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Conserved domains on  [gi|1443700932|ref|XP_025903157|]
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histone-lysine N-methyltransferase 2D [Nothoprocta perdicaria]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SET_KMT2C_2D cd19171
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C), ...
 4957-5109 2.86e-110

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C), 2D (KMT2D) and similar proteins; This family includes KMT2C and KMT2D. Both, KMT2C (also termed HALR or MLL3) and KMT2D (also termed ALR or MLL2), act as histone methyltransferases that methylate 'Lys-4' of histone H3 (H3K4me). They are subunits of MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation.


:

Pssm-ID: 380948 [Multi-domain]  Cd Length: 153  Bit Score: 348.27  E-value: 2.86e-110
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4957 KSSQYRRLKTEWKNNVYLARSRIQGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVIDA 5036
Cdd:cd19171      1 KSSQYRKLKTEWRSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGEIIRNEVANRREKIYESQNRGIYMFRIDNDWVIDA 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1443700932 5037 TLTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWM 5109
Cdd:cd19171     81 TMTGGPARYINHSCNPNCVAEVVTFDKEKKIIIISNRRIAKGEELTYDYKFDFEDDQHKIPCLCGAPNCRKWM 153
ePHD2_KMT2D cd15698
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 4605-4711 3.08e-75

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2D. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions.


:

Pssm-ID: 277168  Cd Length: 107  Bit Score: 246.12  E-value: 3.08e-75
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4605 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALINVEVALHRGLLTKCSLCQKTGATNSCNRIRCPS 4684
Cdd:cd15698      1 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQKTGATNSCNRLRCPN 80

                           90       100
                   ....*....|....*....|....*..
gi 1443700932 4685 VYHFACAIRAKCMFFKDKTMLCPLHKL 4711
Cdd:cd15698     81 VYHFACAIRAKCMFFKDKTMLCPMHKL 107
HMG-box_KMT2D cd22027
high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2D (KMT2D) and ...
 1615-1698 2.85e-60

high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2D (KMT2D) and similar proteins; KMT2D, also called ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis.


:

Pssm-ID: 438836  Cd Length: 84  Bit Score: 202.24  E-value: 2.85e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1615 GLSYNQRSLQRWEKDEELGELSTISPVLYANMNFPNLKQDYPDWSSRCKQIMKLWRKVPATDKAPYLQKAKDNRAAHRIN 1694
Cdd:cd22027      1 GLSYNQRSLQRWEKDEELGELSTISPVLYANINFPNLKQDYPDWSSRCKQIMKLWRKVPAADKAPYLQKAKDNRAAHRIN 80


                   ....
gi 1443700932 1695 KVQK 1698
Cdd:cd22027     81 KVQK 84
PHD_SF super family cl22851
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 130-212 7.33e-44

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


The actual alignment was detected with superfamily member cd15695:

Pssm-ID: 473978  Cd Length: 90  Bit Score: 155.46  E-value: 7.33e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932  130 GHCWVHRCCAAWSADVLPG-ATGLTHVDRAVFSGISQKCEHCQRMGATIPCRADGCPRLYHFPCAAASGCFQSMKTLRLL 208
Cdd:cd15695      7 GECWVHHWCAAWSAGVKQHeGDGLIGVDKAVFSGISQKCEHCKRLGATIQCHAEGCPRFYHFPCAAASGSFQSMKTLLLL 86


                   ....
gi 1443700932  209 CPEH 212
Cdd:cd15695     87 CPEH 90
PHD3_KMT2D cd15597
PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 954-1004 7.62e-33

PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the third PHD finger.


:

Pssm-ID: 277072  Cd Length: 51  Bit Score: 122.84  E-value: 7.62e-33
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1443700932  954 DMCVVCGSFGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVECI 1004
Cdd:cd15597      1 DMCVVCGSFGRGSEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVECI 51
FYRC smart00542
FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region ...
 4813-4900 5.86e-32

FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region (FYRN), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.


:

Pssm-ID: 197781  Cd Length: 86  Bit Score: 121.25  E-value: 5.86e-32
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932  4813 EFVVQVIEQGleDLIFSDSSPQAVWNRIIEPVAMMRKEADMLRLFPEYLKGEELFGLTVHAVLRIAESLPGVESCQNYLF 4892
Cdd:smart00542    1 LFRVEIESDP--GEVFKGESPEKCWEMVLERVQEARIAADLLQLLPEGVSGEEMFGLSSPAVVKLIEALPGVHQCTNYWF 78


                    ....*...
gi 1443700932  4893 RYGRHPLM 4900
Cdd:smart00542   79 RYHRSPLL 86
PHD_SF super family cl22851
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 1083-1132 2.73e-30

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


The actual alignment was detected with superfamily member cd15601:

Pssm-ID: 473978  Cd Length: 51  Bit Score: 115.39  E-value: 2.73e-30
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1083 CPVCREKYVEDDLLIQCRHCERWLHAACDSLFTEEEVEQAADEGFDCSAC 1132
Cdd:cd15601      2 CPVCRAKYVEEDLLIQCRHCDRWVHAVCESLFTEDEVEQAADEGFDCSSC 51
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
 1005-1051 6.53e-30

PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger of KMT2C and the fourth PHD finger of KMT2D.


:

Pssm-ID: 276988  Cd Length: 47  Bit Score: 114.11  E-value: 6.53e-30
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1443700932 1005 VCEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 1051
Cdd:cd15513      1 VCEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 47
PHD_SF super family cl22851
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 270-315 3.63e-25

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


The actual alignment was detected with superfamily member cd15595:

Pssm-ID: 473978  Cd Length: 46  Bit Score: 100.84  E-value: 3.63e-25
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932  270 VCQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIETLPAASWKCKNC 315
Cdd:cd15595      1 VCQTCRKPGEDSKMLVCEACDKGYHTFCLKPAMESLPTDSWKCKAC 46
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 223-268 7.12e-22

PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the first PHD finger.


:

Pssm-ID: 276984  Cd Length: 48  Bit Score: 91.22  E-value: 7.12e-22
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1443700932  223 RCVVCDGPGDLRDLLFCTSCGQHYHGACLD--VVLAPHKRAGWQCPEC 268
Cdd:cd15509      1 NCAVCDSPGDLSDLLFCTSCGQHYHGSCLDpaVRPTPLVRAGWQCPEC 48
FYRN pfam05964
F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 4754-4805 3.76e-18

F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00541.


:

Pssm-ID: 461787  Cd Length: 51  Bit Score: 81.01  E-value: 3.76e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1443700932 4754 GGLVFHAIGQLLPHQMAdFHSVTALYPVGYEATRIYWSLRTNNRRCCYRCTI 4805
Cdd:pfam05964    1 GSLTVLSLGEIVPDRPA-FHTERYIYPVGYKSTRLYWSTKDPRKRCRYTCEI 51
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 1788-2358 2.35e-15

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 84.22  E-value: 2.35e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1788 APEPRFPSPLGQSPTVGAAFQPFPGQPLAGARTQPPDFHPTPPGTPRHqsgtpdPFLKPRCPSLDNLSGPGSPGARPPEA 1867
Cdd:PHA03247  2483 PAEARFPFAAGAAPDPGGGGPPDPDAPPAPSRLAPAILPDEPVGEPVH------PRMLTWIRGLEELASDDAGDPPPPLP 2556

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1868 LLSPLPFSEQKkglevkkedggalgvcspgyVPATGYSDSPGCTHIPSTELKvADVFKAPLTPRV----SQVEPQSPGLG 1943
Cdd:PHA03247  2557 PAAPPAAPDRS--------------------VPPPRPAPRPSEPAVTSRARR-PDAPPQSARPRApvddRGDPRGPAPPS 2615

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1944 HRPPDAHPLAPSPPGhadlfRQSPYSDPYAQPPLTPRPQPPEGCCTAPPRSLPSEpfsRIPASPQSQSSSQSPLTPRPLS 2023
Cdd:PHA03247  2616 PLPPDTHAPDPPPPS-----PSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPR---RARRLGRAAQASSPPQRPRRRA 2687

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2024 NEAfCQSPVTPRFQSPDPYSQPPSRPQSRDPFTPLHKPP---RAQLPAAPLSHSPAGSGGFGGAATGEPPAKAPGVPQQP 2100
Cdd:PHA03247  2688 ARP-TVGSLTSLADPPPPPPTPEPAPHALVSATPLPPGPaaaRQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGP 2766

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2101 PFARSPGAgifTTGQPPMRFTFPPAvseplkGSPSHQLHGLNSHYVPSKPQSAGYTSSPSFHQAGSPLGPgagaaetysL 2180
Cdd:PHA03247  2767 PAPAPPAA---PAAGPPRRLTRPAV------ASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGP---------L 2828

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2181 SPlrPPSVLPQASPSAPQPQDASV----AYVPRAAVLTTPADKREVAATTALSAPLNRDLGELPSAQDGALGAMSQSELE 2256
Cdd:PHA03247  2829 PP--PTSAQPTAPPPPPGPPPPSLplggSVAPGGDVRRRPPSRSPAAKPAAPARPPVRRLARPAVSRSTESFALPPDQPE 2906

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2257 KQRQRQrlrellirqqiqrnsLRQEKESAAAAAGPAGWVPEPSGQAFGMAPYQPAQDKSLLGPLAGTAKLP--------- 2327
Cdd:PHA03247  2907 RPPQPQ---------------APPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPwlgalvpgr 2971

                          570       580       590
                   ....*....|....*....|....*....|.
gi 1443700932 2328 VPVQAAFTQDERIARPPPATTPAALDINSSP 2358
Cdd:PHA03247  2972 VAVPRFRVPQPAPSREAPASSTPPLTGHSLS 3002
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 3483-4016 3.55e-15

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 83.83  E-value: 3.55e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3483 APPAQGAIGQPVG----PKQPALPQSLLVQQLSPQPPALLGHAQTPALQHPSGLGSGAPQRPLLLTPQQQQQQQRVLGSP 3558
Cdd:PHA03247  2591 APPQSARPRAPVDdrgdPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRL 2670

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3559 QLAPQSPAMLghRLVLGQPLHPPQAPLQHFA----QPRVPGQAPSGLQLAQGMQPLAAGKEQPMDGPPAEGTEgPPEPQG 3634
Cdd:PHA03247  2671 GRAAQASSPP--QRPRRRAARPTVGSLTSLAdpppPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAP-PAVPAG 2747

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3635 APGLGAAESPAVLGLPTAPKHPTelgqgqqlllaSPQPGSLGTSARLLHQPLPSPGAARPELPQSHGDVAGSALVTelpp 3714
Cdd:PHA03247  2748 PATPGGPARPARPPTTAGPPAPA-----------PPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVL---- 2812

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3715 apqppspeqpgkglPGSGALPPPrlqspgqqkAGPAPQPAPTLPPSILGPVPAPVMGQIRAQLQGVLAKNPQLRHLTPQQ 3794
Cdd:PHA03247  2813 --------------APAAALPPA---------ASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSR 2869

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3795 QQQLQALLVQRHQQSLLQQNQALRQSGPFPgtVPEQGLPPGRQPSRPQFPvRPPVLTEAPTGFAADPGTGGRSQPGQQPL 3874
Cdd:PHA03247  2870 SPAAKPAAPARPPVRRLARPAVSRSTESFA--LPPDQPERPPQPQAPPPP-QPQPQPPPPPQPQPPPPPPPRPQPPLAPT 2946

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3875 AELVQAALATRGPQ--------PGFVRLSTPPALSPLDSQPSPEQSPHEPKTPTPTTTGGLAPSPV-------APLELPQ 3939
Cdd:PHA03247  2947 TDPAGAGEPSGAVPqpwlgalvPGRVAVPRFRVPQPAPSREAPASSTPPLTGHSLSRVSSWASSLAlheetdpPPVSLKQ 3026

                          490       500       510       520       530       540       550
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1443700932 3940 SPWgsePPALDDDVAETSVngqgVEGTPDECPQLPVKQEPREETALPAaarepEPQEPVKPEANGDAVGGALAGSPP 4016
Cdd:PHA03247  3027 TLW---PPDDTEDSDADSL----FDSDSERSDLEALDPLPPEPHDPFA-----HEPDPATPEAGARESPSSQFGPPP 3091
Med15 super family cl26621
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 3159-3616 1.18e-12

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


The actual alignment was detected with superfamily member pfam09606:

Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 74.66  E-value: 1.18e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3159 GVQQPLSQPAAAAQGLgqqsgqPGGLRLPQGGVSMAV-PQGLsfMGQQAVGSAPVPGTSSTFFPGNPALRGLAADNRLMQ 3237
Cdd:pfam09606   74 GGQQGMPDPINALQNL------AGQGTRPQMMGPMGPgPGGP--MGQQMGGPGTASNLLASLGRPQMPMGGAGFPSQMSR 145

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3238 ERQLQRMQLAQKLQQQQQQNMLGQVSLQQQQQPPGIMGQTSMQQPGIMGQASMQQPGVMGQVSMQQTGVMG-QMSIQQPS 3316
Cdd:pfam09606  146 VGRMQPGGQAGGMMQPSSGQPGSGTPNQMGPNGGPGQGQAGGMNGGQQGPMGGQMPPQMGVPGMPGPADAGaQMGQQAQA 225

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3317 MAGQASMQQTGVLGQVSMQQSGIMGQASMQQPGVLgqvsMQQPGVMGQtmqqpgvmGQTSMQPPGVMGQTsmqqtsvmGQ 3396
Cdd:pfam09606  226 NGGMNPQQMGGAPNQVAMQQQQPQQQGQQSQLGMG----INQMQQMPQ--------GVGGGAGQGGPGQP--------MG 285

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3397 VSMQQPGAVGqASMQPQGIMAQASLQQSGVMGQTALQQPGILPQPSLQPQGLMAQpaMQPAGSLAQPPLPQQPPMQQPGL 3476
Cdd:pfam09606  286 PPGQQPGAMP-NVMSIGDQNNYQQQQTRQQQQQQGGNHPAAHQQQMNQSVGQGGQ--VVALGGLNHLETWNPGNFGGLGA 362

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3477 GvQQVAAPPAQGAIGQPVGPKQPALPQSLlvQQLSPQPPALLGHAQTPALQHPSglgsgapqrpllltpqqqqqqqrvLG 3556
Cdd:pfam09606  363 N-PMQRGQPGMMSSPSPVPGQQVRQVTPN--QFMRQSPQPSVPSPQGPGSQPPQ------------------------SH 415

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1443700932 3557 SPQLAPqSPAMlghrlvlgQPLHPPQaPLQHFAQPRVPGQAPSGLQL-----AQGMQPLAAGKEQ 3616
Cdd:pfam09606  416 PGGMIP-SPAL--------IPSPSPQ-MSQQPAQQRTIGQDSPGGSLntpgqSAVNSPLNPQEEQ 470
PAT1 super family cl37801
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 2780-2926 6.05e-05

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


The actual alignment was detected with superfamily member pfam09770:

Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 49.65  E-value: 6.05e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2780 LLEHEKKELQKKQQMSVQLPRGAP-QHLPAAGHPLLHPGAPGQPPEGQGPRLGTPQPTLQLGLMARQQLLQPQQSRLGGP 2858
Cdd:pfam09770  203 MRAQAKKPAQQPAPAPAQPPAAPPaQQAQQQQQFPPQIQQQQQPQQQPQQPQQHPGQGHPVTILQRPQSPQPDPAQPSIQ 282

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1443700932 2859 QQGLPLAGHMGMAPAQP-HVLAAP--HGVQVALPPQQGQQPVLMQKPMGAG-QPPGLGLKPPQLVMQQQLAN 2926
Cdd:pfam09770  283 PQAQQFHQQPPPVPVQPtQILQNPnrLSAARVGYPQNPQPGVQPAPAHQAHrQQGSFGRQAPIITHPQQLAQ 354
 
Name Accession Description Interval E-value
SET_KMT2C_2D cd19171
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C), ...
 4957-5109 2.86e-110

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C), 2D (KMT2D) and similar proteins; This family includes KMT2C and KMT2D. Both, KMT2C (also termed HALR or MLL3) and KMT2D (also termed ALR or MLL2), act as histone methyltransferases that methylate 'Lys-4' of histone H3 (H3K4me). They are subunits of MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation.


Pssm-ID: 380948 [Multi-domain]  Cd Length: 153  Bit Score: 348.27  E-value: 2.86e-110
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4957 KSSQYRRLKTEWKNNVYLARSRIQGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVIDA 5036
Cdd:cd19171      1 KSSQYRKLKTEWRSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGEIIRNEVANRREKIYESQNRGIYMFRIDNDWVIDA 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1443700932 5037 TLTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWM 5109
Cdd:cd19171     81 TMTGGPARYINHSCNPNCVAEVVTFDKEKKIIIISNRRIAKGEELTYDYKFDFEDDQHKIPCLCGAPNCRKWM 153
ePHD2_KMT2D cd15698
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 4605-4711 3.08e-75

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2D. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions.


Pssm-ID: 277168  Cd Length: 107  Bit Score: 246.12  E-value: 3.08e-75
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4605 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALINVEVALHRGLLTKCSLCQKTGATNSCNRIRCPS 4684
Cdd:cd15698      1 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQKTGATNSCNRLRCPN 80

                           90       100
                   ....*....|....*....|....*..
gi 1443700932 4685 VYHFACAIRAKCMFFKDKTMLCPLHKL 4711
Cdd:cd15698     81 VYHFACAIRAKCMFFKDKTMLCPMHKL 107
HMG-box_KMT2D cd22027
high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2D (KMT2D) and ...
 1615-1698 2.85e-60

high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2D (KMT2D) and similar proteins; KMT2D, also called ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis.


Pssm-ID: 438836  Cd Length: 84  Bit Score: 202.24  E-value: 2.85e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1615 GLSYNQRSLQRWEKDEELGELSTISPVLYANMNFPNLKQDYPDWSSRCKQIMKLWRKVPATDKAPYLQKAKDNRAAHRIN 1694
Cdd:cd22027      1 GLSYNQRSLQRWEKDEELGELSTISPVLYANINFPNLKQDYPDWSSRCKQIMKLWRKVPAADKAPYLQKAKDNRAAHRIN 80


                   ....
gi 1443700932 1695 KVQK 1698
Cdd:cd22027     81 KVQK 84
ePHD1_KMT2D cd15695
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 130-212 7.33e-44

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMT2D. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 at Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions.


Pssm-ID: 277165  Cd Length: 90  Bit Score: 155.46  E-value: 7.33e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932  130 GHCWVHRCCAAWSADVLPG-ATGLTHVDRAVFSGISQKCEHCQRMGATIPCRADGCPRLYHFPCAAASGCFQSMKTLRLL 208
Cdd:cd15695      7 GECWVHHWCAAWSAGVKQHeGDGLIGVDKAVFSGISQKCEHCKRLGATIQCHAEGCPRFYHFPCAAASGSFQSMKTLLLL 86


                   ....
gi 1443700932  209 CPEH 212
Cdd:cd15695     87 CPEH 90
PHD3_KMT2D cd15597
PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 954-1004 7.62e-33

PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the third PHD finger.


Pssm-ID: 277072  Cd Length: 51  Bit Score: 122.84  E-value: 7.62e-33
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1443700932  954 DMCVVCGSFGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVECI 1004
Cdd:cd15597      1 DMCVVCGSFGRGSEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVECI 51
SET COG2940
SET domain-containing protein (function unknown) [General function prediction only];
4971-5108 1.15e-32

SET domain-containing protein (function unknown) [General function prediction only];


Pssm-ID: 442183 [Multi-domain]  Cd Length: 134  Bit Score: 125.46  E-value: 1.15e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4971 NVYLARSRIQGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEEQNRgiYMFRINNEHVIDATLTGGPARYINHSC 5050
Cdd:COG2940      7 RIEVRPSPIHGRGVFATRDIPKGTLIGEYPGEVITWAEAERREPHKEPLHT--YLFELDDDGVIDGALGGNPARFINHSC 84

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1443700932 5051 APNCVAEVVTFD-----KEDkiiiissrrIPKGEELTYDYQFDFEDDQHkiPCHCGawNCRKW 5108
Cdd:COG2940     85 DPNCEADEEDGRifivaLRD---------IAAGEELTYDYGLDYDEEEY--PCRCP--NCRGT 134
SET smart00317
SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Putative methyl transferase, based on ...
 4970-5092 4.34e-32

SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Putative methyl transferase, based on outlier plant homologues


Pssm-ID: 214614 [Multi-domain]  Cd Length: 124  Bit Score: 123.21  E-value: 4.34e-32
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932  4970 NNVYLARSRIQGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYE-EQNRGIYMFRINNEHVIDATLTGGPARYINH 5048
Cdd:smart00317    1 NKLEVFKSPGKGWGVRATEDIPKGEFIGEYVGEIITSEEAEERPKAYDtDGAKAFYLFDIDSDLCIDARRKGNLARFINH 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....
gi 1443700932  5049 SCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDD 5092
Cdd:smart00317   81 SCEPNCELLFVEVNGDDRIVIFALRDIKPGEELTIDYGSDYANE 124
FYRC smart00542
FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region ...
 4813-4900 5.86e-32

FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region (FYRN), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.


Pssm-ID: 197781  Cd Length: 86  Bit Score: 121.25  E-value: 5.86e-32
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932  4813 EFVVQVIEQGleDLIFSDSSPQAVWNRIIEPVAMMRKEADMLRLFPEYLKGEELFGLTVHAVLRIAESLPGVESCQNYLF 4892
Cdd:smart00542    1 LFRVEIESDP--GEVFKGESPEKCWEMVLERVQEARIAADLLQLLPEGVSGEEMFGLSSPAVVKLIEALPGVHQCTNYWF 78


                    ....*...
gi 1443700932  4893 RYGRHPLM 4900
Cdd:smart00542   79 RYHRSPLL 86
PHD5_KMT2D cd15601
PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 1083-1132 2.73e-30

PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such asHOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is downregulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger.


Pssm-ID: 277074  Cd Length: 51  Bit Score: 115.39  E-value: 2.73e-30
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1083 CPVCREKYVEDDLLIQCRHCERWLHAACDSLFTEEEVEQAADEGFDCSAC 1132
Cdd:cd15601      2 CPVCRAKYVEEDLLIQCRHCDRWVHAVCESLFTEDEVEQAADEGFDCSSC 51
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
 1005-1051 6.53e-30

PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger of KMT2C and the fourth PHD finger of KMT2D.


Pssm-ID: 276988  Cd Length: 47  Bit Score: 114.11  E-value: 6.53e-30
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1443700932 1005 VCEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 1051
Cdd:cd15513      1 VCEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 47
FYRC pfam05965
F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 4811-4895 5.27e-27

F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00542.


Pssm-ID: 461788  Cd Length: 83  Bit Score: 107.31  E-value: 5.27e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4811 RPEFVVQVIEQglEDLIFSDSSPQAVWNRIIEPVAMMRKEADMLRLFPEYLKGEELFGLTVHAVLRIAESLPGVESCQNY 4890
Cdd:pfam05965    1 GPLFRVTVEED--PDESFEGSSPTKCWSMVLERVQELRREAGLKLKLPESISGEDMFGLTHPAVVRLIESLPGAEKCTNY 78


                   ....*
gi 1443700932 4891 LFRYG 4895
Cdd:pfam05965   79 KFRYG 83
PHD2_KMT2D cd15595
PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 270-315 3.63e-25

PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such asHOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 277070  Cd Length: 46  Bit Score: 100.84  E-value: 3.63e-25
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932  270 VCQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIETLPAASWKCKNC 315
Cdd:cd15595      1 VCQTCRKPGEDSKMLVCEACDKGYHTFCLKPAMESLPTDSWKCKAC 46
SET pfam00856
SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be ...
 4981-5085 6.81e-22

SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure.


Pssm-ID: 459965 [Multi-domain]  Cd Length: 115  Bit Score: 93.74  E-value: 6.81e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4981 GLGLYAAKDIEKHTMVIEYIGT-IIRNEVANRREKIYEEQNR----GIYMFRIN--NEHVIDATLT--GGPARYINHSCA 5051
Cdd:pfam00856    1 GRGLFATEDIPKGEFIGEYVEVlLITKEEADKRELLYYDKLElrlwGPYLFTLDedSEYCIDARALyyGNWARFINHSCD 80

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1443700932 5052 PNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDY 5085
Cdd:pfam00856   81 PNCEVRVVYVNGGPRIVIFALRDIKPGEELTIDY 114
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 223-268 7.12e-22

PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the first PHD finger.


Pssm-ID: 276984  Cd Length: 48  Bit Score: 91.22  E-value: 7.12e-22
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1443700932  223 RCVVCDGPGDLRDLLFCTSCGQHYHGACLD--VVLAPHKRAGWQCPEC 268
Cdd:cd15509      1 NCAVCDSPGDLSDLLFCTSCGQHYHGSCLDpaVRPTPLVRAGWQCPEC 48
FYRN pfam05964
F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 4754-4805 3.76e-18

F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00541.


Pssm-ID: 461787  Cd Length: 51  Bit Score: 81.01  E-value: 3.76e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1443700932 4754 GGLVFHAIGQLLPHQMAdFHSVTALYPVGYEATRIYWSLRTNNRRCCYRCTI 4805
Cdd:pfam05964    1 GSLTVLSLGEIVPDRPA-FHTERYIYPVGYKSTRLYWSTKDPRKRCRYTCEI 51
FYRN smart00541
FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region ...
 4764-4805 2.02e-15

FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region (FYRC), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.


Pssm-ID: 128814  Cd Length: 44  Bit Score: 72.70  E-value: 2.02e-15
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|..
gi 1443700932  4764 LLPHQMADFHSVTALYPVGYEATRIYWSLRTNNRRCCYRCTI 4805
Cdd:smart00541    1 LLPIQGKLFHSESAIFPVGYKSTRKYWSVKDPNRRCLYSCVI 42
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1788-2358 2.35e-15

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 84.22  E-value: 2.35e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1788 APEPRFPSPLGQSPTVGAAFQPFPGQPLAGARTQPPDFHPTPPGTPRHqsgtpdPFLKPRCPSLDNLSGPGSPGARPPEA 1867
Cdd:PHA03247  2483 PAEARFPFAAGAAPDPGGGGPPDPDAPPAPSRLAPAILPDEPVGEPVH------PRMLTWIRGLEELASDDAGDPPPPLP 2556

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1868 LLSPLPFSEQKkglevkkedggalgvcspgyVPATGYSDSPGCTHIPSTELKvADVFKAPLTPRV----SQVEPQSPGLG 1943
Cdd:PHA03247  2557 PAAPPAAPDRS--------------------VPPPRPAPRPSEPAVTSRARR-PDAPPQSARPRApvddRGDPRGPAPPS 2615

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1944 HRPPDAHPLAPSPPGhadlfRQSPYSDPYAQPPLTPRPQPPEGCCTAPPRSLPSEpfsRIPASPQSQSSSQSPLTPRPLS 2023
Cdd:PHA03247  2616 PLPPDTHAPDPPPPS-----PSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPR---RARRLGRAAQASSPPQRPRRRA 2687

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2024 NEAfCQSPVTPRFQSPDPYSQPPSRPQSRDPFTPLHKPP---RAQLPAAPLSHSPAGSGGFGGAATGEPPAKAPGVPQQP 2100
Cdd:PHA03247  2688 ARP-TVGSLTSLADPPPPPPTPEPAPHALVSATPLPPGPaaaRQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGP 2766

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2101 PFARSPGAgifTTGQPPMRFTFPPAvseplkGSPSHQLHGLNSHYVPSKPQSAGYTSSPSFHQAGSPLGPgagaaetysL 2180
Cdd:PHA03247  2767 PAPAPPAA---PAAGPPRRLTRPAV------ASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGP---------L 2828

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2181 SPlrPPSVLPQASPSAPQPQDASV----AYVPRAAVLTTPADKREVAATTALSAPLNRDLGELPSAQDGALGAMSQSELE 2256
Cdd:PHA03247  2829 PP--PTSAQPTAPPPPPGPPPPSLplggSVAPGGDVRRRPPSRSPAAKPAAPARPPVRRLARPAVSRSTESFALPPDQPE 2906

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2257 KQRQRQrlrellirqqiqrnsLRQEKESAAAAAGPAGWVPEPSGQAFGMAPYQPAQDKSLLGPLAGTAKLP--------- 2327
Cdd:PHA03247  2907 RPPQPQ---------------APPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPwlgalvpgr 2971

                          570       580       590
                   ....*....|....*....|....*....|.
gi 1443700932 2328 VPVQAAFTQDERIARPPPATTPAALDINSSP 2358
Cdd:PHA03247  2972 VAVPRFRVPQPAPSREAPASSTPPLTGHSLS 3002
PHA03247 PHA03247
large tegument protein UL36; Provisional
 3483-4016 3.55e-15

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 83.83  E-value: 3.55e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3483 APPAQGAIGQPVG----PKQPALPQSLLVQQLSPQPPALLGHAQTPALQHPSGLGSGAPQRPLLLTPQQQQQQQRVLGSP 3558
Cdd:PHA03247  2591 APPQSARPRAPVDdrgdPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRL 2670

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3559 QLAPQSPAMLghRLVLGQPLHPPQAPLQHFA----QPRVPGQAPSGLQLAQGMQPLAAGKEQPMDGPPAEGTEgPPEPQG 3634
Cdd:PHA03247  2671 GRAAQASSPP--QRPRRRAARPTVGSLTSLAdpppPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAP-PAVPAG 2747

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3635 APGLGAAESPAVLGLPTAPKHPTelgqgqqlllaSPQPGSLGTSARLLHQPLPSPGAARPELPQSHGDVAGSALVTelpp 3714
Cdd:PHA03247  2748 PATPGGPARPARPPTTAGPPAPA-----------PPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVL---- 2812

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3715 apqppspeqpgkglPGSGALPPPrlqspgqqkAGPAPQPAPTLPPSILGPVPAPVMGQIRAQLQGVLAKNPQLRHLTPQQ 3794
Cdd:PHA03247  2813 --------------APAAALPPA---------ASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSR 2869

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3795 QQQLQALLVQRHQQSLLQQNQALRQSGPFPgtVPEQGLPPGRQPSRPQFPvRPPVLTEAPTGFAADPGTGGRSQPGQQPL 3874
Cdd:PHA03247  2870 SPAAKPAAPARPPVRRLARPAVSRSTESFA--LPPDQPERPPQPQAPPPP-QPQPQPPPPPQPQPPPPPPPRPQPPLAPT 2946

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3875 AELVQAALATRGPQ--------PGFVRLSTPPALSPLDSQPSPEQSPHEPKTPTPTTTGGLAPSPV-------APLELPQ 3939
Cdd:PHA03247  2947 TDPAGAGEPSGAVPqpwlgalvPGRVAVPRFRVPQPAPSREAPASSTPPLTGHSLSRVSSWASSLAlheetdpPPVSLKQ 3026

                          490       500       510       520       530       540       550
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1443700932 3940 SPWgsePPALDDDVAETSVngqgVEGTPDECPQLPVKQEPREETALPAaarepEPQEPVKPEANGDAVGGALAGSPP 4016
Cdd:PHA03247  3027 TLW---PPDDTEDSDADSL----FDSDSERSDLEALDPLPPEPHDPFA-----HEPDPATPEAGARESPSSQFGPPP 3091
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1005-1053 2.84e-14

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 69.83  E-value: 2.84e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1443700932 1005 VCEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQT--VPKGGWKCKWCVCC 1053
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPaeIPSGEWLCPECKPK 51
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 3159-3616 1.18e-12

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 74.66  E-value: 1.18e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3159 GVQQPLSQPAAAAQGLgqqsgqPGGLRLPQGGVSMAV-PQGLsfMGQQAVGSAPVPGTSSTFFPGNPALRGLAADNRLMQ 3237
Cdd:pfam09606   74 GGQQGMPDPINALQNL------AGQGTRPQMMGPMGPgPGGP--MGQQMGGPGTASNLLASLGRPQMPMGGAGFPSQMSR 145

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3238 ERQLQRMQLAQKLQQQQQQNMLGQVSLQQQQQPPGIMGQTSMQQPGIMGQASMQQPGVMGQVSMQQTGVMG-QMSIQQPS 3316
Cdd:pfam09606  146 VGRMQPGGQAGGMMQPSSGQPGSGTPNQMGPNGGPGQGQAGGMNGGQQGPMGGQMPPQMGVPGMPGPADAGaQMGQQAQA 225

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3317 MAGQASMQQTGVLGQVSMQQSGIMGQASMQQPGVLgqvsMQQPGVMGQtmqqpgvmGQTSMQPPGVMGQTsmqqtsvmGQ 3396
Cdd:pfam09606  226 NGGMNPQQMGGAPNQVAMQQQQPQQQGQQSQLGMG----INQMQQMPQ--------GVGGGAGQGGPGQP--------MG 285

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3397 VSMQQPGAVGqASMQPQGIMAQASLQQSGVMGQTALQQPGILPQPSLQPQGLMAQpaMQPAGSLAQPPLPQQPPMQQPGL 3476
Cdd:pfam09606  286 PPGQQPGAMP-NVMSIGDQNNYQQQQTRQQQQQQGGNHPAAHQQQMNQSVGQGGQ--VVALGGLNHLETWNPGNFGGLGA 362

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3477 GvQQVAAPPAQGAIGQPVGPKQPALPQSLlvQQLSPQPPALLGHAQTPALQHPSglgsgapqrpllltpqqqqqqqrvLG 3556
Cdd:pfam09606  363 N-PMQRGQPGMMSSPSPVPGQQVRQVTPN--QFMRQSPQPSVPSPQGPGSQPPQ------------------------SH 415

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1443700932 3557 SPQLAPqSPAMlghrlvlgQPLHPPQaPLQHFAQPRVPGQAPSGLQL-----AQGMQPLAAGKEQ 3616
Cdd:pfam09606  416 PGGMIP-SPAL--------IPSPSPQ-MSQQPAQQRTIGQDSPGGSLntpgqSAVNSPLNPQEEQ 470
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1005-1050 1.97e-12

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 64.54  E-value: 1.97e-12
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 1443700932  1005 VCEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQT-VPKGGWKCKWC 1050
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 4632-4709 5.88e-12

PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH.


Pssm-ID: 463977 [Multi-domain]  Cd Length: 88  Bit Score: 64.66  E-value: 5.88e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4632 HLNCALWSTEVY----ETQGGALINVEVALHRGLLTKCSLC-QKTGATNSCNRIRCPSVYHFACAIRAKCMF-FKDKT-- 4703
Cdd:pfam13771    1 HVVCALWSPELVqrgnDSMGFPIEDIEKIPKRRWKLKCYLCkKKGGACIQCSKKNCRRAFHVTCALEAGLLMqFDEDNgt 80


                   ....*...
gi 1443700932 4704 --MLCPLH 4709
Cdd:pfam13771   81 fkSYCKKH 88
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 223-271 1.11e-11

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 62.51  E-value: 1.11e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1443700932  223 RCVVCDGPGDLRDLLFCTSCGQHYHGACLDVVL--APHKRAGWQCPECKVC 271
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPPLdpAEIPSGEWLCPECKPK 51
Glutenin_hmw pfam03157
High molecular weight glutenin subunit; Members of this family include high molecular weight ...
 3312-3994 6.83e-11

High molecular weight glutenin subunit; Members of this family include high molecular weight subunits of glutenin. This group of gluten proteins is thought to be largely responsible for the elastic properties of gluten, and hence, doughs. Indeed, glutenin high molecular weight subunits are classified as elastomeric proteins, because the glutenin network can withstand significant deformations without breaking, and return to the original conformation when the stress is removed. Elastomeric proteins differ considerably in amino acid sequence, but they are all polymers whose subunits consist of elastomeric domains, composed of repeated motifs, and non-elastic domains that mediate cross-linking between the subunits. The elastomeric domain motifs are all rich in glycine residues in addition to other hydrophobic residues. High molecular weight glutenin subunits have an extensive central elastomeric domain, flanked by two terminal non-elastic domains that form disulphide cross-links. The central elastomeric domain is characterized by the following three repeated motifs: PGQGQQ, GYYPTS[P/L]QQ, GQQ. It possesses overlapping beta-turns within and between the repeated motifs, and assumes a regular helical secondary structure with a diameter of approx. 1.9 nm and a pitch of approx. 1.5 nm.


Pssm-ID: 367362 [Multi-domain]  Cd Length: 786  Bit Score: 69.21  E-value: 6.83e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3312 IQQPSMAGQASMQQTGVLGQVSMQQ-SGIMGQASMQQPGVLGQVSMQQPGVMGQTMQQPGVMGQTSMQPPGVMgQTSMQQ 3390
Cdd:pfam03157   94 LQQGIFWGIPALLQRYYPGVTSPQQvSYYPGQASPQRPGQGQQPGQGQQWYYPTSPQQPGQWQQPGQGQQGYY-PTSPQQ 172

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3391 TSVMGQVSMQQ---PGAVGQASMQPQGIMAQASLQQSGVMGQTALQQPGILPQPSLQPQ--GLMAQPAMQPAGSLAQPPL 3465
Cdd:pfam03157  173 SGQRQQPGQGQqlrQGQQGQQSGQGQPGYYPTSSQQPGQLQQTGQGQQGQQPERGQQGQqpGQGQQPGQGQQGQQPGQPQ 252

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3466 PQQPPMQQPGLGVQQVAAPPAQGAIGQ----PVGPKQPALPQS-----LLVQQLSPQPPALLGHAQTPALQHPSGLGSGA 3536
Cdd:pfam03157  253 QLGQGQQGYYPISPQQPRQWQQSGQGQqgyyPTSLQQPGQGQSgyyptSQQQAGQLQQEQQLGQEQQDQQPGQGRQGQQP 332

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3537 PQRPLLLTPQQQQQQQRvlGSPQLAPQSPAMLGHrlvlGQPLHPPQAPlQHFAQPRVPGQAPSGLQLAQGMQPLAAGK-E 3615
Cdd:pfam03157  333 GQGQQGQQPAQGQQPGQ--GQPGYYPTSPQQPGQ----GQPGYYPTSQ-QQPQQGQQPEQGQQGQQQGQGQQGQQPGQgQ 405

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3616 QPMDGPPAEGTEGPPEP-QGAPGLgAAESPAVLGLPTAPKHPTELGQGQQLLLASP---QPGSLGTSARLLHQPLPSPGA 3691
Cdd:pfam03157  406 QPGQGQPGYYPTSPQQSgQGQPGY-YPTSPQQSGQGQQPGQGQQPGQEQPGQGQQPgqgQQGQQPGQPEQGQQPGQGQPG 484

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3692 ARPELPQSHGDvagsalvtelppAPQPPSPEQPGKGLPGSgalPPPRLQSPGQQKAGPAP-QPAPTLPPSILGPVPAPVM 3770
Cdd:pfam03157  485 YYPTSPQQSGQ------------GQQLGQWQQQGQGQPGY---YPTSPLQPGQGQPGYYPtSPQQPGQGQQLGQLQQPTQ 549

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3771 GQiraqlQGVLAKNPQLRHLTPQQQQQLQALLVQRHQQSLLQQNQALRQSGPFPGTVPEQGlpPGRQPSRPQFPVRPpvl 3850
Cdd:pfam03157  550 GQ-----QGQQSGQGQQGQQPGQGQQGQQPGQGQQGQQPGQGQQPGQGQPGYYPTSPQQSG--QGQQPGQWQQPGQG--- 619

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3851 teAPTGFAADPGTGGRSQPGQQPLAElvqaALATRGPQPGFVRLS---------TPPALSPLDSQPSPEQSPHEPKTPTP 3921
Cdd:pfam03157  620 --QPGYYPTSSLQLGQGQQGYYPTSP----QQPGQGQQPGQWQQSgqgqqgyypTSPQQSGQAQQPGQGQQPGQWLQPGQ 693

                          650       660       670       680       690       700       710
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1443700932 3922 TTTGGLAPSPVAPLELPQSPWGSEPPALDDDVAETSVNGQGVEGTPDECPQLPVKQEPREETALPAAAREPEP 3994
Cdd:pfam03157  694 GQQGYYPTSPQQPGQGQQLGQGQQSGQGQQGYYPTSPGQGQQSGQGQQGYDSPYHVSAEHQAASLKVAKAQQL 766
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 956-1006 4.33e-10

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 57.89  E-value: 4.33e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1443700932  956 CVVCGsfGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKG-WRCVECIVC 1006
Cdd:pfam00628    2 CAVCG--KSDDGGELVQCDGCDDWFHLACLGPPLDPAEIPSGeWLCPECKPK 51
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 135-212 6.10e-10

PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH.


Pssm-ID: 463977 [Multi-domain]  Cd Length: 88  Bit Score: 58.88  E-value: 6.10e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932  135 HRCCAAWSADVLPGAT-----GLTHVDRAVFSGISQKCEHC-QRMGATIPCRADGCPRLYHFPCAAASGCFQSMK----T 204
Cdd:pfam13771    1 HVVCALWSPELVQRGNdsmgfPIEDIEKIPKRRWKLKCYLCkKKGGACIQCSKKNCRRAFHVTCALEAGLLMQFDedngT 80


                   ....*...
gi 1443700932  205 LRLLCPEH 212
Cdd:pfam13771   81 FKSYCKKH 88
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 955-1003 8.04e-10

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 57.22  E-value: 8.04e-10
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*....
gi 1443700932   955 MCVVCGsfGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVEC 1003
Cdd:smart00249    1 YCSVCG--KPDDGGELLQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 223-268 1.02e-09

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 56.84  E-value: 1.02e-09
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 1443700932   223 RCVVCDGPGDLRDLLFCTSCGQHYHGACLDVVLAPH-KRAGWQCPEC 268
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEEePDGKWYCPKC 47
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 270-318 1.93e-09

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 56.35  E-value: 1.93e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1443700932  270 VCQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIET--LPAASWKCKNCRVC 318
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPaeIPSGEWLCPECKPK 51
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 270-315 6.58e-08

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 51.83  E-value: 6.58e-08
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 1443700932   270 VCQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIET-LPAASWKCKNC 315
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
HMG smart00398
high mobility group;
1641-1692 1.62e-07

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 51.16  E-value: 1.62e-07
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....
gi 1443700932  1641 VLYANMNFPNLKQDYPDWSS--RCKQIMKLWRKVPATDKAPYLQKAKDNRAAHR 1692
Cdd:smart00398   10 MLFSQENRAKIKAENPDLSNaeISKKLGERWKLLSEEEKAPYEEKAKKDKERYE 63
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1082-1132 5.68e-07

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 49.13  E-value: 5.68e-07
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|.
gi 1443700932  1082 VCPVCREKYvEDDLLIQCRHCERWLHAACDSLFTEEEVEqaaDEGFDCSAC 1132
Cdd:smart00249    1 YCSVCGKPD-DGGELLQCDGCDRWYHQTCLGPPLLEEEP---DGKWYCPKC 47
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1082-1134 3.85e-05

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 44.02  E-value: 3.85e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1443700932 1082 VCPVCReKYVEDDLLIQCRHCERWLHAACDSLftEEEVEQAADEGFDCSACQP 1134
Cdd:pfam00628    1 YCAVCG-KSDDGGELVQCDGCDDWFHLACLGP--PLDPAEIPSGEWLCPECKP 50
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 2780-2926 6.05e-05

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 49.65  E-value: 6.05e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2780 LLEHEKKELQKKQQMSVQLPRGAP-QHLPAAGHPLLHPGAPGQPPEGQGPRLGTPQPTLQLGLMARQQLLQPQQSRLGGP 2858
Cdd:pfam09770  203 MRAQAKKPAQQPAPAPAQPPAAPPaQQAQQQQQFPPQIQQQQQPQQQPQQPQQHPGQGHPVTILQRPQSPQPDPAQPSIQ 282

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1443700932 2859 QQGLPLAGHMGMAPAQP-HVLAAP--HGVQVALPPQQGQQPVLMQKPMGAG-QPPGLGLKPPQLVMQQQLAN 2926
Cdd:pfam09770  283 PQAQQFHQQPPPVPVQPtQILQNPnrLSAARVGYPQNPQPGVQPAPAHQAHrQQGSFGRQAPIITHPQQLAQ 354
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 4665-4709 2.36e-04

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 41.81  E-value: 2.36e-04
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 1443700932  4665 CSLCQKTGATN---SCNRirCPSVYHFACAIRAKCMFFKDKTMLCPLH 4709
Cdd:smart00249    2 CSVCGKPDDGGellQCDG--CDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
HMG_box pfam00505
HMG (high mobility group) box;
1641-1692 3.92e-04

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 41.83  E-value: 3.92e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1443700932 1641 VLYANMNFPNLKQDYPDWSSR--CKQIMKLWRKVPATDKAPYLQKAKDNRAAHR 1692
Cdd:pfam00505    9 FLFSKEQRAKLKAENPGLKNAeiSKILGEKWKALSEEEKKPYEEKAEKEKARYE 62
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 2003-2199 6.46e-04

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 46.30  E-value: 6.46e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2003 IPASPQSQSSSQSPLTPRPLSNEAFCQSPVTPRFQSPDPYSQPPSRPQSRDPFTPLHKPPRAQLPAAPLSHSPAGSggfg 2082
Cdd:pfam03154  181 ASPPSPPPPGTTQAATAGPTPSAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQTPTLHPQRLPSPHPPLQPMTQPP---- 256

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2083 gaatgePPAKAPGVPQQPPFARSPGagifttgqPPMrftfppavSEPLKGSPSHQLHGLNSHYVPSKPQSAgytsspsfh 2162
Cdd:pfam03154  257 ------PPSQVSPQPLPQPSLHGQM--------PPM--------PHSLQTGPSHMQHPVPPQPFPLTPQSS--------- 305

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 1443700932 2163 QAGSPLGPGAGAAETYSLSPLRPPsvlPQASPSAPQP 2199
Cdd:pfam03154  306 QSQVPPGPSPAAPGQSQQRIHTPP---SQSQLQSQQP 339
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 3411-3568 1.47e-03

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 44.80  E-value: 1.47e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3411 QPQGIMAQASLQQSGVMGQTALQQPGIL----PQPSLQPQGLMAQPAMQPAGSLAQPPLPQQPPMQQPGLGVQQVAAPPA 3486
Cdd:TIGR01628  379 QPRMRQLPMGSPMGGAMGQPPYYGQGPQqqfnGQPLGWPRMSMMPTPMGPGGPLRPNGLAPMNAVRAPSRNAQNAAQKPP 458

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3487 QGAIgqpvgPKQPALPQSLLVQQLsPQPPALLGHaQTPALQHPSGLGSGAPQrpllltpqqqqQQQRVLG---------- 3556
Cdd:TIGR01628  459 MQPV-----MYPPNYQSLPLSQDL-PQPQSTASQ-GGQNKKLAQVLASATPQ-----------MQKQVLGerlfplveai 520

                          170
                   ....*....|..
gi 1443700932 3557 SPQLAPQSPAML 3568
Cdd:TIGR01628  521 EPALAAKITGML 532
SP1-4_arthropods_N cd22553
N-terminal domain of transcription factor Specificity Protein (SP) 1-4 from arthropods; ...
 3273-3619 7.45e-03

N-terminal domain of transcription factor Specificity Protein (SP) 1-4 from arthropods; Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. There are many SPs in vertebrates (9 SPs in humans and mice, 7 SPs in the chicken, and 11 SPs in teleost fish), but arthropods only have 3 SPs. One SP is clade SP1-4, which is expressed ubiquitously throughout development. SP1-4 belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. This model represents the N-terminal domain of SP1-4 from arthropods.


Pssm-ID: 411778 [Multi-domain]  Cd Length: 384  Bit Score: 42.32  E-value: 7.45e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3273 IMGQTSMQQPGIMGQASMQQPGVMGQVSMQQTGVMGQMSIQQPSMAGQASMQQTGVLGQVsmQQSGIMGQAS--MQQPGV 3350
Cdd:cd22553     14 QVATTASNIGGQQKQAQSDSSETHDPLILSPPLSQPQQIITAQSSGSAAGGVAYSVSPAV--QTVTVDGHEAifIPANSG 91

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3351 LGQVSMQQPGVM--GQTMQQPgVMGQTSMQPPGVMGQTsmQQTSVMGQVSmqQPGAVGQASMQPQGIMAQASLQQ---SG 3425
Cdd:cd22553     92 LLQTNNQQAIQLapGGTQAIL-ANQQTLIRPNTVQGQA--NASNVLQNIA--QIASGGNAVQLPLNNMTQTIPVQvpvST 166

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3426 VMGQTALQ------QPGILPQPSLQPQGLMAQ--PAMQPAGSLAQpplpqqppmqqpglgvQQVAAPPAQGAIGQPVGPK 3497
Cdd:cd22553    167 ANGQTVYQtiqvpiQAIQSGNAGGGNQALQAQviPQLAQAAQLQP----------------QQLAQVSSQGYIQQIPANA 230

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3498 QPALPQslLVQQLSPQPPALLGhaqtpalQHPSGLGSGAPQRPllLTPQQQQQQQRVLGSPQLAPQSPAMLGHRLVLGQP 3577
Cdd:cd22553    231 SQQQPQ--MVQQGPNQSGQIIG-------QVASASSIQAAAIP--LTVYTGALAGQNGSNQQQVGQIVTSPIQGMTQGLT 299

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|..
gi 1443700932 3578 LHPPQAPLQHFAQprvpgQAPSGLQLAQGMQPLAAGKEQPMD 3619
Cdd:cd22553    300 APASSSIPTVVQQ-----QAIQGNPLPPGTQIIAAGQQLQQD 336
PRK14971 PRK14971
DNA polymerase III subunit gamma/tau;
3358-3456 7.68e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237874 [Multi-domain]  Cd Length: 614  Bit Score: 42.46  E-value: 7.68e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3358 QPGVMGQTMQQPGVMGQTSMQPPGVMGQTSMQQTSVMGQVSMQQPGAVGQASMQPQGIMAQASLQQSGVMGQTALQQPGI 3437
Cdd:PRK14971   370 SGGRGPKQHIKPVFTQPAAAPQPSAAAAASPSPSQSSAAAQPSAPQSATQPAGTPPTVSVDPPAAVPVNPPSTAPQAVRP 449

                           90
                   ....*....|....*....
gi 1443700932 3438 LPQPSLQPQGLMAQPAMQP 3456
Cdd:PRK14971   450 AQFKEEKKIPVSKVSSLGP 468
 
Name Accession Description Interval E-value
SET_KMT2C_2D cd19171
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C), ...
 4957-5109 2.86e-110

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C), 2D (KMT2D) and similar proteins; This family includes KMT2C and KMT2D. Both, KMT2C (also termed HALR or MLL3) and KMT2D (also termed ALR or MLL2), act as histone methyltransferases that methylate 'Lys-4' of histone H3 (H3K4me). They are subunits of MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation.


Pssm-ID: 380948 [Multi-domain]  Cd Length: 153  Bit Score: 348.27  E-value: 2.86e-110
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4957 KSSQYRRLKTEWKNNVYLARSRIQGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVIDA 5036
Cdd:cd19171      1 KSSQYRKLKTEWRSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGEIIRNEVANRREKIYESQNRGIYMFRIDNDWVIDA 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1443700932 5037 TLTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWM 5109
Cdd:cd19171     81 TMTGGPARYINHSCNPNCVAEVVTFDKEKKIIIISNRRIAKGEELTYDYKFDFEDDQHKIPCLCGAPNCRKWM 153
SET_KMT2D cd19209
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2D (KMT2D) ...
 4955-5109 9.50e-109

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2D (KMT2D) and similar proteins; KMT2D (EC2.1.1.43; also termed lysine N-methyltransferase 2D, ALL1-related protein (ALR), or myeloid/lymphoid or mixed-lineage leukemia protein 2 (MLL2)), acts as histone methyltransferase that methylates 'Lys-4' of histone H3 (H3K4me). It is a coactivator for estrogen receptor by being recruited by ESR1, thereby activating transcription. KMT2D is a subunit of MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation.


Pssm-ID: 380986 [Multi-domain]  Cd Length: 155  Bit Score: 343.99  E-value: 9.50e-109
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4955 HSKSSQYRRLKTEWKNNVYLARSRIQGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVI 5034
Cdd:cd19209      1 HSKSSQYRRLKTEWKNNVYLARSRIQGLGLYAAKDLEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVI 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1443700932 5035 DATLTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWM 5109
Cdd:cd19209     81 DATLTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWM 155
SET_KMT2C cd19208
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C) ...
 4956-5109 8.90e-91

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C) and similar proteins; KMT2C (EC2.1.1.43; also termed lysine N-methyltransferase 2C, homologous to ALR protein (HALR) myeloid/lymphoid, or mixed-lineage leukemia protein 3 (MLL3)), acts as a histone methyltransferase that methylates 'Lys-4' of histone H3 (H3K4me) and may be involved in leukemogenesis and developmental disorder. KMT2C is a catalytic subunit of MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation. Overexpression of KMT2C is associated with estrogen receptor-positive breast cancer; KMT2C mediates the estrogen dependence of breast cancer through regulation of estrogen receptor alpha (ERalpha) enhancer function. KMT2C is frequently mutated in certain populations with diffuse-type gastric adenocarcinomas (DGA); its loss promotes epithelial-to-mesenchymal transition (EMT) and is associated with worse overall survival.


Pssm-ID: 380985 [Multi-domain]  Cd Length: 154  Bit Score: 292.30  E-value: 8.90e-91
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4956 SKSSQYRRLKTEWKNNVYLARSRIQGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVID 5035
Cdd:cd19208      1 SKSSQYRKMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNEVANRKEKLYESQNRGVYMFRIDNDHVID 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1443700932 5036 ATLTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWM 5109
Cdd:cd19208     81 ATLTGGPARYINHSCAPNCVAEVVTFEKGHKIIISSSRRIQKGEELCYDYKFDFEDDQHKIPCHCGAVNCRKWM 154
ePHD2_KMT2D cd15698
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 4605-4711 3.08e-75

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2D. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions.


Pssm-ID: 277168  Cd Length: 107  Bit Score: 246.12  E-value: 3.08e-75
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4605 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALINVEVALHRGLLTKCSLCQKTGATNSCNRIRCPS 4684
Cdd:cd15698      1 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALMNVEVALHRGLLTKCSLCQKTGATNSCNRLRCPN 80

                           90       100
                   ....*....|....*....|....*..
gi 1443700932 4685 VYHFACAIRAKCMFFKDKTMLCPLHKL 4711
Cdd:cd15698     81 VYHFACAIRAKCMFFKDKTMLCPMHKL 107
SET_SETD1-like cd10518
SET domain (including post-SET domain) found in SET domain-containing proteins (SETD1A/SETD1B), ...
 4958-5106 1.52e-70

SET domain (including post-SET domain) found in SET domain-containing proteins (SETD1A/SETD1B), histone-lysine N-methyltransferases (KMT2A/KMT2B/KMT2C/KMT2D) and similar proteins; This family includes SET domain-containing protein 1A (SETD1A), 1B (SETD1B), as well as histone-lysine N-methyltransferase 2A (KMT2A), 2B (KMT2B), 2C (KMT2C), 2D (KMT2D). These proteins are histone-lysine N-methyltransferases (EC 2.1.1.43) that specifically methylate 'Lys-4' of histone H3 (H3K4me).


Pssm-ID: 380916  Cd Length: 150  Bit Score: 234.41  E-value: 1.52e-70
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4958 SSQYRRLKTEWKNNVYLARSRIQGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEEQN-RGIYMFRINNEHVIDA 5036
Cdd:cd10518      2 SKRFRQLRSRLKERLRVGKSGIHGWGLFAKRPIAAGEMVIEYVGEVIRPIVADKREKRYDEEGgGGTYMFRIDEDLVIDA 81

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 5037 TLTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQhKIPCHCGAWNCR 5106
Cdd:cd10518     82 TKKGNIARFINHSCDPNCYAKIITVDGEKHIVIFAKRDIAPGEELTYDYKFPIEDEE-KIPCLCGAPNCR 150
ePHD2_KMT2C_like cd15666
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
 4605-4709 2.45e-67

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2C, and KMT2D. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions.


Pssm-ID: 277136  Cd Length: 105  Bit Score: 223.33  E-value: 2.45e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4605 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALINVEVALHRGLLTKCSLCQKTGATNSCNRIRCPS 4684
Cdd:cd15666      1 CVLCGGEGDGDTDGPGRLLNLDVDKWVHLNCALWSYEVYETQNGALMNVEEALRRALTTTCSHCGRTGATVPCFKPRCAN 80

                           90       100
                   ....*....|....*....|....*
gi 1443700932 4685 VYHFACAIRAKCMFFKDKTMLCPLH 4709
Cdd:cd15666     81 VYHLPCAIKDGCMFFKDKTMLCPSH 105
ePHD2_KMT2C cd15697
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 4605-4709 2.58e-61

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2C. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains PHD fingers, two ePHD fingers, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains.


Pssm-ID: 277167  Cd Length: 105  Bit Score: 206.05  E-value: 2.58e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4605 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALINVEVALHRGLLTKCSLCQKTGATNSCNRIRCPS 4684
Cdd:cd15697      1 CCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALINVELALRRGLQMKCVFCHKTGATSGCHRLRCTN 80

                           90       100
                   ....*....|....*....|....*
gi 1443700932 4685 VYHFACAIRAKCMFFKDKTMLCPLH 4709
Cdd:cd15697     81 VYHFTCAIKAQCMFFKDKTMLCPMH 105
HMG-box_KMT2D cd22027
high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2D (KMT2D) and ...
 1615-1698 2.85e-60

high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2D (KMT2D) and similar proteins; KMT2D, also called ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis.


Pssm-ID: 438836  Cd Length: 84  Bit Score: 202.24  E-value: 2.85e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1615 GLSYNQRSLQRWEKDEELGELSTISPVLYANMNFPNLKQDYPDWSSRCKQIMKLWRKVPATDKAPYLQKAKDNRAAHRIN 1694
Cdd:cd22027      1 GLSYNQRSLQRWEKDEELGELSTISPVLYANINFPNLKQDYPDWSSRCKQIMKLWRKVPAADKAPYLQKAKDNRAAHRIN 80


                   ....
gi 1443700932 1695 KVQK 1698
Cdd:cd22027     81 KVQK 84
SET_KMT2A_2B cd19170
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A), ...
 4958-5110 6.42e-52

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A), 2B (KMT2B) and similar proteins; This family includes KMT2A and KMT2B. Both KMT2A (also termed ALL-1 or CXXC7 or MLL or MLL1 or TRX1 or HRX) and KMT2B (also termed MLL4 or TRX2) act as histone methyltransferases that methylate 'Lys-4' of histone H3 (H3K4me).


Pssm-ID: 380947 [Multi-domain]  Cd Length: 152  Bit Score: 181.05  E-value: 6.42e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4958 SSQYRRLKTEWKNNVYLARSRIQGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVIDAT 5037
Cdd:cd19170      2 AMRFRHLRKTAKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGEVIRSVLTDKREKYYESKGIGCYMFRIDDDEVVDAT 81

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1443700932 5038 LTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDqhKIPCHCGAWNCRKWMN 5110
Cdd:cd19170     82 MHGNAARFINHSCEPNCYSRVVNIDGKKHIVIFALRRILRGEELTYDYKFPIEDV--KIPCTCGSKKCRKYLN 152
SET_SETD1 cd19169
SET domain (including post-SET domain) found in SET domain-containing protein 1 (SETD1) and ...
 4960-5106 9.39e-49

SET domain (including post-SET domain) found in SET domain-containing protein 1 (SETD1) and similar proteins; This family includes SET domain-containing protein 1A (SETD1A) and SET domain-containing protein 1B (SETD1B). These proteins are histone-lysine N-methyltransferases that specifically methylate 'Lys-4' of histone H3 (H3K4me) when part of the SET1 histone methyltransferase (HMT) complex, but not if the neighboring 'Lys-9' residue is already methylated.


Pssm-ID: 380946  Cd Length: 148  Bit Score: 171.75  E-value: 9.39e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4960 QYRRLKTEwKNNVYLARSRIQGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEEqnRGI---YMFRINNEHVIDA 5036
Cdd:cd19169      4 KFNQLKFR-KKQLKFAKSRIHDWGLFALEPIAADEMVIEYVGQVIRQSVADEREKRYEA--IGIgssYLFRVDDDTIIDA 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 5037 TLTGGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDqhKIPCHCGAWNCR 5106
Cdd:cd19169     81 TKCGNLARFINHSCNPNCYAKIITVESQKKIVIYSKRPIAVNEEITYDYKFPIEDE--KIPCLCGAPQCR 148
ePHD1_KMT2D cd15695
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 130-212 7.33e-44

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMT2D. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 at Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions.


Pssm-ID: 277165  Cd Length: 90  Bit Score: 155.46  E-value: 7.33e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932  130 GHCWVHRCCAAWSADVLPG-ATGLTHVDRAVFSGISQKCEHCQRMGATIPCRADGCPRLYHFPCAAASGCFQSMKTLRLL 208
Cdd:cd15695      7 GECWVHHWCAAWSAGVKQHeGDGLIGVDKAVFSGISQKCEHCKRLGATIQCHAEGCPRFYHFPCAAASGSFQSMKTLLLL 86


                   ....
gi 1443700932  209 CPEH 212
Cdd:cd15695     87 CPEH 90
SET_KMT2A cd19206
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A) ...
 4960-5110 1.46e-43

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A) and similar proteins; KMT2A (EC2.1.1.43; also termed lysine N-methyltransferase 2A, ALL-1, CXXC-type zinc finger protein 7 (CXXC7), myeloid/lymphoid or mixed-lineage leukemia (MLL), myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), trithorax-like protein (TRX1), or zinc finger protein HRX) acts as a histone methyltransferase that plays an essential role in early development and hematopoiesis. It is a catalytic subunit of the MLL1/MLL complex, a multiprotein complex that mediates both methylation of 'Lys-4' of histone H3 (H3K4me) complex and acetylation of 'Lys-16' of histone H4 (H4K16ac).


Pssm-ID: 380983 [Multi-domain]  Cd Length: 154  Bit Score: 157.49  E-value: 1.46e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4960 QYRRLKTEWKNNVYLARSRIQGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVIDATLT 5039
Cdd:cd19206      4 RFRHLKKTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYSGNVIRSILTDKREKYYDSKGIGCYMFRIDDSEVVDATMH 83

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1443700932 5040 GGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWMN 5110
Cdd:cd19206     84 GNAARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDASNKLPCNCGAKKCRKFLN 154
SET_SET1 cd20072
SET domain (including post-SET domain) found in catalytic component of the Saccharomyces ...
 4969-5106 2.76e-43

SET domain (including post-SET domain) found in catalytic component of the Saccharomyces cerevisiae COMPASS complex and similar proteins; The family contains mostly fungal SET domains, including SET1 found in the catalytic component of the Saccharomyces cerevisiae COMPASS (complex of proteins associated with Set1). SET1 is a histone-lysine N-methyltransferase that specifically methylates 'Lys-4' of histone H3 (H3K4me), when part of the SET1 histone methyltransferase (HMT) complex. The activity of this catalytic domain is established through forming a complex with a set of core proteins; it is extensively contacted by Cps60 (Bre2), Cps50 (Swd1), and Cps30 (Swd3).


Pssm-ID: 380998  Cd Length: 148  Bit Score: 156.43  E-value: 2.76e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4969 KNNVYLARSRIQGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEEQNRG-IYMFRINNEHVIDATLTGGPARYIN 5047
Cdd:cd20072     12 KKQLKFARSAIHNWGLYAMENISAKDMVIEYVGEVIRQQVADEREKRYLRQGIGsSYLFRIDDDTVVDATKKGNIARFIN 91

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1443700932 5048 HSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDqhKIPCHCGAWNCR 5106
Cdd:cd20072     92 HCCDPNCTAKIIKVEGEKRIVIYAKRDIAAGEELTYDYKFPREED--KIPCLCGAPNCR 148
HMG_KMT2C-like cd21997
high mobility group (HMG)-box found in histone-lysine N-methyltransferases KMT2C, KMT2D and ...
 1625-1691 9.51e-42

high mobility group (HMG)-box found in histone-lysine N-methyltransferases KMT2C, KMT2D and similar proteins; This subfamily includes KMT2C and KMT2D. KMT2C, also called myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, and farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also called ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. All subfamily members contain one HMG-box domain.


Pssm-ID: 438813  Cd Length: 67  Bit Score: 148.66  E-value: 9.51e-42
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1443700932 1625 RWEKDEELGELSTISPVLYANMNFPNLKQDYPDWSSRCKQIMKLWRKVPATDKAPYLQKAKDNRAAH 1691
Cdd:cd21997      1 KWEKDEPLGDMATISPVLYANINHPNLKQEYPDWTDRAKQIAKLWRKLSAEERAPYLQKARENRAAL 67
ePHD1_KMT2C_like cd15665
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
 130-212 1.65e-39

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMTC2C and KMTC2D. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five plant PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions.


Pssm-ID: 277135  Cd Length: 90  Bit Score: 143.23  E-value: 1.65e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932  130 GHCWVHRCCAAWSADVLPGATG-LTHVDRAVFSGISQKCEHCQRMGATIPCRADGCPRLYHFPCAAASGCFQSMKTLRLL 208
Cdd:cd15665      7 GEVYAHHCCAAWSEGVCQTEDGaLENVDKAVAKALSQKCSFCLRYGASISCRMPSCSKSFHFPCAAAAGCFQDIKTLTLF 86


                   ....
gi 1443700932  209 CPEH 212
Cdd:cd15665     87 CPEH 90
HMG-box_KMT2C cd22026
high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2C (KMT2C) and ...
 1620-1697 1.45e-38

high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2C (KMT2C) and similar proteins; KMT2C, also called myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis.


Pssm-ID: 438835  Cd Length: 81  Bit Score: 140.30  E-value: 1.45e-38
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1443700932 1620 QRSLQRWEKDEELGELSTISPVLYANMNFPNLKQDYPDWSSRCKQIMKLWRKVPATDKAPYLQKAKDNRAAHRINKVQ 1697
Cdd:cd22026      1 QRSTLKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIAKLWRKASSQERAPYVQKARDNRAALRINKVQ 78
SET_KMT2B cd19207
SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2B (KMT2B) ...
 4960-5110 3.23e-38

SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2B (KMT2B) and similar proteins; KMT2B (EC2.1.1.43; also termed lysine N-methyltransferase 2B, myeloid/lymphoid or mixed-lineage leukemia protein 4 (MLL2/MLL4), trithorax homolog 2 (TRX2), or WW domain-binding protein 7 (WBP-7)), acts as a histone methyltransferase that methylates 'Lys-4' of histone H3 (H3K4me). It is required during the transcriptionally active period of oocyte growth for the establishment and/or maintenance of bulk H3K4 trimethylation (H3K4me3), global transcriptional silencing that precedes resumption of meiosis, oocyte survival and normal zygotic genome activation.


Pssm-ID: 380984 [Multi-domain]  Cd Length: 154  Bit Score: 142.08  E-value: 3.23e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4960 QYRRLKTEWKNNVYLARSRIQGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVIDATLT 5039
Cdd:cd19207      4 RFRHLKKTSKEAVGVYRSAIHGRGLFCKRNIDAGEMVIEYSGIVIRSVLTDKREKFYDSKGIGCYMFRIDDFDVVDATMH 83

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1443700932 5040 GGPARYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWMN 5110
Cdd:cd19207     84 GNAARFINHSCEPNCYSRVIHVEGQKHIVIFALRKIYRGEELTYDYKFPIEDASNKLPCNCGAKRCRRFLN 154
ePHD_KMT2A_like cd15664
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); The ...
 4605-4709 5.71e-36

Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A/MLL1 and KMT2B/MLL2. KMT2A and KMT2B comprise the mammalian Trx branch of COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation by mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three PHD fingers, this extended PHD (ePHD) finger, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain.


Pssm-ID: 277134  Cd Length: 105  Bit Score: 133.68  E-value: 5.71e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4605 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALINVEVALHRGLLTKCSLCQKTGATNSCNRIRCPS 4684
Cdd:cd15664      1 CALCGVYGDDEPNDAGRLLYCGQDEWVHINCALWSAEVFEEDDGSLQNVHSAVSRGRMMKCELCGKPGATVGCCLKSCPA 80

                           90       100
                   ....*....|....*....|....*
gi 1443700932 4685 VYHFACAIRAKCMFFKDKTMLCPLH 4709
Cdd:cd15664     81 NYHFMCARKAECVFQDDKKVFCPAH 105
SET_SETD1A cd19204
SET domain (including post-SET domain) found in SET domain-containing protein 1A (SETD1A) and ...
 4969-5110 4.13e-35

SET domain (including post-SET domain) found in SET domain-containing protein 1A (SETD1A) and similar proteins; SETD1A (EC2.1.1.43), also termed lysine N-methyltransferase 2F, or Set1/Ash2 histone methyltransferase complex subunit SET1, is a histone-lysine N-methyltransferase that specifically methylates 'Lys-4' of histone H3 (H3K4me), when part of the SET1 histone methyltransferase (HMT) complex, but not if the neighboring 'Lys-9' residue is already methylated. Human SET domain containing protein 1A (hSETD1A) expression occurs at a high rate in hepatocellular carcinoma patients and controls tumor metastasis in breast cancer by activating MMP expression.


Pssm-ID: 380981 [Multi-domain]  Cd Length: 153  Bit Score: 133.23  E-value: 4.13e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4969 KNNVYLARSRIQGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGI-YMFRINNEHVIDATLTGGPARYIN 5047
Cdd:cd19204     13 KKKLRFGRSRIHEWGLFAMEPIAADEMVIEYVGQNIRQVVADMREKRYVQEGIGSsYLFRVDHDTIIDATKCGNLARFIN 92

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1443700932 5048 HSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDqhKIPCHCGAWNCRKWMN 5110
Cdd:cd19204     93 HCCTPNCYAKVITIESQKKIVIYSKQPIGVNEEITYDYKFPIEDN--KIPCLCGTENCRGTLN 153
SET_SETD1B cd19205
SET domain (including post-SET domain) found in SET domain-containing protein 1B (SETD1B) and ...
 4969-5110 2.10e-34

SET domain (including post-SET domain) found in SET domain-containing protein 1B (SETD1B) and similar proteins; SETD1B (EC2.1.1.43), also termed lysine N-methyltransferase 2G, is a histone-lysine N-methyltransferase that specifically methylates 'Lys-4' of histone H3 (H3K4me) when part of the SET1 histone methyltransferase (HMT) complex, but not if the neighboring 'Lys-9' residue is already methylated. Loss of SETD1B occurs in up to half the gastric and colorectal cancers, most commonly via SETD1B mutations, while de novo variants in SETD1B are associated with intellectual disability, epilepsy and autism.


Pssm-ID: 380982 [Multi-domain]  Cd Length: 153  Bit Score: 130.95  E-value: 2.10e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4969 KNNVYLARSRIQGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGI-YMFRINNEHVIDATLTGGPARYIN 5047
Cdd:cd19205     13 KKKLKFCKSHIHDWGLFAMEPIAADEMVIEYVGQNIRQVIADMREKRYEDEGIGSsYMFRVDHDTIIDATKCGNFARFIN 92

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1443700932 5048 HSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDqhKIPCHCGAWNCRKWMN 5110
Cdd:cd19205     93 HSCNPNCYAKVITVESQKKIVIYSKQHINVNEEITYDYKFPIEDV--KIPCLCGSENCRGTLN 153
PHD3_KMT2D cd15597
PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 954-1004 7.62e-33

PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the third PHD finger.


Pssm-ID: 277072  Cd Length: 51  Bit Score: 122.84  E-value: 7.62e-33
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1443700932  954 DMCVVCGSFGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVECI 1004
Cdd:cd15597      1 DMCVVCGSFGRGSEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVECI 51
SET COG2940
SET domain-containing protein (function unknown) [General function prediction only];
4971-5108 1.15e-32

SET domain-containing protein (function unknown) [General function prediction only];


Pssm-ID: 442183 [Multi-domain]  Cd Length: 134  Bit Score: 125.46  E-value: 1.15e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4971 NVYLARSRIQGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEEQNRgiYMFRINNEHVIDATLTGGPARYINHSC 5050
Cdd:COG2940      7 RIEVRPSPIHGRGVFATRDIPKGTLIGEYPGEVITWAEAERREPHKEPLHT--YLFELDDDGVIDGALGGNPARFINHSC 84

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1443700932 5051 APNCVAEVVTFD-----KEDkiiiissrrIPKGEELTYDYQFDFEDDQHkiPCHCGawNCRKW 5108
Cdd:COG2940     85 DPNCEADEEDGRifivaLRD---------IAAGEELTYDYGLDYDEEEY--PCRCP--NCRGT 134
SET smart00317
SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Putative methyl transferase, based on ...
 4970-5092 4.34e-32

SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Putative methyl transferase, based on outlier plant homologues


Pssm-ID: 214614 [Multi-domain]  Cd Length: 124  Bit Score: 123.21  E-value: 4.34e-32
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932  4970 NNVYLARSRIQGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYE-EQNRGIYMFRINNEHVIDATLTGGPARYINH 5048
Cdd:smart00317    1 NKLEVFKSPGKGWGVRATEDIPKGEFIGEYVGEIITSEEAEERPKAYDtDGAKAFYLFDIDSDLCIDARRKGNLARFINH 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....
gi 1443700932  5049 SCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDD 5092
Cdd:smart00317   81 SCEPNCELLFVEVNGDDRIVIFALRDIKPGEELTIDYGSDYANE 124
FYRC smart00542
FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region ...
 4813-4900 5.86e-32

FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region (FYRN), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.


Pssm-ID: 197781  Cd Length: 86  Bit Score: 121.25  E-value: 5.86e-32
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932  4813 EFVVQVIEQGleDLIFSDSSPQAVWNRIIEPVAMMRKEADMLRLFPEYLKGEELFGLTVHAVLRIAESLPGVESCQNYLF 4892
Cdd:smart00542    1 LFRVEIESDP--GEVFKGESPEKCWEMVLERVQEARIAADLLQLLPEGVSGEEMFGLSSPAVVKLIEALPGVHQCTNYWF 78


                    ....*...
gi 1443700932  4893 RYGRHPLM 4900
Cdd:smart00542   79 RYHRSPLL 86
SET_SETD2 cd19172
SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2) and ...
 4965-5109 6.63e-32

SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2) and similar proteins; SETD2 (also termed HIF-1, huntingtin yeast partner B, huntingtin-interacting protein 1 (HIP-1), huntingtin-interacting protein B, lysine N-methyltransferase 3A or protein-lysine N-methyltransferase SETD2) acts as histone-lysine N-methyltransferase that specifically trimethylates 'Lys-36' of histone H3 (H3K36me3) using demethylated 'Lys-36' (H3K36me2) as substrate. It has been shown that methylation is a posttranslational modification of dynamic microtubules and that SETD2 methylates alpha-tubulin at lysine 40, the same lysine that is marked by acetylation on microtubules. Methylation of microtubules occurs during mitosis and cytokinesis and can be ablated by SETD2 deletion, which causes mitotic spindle and cytokinesis defects, micronuclei, and polyploidy.


Pssm-ID: 380949 [Multi-domain]  Cd Length: 142  Bit Score: 123.46  E-value: 6.63e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4965 KTEWKnnvylarsriqGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYE-EQNRGIYMFRINNEHVIDATLTGGPA 5043
Cdd:cd19172      8 RTEKK-----------GWGLRAAEDLPKGTFVIEYVGEVLDEKEFKRRMKEYArEGNRHYYFMALKSDEIIDATKKGNLS 76

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1443700932 5044 RYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFD--FEDDQhkiPCHCGAWNCRKWM 5109
Cdd:cd19172     77 RFINHSCEPNCETQKWTVNGELRVGFFAKRDIPAGEELTFDYQFEryGKEAQ---KCYCGSPNCRGYI 141
SET_SETD2-like cd10531
SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2), ...
 4971-5106 4.01e-31

SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2), nuclear SETD2 (NSD2), ASH1-like protein (ASH1L) and similar proteins; This family includes SET domain-containing protein 2 (SETD2), nuclear SETD2 (NSD2) and ASH1-like protein (ASH1L), which function as histone-lysine N-methyltransferases. SETD2 specifically trimethylates 'Lys-36' of histone H3 (H3K36me3) using demethylated 'Lys-36' (H3K36me2) as substrate. NSD2 shows histone H3 'Lys-27' (H3K27me) methyltransferase activity. ASH1L specifically methylates 'Lys-36' of histone H3 (H3K36me). The family also includes Arabidopsis thaliana ASH1-related protein 3 (ASHR3) and similar proteins.


Pssm-ID: 380929  Cd Length: 136  Bit Score: 120.82  E-value: 4.01e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4971 NVYLARSRIQGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRR-EKIYEEQNRGIYMFRINNEHVIDATLTGGPARYINHS 5049
Cdd:cd10531      1 KLELFRTEKKGWGVKAKEDIQKGEFIIEYVGEVIDKKEFKERlDEYEELGKSNFYILSLSDDVVIDATRKGNLSRFINHS 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1443700932 5050 CAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQhKIPCHCGAWNCR 5106
Cdd:cd10531     81 CEPNCETQKWIVNGEYRIGIFALRDIPAGEELTFDYNFVNYNEA-KQVCLCGAQNCR 136
PHD4_KMT2C cd15596
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 948-1003 2.05e-30

PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the fourth PHD finger.


Pssm-ID: 277071  Cd Length: 57  Bit Score: 115.88  E-value: 2.05e-30
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1443700932  948 KFVLMQDMCVVCGSFGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVEC 1003
Cdd:cd15596      1 KFTLNQDMCVVCGSFGQGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLEC 56
PHD5_KMT2D cd15601
PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 1083-1132 2.73e-30

PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such asHOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is downregulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger.


Pssm-ID: 277074  Cd Length: 51  Bit Score: 115.39  E-value: 2.73e-30
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1083 CPVCREKYVEDDLLIQCRHCERWLHAACDSLFTEEEVEQAADEGFDCSAC 1132
Cdd:cd15601      2 CPVCRAKYVEEDLLIQCRHCDRWVHAVCESLFTEDEVEQAADEGFDCSSC 51
ePHD_KMT2A cd15693
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A); The extended plant ...
 4603-4713 6.11e-30

Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of KMT2A. KMT2A also termed ALL-1, or CXXC-type zinc finger protein 7, or myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), or trithorax-like protein (Htrx), or zinc finger protein HRX, is a histone methyltransferase that belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2). It regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex, which also contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL1 complex is highly active and specific for H3K4methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three PHD fingers, a Bromodomain domain, this extended PHD finger, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain.


Pssm-ID: 277163  Cd Length: 113  Bit Score: 116.64  E-value: 6.11e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4603 RKCCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALINVEVALHRGLLTKCSLCQKTGATNSCNRIRC 4682
Cdd:cd15693      1 RQCALCLKYGDDSANDAGRLLYIGQNEWTHVNCALWSAEVFEDDDGSLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSC 80

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1443700932 4683 PSVYHFACAIRAKCMFFKDKTMLCPLHK--LKG 4713
Cdd:cd15693     81 TSNYHFMCSRAKNCVFLEDKKVYCQRHKdlIKG 113
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
 1005-1051 6.53e-30

PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger of KMT2C and the fourth PHD finger of KMT2D.


Pssm-ID: 276988  Cd Length: 47  Bit Score: 114.11  E-value: 6.53e-30
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1443700932 1005 VCEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 1051
Cdd:cd15513      1 VCEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 47
SET_ASHR3-like cd19175
SET domain (including post-SET domain) found in Arabidopsis thaliana ASH1-related protein 3 ...
 4981-5109 6.60e-30

SET domain (including post-SET domain) found in Arabidopsis thaliana ASH1-related protein 3 (ASHR3) and similar proteins; This family includes Arabidopsis thaliana ASH1-related protein 3 (ASHR3, also termed protein SET DOMAIN GROUP 4 or protein stamen loss), ASH1 homolog 3 (ASHH3, also termed protein SET DOMAIN GROUP 7) and homolog 4 (ASHH4, also termed protein SET DOMAIN GROUP 24). They all function as histone-lysine N-methyltransferases (EC 2.1.1.43).


Pssm-ID: 380952 [Multi-domain]  Cd Length: 139  Bit Score: 117.52  E-value: 6.60e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4981 GLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEEQ-NRGIYMFRINNEHVIDATLTGGPARYINHSCAPNCVAEVV 5059
Cdd:cd19175     11 GWGLVADEDINAGEFIIEYVGEVIDDKTCEERLWDMKHKgEKNFYMCEIDKDMVIDATFKGNLSRFINHSCDPNCELQKW 90

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1443700932 5060 TFDKEDKIIIISSRRIPKGEELTYDYQF-DFEDDQHkipCHCGAWNCRKWM 5109
Cdd:cd19175     91 QVDGETRIGVFAIRDIKKGEELTYDYQFvQFGADQD---CHCGSKNCRGKL 138
SET_EZH cd10519
SET domain found in enhancer of zeste homolog 1 (EZH1), zeste homolog 2 (EZH2) and similar ...
 4972-5087 1.47e-28

SET domain found in enhancer of zeste homolog 1 (EZH1), zeste homolog 2 (EZH2) and similar proteins; The family includes EZH1 and EZH2. EZH1 (EC 2.1.1.43; also termed ENX-2, or histone-lysine N-methyltransferase EZH1) is a catalytic subunit of the PRC2/EED-EZH1 complex, which methylates 'Lys-27' of histone H3, leading to transcriptional repression of the affected target gene. EZH2 (EC 2.1.1.43; also termed lysine N-methyltransferase 6, ENX-1, or histone-lysine N-methyltransferase EZH2) is a catalytic subunit of the PRC2/EED-EZH2 complex, which methylates 'Lys-9' (H3K9me) and 'Lys-27' (H3K27me) of histone H3, leading to transcriptional repression of the affected target gene. Both, EZH1 and EZH2, can mono-, di- and trimethylate 'Lys-27' of histone H3 to form H3K27me1, H3K27me2 and H3K27me3, respectively.


Pssm-ID: 380917  Cd Length: 117  Bit Score: 112.72  E-value: 1.47e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4972 VYLARSRIQGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGiYMFRINNEHVIDATLTGGPARYINHSCA 5051
Cdd:cd10519      3 LLLGKSDVAGWGLFLKEPIKKDEFIGEYTGELISQDEADRRGKIYDKYNSS-YLFNLNDQFVVDATRKGNKIRFANHSSN 81

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1443700932 5052 PNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQF 5087
Cdd:cd10519     82 PNCYAKVMMVNGDHRIGIFAKRDIEAGEELFFDYGY 117
PHD4_KMT2C_like cd15512
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD domain 3 found in ...
 955-1003 4.44e-28

PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD domain 3 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, two extended PHD (ePHD) fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fourth PHD finger of KMT2C and the third domain of KMT2D.


Pssm-ID: 276987  Cd Length: 49  Bit Score: 109.09  E-value: 4.44e-28
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1443700932  955 MCVVCGSFGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVEC 1003
Cdd:cd15512      1 MCVSCGSFGRGAEGRLIACSQCGQCYHPYCVNVKVTKVILSKGWRCLDC 49
SET_NSD cd19173
SET domain (including post-SET domain) found in nuclear SET domain-containing proteins, NSD1, ...
 4981-5105 1.83e-27

SET domain (including post-SET domain) found in nuclear SET domain-containing proteins, NSD1, NSD2, NSD3 and similar proteins; The nuclear receptor-binding SET Domain (NSD) family of histone H3 lysine 36 methyltransferases is comprised of NSD1, NSD2, and NSD3, which are primarily known to be involved in chromatin integrity and gene expression through mono-, di-, or tri-methylating lysine 36 of histone H3 (H3K36), respectively. NSD1 (EC 2.1.1.43; also termed histone-lysine N-methyltransferase H3 lysine-36 and H4 lysine-20 specific, androgen receptor coactivator 267 kDa protein (ARA267), androgen receptor-associated protein of 267 kDa, H3-K36-HMTase, H4-K20-HMTase, lysine N-methyltransferase 3B (KMT3B) or NR-binding SET domain-containing protein 1) functions as a histone-lysine N-methyltransferase that preferentially methylates 'Lys-36' of histone H3 and 'Lys-20' of histone H4. NSD2 (EC 2.1.1.43; also termed multiple myeloma SET domain-containing protein (MMSET), protein trithorax-5 (TRX5), or wolf-Hirschhorn syndrome candidate 1 protein (WHSC1)) acts as histone-lysine N-methyltransferase with histone H3 'Lys-27' (H3K27me) methyltransferase activity. NSD3 (EC 2.1.1.43; also termed protein whistle, WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1L1), or WHSC1-like protein 1) functions as a histone-lysine N-methyltransferase that preferentially methylates 'Lys-4' and 'Lys-27' of histone H3.


Pssm-ID: 380950 [Multi-domain]  Cd Length: 142  Bit Score: 110.87  E-value: 1.83e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4981 GLGLYAAKDIEKHTMVIEYIGTIIRNEVANRR-EKIYEEQNRGIYMFRINNEHVIDATLTGGPARYINHSCAPNCVAEVV 5059
Cdd:cd19173     13 GWGLRTKRDIKKGDFVIEYVGELIDEEECRRRlKKAHENNITNFYMLTLDKDRIIDAGPKGNLSRFMNHSCQPNCETQKW 92

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932 5060 TFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQhKIPCHCGAWNC 5105
Cdd:cd19173     93 TVNGDTRVGLFAVRDIPAGEELTFNYNLDCLGNE-KKVCRCGAPNC 137
PHD6_KMT2C_like cd15514
PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 5 found in ...
 1082-1132 1.96e-27

PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 5 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the sixth PHD finger of KMT2C and the fifth PHD finger of KMT2D.


Pssm-ID: 276989  Cd Length: 51  Bit Score: 107.37  E-value: 1.96e-27
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1443700932 1082 VCPVCREKYVEDDLLIQCRHCERWLHAACDSLFTEEEVEQAADEGFDCSAC 1132
Cdd:cd15514      1 KCPVCSRSYNEGELIIQCSQCERWLHGACDSLRTEEEAERAADNGYRCLLC 51
FYRC pfam05965
F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 4811-4895 5.27e-27

F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00542.


Pssm-ID: 461788  Cd Length: 83  Bit Score: 107.31  E-value: 5.27e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4811 RPEFVVQVIEQglEDLIFSDSSPQAVWNRIIEPVAMMRKEADMLRLFPEYLKGEELFGLTVHAVLRIAESLPGVESCQNY 4890
Cdd:pfam05965    1 GPLFRVTVEED--PDESFEGSSPTKCWSMVLERVQELRREAGLKLKLPESISGEDMFGLTHPAVVRLIESLPGAEKCTNY 78


                   ....*
gi 1443700932 4891 LFRYG 4895
Cdd:pfam05965   79 KFRYG 83
ePHD cd15571
Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is ...
 4605-4709 9.10e-27

Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. The extended PHD finger is characterized as Cys2HisCys5HisCys2His, which has been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors.


Pssm-ID: 277046 [Multi-domain]  Cd Length: 112  Bit Score: 107.67  E-value: 9.10e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4605 CCFCHEEGdGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGAL--INVEVALHRGLLTKCSLCQKT-GATNSCNRIR 4681
Cdd:cd15571      1 CALCPRSG-GALKGGGALKTTSDGLWVHVVCALWSPEVYFDDGTLLevEGVSKIPKRRKKLKCSICGKRgGACIQCSYPG 79

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1443700932 4682 CPSVYHFACAIRAKCMF-----FKDKTMLCPLH 4709
Cdd:cd15571     80 CPRSFHVSCAIRAGCLFefedgPGNFVVYCPKH 112
ePHD_KMT2B cd15694
Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B); The extended plant ...
 4605-4709 4.49e-26

Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of KMT2B. KMT2B is also called trithorax homolog 2 or WW domain-binding protein 7 (WBP-7). KMT2B is encoded by the gene that was first named myeloid/lymphoid or mixed-lineage leukemia 2 (MLL2), a second human homolog of Drosophila trithorax, located on chromosome 19. It belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2) and is vital for normal mammalian embryonic development. KMT2B functions as the catalytic subunit in the MLL2 complex, which contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL2 complex is highly active and specific for histone 3 lysine 4 (H3K4) methylation, which stimulates chromatin transcription in a SAM- and H3K4-dependent manner. Moreover, KMT2B plays a critical role in memory formation by mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. KMT2B contains a CxxC (x for any residue) zinc finger domain, three PHD fingers, this ePHD finger, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain.


Pssm-ID: 277164  Cd Length: 105  Bit Score: 105.51  E-value: 4.49e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4605 CCFCHEEGDGATDGPARLLNLDLDLWVHLNCALWSTEVYETQGGALINVEVALHRGLLTKCSLCQKTGATNSCNRIRCPS 4684
Cdd:cd15694      1 CALCLKYGDADSKDAGRLLYIGQNEWTHVNCAIWSAEVFEENDGSLKNVHAAVARGRQMRCEHCQKIGATVGCCLSACLS 80

                           90       100
                   ....*....|....*....|....*
gi 1443700932 4685 VYHFACAIRAKCMFFKDKTMLCPLH 4709
Cdd:cd15694     81 NFHFMCARASRCCFQDDKKVFCQKH 105
ePHD1_KMT2C cd15696
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 130-212 2.46e-25

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMT2C. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several PHD fingers, two ePHD fingers, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains.


Pssm-ID: 277166  Cd Length: 90  Bit Score: 102.72  E-value: 2.46e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932  130 GHCWVHRCCAAWSADVLPG-ATGLTHVDRAVFSGISQKCEHCQRMGATIPCRADGCPRLYHFPCAAASGCFQSMKTLRLL 208
Cdd:cd15696      7 GECWAHLRCAEWSLGVCQGeEQLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQDFSRRLLL 86


                   ....
gi 1443700932  209 CPEH 212
Cdd:cd15696     87 CPTH 90
PHD2_KMT2D cd15595
PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 270-315 3.63e-25

PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such asHOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 277070  Cd Length: 46  Bit Score: 100.84  E-value: 3.63e-25
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932  270 VCQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIETLPAASWKCKNC 315
Cdd:cd15595      1 VCQTCRKPGEDSKMLVCEACDKGYHTFCLKPAMESLPTDSWKCKAC 46
SET_SUV39H cd10542
SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 ...
 4981-5109 1.37e-24

SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homologs, SUV39H1, SUV39H2 and similar proteins; This family includes SUV39H1 (also termed histone H3-K9 methyltransferase 1, H3-K9-HMTase 1, lysine N-methyltransferase 1A, KMT1A, position-effect variegation 3-9 homolog, SUV39H, or Su(var)3-9 homolog 1) and SUV39H2 (also termed histone H3-K9 methyltransferase 2, H3-K9-HMTase 2, lysine N-methyltransferase 1B, KMT1B, or Su(var)3-9 homolog 2), both act as histone-lysine N-methyltransferases that specifically trimethylate 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. They mainly function in heterochromatin regions, thereby playing central roles in the establishment of constitutive heterochromatin at pericentric and telomere regions. Also included are Schizosaccharomyces pombe H3K9 methyltransferase Clr4 (SUV39H homolog) and Neurospora crassa DIM-5, both of which also methylate 'Lys-9' of histone H3.


Pssm-ID: 380940 [Multi-domain]  Cd Length: 245  Bit Score: 105.84  E-value: 1.37e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4981 GLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEEQNRgIYMFRIN-----NEHVIDATLTGGPARYINHSCAPN-- 5053
Cdd:cd10542     99 GWGVKTLEDIKKGTFVMEYVGEIITSEEAERRGKIYDANGR-TYLFDLDyndddCEYTVDAAYYGNISHFINHSCDPNla 177

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1443700932 5054 ---CVAE--------VVTFDKEDkiiiissrrIPKGEELTYDYQFDFEDDQH----------KIPCHCGAWNCRKWM 5109
Cdd:cd10542    178 vyaVWINhldprlprIAFFAKRD---------IKAGEELTFDYLMTGTGGSSestipkpkdvRVPCLCGSKNCRKYL 245
ePHD2_KMT2C_like cd15666
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
 133-212 1.16e-22

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2C, and KMT2D. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions.


Pssm-ID: 277136  Cd Length: 105  Bit Score: 95.45  E-value: 1.16e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932  133 WVHRCCAAWSADVLPGATG-LTHVDRAVFSGISQKCEHCQRMGATIPCRADGCPRLYHFPCAAASGC-FQSMKTlrLLCP 210
Cdd:cd15666     26 WVHLNCALWSYEVYETQNGaLMNVEEALRRALTTTCSHCGRTGATVPCFKPRCANVYHLPCAIKDGCmFFKDKT--MLCP 103


                   ..
gi 1443700932  211 EH 212
Cdd:cd15666    104 SH 105
SET_ASH1L cd19174
SET domain (including post-SET domain) found in ASH1-like protein (ASH1L) and similar proteins; ...
 4981-5110 1.26e-22

SET domain (including post-SET domain) found in ASH1-like protein (ASH1L) and similar proteins; ASH1L (EC 2.1.1.43; also termed absent small and homeotic disks protein 1 homolog, KMT2H, or lysine N-methyltransferase 2H) acts as histone-lysine N-methyltransferase that specifically methylates 'Lys-36' of histone H3 (H3K36me). It plays important roles in development; heterozygous mutation of ASH1L is associated with severe intellectual disability (ID) and multiple congenital anomaly (MCA).


Pssm-ID: 380951 [Multi-domain]  Cd Length: 141  Bit Score: 96.98  E-value: 1.26e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4981 GLGLYAAKDIEKHTMVIEYIGTII-RNEVANRREKIYEeQNRGIYMFRINNEHVIDATLTGGPARYINHSCAPNC----- 5054
Cdd:cd19174     11 GWGVRTKEPIKAGQFIIEYVGEVVsEQEFRRRMIEQYH-NHSHHYCLNLDSGMVIDGYRMGNEARFVNHSCDPNCemqkw 89

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 5055 ----VAEVVTFDKEDkiiiissrrIPKGEELTYDYQFDFEDDQHKIPCHCGAWNCRKWMN 5110
Cdd:cd19174     90 svngVYRIGLFALKD---------IPAGEELTYDYNFHSFNVEKQQPCKCGSPNCRGVIG 140
PHD2_KMT2C cd15594
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 270-315 5.27e-22

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the second PHD finger.


Pssm-ID: 277069  Cd Length: 46  Bit Score: 91.54  E-value: 5.27e-22
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932  270 VCQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIETLPAASWKCKNC 315
Cdd:cd15594      1 VCQTCRQPGDDNKMLVCDTCDKGYHTFCLQPVMTTIPKNGWKCKNC 46
SET pfam00856
SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be ...
 4981-5085 6.81e-22

SET domain; SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure.


Pssm-ID: 459965 [Multi-domain]  Cd Length: 115  Bit Score: 93.74  E-value: 6.81e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4981 GLGLYAAKDIEKHTMVIEYIGT-IIRNEVANRREKIYEEQNR----GIYMFRIN--NEHVIDATLT--GGPARYINHSCA 5051
Cdd:pfam00856    1 GRGLFATEDIPKGEFIGEYVEVlLITKEEADKRELLYYDKLElrlwGPYLFTLDedSEYCIDARALyyGNWARFINHSCD 80

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1443700932 5052 PNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDY 5085
Cdd:pfam00856   81 PNCEVRVVYVNGGPRIVIFALRDIKPGEELTIDY 114
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 223-268 7.12e-22

PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the first PHD finger.


Pssm-ID: 276984  Cd Length: 48  Bit Score: 91.22  E-value: 7.12e-22
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1443700932  223 RCVVCDGPGDLRDLLFCTSCGQHYHGACLD--VVLAPHKRAGWQCPEC 268
Cdd:cd15509      1 NCAVCDSPGDLSDLLFCTSCGQHYHGSCLDpaVRPTPLVRAGWQCPEC 48
PHD6_KMT2C cd15600
PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 1083-1132 1.24e-21

PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the sixth PHD finger.


Pssm-ID: 277073  Cd Length: 51  Bit Score: 90.76  E-value: 1.24e-21
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1083 CPVCREKYVEDDLLIQCRHCERWLHAACDSLFTEEEVEQAADEGFDCSAC 1132
Cdd:cd15600      2 CPICYRNYREEELILQCRQCDRWMHASCQNLNTEEEVENAADNGFDCTMC 51
PHD2_KMT2C_like cd15510
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 270-315 7.02e-21

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 276985  Cd Length: 46  Bit Score: 88.64  E-value: 7.02e-21
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932  270 VCQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIETLPAASWKCKNC 315
Cdd:cd15510      1 VCQACRQPGDDTKMLVCETCDKGYHTSCLRPVMSSIPKYGWKCKNC 46
ePHD cd15571
Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is ...
 107-212 2.56e-20

Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. The extended PHD finger is characterized as Cys2HisCys5HisCys2His, which has been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors.


Pssm-ID: 277046 [Multi-domain]  Cd Length: 112  Bit Score: 89.18  E-value: 2.56e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932  107 PPDDPAPVGFPEPVTPSRCQlpaghcWVHRCCAAWSADV---LPGATGLTHVDRAVFSGISQKCEHC-QRMGATIPCRAD 182
Cdd:cd15571      5 PRSGGALKGGGALKTTSDGL------WVHVVCALWSPEVyfdDGTLLEVEGVSKIPKRRKKLKCSICgKRGGACIQCSYP 78

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1443700932  183 GCPRLYHFPCAAASGCFQSMKT----LRLLCPEH 212
Cdd:cd15571     79 GCPRSFHVSCAIRAGCLFEFEDgpgnFVVYCPKH 112
SET_NSD2 cd19211
SET domain (including post-SET domain) found in nuclear SET domain-containing protein 2 (NSD2) ...
 4974-5105 1.15e-19

SET domain (including post-SET domain) found in nuclear SET domain-containing protein 2 (NSD2) and similar proteins; NSD2 (EC 2.1.1.43; also termed multiple myeloma SET domain-containing protein (MMSET), protein trithorax-5 (TRX5), or wolf-Hirschhorn syndrome candidate 1 protein (WHSC1)) acts as histone-lysine N-methyltransferase with histone H3 'Lys-36' (H3K36me) methyltransferase activity. NSD2 has been shown to mediate di- and trimethylation of H3K36 and dimethylation of H4K20 in different systems, and has been characterized as a transcriptional repressor interacting with histone deacetylase HDAC1 and histone demethylase LSD1. NSD2 mediates constitutive NF-kappaB signaling for cancer cell proliferation, survival and tumor growth. It is highly overexpressed in several types of human cancers, including small-cell lung cancers, neuroblastoma, carcinomas of stomach and colon, and bladder cancers, and its overexpression tends to be associated with tumor aggressiveness. WHSC1 is frequently deleted in Wolf-Hirschhorn syndrome (WHS).


Pssm-ID: 380988 [Multi-domain]  Cd Length: 142  Bit Score: 88.51  E-value: 1.15e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4974 LARSRIQGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEEQN-RGIYMFRINNEHVIDATLTGGPARYINHSCAP 5052
Cdd:cd19211      6 IIKTEGKGWGLIAKRDIKKGEFVNEYVGELIDEEECMARIKHAHENDiTHFYMLTIDKDRIIDAGPKGNYSRFMNHSCQP 85

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1443700932 5053 NCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIpCHCGAWNC 5105
Cdd:cd19211     86 NCETQKWTVNGDTRVGLFAVCDIPAGTELTFNYNLDCLGNEKTV-CRCGAPNC 137
ePHD1_KMT2C_like cd15665
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
 4605-4709 2.51e-19

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMTC2C and KMTC2D. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five plant PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions.


Pssm-ID: 277135  Cd Length: 90  Bit Score: 85.45  E-value: 2.51e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4605 CCFCheegdgatdgparllNLDlDLWVHLNCALWSTEVYETQGGALINVEVALHRGLLTKCSLCQKTGATNSCNRIRCPS 4684
Cdd:cd15665      1 CALC---------------NLG-EVYAHHCCAAWSEGVCQTEDGALENVDKAVAKALSQKCSFCLRYGASISCRMPSCSK 64

                           90       100
                   ....*....|....*....|....*..
gi 1443700932 4685 VYHFACAIRAKCmF--FKDKTMLCPLH 4709
Cdd:cd15665     65 SFHFPCAAAAGC-FqdIKTLTLFCPEH 90
SET_EZH2 cd19218
SET domain found in enhancer of zeste homolog 2 (EZH2) and similar proteins; EZH2 (EC 2.1.1.43) ...
 4968-5087 4.70e-19

SET domain found in enhancer of zeste homolog 2 (EZH2) and similar proteins; EZH2 (EC 2.1.1.43), also termed lysine N-methyltransferase 6, or ENX-1, or histone-lysine N-methyltransferase EZH2, is a catalytic subunit of the polycomb repressive complex 2 (PRC2)/EED-EZH2 complex, which methylates 'Lys-9' (H3K9me) and 'Lys-27' (H3K27me) of histone H3, leading to transcriptional repression of the affected target gene. It can mono-, di- and trimethylate 'Lys-27' of histone H3 to form H3K27me1, H3K27me2 and H3K27me3, respectively. PRC2 is involved in several cancers; EZH2 is overexpressed in breast, liver and prostate cancer, while point mutations in EZH2 alter the substrate preference and product specificity of PRC2 in Non-Hodgkin lymphomas (NHLs). Thus, PRC2 is a popular target for cancer therapeutics.


Pssm-ID: 380995  Cd Length: 120  Bit Score: 86.12  E-value: 4.70e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4968 WKNNVYLARSRIQGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEEqnrgiYM----FRINNEHVIDATLTGGPA 5043
Cdd:cd19218      2 SKKHLLLAPSDVAGWGIFIKDPVQKNEFISEYCGEIISQDEADRRGKVYDK-----YMcsflFNLNNDFVVDATRKGNKI 76

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 1443700932 5044 RYINHSCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQF 5087
Cdd:cd19218     77 RFANHSVNPNCYAKVMMVNGDHRIGIFAKRAIQTGEELFFDYRY 120
SET_EZH1 cd19217
SET domain found in enhancer of zeste homolog 1 (EZH1) and similar proteins; EZH1 (EC 2.1.1.43) ...
 4969-5091 3.55e-18

SET domain found in enhancer of zeste homolog 1 (EZH1) and similar proteins; EZH1 (EC 2.1.1.43), also termed ENX-2, or histone-lysine N-methyltransferase EZH1, is a catalytic subunit of the PRC2/EED-EZH1 complex, which methylates 'Lys-27' of histone H3, leading to transcriptional repression of the affected target gene. It can mono-, di- and trimethylate 'Lys-27' of histone H3 to form H3K27me1, H3K27me2 and H3K27me3, respectively.


Pssm-ID: 380994  Cd Length: 136  Bit Score: 83.96  E-value: 3.55e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4969 KNNVYLARSRIQGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGiYMFRINNEHVIDATLTGGPARYINH 5048
Cdd:cd19217      5 KKHLLLAPSDVAGWGTFIKESVQKNEFISEYCGELISQDEADRRGKVYDKYMSS-FLFNLNNDFVVDATRKGNKIRFANH 83

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1443700932 5049 SCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFED 5091
Cdd:cd19217     84 SVNPNCYAKVVMVNGDHRIGIFAKRAIQQGEELFFDYRYSQAD 126
FYRN pfam05964
F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 4754-4805 3.76e-18

F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00541.


Pssm-ID: 461787  Cd Length: 51  Bit Score: 81.01  E-value: 3.76e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1443700932 4754 GGLVFHAIGQLLPHQMAdFHSVTALYPVGYEATRIYWSLRTNNRRCCYRCTI 4805
Cdd:pfam05964    1 GSLTVLSLGEIVPDRPA-FHTERYIYPVGYKSTRLYWSTKDPRKRCRYTCEI 51
ePHD_RAI1_like cd15668
Extended PHD finger found in retinoic acid-induced protein 1 (RAI1), transcription factor 20 ...
 4605-4709 4.70e-18

Extended PHD finger found in retinoic acid-induced protein 1 (RAI1), transcription factor 20 (TCF-20) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of RAI1 and TCF-20. RAI1, a homolog of stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPBP, also termed TCF-20), is a chromatin-binding protein implicated in the regulation of gene expression. TCF-20 is involved in transcriptional activation of the MMP3 (matrix metalloprotease 3) promoter. It also functions as a transcriptional co-regulator that enhances or represses the transcriptional activity of certain transcription factors/cofactors, such as specificity protein 1 (Sp1), E twenty-six 1 (Ets1), paired box protein 6 (Pax6), small nuclear RING-finger (SNURF)/RNF4, c-Jun, androgen receptor (AR) and estrogen receptor alpha (ERalpha). Both RAI1 and TCF-20 are strongly enriched in chromatin in interphase HeLa cells, and display low nuclear mobility, and have been implicated in Smith-Magenis syndrome and Potocki-Lupski syndrome.


Pssm-ID: 277138  Cd Length: 103  Bit Score: 82.36  E-value: 4.70e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4605 CCFC----HEEGDGATDGPArllnldLDLWVHLNCALWSTEVYETqGGALINVEVALHRGLLTKCSLCQKTGATNSCNRI 4680
Cdd:cd15668      1 CVFCkrgpHYKGLGDLFGPY------YEVWVHEDCAVWAPGVYLV-GGKLYGLEEAVWVAKQSVCSSCQQTGATIGCLHK 73

                           90       100       110
                   ....*....|....*....|....*....|
gi 1443700932 4681 RCPSVYHFACAIRAKCMFFKDK-TMLCPLH 4709
Cdd:cd15668     74 GCKAKYHYPCAVESGCQLDEENfSLLCPKH 103
SET_SETDB-like cd10538
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) ...
 4976-5086 6.39e-18

SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and 2 (SETDB2), suppressor of variegation 3-9 homologs, SUV39H1 and SUV39H2, euchromatic histone-lysine N-methyltransferase EHMT1 and EHMT2, and similar proteins; The family includes SET domain bifurcated 1 (SETDB1) and 2 (SETDB2), suppressor of variegation 3-9 homologs, SUV39H1 and SUV39H2, euchromatic histone-lysine N-methyltransferase EHMT1 and EHMT2. SETDB1 (EC 2.1.1.43; also termed ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. SETDB2 (EC 2.1.1.43; also termed chronic lymphocytic leukemia deletion region gene 8 protein (CLLD8), or lysine N-methyltransferase 1F (KMT1F)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It is involved in left-right axis specification in early development and mitosis. SUV39H1 (also termed histone H3-K9 methyltransferase 1, H3-K9-HMTase 1, lysine N-methyltransferase 1A, KMT1A, position-effect variegation 3-9 homolog, SUV39H, or Su(var)3-9 homolog 1) and SUV39H2 (also termed histone H3-K9 methyltransferase 2, H3-K9-HMTase 2, lysine N-methyltransferase 1B, KMT1B, or Su(var)3-9 homolog 2), both act as histone-lysine N-methyltransferases that specifically trimethylate 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. They mainly function in heterochromatin regions, thereby playing central roles in the establishment of constitutive heterochromatin at pericentric and telomere regions. EHMT1 (also termed Eu-HMTase1, G9a-like protein 1, GLP, GLP1, histone H3-K9 methyltransferase 5, H3-K9-HMTase 5, lysine N-methyltransferase 1D, or KMT1D) and EHMT2 (also termed Eu-HMTase2, HLA-B-associated transcript 8, histone H3-K9 methyltransferase 3, H3-K9-HMTase 3, lysine N-methyltransferase 1C, KMT1C, or protein G9a), both act as histone-lysine N-methyltransferases that specifically mono- and dimethylate 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin. This family also includes the pre-SET domain, which is found in a number of histone methyltransferases (HMTase), N-terminal to the SET domain. Pre-SET domain is a zinc binding motif which contains 9 conserved cysteines that coordinate three zinc ions. It is thought that this region plays a structural role in stabilizing SET domains. Most family members, except for Arabidopsis thaliana SUVH9, contain a post-SET domain which harbors a zinc-binding site.


Pssm-ID: 380936 [Multi-domain]  Cd Length: 217  Bit Score: 85.89  E-value: 6.39e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4976 RSRIQGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEeQNRGIYMFRINN---------EHVIDATLTGGPARYI 5046
Cdd:cd10538     95 RTSKKGWGVRSLEFIPKGSFVCEYVGEVITTSEADRRGKIYD-KSGGSYLFDLDEfsdsdgdgeELCVDATFCGNVSRFI 173

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 1443700932 5047 NHSCAPNCVAEVVTFDKEDKIIII----SSRRIPKGEELTYDYQ 5086
Cdd:cd10538    174 NHSCDPNLFPFNVVIDHDDLRYPRialfATRDILPGEELTFDYG 217
ePHD_KMT2A_like cd15664
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); The ...
 127-212 1.13e-17

Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A/MLL1 and KMT2B/MLL2. KMT2A and KMT2B comprise the mammalian Trx branch of COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation by mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three PHD fingers, this extended PHD (ePHD) finger, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain.


Pssm-ID: 277134  Cd Length: 105  Bit Score: 81.30  E-value: 1.13e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932  127 LPAGH-CWVHRCCAAWSADVLPGATG-LTHVDRAVFSGISQKCEHCQRMGATIPCRADGCPRLYHFPCAAASGC-FQSMK 203
Cdd:cd15664     19 LYCGQdEWVHINCALWSAEVFEEDDGsLQNVHSAVSRGRMMKCELCGKPGATVGCCLKSCPANYHFMCARKAECvFQDDK 98


                   ....*....
gi 1443700932  204 tlRLLCPEH 212
Cdd:cd15664     99 --KVFCPAH 105
SET_NSD3 cd19212
SET domain (including post-SET domain) found in nuclear receptor-binding SET domain-containing ...
 4980-5105 1.15e-17

SET domain (including post-SET domain) found in nuclear receptor-binding SET domain-containing protein 3 (NSD3) and similar proteins; NSD3 (EC 2.1.1.43; also termed protein whistle, WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1L1), or WHSC1-like protein 1) functions as a histone-lysine N-methyltransferase that preferentially methylates 'Lys-4' and 'Lys-27' of histone H3. NSD3 is amplified and overexpressed in multiple cancer types, including acute myeloid leukemia (AML), breast, lung, pancreatic and bladder cancers, as well as squamous cell carcinoma of the head and neck (SCCHN). NSD3 contributes to tumorigenesis by interacting with bromodomain-containing protein 4 (BRD4), the bromodomain and extraterminal (BET) protein, which is a potential therapeutic target in acute myeloid leukemia (AML). NSD3 is amplified in primary tumors and cell lines from breast carcinoma, and can promote the cell viability of small-cell lung cancer and pancreatic ductal adenocarcinoma. High NSD3 expression is implicated in poor grade and heavy smoking history in SCCHN. Thus, NSD3 may serve as a potential druggable target for selective cancer therapy.


Pssm-ID: 380989 [Multi-domain]  Cd Length: 142  Bit Score: 82.67  E-value: 1.15e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4980 QGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEEQN-RGIYMFRINNEHVIDATLTGGPARYINHSCAPNCVAEV 5058
Cdd:cd19212     12 RGWGLRTKRSIKKGEFVNEYVGELIDEEECRLRIKRAHENSvTNFYMLTVTKDRIIDAGPKGNYSRFMNHSCNPNCETQK 91

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1443700932 5059 VTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIpCHCGAWNC 5105
Cdd:cd19212     92 WTVNGDVRVGLFALCDIPAGMELTFNYNLDCLGNGRTE-CHCGADNC 137
SET_NSD1 cd19210
SET domain (including post-SET domain) found in nuclear receptor-binding SET domain-containing ...
 4972-5105 1.09e-16

SET domain (including post-SET domain) found in nuclear receptor-binding SET domain-containing protein 1 (NSD1) and similar proteins; NSD1 (EC 2.1.1.43; also termed Histone-lysine N-methyltransferase H3 lysine-36 and H4 lysine-20 specific, androgen receptor coactivator 267 kDa protein (ARA267), androgen receptor-associated protein of 267 kDa, H3-K36-HMTase, H4-K20-HMTase, lysine N-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein 1) functions as a histone-lysine N-methyltransferase that preferentially methylates 'Lys-36' of histone H3 and 'Lys-20' of histone H4. NSD1 is altered in approximately 10% of head and neck cancer patients with 55% decrease in risk of death in NSD1-mutated versus non-mutated patients; its disruption promotes favorable chemotherapeutic responses linked to hypomethylation.


Pssm-ID: 380987 [Multi-domain]  Cd Length: 142  Bit Score: 79.97  E-value: 1.09e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4972 VYLARSRIQGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEEQN-RGIYMFRINNEHVIDATLTGGPARYINHSC 5050
Cdd:cd19210      4 VEIFRTLGRGWGLRCKTDIKKGEFVNEYVGELIDEEECRARIRYAQEHDiTNFYMLTLDKDRIIDAGPKGNYARFMNHCC 83

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1443700932 5051 APNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFEDDQhKIPCHCGAWNC 5105
Cdd:cd19210     84 QPNCETQKWTVNGDTRVGLFALCDIKAGTELTFNYNLECLGNG-KTVCKCGAPNC 137
ePHD_RAI1 cd15700
Extended PHD finger (ePHD) found in retinoic acid-induced protein 1 (RAI1); The extended plant ...
 133-212 1.14e-15

Extended PHD finger (ePHD) found in retinoic acid-induced protein 1 (RAI1); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of RAI1. RAI1, a homolog of stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPBP, also termed TCF-20), is a chromatin-binding protein implicated in the regulation of gene expression. It is strongly enriched on chromatin in interphase HeLa cells, and displays low nuclear mobility, and has been implicated in Smith-Magenis syndrome, Potocki-Lupski syndrome, and non-syndromic autism. RAI1 contains a region with homology to the novel nucleosome-binding region SPBP and an ePHD/ADD domain with ability to bind nucleosomes.


Pssm-ID: 277170  Cd Length: 104  Bit Score: 75.68  E-value: 1.14e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932  133 WVHRCCAAWSADVLPGATGLTHVDRAVFSGISQKCEHCQRMGATIPCRADGCPRLYHFPCAAASGCFQSMKTLRLLCPEH 212
Cdd:cd15700     25 WVHEACAVWTTGVYLVAGKLFGLQEAVQKAADAKCSSCQGAGATVGCCHKGCTQSYHYICAVEAGCLFEEENFSLRCPKH 104
SET_SUV39H_Clr4-like cd20073
SET domain (including pre-SET and post-SET domains) found in of Schizosaccharomyces pombe H3K9 ...
 4980-5109 1.17e-15

SET domain (including pre-SET and post-SET domains) found in of Schizosaccharomyces pombe H3K9 methyltransferase Clr4, and similar proteins; This subfamily contains fission yeast Schizosaccharomyces pombe H3K9 methyltransferase Clr4 (also known as Suv39h), the sole homolog of the mammalian SUV39H1 and SUV39H2 enzymes, that has a critical role in preventing aberrant heterochromatin formation. It is known to di- and tri-methylate Lys-9 of histone H3, a central heterochromatic histone modification, with its specificity profile most similar to that of the human SUV39H2 homolog.


Pssm-ID: 380999 [Multi-domain]  Cd Length: 259  Bit Score: 80.31  E-value: 1.17e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4980 QGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEeqNRGI-YMF-------RINNEHVIDATLTGGPARYINHSCA 5051
Cdd:cd20073    103 KGWGLRCPRFIKAGTFIGVYLGEVITQSEAEIRGKKYD--NVGVtYLFdldlfedQVDEYYTVDAQYCGDVTRFINHSCD 180

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1443700932 5052 PNCVAEVVTFDKEDKIIIISS----RRIPKGEELTYDYQFDFEDDQ----------------HKIPCHCGAWNCRKWM 5109
Cdd:cd20073    181 PNLAIYSVLRDKSDSKIYDLAffaiKDIPALEELTFDYSGRNNFDQlgfignrsnskyinlkNKRPCYCGSANCRGWL 258
PHD1_KDM5B cd15603
PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
 1005-1050 1.45e-15

PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis antigen 31 (CT31), Histone demethylase JARID1B, Jumonji/ARID domain-containing protein 1B (JARID1B), PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A)) is a member of the JARID subfamily within the JmjC proteins. It has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of pregnant females and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well as TIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277076  Cd Length: 46  Bit Score: 73.45  E-value: 1.45e-15
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932 1005 VCEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1050
Cdd:cd15603      1 VCLVCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 46
PHD1_KDM5A_like cd15515
PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar ...
 1005-1050 1.78e-15

PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar proteins; The JARID subfamily within the JmjC proteins includes Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and a Drosophila homolog, protein little imaginal discs (Lid). KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. KDM5C is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me2 and H3K4me3), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. This family also includes Drosophila melanogaster protein little imaginal discs (Lid) that functions as a JmjC-dependent H3K4me3 demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Members in this family contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two or three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 276990  Cd Length: 46  Bit Score: 73.20  E-value: 1.78e-15
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932 1005 VCEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1050
Cdd:cd15515      1 ICQVCGRGDDEDKLLLCDGCDDSYHTFCLIPPLPDIPPGDWRCPKC 46
SET_SETMAR cd10544
SET domain (including pre-SET and post-SET domains) found in SET domain and mariner ...
 4981-5109 1.90e-15

SET domain (including pre-SET and post-SET domains) found in SET domain and mariner transposase fusion protein (SETMAR) and similar proteins; SETMAR (also termed metnase) is a DNA-binding protein that is indirectly recruited to sites of DNA damage through protein-protein interactions. It has a sequence-specific DNA-binding activity recognizing the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element and displays a DNA nicking and end joining activity. SETMAR also acts as a histone-lysine N-methyltransferase that methylates 'Lys-4' and 'Lys-36' of histone H3. It specifically mediates dimethylation of H3 'Lys-36' at sites of DNA double-strand break and may recruit proteins required for efficient DSB repair through non-homologous end-joining.


Pssm-ID: 380942 [Multi-domain]  Cd Length: 254  Bit Score: 79.65  E-value: 1.90e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4981 GLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKiyeEQNRGI--YMFRINnEHV---------IDATLTGGPARYINHS 5049
Cdd:cd10544    101 GWGLRTLEFIPKGRFVCEYAGEVIGFEEARRRTK---SQTKGDmnYIIVLR-EHLssgkvletfVDPTYIGNIGRFLNHS 176

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 5050 CAPNC----------VAEVVTFDKEDkiiiissrrIPKGEELTYDY------------QFDFEDDQHKIPCHCGAWNCRK 5107
Cdd:cd10544    177 CEPNLfmvpvrvdsmVPKLALFAARD---------IVAGEELSFDYsgefsnsvesvtLARQDESKSRKPCLCGAENCRG 247


                   ..
gi 1443700932 5108 WM 5109
Cdd:cd10544    248 FL 249
ePHD_RAI1_like cd15668
Extended PHD finger found in retinoic acid-induced protein 1 (RAI1), transcription factor 20 ...
 133-212 1.99e-15

Extended PHD finger found in retinoic acid-induced protein 1 (RAI1), transcription factor 20 (TCF-20) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of RAI1 and TCF-20. RAI1, a homolog of stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPBP, also termed TCF-20), is a chromatin-binding protein implicated in the regulation of gene expression. TCF-20 is involved in transcriptional activation of the MMP3 (matrix metalloprotease 3) promoter. It also functions as a transcriptional co-regulator that enhances or represses the transcriptional activity of certain transcription factors/cofactors, such as specificity protein 1 (Sp1), E twenty-six 1 (Ets1), paired box protein 6 (Pax6), small nuclear RING-finger (SNURF)/RNF4, c-Jun, androgen receptor (AR) and estrogen receptor alpha (ERalpha). Both RAI1 and TCF-20 are strongly enriched in chromatin in interphase HeLa cells, and display low nuclear mobility, and have been implicated in Smith-Magenis syndrome and Potocki-Lupski syndrome.


Pssm-ID: 277138  Cd Length: 103  Bit Score: 75.04  E-value: 1.99e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932  133 WVHRCCAAWSADVLPGATGLTHVDRAVFSGISQKCEHCQRMGATIPCRADGCPRLYHFPCAAASGCFQSMKTLRLLCPEH 212
Cdd:cd15668     24 WVHEDCAVWAPGVYLVGGKLYGLEEAVWVAKQSVCSSCQQTGATIGCLHKGCKAKYHYPCAVESGCQLDEENFSLLCPKH 103
FYRN smart00541
FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region ...
 4764-4805 2.02e-15

FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region (FYRC), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.


Pssm-ID: 128814  Cd Length: 44  Bit Score: 72.70  E-value: 2.02e-15
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|..
gi 1443700932  4764 LLPHQMADFHSVTALYPVGYEATRIYWSLRTNNRRCCYRCTI 4805
Cdd:smart00541    1 LLPIQGKLFHSESAIFPVGYKSTRKYWSVKDPNRRCLYSCVI 42
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1788-2358 2.35e-15

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 84.22  E-value: 2.35e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1788 APEPRFPSPLGQSPTVGAAFQPFPGQPLAGARTQPPDFHPTPPGTPRHqsgtpdPFLKPRCPSLDNLSGPGSPGARPPEA 1867
Cdd:PHA03247  2483 PAEARFPFAAGAAPDPGGGGPPDPDAPPAPSRLAPAILPDEPVGEPVH------PRMLTWIRGLEELASDDAGDPPPPLP 2556

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1868 LLSPLPFSEQKkglevkkedggalgvcspgyVPATGYSDSPGCTHIPSTELKvADVFKAPLTPRV----SQVEPQSPGLG 1943
Cdd:PHA03247  2557 PAAPPAAPDRS--------------------VPPPRPAPRPSEPAVTSRARR-PDAPPQSARPRApvddRGDPRGPAPPS 2615

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1944 HRPPDAHPLAPSPPGhadlfRQSPYSDPYAQPPLTPRPQPPEGCCTAPPRSLPSEpfsRIPASPQSQSSSQSPLTPRPLS 2023
Cdd:PHA03247  2616 PLPPDTHAPDPPPPS-----PSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPR---RARRLGRAAQASSPPQRPRRRA 2687

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2024 NEAfCQSPVTPRFQSPDPYSQPPSRPQSRDPFTPLHKPP---RAQLPAAPLSHSPAGSGGFGGAATGEPPAKAPGVPQQP 2100
Cdd:PHA03247  2688 ARP-TVGSLTSLADPPPPPPTPEPAPHALVSATPLPPGPaaaRQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGP 2766

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2101 PFARSPGAgifTTGQPPMRFTFPPAvseplkGSPSHQLHGLNSHYVPSKPQSAGYTSSPSFHQAGSPLGPgagaaetysL 2180
Cdd:PHA03247  2767 PAPAPPAA---PAAGPPRRLTRPAV------ASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGP---------L 2828

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2181 SPlrPPSVLPQASPSAPQPQDASV----AYVPRAAVLTTPADKREVAATTALSAPLNRDLGELPSAQDGALGAMSQSELE 2256
Cdd:PHA03247  2829 PP--PTSAQPTAPPPPPGPPPPSLplggSVAPGGDVRRRPPSRSPAAKPAAPARPPVRRLARPAVSRSTESFALPPDQPE 2906

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2257 KQRQRQrlrellirqqiqrnsLRQEKESAAAAAGPAGWVPEPSGQAFGMAPYQPAQDKSLLGPLAGTAKLP--------- 2327
Cdd:PHA03247  2907 RPPQPQ---------------APPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPwlgalvpgr 2971

                          570       580       590
                   ....*....|....*....|....*....|.
gi 1443700932 2328 VPVQAAFTQDERIARPPPATTPAALDINSSP 2358
Cdd:PHA03247  2972 VAVPRFRVPQPAPSREAPASSTPPLTGHSLS 3002
SET_SETD8 cd10528
SET domain found in SET domain-containing protein 8 (SETD8) and similar proteins; SETD8 (EC 2. ...
 4978-5085 2.51e-15

SET domain found in SET domain-containing protein 8 (SETD8) and similar proteins; SETD8 (EC 2.1.1.43; also termed N-lysine methyltransferase KMT5A, H4-K20-HMTase KMT5A, lysine N-methyltransferase 5A, lysine-specific methylase 5A, PR/SET domain-containing protein 07, PR-Set7 or PR/SET07) is a nucleosomal histone-lysine N-methyltransferase that specifically monomethylates 'Lys-20' of histone H4 (H4K20me1). It plays a central role in the silencing of euchromatic genes.


Pssm-ID: 380926 [Multi-domain]  Cd Length: 141  Bit Score: 76.08  E-value: 2.51e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4978 RIQGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEE-QNRGIYM--FRINNE-HVIDATL-TGGPARYINHSC-A 5051
Cdd:cd10528     25 DGKGRGVIATRPFEKGDFVVEYHGDLITITEAKKREALYAKdPSTGCYMyyFQYKGKtYCVDATKeSGRLGRLINHSKkK 104

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1443700932 5052 PNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDY 5085
Cdd:cd10528    105 PNLKTKLLVIDGVPHLILVAKRDIKPGEELLYDY 138
PHA03247 PHA03247
large tegument protein UL36; Provisional
 3483-4016 3.55e-15

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 83.83  E-value: 3.55e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3483 APPAQGAIGQPVG----PKQPALPQSLLVQQLSPQPPALLGHAQTPALQHPSGLGSGAPQRPLLLTPQQQQQQQRVLGSP 3558
Cdd:PHA03247  2591 APPQSARPRAPVDdrgdPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRL 2670

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3559 QLAPQSPAMLghRLVLGQPLHPPQAPLQHFA----QPRVPGQAPSGLQLAQGMQPLAAGKEQPMDGPPAEGTEgPPEPQG 3634
Cdd:PHA03247  2671 GRAAQASSPP--QRPRRRAARPTVGSLTSLAdpppPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAP-PAVPAG 2747

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3635 APGLGAAESPAVLGLPTAPKHPTelgqgqqlllaSPQPGSLGTSARLLHQPLPSPGAARPELPQSHGDVAGSALVTelpp 3714
Cdd:PHA03247  2748 PATPGGPARPARPPTTAGPPAPA-----------PPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVL---- 2812

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3715 apqppspeqpgkglPGSGALPPPrlqspgqqkAGPAPQPAPTLPPSILGPVPAPVMGQIRAQLQGVLAKNPQLRHLTPQQ 3794
Cdd:PHA03247  2813 --------------APAAALPPA---------ASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSR 2869

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3795 QQQLQALLVQRHQQSLLQQNQALRQSGPFPgtVPEQGLPPGRQPSRPQFPvRPPVLTEAPTGFAADPGTGGRSQPGQQPL 3874
Cdd:PHA03247  2870 SPAAKPAAPARPPVRRLARPAVSRSTESFA--LPPDQPERPPQPQAPPPP-QPQPQPPPPPQPQPPPPPPPRPQPPLAPT 2946

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3875 AELVQAALATRGPQ--------PGFVRLSTPPALSPLDSQPSPEQSPHEPKTPTPTTTGGLAPSPV-------APLELPQ 3939
Cdd:PHA03247  2947 TDPAGAGEPSGAVPqpwlgalvPGRVAVPRFRVPQPAPSREAPASSTPPLTGHSLSRVSSWASSLAlheetdpPPVSLKQ 3026

                          490       500       510       520       530       540       550
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1443700932 3940 SPWgsePPALDDDVAETSVngqgVEGTPDECPQLPVKQEPREETALPAaarepEPQEPVKPEANGDAVGGALAGSPP 4016
Cdd:PHA03247  3027 TLW---PPDDTEDSDADSL----FDSDSERSDLEALDPLPPEPHDPFA-----HEPDPATPEAGARESPSSQFGPPP 3091
PHD2_KMT2C cd15594
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 1005-1050 4.17e-15

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the second PHD finger.


Pssm-ID: 277069  Cd Length: 46  Bit Score: 72.28  E-value: 4.17e-15
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932 1005 VCEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1050
Cdd:cd15594      1 VCQTCRQPGDDNKMLVCDTCDKGYHTFCLQPVMTTIPKNGWKCKNC 46
PHD_BAZ1A cd15627
PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also ...
 1006-1050 1.01e-14

PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1A contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277097 [Multi-domain]  Cd Length: 46  Bit Score: 70.88  E-value: 1.01e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932 1006 CEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1050
Cdd:cd15627      2 CRICRRKGDAEKMLLCDGCDRGHHMYCLRPPLKKVPEGDWFCPDC 46
PHD2_KMT2C_like cd15510
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 1005-1050 1.32e-14

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 276985  Cd Length: 46  Bit Score: 70.54  E-value: 1.32e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932 1005 VCEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1050
Cdd:cd15510      1 VCQACRQPGDDTKMLVCETCDKGYHTSCLRPVMSSIPKYGWKCKNC 46
SET_SUV39H_DIM5-like cd19473
SET domain (including pre-SET domain) found in Neurospora crassa (DIM-5) and similar proteins; ...
 4981-5109 1.40e-14

SET domain (including pre-SET domain) found in Neurospora crassa (DIM-5) and similar proteins; This subfamily contains Neurospora crassa DIM-5 (also termed H3-K9-HMTase dim-5, or HKMT) which functions as histone-lysine N-methyltransferase that specifically trimethylates histone H3 to form H3K9me3.


Pssm-ID: 380996 [Multi-domain]  Cd Length: 274  Bit Score: 77.36  E-value: 1.40e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4981 GLGLYAAKDIEKHTMVIEYIGTIIRNEVAN-RREKIYEEQNRGIYMF-------------RINNE-HVIDATLTGGPARY 5045
Cdd:cd19473    117 GWGVRSTVDIKRGQFVDCYVGEIITPEEAQrRRDAATIAQRKDVYLFaldkfsdpdsldpRLRGDpYEIDGEFMSGPTRF 196

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1443700932 5046 INHSCAPNC-VAEVVTfDKEDKIIII----SSRRIPKGEELTYDY----------QFDFEDDQHKIPCHCGAWNCRKWM 5109
Cdd:cd19473    197 INHSCDPNLrIFARVG-DHADKHIHDlaffAIKDIPRGTELTFDYvdgvtgldddAGDEEKEKEMTKCLCGSPKCRGYL 274
PHD1_Lid2p_like cd15519
PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
 1005-1050 1.45e-14

PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar proteins; Lid2p is a trimethyl H3K4 (H3K4me3) demethylase responsible for H3K4 hypomethylation in heterochromatin. It interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, and mediates H3K9 methylation and small RNA production. It also acts cooperatively with the histone modification enzymes Set1 and Lsd1 and plays an essential role in cross-talk between H3K4 and H3K9 methylation in euchromatin. Lid2p contains a JmjC domain, three PHD fingers and a JmjN domain. This model corresponds to the first PHD finger.


Pssm-ID: 276994 [Multi-domain]  Cd Length: 46  Bit Score: 70.57  E-value: 1.45e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932 1005 VCEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1050
Cdd:cd15519      1 GCEVCGLDDNEGEVLLCDGCDAEYHTSCLDPPLGEIPPGTWFCPSC 46
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1005-1053 2.84e-14

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 69.83  E-value: 2.84e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1443700932 1005 VCEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQT--VPKGGWKCKWCVCC 1053
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPaeIPSGEWLCPECKPK 51
PHD_BAZ1A_like cd15544
PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, ...
 1006-1050 4.24e-14

PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. Both BAZ1A and BAZ1B contain a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277019  Cd Length: 46  Bit Score: 69.36  E-value: 4.24e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932 1006 CEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1050
Cdd:cd15544      2 CKVCRKKGDPDNMILCDGCDKAFHLYCLRPALREVPSGDWFCPAC 46
PHD_RSF1 cd15543
PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV ...
 1006-1050 5.31e-14

PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV pX-associated protein 8, or Hepatitis B virus X-associated protein alpha (HBxAPalpha), or p325 subunit of RSF chromatin-remodeling complex, is a novel nuclear protein with histone chaperon function. It is a subunit of an ISWI chromatin remodeling complex, remodeling and spacing factor (RSF), and plays a role in mediating ATPase-dependent chromatin remodeling and conferring tumor aggressiveness in common carcinomas. As an ataxia-telangiectasia mutated (ATM)-dependent chromatin remodeler, Rsf-1 facilitates DNA damage checkpoints and homologous recombination repair. It regulates the mitotic spindle checkpoint and chromosome instability through the association with serine/threonine kinase BubR1 (BubR1) and Hepatitis B virus (HBV) X protein (HBx) in the chromatin fraction during mitosis. It also interacts with cyclin E1 and promotes tumor development. Rsf-1 contains a plant homeodomain (PHD) finger.


Pssm-ID: 277018 [Multi-domain]  Cd Length: 46  Bit Score: 68.84  E-value: 5.31e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932 1006 CEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1050
Cdd:cd15543      2 CRKCGLSDHPEWILLCDRCDAGYHTACLRPPLMIIPDGNWFCPPC 46
ePHD_KMT2B cd15694
Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B); The extended plant ...
 133-212 7.61e-14

Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of KMT2B. KMT2B is also called trithorax homolog 2 or WW domain-binding protein 7 (WBP-7). KMT2B is encoded by the gene that was first named myeloid/lymphoid or mixed-lineage leukemia 2 (MLL2), a second human homolog of Drosophila trithorax, located on chromosome 19. It belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2) and is vital for normal mammalian embryonic development. KMT2B functions as the catalytic subunit in the MLL2 complex, which contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL2 complex is highly active and specific for histone 3 lysine 4 (H3K4) methylation, which stimulates chromatin transcription in a SAM- and H3K4-dependent manner. Moreover, KMT2B plays a critical role in memory formation by mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. KMT2B contains a CxxC (x for any residue) zinc finger domain, three PHD fingers, this ePHD finger, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain.


Pssm-ID: 277164  Cd Length: 105  Bit Score: 70.45  E-value: 7.61e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932  133 WVHRCCAAWSADVLPGATG-LTHVDRAVFSGISQKCEHCQRMGATIPCRADGCPRLYHFPCAAASGC-FQSMKtlRLLCP 210
Cdd:cd15694     26 WTHVNCAIWSAEVFEENDGsLKNVHAAVARGRQMRCEHCQKIGATVGCCLSACLSNFHFMCARASRCcFQDDK--KVFCQ 103


                   ..
gi 1443700932  211 EH 212
Cdd:cd15694    104 KH 105
PHD1_Lid_like cd15605
PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar ...
 1005-1050 8.17e-14

PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar proteins; Drosophila melanogaster Lid, also termed Retinoblastoma-binding protein 2 homolog, is identified genetically as a trithorax group (trxG) protein that is a Drosophila homolog of the human protein JARID1A/kdm5A, a member of the JARID subfamily within the JmjC proteins. Lid functions as a JmjC-dependent trimethyl histone H3K4 (H3K4me3) demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Lid contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger of Lid.


Pssm-ID: 277078  Cd Length: 46  Bit Score: 68.24  E-value: 8.17e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932 1005 VCEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1050
Cdd:cd15605      1 VCHTCGRGDGEESMLLCDGCDDSYHTFCLLPPLSEVPKGDWRCPKC 46
SET_EHMT cd10543
SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine ...
 4974-5106 1.06e-13

SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine N-methyltransferase EHMT1, EHMT2 and similar proteins; This family includes EHMT1 (also termed Eu-HMTase1, G9a-like protein 1, GLP, GLP1, histone H3-K9 methyltransferase 5, H3-K9-HMTase 5, lysine N-methyltransferase 1D, or KMT1D) and EHMT2 (also termed Eu-HMTase2, HLA-B-associated transcript 8, histone H3-K9 methyltransferase 3, H3-K9-HMTase 3, lysine N-methyltransferase 1C, KMT1C, or protein G9a), both act as histone-lysine N-methyltransferases that specifically mono- and dimethylate 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin.


Pssm-ID: 380941 [Multi-domain]  Cd Length: 231  Bit Score: 73.91  E-value: 1.06e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4974 LARSRIQGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKiyeeqnrGIYMFRINNE----HVIDATLTGGPARYINHS 5049
Cdd:cd10543     95 LFRTRGMGWGVRALQDIPKGTFVCEYIGELISDSEADSRED-------DSYLFDLDNKdgetYCIDARRYGNISRFINHL 167

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1443700932 5050 CAPNCVAEVVTFDKED----KIIIISSRRIPKGEELTYDYQFDFEDDQHK-IPCHCGAWNCR 5106
Cdd:cd10543    168 CEPNLIPVRVFVEHQDlrfpRIAFFASRDIKAGEELGFDYGEKFWRIKGKyFTCRCGSPKCK 229
ePHD2_KMT2D cd15698
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 133-212 1.20e-13

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2D. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions.


Pssm-ID: 277168  Cd Length: 107  Bit Score: 70.08  E-value: 1.20e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932  133 WVHRCCAAWSADVLPGATG-LTHVDRAVFSGISQKCEHCQRMGATIPCRADGCPRLYHFPCAAASGCFqSMKTLRLLCPE 211
Cdd:cd15698     26 WVHLNCALWSTEVYETQGGaLMNVEVALHRGLLTKCSLCQKTGATNSCNRLRCPNVYHFACAIRAKCM-FFKDKTMLCPM 104


                   .
gi 1443700932  212 H 212
Cdd:cd15698    105 H 105
SET_SUV39H2 cd10532
SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 ...
 4980-5109 2.17e-13

SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homolog 2 (SUV39H2) and similar proteins; SUV39H2 (EC 2.1.1.43; also termed histone H3-K9 methyltransferase 2, H3-K9-HMTase 2, lysine N-methyltransferase 1B (KMT1B), or Su(var)3-9 homolog 2) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. It mainly functions in heterochromatin regions, thereby playing a central role in the establishment of constitutive heterochromatin at pericentric and telomere regions.


Pssm-ID: 380930 [Multi-domain]  Cd Length: 243  Bit Score: 73.39  E-value: 2.17e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4980 QGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEeqNRGI-YMFRIN---NEHVIDATLTGGPARYINHSCAPNCV 5055
Cdd:cd10532     95 RGWGVKTLQKIKKNSFVMEYVGEVITSEEAERRGQFYD--SKGItYLFDLDyesDEFTVDAARYGNVSHFVNHSCDPNLQ 172

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1443700932 5056 AEVVTFDKED----KIIIISSRRIPKGEELTYDYQFDFEDD-------------QHKIPCHCGAWNCRKWM 5109
Cdd:cd10532    173 VFNVFIDNLDtrlpRIALFSTRTIKAGEELTFDYQMKGSGDlssdsidnspakkRVRTVCKCGAVTCRGYL 243
ePHD1_KMT2D cd15695
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 4628-4709 2.18e-13

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMT2D. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 at Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions.


Pssm-ID: 277165  Cd Length: 90  Bit Score: 68.79  E-value: 2.18e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4628 DLWVHLNCALWSTEVYETQGGALINVEVALHRGLLTKCSLCQKTGATNSCNRIRCPSVYHFACAIrAKCMFFKDKT--ML 4705
Cdd:cd15695      8 ECWVHHWCAAWSAGVKQHEGDGLIGVDKAVFSGISQKCEHCKRLGATIQCHAEGCPRFYHFPCAA-ASGSFQSMKTllLL 86


                   ....
gi 1443700932 4706 CPLH 4709
Cdd:cd15695     87 CPEH 90
SET_SUV39H1 cd10525
SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 ...
 4980-5109 2.32e-13

SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homolog 1 (SUV39H1) and similar proteins; SUV39H1 (EC 2.1.1.43; also termed histone H3-K9 methyltransferase 1, H3-K9-HMTase 1, lysine N-methyltransferase 1A (KMT1A), position-effect variegation 3-9 homolog (SUV39H), or Su(var)3-9 homolog 1) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. It mainly functions in heterochromatin regions, thereby playing a central role in the establishment of constitutive heterochromatin at pericentric and telomere regions.


Pssm-ID: 380923 [Multi-domain]  Cd Length: 255  Bit Score: 73.39  E-value: 2.32e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4980 QGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEEQNrGIYMFR---INNEHVIDATLTGGPARYINHSCAPNCVA 5056
Cdd:cd10525     97 RGWGVRTLEKIRKNSFVMEYVGEIITSEEAERRGQIYDRQG-ATYLFDldyVEDVYTVDAAYYGNISHFVNHSCDPNLQV 175

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1443700932 5057 EVVTFDKEDKIIIISSRRIPK----GEELTYDYQF-----DFEDDQH-----------------KIPCHCGAWNCRKWM 5109
Cdd:cd10525    176 YNVFIDNLDERLPRIALFATRtiraGEELTFDYNMqvdpvDAESTKMdsnfglaglpgspkkrvRIECKCGVRSCRKYL 254
SET_EZH-like cd19168
SET domain found in enhancer of zeste homolog 1 (EZH1) and zeste homolog 2 (EZH2) of polycomb ...
 4972-5089 2.48e-13

SET domain found in enhancer of zeste homolog 1 (EZH1) and zeste homolog 2 (EZH2) of polycomb repressive complex 2 (PRC2), and similar proteins; The family includes EZH1 and EZH2. EZH1 (EC 2.1.1.43; also termed ENX-2, or histone-lysine N-methyltransferase EZH1) is a catalytic subunit of the PRC2/EED-EZH1 complex, which methylates 'Lys-27' of histone H3, leading to transcriptional repression of the affected target gene. EZH2 (EC 2.1.1.43; also termed lysine N-methyltransferase 6, ENX-1, or histone-lysine N-methyltransferase EZH2) is a catalytic subunit of the PRC2/EED-EZH2 complex, which methylates 'Lys-9' (H3K9me) and 'Lys-27' (H3K27me) of histone H3, leading to transcriptional repression of the affected target gene. Both EZH1 and EZH2 can mono-, di- and trimethylate 'Lys-27' of histone H3 to form H3K27me1, H3K27me2 and H3K27me3, respectively. PRC2 is involved in several cancers; EZH2 is overexpressed in breast, liver and prostate cancer, while point mutations in EZH2 alter the substrate preference and product specificity of PRC2 in Non-Hodgkin lymphomas (NHLs). Thus, PRC2 is a popular target for cancer therapeutics.


Pssm-ID: 380945  Cd Length: 124  Bit Score: 69.91  E-value: 2.48e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4972 VYLARSRIQ-GLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEEQNRgIYMFRINNEHVIDATLTGGPARYINH-- 5048
Cdd:cd19168      3 VVLGKSQLEcGLGLFAAEDIKEGEFVIEYTGELISHDEGVRREHRRGDVSY-LYLFEEQEGIWVDAAIYGNLSRYINHat 81

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1443700932 5049 --SCAPNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDF 5089
Cdd:cd19168     82 dkVKTGNCMPKIMYVNHEWRIKFTAIKDIKIGEELFFNYGDNF 124
PHD1_KDM5A cd15602
PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone ...
 1005-1051 2.55e-13

PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone demethylase JARID1A, Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2)) was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5A functions as a trimethylated histone H3 lysine 4 (H3K4me3) demethylase that belongs to the JARID subfamily within the JmjC proteins. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5A contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277075  Cd Length: 49  Bit Score: 67.28  E-value: 2.55e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1443700932 1005 VCEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 1051
Cdd:cd15602      1 VCLFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKCV 47
PHD_UHRF1_2 cd15525
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and ...
 1006-1050 3.12e-13

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and UHRF2; UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277000  Cd Length: 47  Bit Score: 66.62  E-value: 3.12e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932 1006 CEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQTVPKGG-WKCKWC 1050
Cdd:cd15525      2 CHVCGGKQDPEKQLLCDECDMAYHLYCLDPPLTSLPDDDeWYCPDC 47
PHA03247 PHA03247
large tegument protein UL36; Provisional
 1670-2269 3.38e-13

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 77.29  E-value: 3.38e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1670 RKVPATDKAPYLQKAKDNRAAHRINKVQKQAESQINKQTKGEgLRKPERPSlhlriPVPPGAQPVYMGSPPGVGEGFLKP 1749
Cdd:PHA03247  2566 RSVPPPRPAPRPSEPAVTSRARRPDAPPQSARPRAPVDDRGD-PRGPAPPS-----PLPPDTHAPDPPPPSPSPAANEPD 2639

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1750 PAGTGAGPESPSELFLKLPPQSPAQVPSHDPYGAAGSYAPePRFPSPLGQSPTVGA----AFQPFPGQPLAGARTQPPDF 1825
Cdd:PHA03247  2640 PHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSP-PQRPRRRAARPTVGSltslADPPPPPPTPEPAPHALVSA 2718

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1826 HPTPPGTPRHQSGTPDPFLKPRCPSLDNLS----GPGSPGARP-PEALLSPLPFSEQKKGLE--VKKEDGGALGVCSPGY 1898
Cdd:PHA03247  2719 TPLPPGPAAARQASPALPAAPAPPAVPAGPatpgGPARPARPPtTAGPPAPAPPAAPAAGPPrrLTRPAVASLSESRESL 2798

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1899 VPATGYSDSPGCTHIPSTELKVADVFKAPLTPRVSQVEPQSPGLGHRPPDAHPLAPSPPGHADLFRQSPYSDPYAQPplt 1978
Cdd:PHA03247  2799 PSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKP--- 2875

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1979 prpqppegccTAPPRSlpsePFSRIPASPQSQSSSQSPLTPRPLsneafcQSPVTPrfQSPDPYSQPPSRPQSRDPFTPL 2058
Cdd:PHA03247  2876 ----------AAPARP----PVRRLARPAVSRSTESFALPPDQP------ERPPQP--QAPPPPQPQPQPPPPPQPQPPP 2933

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2059 HKPPRAQLPAAPLSHSPAGSGGFGGAATGEPPAKAPGVPQQPPFARSPGAGIFTTGQPPMRFTFPPAVSEPLKGSPSHQL 2138
Cdd:PHA03247  2934 PPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRVPQPAPSREAPASSTPPLTGHSLSRVSSWASSLAL 3013

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2139 HGLNSHYVPSKPQSAGYTSSPSFHQAGSPLGPGAGAAETYSLSPLRPPSVLPQASPSAPQPQDASVAYVPRAAVLTTPad 2218
Cdd:PHA03247  3014 HEETDPPPVSLKQTLWPPDDTEDSDADSLFDSDSERSDLEALDPLPPEPHDPFAHEPDPATPEAGARESPSSQFGPPP-- 3091

                          570       580       590       600       610
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1443700932 2219 kreVAATTALSAPLNRDLGElpsaqdGALGAMSQSELEKQRQRQRLRELLI 2269
Cdd:PHA03247  3092 ---LSANAALSRRYVRSTGR------SALAVLIEACRRIRRQLRRTRHALL 3133
PHD1_KDM5C_5D cd15604
PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family ...
 1005-1050 6.53e-13

PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family includes KDM5C and KDM5D, both of which belong to the JARID subfamily within the JmjC proteins. KDM5C (also termed Histone demethylase JARID1C, Jumonji/ARID domain-containing protein 1C, SmcX, or Xe169) is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D (also termed Histocompatibility Y antigen (H-Y), Histone demethylase JARID1D, Jumonji/ARID domain-containing protein 1D, or SmcY) is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me3 andH3K4me2), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. Both KDM5C and KDM5D contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277077  Cd Length: 46  Bit Score: 66.02  E-value: 6.53e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932 1005 VCEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1050
Cdd:cd15604      1 VCRMCSRGDEDDKLLLCDGCDDNYHTFCLLPPLPEPPKGIWRCPKC 46
ePHD1_KMT2C cd15696
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 4628-4709 9.96e-13

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMT2C. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several PHD fingers, two ePHD fingers, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains.


Pssm-ID: 277166  Cd Length: 90  Bit Score: 66.89  E-value: 9.96e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4628 DLWVHLNCALWSTEVYETQGGALINVEVALHRGLLTKCSLCQKTGATNSCNRIRCPSVYHFACAIRAKCMF-FKDKTMLC 4706
Cdd:cd15696      8 ECWAHLRCAEWSLGVCQGEEQLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTQMYHYPCAAGAGTFQdFSRRLLLC 87


                   ...
gi 1443700932 4707 PLH 4709
Cdd:cd15696     88 PTH 90
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 3159-3616 1.18e-12

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 74.66  E-value: 1.18e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3159 GVQQPLSQPAAAAQGLgqqsgqPGGLRLPQGGVSMAV-PQGLsfMGQQAVGSAPVPGTSSTFFPGNPALRGLAADNRLMQ 3237
Cdd:pfam09606   74 GGQQGMPDPINALQNL------AGQGTRPQMMGPMGPgPGGP--MGQQMGGPGTASNLLASLGRPQMPMGGAGFPSQMSR 145

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3238 ERQLQRMQLAQKLQQQQQQNMLGQVSLQQQQQPPGIMGQTSMQQPGIMGQASMQQPGVMGQVSMQQTGVMG-QMSIQQPS 3316
Cdd:pfam09606  146 VGRMQPGGQAGGMMQPSSGQPGSGTPNQMGPNGGPGQGQAGGMNGGQQGPMGGQMPPQMGVPGMPGPADAGaQMGQQAQA 225

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3317 MAGQASMQQTGVLGQVSMQQSGIMGQASMQQPGVLgqvsMQQPGVMGQtmqqpgvmGQTSMQPPGVMGQTsmqqtsvmGQ 3396
Cdd:pfam09606  226 NGGMNPQQMGGAPNQVAMQQQQPQQQGQQSQLGMG----INQMQQMPQ--------GVGGGAGQGGPGQP--------MG 285

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3397 VSMQQPGAVGqASMQPQGIMAQASLQQSGVMGQTALQQPGILPQPSLQPQGLMAQpaMQPAGSLAQPPLPQQPPMQQPGL 3476
Cdd:pfam09606  286 PPGQQPGAMP-NVMSIGDQNNYQQQQTRQQQQQQGGNHPAAHQQQMNQSVGQGGQ--VVALGGLNHLETWNPGNFGGLGA 362

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3477 GvQQVAAPPAQGAIGQPVGPKQPALPQSLlvQQLSPQPPALLGHAQTPALQHPSglgsgapqrpllltpqqqqqqqrvLG 3556
Cdd:pfam09606  363 N-PMQRGQPGMMSSPSPVPGQQVRQVTPN--QFMRQSPQPSVPSPQGPGSQPPQ------------------------SH 415

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1443700932 3557 SPQLAPqSPAMlghrlvlgQPLHPPQaPLQHFAQPRVPGQAPSGLQL-----AQGMQPLAAGKEQ 3616
Cdd:pfam09606  416 PGGMIP-SPAL--------IPSPSPQ-MSQQPAQQRTIGQDSPGGSLntpgqSAVNSPLNPQEEQ 470
PHD_BAZ2A_like cd15545
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B ...
 1006-1050 1.21e-12

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B (BAZ2B); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A. Both BAZ2A and BAZ2B contain a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain. BAZ2B also harbors an extra Apolipophorin-III like domain in its N-terminal region.


Pssm-ID: 277020 [Multi-domain]  Cd Length: 46  Bit Score: 65.02  E-value: 1.21e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932 1006 CEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1050
Cdd:cd15545      2 CQICRSGDNEDQLLLCDGCDRGYHTYCFKPKMTNVPEGDWFCPEC 46
ePHD_TCF20 cd15699
Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20); The extended plant ...
 4605-4709 1.29e-12

Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of TCF-20. TCF-20, also termed nuclear factor SPBP, or protein AR1, or stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPRE-binding protein), is involved in transcriptional activation of the MMP3 (matrix metalloprotease 3) promoter. It is strongly enriched on chromatin in interphase HeLa cells, and displays low nuclear mobility, and has been implicated in Smith-Magenis syndrome and Potocki-Lupski syndrome. As a chromatin-binding protein, TCF-20 plays a role in the regulation of gene expression. It also functions as a transcriptional co-regulator that enhances or represses the transcriptional activity of certain transcription factors/cofactors, such as specificity protein 1 (Sp1), E twenty-six 1 (Ets1), paired box protein 6 (Pax6), small nuclear RING-finger (SNURF)/RNF4, c-Jun, androgen receptor (AR) and estrogen receptor alpha (ERalpha). TCF-20 contains an N-terminal transactivation domain, a novel DNA-binding domain with an AT-hook motif, three nuclear localization signals (NLSs) and a C-terminal ePHD/ADD domain.


Pssm-ID: 277169  Cd Length: 103  Bit Score: 66.86  E-value: 1.29e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4605 CCFCHEEGD----GATDGPArllnldLDLWVHLNCALWSTEVYETQGgALINVEVALHRGLLTKCSLCQKTGATNSCNRI 4680
Cdd:cd15699      1 CCLCGKWANyrnlGDLFGPF------YEFWVHEGCILWANGIYLVCG-RLYGLQEALDIAREMKCSHCQEAGATLGCYNK 73

                           90       100       110
                   ....*....|....*....|....*....|
gi 1443700932 4681 RCPSVYHFACAIRAKCMFFKDK-TMLCPLH 4709
Cdd:cd15699     74 GCSFRYHYPCAIDADCLLNEENfSVRCPKH 103
ePHD_TCF20 cd15699
Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20); The extended plant ...
 133-212 1.82e-12

Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of TCF-20. TCF-20, also termed nuclear factor SPBP, or protein AR1, or stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPRE-binding protein), is involved in transcriptional activation of the MMP3 (matrix metalloprotease 3) promoter. It is strongly enriched on chromatin in interphase HeLa cells, and displays low nuclear mobility, and has been implicated in Smith-Magenis syndrome and Potocki-Lupski syndrome. As a chromatin-binding protein, TCF-20 plays a role in the regulation of gene expression. It also functions as a transcriptional co-regulator that enhances or represses the transcriptional activity of certain transcription factors/cofactors, such as specificity protein 1 (Sp1), E twenty-six 1 (Ets1), paired box protein 6 (Pax6), small nuclear RING-finger (SNURF)/RNF4, c-Jun, androgen receptor (AR) and estrogen receptor alpha (ERalpha). TCF-20 contains an N-terminal transactivation domain, a novel DNA-binding domain with an AT-hook motif, three nuclear localization signals (NLSs) and a C-terminal ePHD/ADD domain.


Pssm-ID: 277169  Cd Length: 103  Bit Score: 66.48  E-value: 1.82e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932  133 WVHRCCAAWSADVLPGATGLTHVDRAVFSGISQKCEHCQRMGATIPCRADGCPRLYHFPCAAASGCFQSMKTLRLLCPEH 212
Cdd:cd15699     24 WVHEGCILWANGIYLVCGRLYGLQEALDIAREMKCSHCQEAGATLGCYNKGCSFRYHYPCAIDADCLLNEENFSVRCPKH 103
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1005-1050 1.97e-12

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 64.54  E-value: 1.97e-12
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 1443700932  1005 VCEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQT-VPKGGWKCKWC 1050
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
PHD_UHRF1 cd15616
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); ...
 1006-1050 2.06e-12

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); UHRF1 (also termed inverted CCAAT box-binding protein of 90 kDa, nuclear protein 95, nuclear zinc finger protein Np95 (Np95), RING finger protein 106, transcription factor ICBP90, or E3 ubiquitin-protein ligase UHRF1) is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF1 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET and RING finger associated (SRA) domain, and a C-terminal RING-finger domain. It specifically binds to hemimethylated DNA, double-stranded CpG dinucleotides, and recruits the maintenance methyltransferase DNMT1 to its hemimethylated DNA substrate through its SRA domain. UHRF1-dependent H3K23 ubiquitylation has an essential role in maintaining DNA methylation and replication. The tandem Tudor domain directs UHRF1 binding to the heterochromatin mark histone H3K9me3 and the PHD finger targets UHRF1 to unmodified histone H3 in euchromatic regions. The RING-finger domain exhibit both autocatalytic E3 ubiquitin (Ub) ligase activity and activity against histone H3 and DNMT1.


Pssm-ID: 277088  Cd Length: 47  Bit Score: 64.60  E-value: 2.06e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932 1006 CEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQTVP-KGGWKCKWC 1050
Cdd:cd15616      2 CHVCGGKQDPDKQLMCDECDMAFHIYCLNPPLSSIPdDEDWYCPEC 47
SET_LegAS4-like cd10522
SET domain found in Legionella pneumophila type IV secretion system effector LegAS4 and ...
 4981-5091 2.12e-12

SET domain found in Legionella pneumophila type IV secretion system effector LegAS4 and similar proteins; LegAS4 is a type IV secretion system effector of Legionella pneumophila. It contains a SET domain that is involved in the modification of Lys4 of histone H3 (H3K4) in the nucleolus of the host cell, thereby enhancing heterochromatic rDNA transcription. It also contains an ankyrin repeat domain of unknown function at its C-terminal region.


Pssm-ID: 380920 [Multi-domain]  Cd Length: 122  Bit Score: 66.98  E-value: 2.12e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4981 GLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEEQNrgiYMFRINNEH-VIDATLTGGPARYINHSCAPNCVAEVV 5059
Cdd:cd10522     14 GLGLFAAETIAKGEFVGEYTGEVLDRWEEDRDSVYHYDPL---YPFDLNGDIlVIDAGKKGNLTRFINHSDQPNLELIVR 90

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1443700932 5060 TFDKEDKIIIISSRRIPKGEELTYDYQFDFED 5091
Cdd:cd10522     91 TLKGEQHIGFVAIRDIKPGEELFISYGPKYWK 122
ePHD2_KMT2C cd15697
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 133-212 2.37e-12

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2C. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains PHD fingers, two ePHD fingers, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains.


Pssm-ID: 277167  Cd Length: 105  Bit Score: 66.22  E-value: 2.37e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932  133 WVHRCCAAWSADVLPGATG-LTHVDRAVFSGISQKCEHCQRMGATIPCRADGCPRLYHFPCAAASGC-FQSMKTlrLLCP 210
Cdd:cd15697     26 WVHLNCALWSTEVYETQAGaLINVELALRRGLQMKCVFCHKTGATSGCHRLRCTNVYHFTCAIKAQCmFFKDKT--MLCP 103


                   ..
gi 1443700932  211 EH 212
Cdd:cd15697    104 MH 105
SET_EHMT1 cd10535
SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine ...
 4957-5106 3.20e-12

SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine N-methyltransferase 1 (EHMT1) and similar proteins; EHMT1 (also termed Eu-HMTase1, G9a-like protein 1, GLP, GLP1, histone H3-K9 methyltransferase 5, H3-K9-HMTase 5, or lysine N-methyltransferase 1D (KMT1D)) acts as a histone-lysine N-methyltransferase that specifically mono- and dimethylates 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin.


Pssm-ID: 380933 [Multi-domain]  Cd Length: 231  Bit Score: 69.58  E-value: 3.20e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4957 KSSQYRRLKTEWKNNVYLARSRIQGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKiyeeqnrGIYMFRINNE----H 5032
Cdd:cd10535     78 RNCRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEYVGELISDSEADVREE-------DSYLFDLDNKdgevY 150

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1443700932 5033 VIDATLTGGPARYINHSCAPNCVAEVVTFDKED----KIIIISSRRIPKGEELTYDYQFDFEDDQHKI-PCHCGAWNCR 5106
Cdd:cd10535    151 CIDARFYGNVSRFINHHCEPNLVPVRVFMAHQDlrfpRIAFFSTRLIEAGEQLGFDYGERFWDIKGKLfSCRCGSPKCR 229
PHD_PHRF1 cd15536
PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also ...
 1006-1050 3.23e-12

PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also termed KIAA1542, or CTD-binding SR-like protein rA9, is a ubiquitin ligase that induces the ubiquitination of TGIF (TG-interacting factor) at lysine 130. It acts as a tumor suppressor that promotes the transforming growth factor (TGF)-beta cytostatic program through selective release of TGIF-driven promyelocytic leukemia protein (PML) inactivation. PHRF1 contains a plant homeodomain (PHD) finger and a RING finger.


Pssm-ID: 277011  Cd Length: 46  Bit Score: 63.97  E-value: 3.23e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932 1006 CEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1050
Cdd:cd15536      2 CEVCGRSDREDRLLLCDGCDAGYHMECLTPPLDEVPIEEWFCPEC 46
PHD_BAZ1A cd15627
PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also ...
 271-315 4.02e-12

PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1A contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277097 [Multi-domain]  Cd Length: 46  Bit Score: 63.57  E-value: 4.02e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932  271 CQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIETLPAASWKCKNC 315
Cdd:cd15627      2 CRICRRKGDAEKMLLCDGCDRGHHMYCLRPPLKKVPEGDWFCPDC 46
PHD2_KMT2D cd15595
PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 1005-1050 5.77e-12

PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such asHOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 277070  Cd Length: 46  Bit Score: 63.09  E-value: 5.77e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932 1005 VCEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1050
Cdd:cd15595      1 VCQTCRKPGEDSKMLVCEACDKGYHTFCLKPAMESLPTDSWKCKAC 46
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 4632-4709 5.88e-12

PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH.


Pssm-ID: 463977 [Multi-domain]  Cd Length: 88  Bit Score: 64.66  E-value: 5.88e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4632 HLNCALWSTEVY----ETQGGALINVEVALHRGLLTKCSLC-QKTGATNSCNRIRCPSVYHFACAIRAKCMF-FKDKT-- 4703
Cdd:pfam13771    1 HVVCALWSPELVqrgnDSMGFPIEDIEKIPKRRWKLKCYLCkKKGGACIQCSKKNCRRAFHVTCALEAGLLMqFDEDNgt 80


                   ....*...
gi 1443700932 4704 --MLCPLH 4709
Cdd:pfam13771   81 fkSYCKKH 88
PHD2_d4 cd15530
PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three ...
 1006-1050 7.94e-12

PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three members of the d4 gene family, DPF1 (neuro-d4), DPF2 (ubi-d4/Requiem), and DPF3 (cer-d4), which function as transcription factors and are involved in transcriptional regulation of genes by changing the condensed/decondensed state of chromatin in the nucleus. DPF2 is ubiquitously expressed and it acts as a transcription factor that may participate in developmentally programmed cell death. DPF1 and DPF3 are expressed predominantly in neural tissues, and they may be involved in the transcription regulation of neuro-specific gene clusters. The d4 family proteins show distinct domain organization with domain 2/3 in the N-terminal region, a Cys2His2 (C2H2) zinc finger or Kruppel-type zinc finger in the central part and two adjacent plant homeodomain (PHD) fingers (d4-domain) in the C-terminal part of the molecule. This model corresponds to the second PHD finger.


Pssm-ID: 277005  Cd Length: 46  Bit Score: 62.79  E-value: 7.94e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932 1006 CEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1050
Cdd:cd15530      2 CSLCGTSENDDQLLFCDDCDRGYHMYCLSPPMSEPPEGSWSCHLC 46
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 223-271 1.11e-11

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 62.51  E-value: 1.11e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1443700932  223 RCVVCDGPGDLRDLLFCTSCGQHYHGACLDVVL--APHKRAGWQCPECKVC 271
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPPLdpAEIPSGEWLCPECKPK 51
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
 1006-1050 1.31e-11

PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, also termed histone acetyltransferase KAT6A, YBF2/SAS3, SAS2 and TIP60 protein 3 (MYST-3), or runt-related transcription factor-binding protein 2, or zinc finger protein 220, is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ-related factor (MORF), also termed MOZ2, or histone acetyltransferase KAT6B, or MOZ, YBF2/SAS3, SAS2 and TIP60 protein 4 (MYST4), is a ubiquitously expressed transcriptional regulator with intrinsic HAT activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. Both MOZ and MORF are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are also implicated in human leukemias. MOZ is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphomagenesis and bone development, and its homologs. MOZ contains a linker histone 1 and histone 5 domains and two plant homeodomain (PHD) fingers. In contrast, MORF contains an N-terminal region containing two PHD fingers, a putative HAT domain, an acidic region, and a C-terminal Ser/Met-rich domain. The family corresponds to the first PHD finger.


Pssm-ID: 277002  Cd Length: 46  Bit Score: 62.01  E-value: 1.31e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932 1006 CEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1050
Cdd:cd15527      2 CSVCQDSGNADNLLFCDACDKGFHMECHDPPLTRMPKGKWVCQIC 46
SET_SETDB1 cd10517
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) ...
 4981-5107 1.46e-11

SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and similar proteins; SETDB1 (EC 2.1.1.43; also termed ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes.


Pssm-ID: 380915 [Multi-domain]  Cd Length: 288  Bit Score: 68.85  E-value: 1.46e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4981 GLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIY-------------EEQNRGIYMfRINNEH--VIDATLTGGPARY 5045
Cdd:cd10517    140 GWGIRCLDDIPKGSFVCIYAGQILTEDEANEEGLQYgdeyfaeldyievVEKLKEGYE-SDVEEHcyIIDAKSEGNLGRY 218

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1443700932 5046 INHSCAPNCVAEVVTFDKEDKIIII----SSRRIPKGEELTYDYQFDFEDDQHKI-PCHCGAWNCRK 5107
Cdd:cd10517    219 LNHSCSPNLFVQNVFVDTHDLRFPWvaffASRYIRAGTELTWDYNYEVGSVPGKVlYCYCGSSNCRG 285
ePHD_RAI1 cd15700
Extended PHD finger (ePHD) found in retinoic acid-induced protein 1 (RAI1); The extended plant ...
 4605-4709 1.70e-11

Extended PHD finger (ePHD) found in retinoic acid-induced protein 1 (RAI1); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of RAI1. RAI1, a homolog of stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPBP, also termed TCF-20), is a chromatin-binding protein implicated in the regulation of gene expression. It is strongly enriched on chromatin in interphase HeLa cells, and displays low nuclear mobility, and has been implicated in Smith-Magenis syndrome, Potocki-Lupski syndrome, and non-syndromic autism. RAI1 contains a region with homology to the novel nucleosome-binding region SPBP and an ePHD/ADD domain with ability to bind nucleosomes.


Pssm-ID: 277170  Cd Length: 104  Bit Score: 63.74  E-value: 1.70e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4605 CCFCHEegdgatdgPARLLNL-DL------DLWVHLNCALWSTEVYETqGGALINVEVALHRGLLTKCSLCQKTGATNSC 4677
Cdd:cd15700      1 CCLCRN--------PANYKDLgDLcgpyypEHWVHEACAVWTTGVYLV-AGKLFGLQEAVQKAADAKCSSCQGAGATVGC 71

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1443700932 4678 NRIRCPSVYHFACAIRAKCMFFKDK-TMLCPLH 4709
Cdd:cd15700     72 CHKGCTQSYHYICAVEAGCLFEEENfSLRCPKH 104
PHD_BAZ2A_like cd15545
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B ...
 271-315 2.78e-11

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B (BAZ2B); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A. Both BAZ2A and BAZ2B contain a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain. BAZ2B also harbors an extra Apolipophorin-III like domain in its N-terminal region.


Pssm-ID: 277020 [Multi-domain]  Cd Length: 46  Bit Score: 61.17  E-value: 2.78e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932  271 CQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIETLPAASWKCKNC 315
Cdd:cd15545      2 CQICRSGDNEDQLLLCDGCDRGYHTYCFKPKMTNVPEGDWFCPEC 46
PHD_UHRF2 cd15617
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); ...
 1006-1050 3.27e-11

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); UHRF2 (also termed Np95/ICBP90-like RING finger protein (NIRF), Np95-like RING finger protein, nuclear protein 97, nuclear zinc finger protein Np97, RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2) was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs,p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277089  Cd Length: 47  Bit Score: 61.12  E-value: 3.27e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932 1006 CEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQTVPKG-GWKCKWC 1050
Cdd:cd15617      2 CYVCGGKQDAHMQLLCDECNMAYHIYCLNPPLDKIPEDeDWYCPSC 47
ePHD_KMT2A cd15693
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A); The extended plant ...
 133-212 4.46e-11

Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of KMT2A. KMT2A also termed ALL-1, or CXXC-type zinc finger protein 7, or myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), or trithorax-like protein (Htrx), or zinc finger protein HRX, is a histone methyltransferase that belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2). It regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex, which also contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL1 complex is highly active and specific for H3K4methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three PHD fingers, a Bromodomain domain, this extended PHD finger, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain.


Pssm-ID: 277163  Cd Length: 113  Bit Score: 63.10  E-value: 4.46e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932  133 WVHRCCAAWSADVLPGATG-LTHVDRAVFSGISQKCEHCQRMGATIPCRADGCPRLYHFPCAAASGCFqSMKTLRLLCPE 211
Cdd:cd15693     28 WTHVNCALWSAEVFEDDDGsLKNVHMAVIRGKQLRCEFCQKPGATVGCCLTSCTSNYHFMCSRAKNCV-FLEDKKVYCQR 106


                   .
gi 1443700932  212 H 212
Cdd:cd15693    107 H 107
PHD_BAZ1A_like cd15544
PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, ...
 271-315 5.39e-11

PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. Both BAZ1A and BAZ1B contain a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277019  Cd Length: 46  Bit Score: 60.50  E-value: 5.39e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932  271 CQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIETLPAASWKCKNC 315
Cdd:cd15544      2 CKVCRKKGDPDNMILCDGCDKAFHLYCLRPALREVPSGDWFCPAC 46
SET_EHMT2 cd10533
SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine ...
 4957-5106 5.71e-11

SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine N-methyltransferase 2 (EHMT2) and similar proteins; EHMT2 (also termed Eu-HMTase2, HLA-B-associated transcript 8, histone H3-K9 methyltransferase 3, H3-K9-HMTase 3, lysine N-methyltransferase 1C (KMT1C), or protein G9a) acts as a histone-lysine N-methyltransferase that specifically mono- and dimethylates 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin.


Pssm-ID: 380931 [Multi-domain]  Cd Length: 239  Bit Score: 66.19  E-value: 5.71e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4957 KSSQYRRLKTEWKNNVYLARSRIQGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKiyeeqnrGIYMFRINNE----H 5032
Cdd:cd10533     78 RNCKNRVVQSGIKVRLQLYRTAKMGWGVRALQTIPQGTFICEYVGELISDAEADVRED-------DSYLFDLDNKdgevY 150

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1443700932 5033 VIDATLTGGPARYINHSCAPNCVAEVVTFDKED----KIIIISSRRIPKGEELTYDYQFDFEDDQHK-IPCHCGAWNCR 5106
Cdd:cd10533    151 CIDARYYGNISRFINHLCDPNIIPVRVFMLHQDlrfpRIAFFSSRDIRTGEELGFDYGDRFWDIKSKyFTCQCGSEKCK 229
Glutenin_hmw pfam03157
High molecular weight glutenin subunit; Members of this family include high molecular weight ...
 3312-3994 6.83e-11

High molecular weight glutenin subunit; Members of this family include high molecular weight subunits of glutenin. This group of gluten proteins is thought to be largely responsible for the elastic properties of gluten, and hence, doughs. Indeed, glutenin high molecular weight subunits are classified as elastomeric proteins, because the glutenin network can withstand significant deformations without breaking, and return to the original conformation when the stress is removed. Elastomeric proteins differ considerably in amino acid sequence, but they are all polymers whose subunits consist of elastomeric domains, composed of repeated motifs, and non-elastic domains that mediate cross-linking between the subunits. The elastomeric domain motifs are all rich in glycine residues in addition to other hydrophobic residues. High molecular weight glutenin subunits have an extensive central elastomeric domain, flanked by two terminal non-elastic domains that form disulphide cross-links. The central elastomeric domain is characterized by the following three repeated motifs: PGQGQQ, GYYPTS[P/L]QQ, GQQ. It possesses overlapping beta-turns within and between the repeated motifs, and assumes a regular helical secondary structure with a diameter of approx. 1.9 nm and a pitch of approx. 1.5 nm.


Pssm-ID: 367362 [Multi-domain]  Cd Length: 786  Bit Score: 69.21  E-value: 6.83e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3312 IQQPSMAGQASMQQTGVLGQVSMQQ-SGIMGQASMQQPGVLGQVSMQQPGVMGQTMQQPGVMGQTSMQPPGVMgQTSMQQ 3390
Cdd:pfam03157   94 LQQGIFWGIPALLQRYYPGVTSPQQvSYYPGQASPQRPGQGQQPGQGQQWYYPTSPQQPGQWQQPGQGQQGYY-PTSPQQ 172

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3391 TSVMGQVSMQQ---PGAVGQASMQPQGIMAQASLQQSGVMGQTALQQPGILPQPSLQPQ--GLMAQPAMQPAGSLAQPPL 3465
Cdd:pfam03157  173 SGQRQQPGQGQqlrQGQQGQQSGQGQPGYYPTSSQQPGQLQQTGQGQQGQQPERGQQGQqpGQGQQPGQGQQGQQPGQPQ 252

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3466 PQQPPMQQPGLGVQQVAAPPAQGAIGQ----PVGPKQPALPQS-----LLVQQLSPQPPALLGHAQTPALQHPSGLGSGA 3536
Cdd:pfam03157  253 QLGQGQQGYYPISPQQPRQWQQSGQGQqgyyPTSLQQPGQGQSgyyptSQQQAGQLQQEQQLGQEQQDQQPGQGRQGQQP 332

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3537 PQRPLLLTPQQQQQQQRvlGSPQLAPQSPAMLGHrlvlGQPLHPPQAPlQHFAQPRVPGQAPSGLQLAQGMQPLAAGK-E 3615
Cdd:pfam03157  333 GQGQQGQQPAQGQQPGQ--GQPGYYPTSPQQPGQ----GQPGYYPTSQ-QQPQQGQQPEQGQQGQQQGQGQQGQQPGQgQ 405

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3616 QPMDGPPAEGTEGPPEP-QGAPGLgAAESPAVLGLPTAPKHPTELGQGQQLLLASP---QPGSLGTSARLLHQPLPSPGA 3691
Cdd:pfam03157  406 QPGQGQPGYYPTSPQQSgQGQPGY-YPTSPQQSGQGQQPGQGQQPGQEQPGQGQQPgqgQQGQQPGQPEQGQQPGQGQPG 484

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3692 ARPELPQSHGDvagsalvtelppAPQPPSPEQPGKGLPGSgalPPPRLQSPGQQKAGPAP-QPAPTLPPSILGPVPAPVM 3770
Cdd:pfam03157  485 YYPTSPQQSGQ------------GQQLGQWQQQGQGQPGY---YPTSPLQPGQGQPGYYPtSPQQPGQGQQLGQLQQPTQ 549

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3771 GQiraqlQGVLAKNPQLRHLTPQQQQQLQALLVQRHQQSLLQQNQALRQSGPFPGTVPEQGlpPGRQPSRPQFPVRPpvl 3850
Cdd:pfam03157  550 GQ-----QGQQSGQGQQGQQPGQGQQGQQPGQGQQGQQPGQGQQPGQGQPGYYPTSPQQSG--QGQQPGQWQQPGQG--- 619

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3851 teAPTGFAADPGTGGRSQPGQQPLAElvqaALATRGPQPGFVRLS---------TPPALSPLDSQPSPEQSPHEPKTPTP 3921
Cdd:pfam03157  620 --QPGYYPTSSLQLGQGQQGYYPTSP----QQPGQGQQPGQWQQSgqgqqgyypTSPQQSGQAQQPGQGQQPGQWLQPGQ 693

                          650       660       670       680       690       700       710
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1443700932 3922 TTTGGLAPSPVAPLELPQSPWGSEPPALDDDVAETSVNGQGVEGTPDECPQLPVKQEPREETALPAAAREPEP 3994
Cdd:pfam03157  694 GQQGYYPTSPQQPGQGQQLGQGQQSGQGQQGYYPTSPGQGQQSGQGQQGYDSPYHVSAEHQAASLKVAKAQQL 766
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
 270-315 1.08e-10

PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger of KMT2C and the fourth PHD finger of KMT2D.


Pssm-ID: 276988  Cd Length: 47  Bit Score: 59.41  E-value: 1.08e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932  270 VCQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIETLPAASWKCKNC 315
Cdd:cd15513      1 VCEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 46
ePHD_PHF7_G2E3_like cd15669
Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ...
 4605-4709 1.14e-10

Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ubiquitin-protein ligase (G2E3); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of PHF7 and G2E3. PHF7, also termed testis development protein NYD-SP6, is a testis-specific PHD finger-containing protein that associates with chromatin and binds histone H3 N-terminal tails with a preference for dimethyl lysine 4 (H3K4me2). It may play an important role in stimulating transcription involved in testicular development and/or spermatogenesis. PHF7 contains a PHD finger and a non-canonical ePHD finger, both of which may be involved in activating transcriptional regulation. G2E3 is a dual function ubiquitin ligase (E3) that may play a possible role in cell cycle regulation and the cellular response to DNA damage. It is essential for prevention of apoptosis in early embryogenesis. It is also a nucleo-cytoplasmic shuttling protein with DNA damage responsive localization. G2E3 contains two distinct RING-like ubiquitin ligase domains that catalyze lysine 48-linked polyubiquitination, and a C-terminal catalytic HECT domain that plays an important role in ubiquitin ligase activity and in the dynamic subcellular localization of the protein. The RING-like ubiquitin ligase domains consist of a PHD finger and an ePHD finger.


Pssm-ID: 277139 [Multi-domain]  Cd Length: 112  Bit Score: 61.50  E-value: 1.14e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4605 CCFCHEEgDGATDGPARLLNLDlDLWVHLNCALWSTEV----YETQG--GALIN-VEVALHRGLLTKCSLCQKTGATNSC 4677
Cdd:cd15669      1 CVLCGRS-DDDPDKYGEKLQKD-GICAHYFCLLFSSGLpqrgEDNEGiyGFLPEdIRKEVRRASRLRCFYCKKKGASIGC 78

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1443700932 4678 NRIRCPSVYHFACAIRAKC--MFFKDKTMLCPLH 4709
Cdd:cd15669     79 AVKGCRRSFHFPCGLENGCvtQFFGEYRSFCWEH 112
ePHD_PHF7_G2E3_like cd15669
Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ...
 165-212 1.26e-10

Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ubiquitin-protein ligase (G2E3); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of PHF7 and G2E3. PHF7, also termed testis development protein NYD-SP6, is a testis-specific PHD finger-containing protein that associates with chromatin and binds histone H3 N-terminal tails with a preference for dimethyl lysine 4 (H3K4me2). It may play an important role in stimulating transcription involved in testicular development and/or spermatogenesis. PHF7 contains a PHD finger and a non-canonical ePHD finger, both of which may be involved in activating transcriptional regulation. G2E3 is a dual function ubiquitin ligase (E3) that may play a possible role in cell cycle regulation and the cellular response to DNA damage. It is essential for prevention of apoptosis in early embryogenesis. It is also a nucleo-cytoplasmic shuttling protein with DNA damage responsive localization. G2E3 contains two distinct RING-like ubiquitin ligase domains that catalyze lysine 48-linked polyubiquitination, and a C-terminal catalytic HECT domain that plays an important role in ubiquitin ligase activity and in the dynamic subcellular localization of the protein. The RING-like ubiquitin ligase domains consist of a PHD finger and an ePHD finger.


Pssm-ID: 277139 [Multi-domain]  Cd Length: 112  Bit Score: 61.50  E-value: 1.26e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1443700932  165 QKCEHCQRMGATIPCRADGCPRLYHFPCAAASGC-FQSMKTLRLLCPEH 212
Cdd:cd15669     64 LRCFYCKKKGASIGCAVKGCRRSFHFPCGLENGCvTQFFGEYRSFCWEH 112
SET_SETD5-like cd10529
SET domain found in SET domain-containing protein 5 (SETD5), inactive histone-lysine ...
 4983-5089 2.58e-10

SET domain found in SET domain-containing protein 5 (SETD5), inactive histone-lysine N-methyltransferase 2E (KMT2E) and similar proteins; SETD5 is a probable transcriptional regulator that acts via the formation of large multiprotein complexes that modify and/or remodel the chromatin. KMT2E (also termed inactive lysine N-methyltransferase 2E or myeloid/lymphoid or mixed-lineage leukemia protein 5 (MLL5)) associates with chromatin regions downstream of transcriptional start sites of active genes and thus regulates gene transcription. The family also includes Saccharomyces cerevisiae SET domain-containing proteins, SET3 and SET4, and Schizosaccharomyces pombe SET3. Most of these family members contain a post-SET domain which harbors a zinc-binding site.


Pssm-ID: 380927  Cd Length: 127  Bit Score: 61.14  E-value: 2.58e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4983 GLYAAKDIEKHTMVIEYIGTI-IRNEVanrrEKIYEEQNRGI-YMFRINNEH----VIDATLTGGPARYINHSCAPNCVA 5056
Cdd:cd10529     18 GLVATEDISPGEPILEYKGEVsLRSEF----KEDNGFFKRPSpFVFFYDGFEglplCVDARKYGNEARFIRRSCRPNAEL 93

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1443700932 5057 EVVTFDK-EDKIIIISSRRIPKGEELTYDYQFDF 5089
Cdd:cd10529     94 RHVVVSNgELRLFIFALKDIRKGTEITIPFDYDY 127
PHD_BAZ1B cd15628
PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also ...
 1006-1050 2.74e-10

PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. BAZ1B contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277098  Cd Length: 46  Bit Score: 58.22  E-value: 2.74e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932 1006 CEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1050
Cdd:cd15628      2 CKVCRKKGEDDKLILCDECNQAFHLFCLRPALYEVPDGEWMCPAC 46
SET_SETDB2 cd10523
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 2 (SETDB2) ...
 4980-5109 4.10e-10

SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 2 (SETDB2) and similar proteins; SETDB2 (EC 2.1.1.43; also termed chronic lymphocytic leukemia deletion region gene 8 protein (CLLD8), or lysine N-methyltransferase 1F (KMT1F)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It is involved in left-right axis specification in early development and mitosis.


Pssm-ID: 380921 [Multi-domain]  Cd Length: 266  Bit Score: 64.08  E-value: 4.10e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4980 QGLGLYAAKDIEKHTMVIEYIGTIIRNEVA--------------NRREKIYEEQNRGIYMFRINNEHVIDATLTGGPARY 5045
Cdd:cd10523    118 KGWGVRCLDDIDKGTFVCIYAGRVLSRARSpteplppklelpseNEVEVVTSWLILSKKRKLRENVCFLDASKEGNVGRF 197

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 5046 INHSCAPNCVAEVVTFDKEDKIIII----SSRRIPKGEELTYDYQFDF--EDDQhKIPCHCGAWNCRKWM 5109
Cdd:cd10523    198 LNHSCCPNLFVQNVFVDTHDKNFPWvaffTNRVVKAGTELTWDYSYDAgtSPEQ-EIPCLCGVNKCQKKI 266
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 956-1006 4.33e-10

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 57.89  E-value: 4.33e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1443700932  956 CVVCGsfGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKG-WRCVECIVC 1006
Cdd:pfam00628    2 CAVCG--KSDDGGELVQCDGCDDWFHLACLGPPLDPAEIPSGeWLCPECKPK 51
ePHD_PHF6_like cd15673
Extended PHD finger found in PHD finger protein 6 (PHF6) and PHD finger protein 11 (PHF11); ...
 4605-4709 5.34e-10

Extended PHD finger found in PHD finger protein 6 (PHF6) and PHD finger protein 11 (PHF11); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the two ePHD fingers of PFH6 and the single ePHD finger of PFH11. PHF6, also termed the X-linked mental retardation disorder Borjeson-Forssman-Lehmann syndrome-associated protein, is a nucleolus, ribosomal RNA promoter-associated protein that regulates cell cycle progression by suppressing ribosomal RNA synthesis. It has been implicated in cell cycle control, genomic maintenance, and tumor suppression. PHF6 shows transcriptional repression activity through directly interacting with the nucleosome remodeling and deacetylation complex component RBBP4. PHF6 contains two non-canonical ePHD fingers. PHF11, also termed BRCA1 C-terminus-associated protein, or renal carcinoma antigen NY-REN-34, is a transcriptional co-activator of the Th1 effector cytokine genes, interleukin-2 (IL2) and interferon-gamma (IFNG), co-operating with nuclear factor kappa B (NF-kappaB). It is involved in T-cell activation and viability. Polymorphisms within PHF11 are associated with total IgE, allergic asthma and eczema.


Pssm-ID: 277143  Cd Length: 116  Bit Score: 60.10  E-value: 5.34e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4605 CCFCHEEGDGATDGParLLNLDLDLWVHLNCALWSTEVYETQ-------GGALIN-VEVALHRGLLTKCSLCQKTGATNS 4676
Cdd:cd15673      1 CGFCKSGEENKETGG--KLASGEKIAAHHNCMLFSSGLVQYVspnendfGGFDIEdVKKEIKRGRKLKCNLCKKTGATIG 78

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1443700932 4677 CNRIRCPSVYHFACAIRAKCMFFKDK-----TMLCPLH 4709
Cdd:cd15673     79 CDVKQCKKTYHYHCAKKDDAKIIERNsqgiyRVYCKNH 116
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 135-212 6.10e-10

PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH.


Pssm-ID: 463977 [Multi-domain]  Cd Length: 88  Bit Score: 58.88  E-value: 6.10e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932  135 HRCCAAWSADVLPGAT-----GLTHVDRAVFSGISQKCEHC-QRMGATIPCRADGCPRLYHFPCAAASGCFQSMK----T 204
Cdd:pfam13771    1 HVVCALWSPELVQRGNdsmgfPIEDIEKIPKRRWKLKCYLCkKKGGACIQCSKKNCRRAFHVTCALEAGLLMQFDedngT 80


                   ....*...
gi 1443700932  205 LRLLCPEH 212
Cdd:pfam13771   81 FKSYCKKH 88
PHD2_PHF10 cd15529
PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
 1005-1050 6.43e-10

PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed BRG1-associated factor 45a (BAF45a), or XAP135, is a ubiquitously expressed transcriptional regulator that is required for maintaining the undifferentiated status of neuroblasts. It contains a SAY (supporter of activation of yellow) domain and two adjacent plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger.


Pssm-ID: 277004  Cd Length: 44  Bit Score: 57.32  E-value: 6.43e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932 1005 VCEVCGKASDPSRLLLCDDCDISYHTYCLDppLQTVPKGGWKCKWC 1050
Cdd:cd15529      1 TCTKCGDPHDEDKMMFCDQCDRGYHTFCVG--LRSIPDGRWICPLC 44
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 1005-1050 7.08e-10

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 57.33  E-value: 7.08e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1443700932 1005 VCEVCGKASD-PSRLLLCDDCDISYHTYCLDPPLQT-VPKGGWKCKWC 1050
Cdd:cd15489      1 SCIVCGKGGDlGGELLQCDGCGKWFHADCLGPPLSSfVPNGKWICPVC 48
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 955-1003 8.04e-10

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 57.22  E-value: 8.04e-10
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*....
gi 1443700932   955 MCVVCGsfGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVEC 1003
Cdd:smart00249    1 YCSVCG--KPDDGGELLQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
PHD2_PHF14 cd15562
PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 1005-1050 8.13e-10

PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the second PHD finger.


Pssm-ID: 277037  Cd Length: 50  Bit Score: 57.03  E-value: 8.13e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1005 VCEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQTVPKG----GWKCKWC 1050
Cdd:cd15562      1 SCGICKKSNDQHLLALCDTCKLYYHLGCLDPPLTRMPKKtknsGWQCSEC 50
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
 271-315 8.53e-10

PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, also termed histone acetyltransferase KAT6A, YBF2/SAS3, SAS2 and TIP60 protein 3 (MYST-3), or runt-related transcription factor-binding protein 2, or zinc finger protein 220, is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ-related factor (MORF), also termed MOZ2, or histone acetyltransferase KAT6B, or MOZ, YBF2/SAS3, SAS2 and TIP60 protein 4 (MYST4), is a ubiquitously expressed transcriptional regulator with intrinsic HAT activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. Both MOZ and MORF are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are also implicated in human leukemias. MOZ is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphomagenesis and bone development, and its homologs. MOZ contains a linker histone 1 and histone 5 domains and two plant homeodomain (PHD) fingers. In contrast, MORF contains an N-terminal region containing two PHD fingers, a putative HAT domain, an acidic region, and a C-terminal Ser/Met-rich domain. The family corresponds to the first PHD finger.


Pssm-ID: 277002  Cd Length: 46  Bit Score: 57.00  E-value: 8.53e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932  271 CQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIETLPAASWKCKNC 315
Cdd:cd15527      2 CSVCQDSGNADNLLFCDACDKGFHMECHDPPLTRMPKGKWVCQIC 46
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 223-268 1.02e-09

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 56.84  E-value: 1.02e-09
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 1443700932   223 RCVVCDGPGDLRDLLFCTSCGQHYHGACLDVVLAPH-KRAGWQCPEC 268
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEEePDGKWYCPKC 47
SET_SETDB cd10541
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1), ...
 4980-5107 1.08e-09

SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1), SET domain bifurcated 2 (SETDB2), and similar proteins; SETDB1 (EC 2.1.1.43; also termed ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. SETDB2 (EC 2.1.1.43; also termed chronic lymphocytic leukemia deletion region gene 8 protein (CLLD8), or lysine N-methyltransferase 1F (KMT1F)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It is involved in left-right axis specification in early development and mitosis.


Pssm-ID: 380939 [Multi-domain]  Cd Length: 236  Bit Score: 62.18  E-value: 1.08e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4980 QGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINNEHVIDATLTGGPARYINHSCAPNCVAEVV 5059
Cdd:cd10541    102 KGWGIRCLDDIAKGTFVCIYAGKILTDDFADKEGLEMGDEYFANLDHIEESCYIIDAKLEGNLGRYLNHSCSPNLFVQNV 181

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1443700932 5060 TFDKEDKIIIISSRRIPK----GEELTYDYQFDFED-DQHKIPCHCGAWNCRK 5107
Cdd:cd10541    182 FVDTHDLRFPWVAFFASKrikaGTELTWDYNYEVGSvEGKELLCCCGSNECRG 234
PHD2_PHF10 cd15529
PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
 270-315 1.15e-09

PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed BRG1-associated factor 45a (BAF45a), or XAP135, is a ubiquitously expressed transcriptional regulator that is required for maintaining the undifferentiated status of neuroblasts. It contains a SAY (supporter of activation of yellow) domain and two adjacent plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger.


Pssm-ID: 277004  Cd Length: 44  Bit Score: 56.55  E-value: 1.15e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932  270 VCQTCRLPGEDSMMLVCEACDKGYHTFCMepAIETLPAASWKCKNC 315
Cdd:cd15529      1 TCTKCGDPHDEDKMMFCDQCDRGYHTFCV--GLRSIPDGRWICPLC 44
PHD_BAZ2A cd15629
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also ...
 271-315 1.20e-09

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. It contains a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277099  Cd Length: 47  Bit Score: 56.78  E-value: 1.20e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932  271 CQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIETLPAASWKCKNC 315
Cdd:cd15629      2 CLVCRKGDNDEYLLLCDGCDRGCHMYCHRPKMLQVPEGDWFCPNC 46
PHA03247 PHA03247
large tegument protein UL36; Provisional
 3482-4055 1.27e-09

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 65.34  E-value: 1.27e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3482 AAP-PAQGAIGQPVGPKQPALPQSLLVQQLS---PQPPALLghAQTPALQHPSGLGSGAPQrPLLLTPQQQQQQQRVLGS 3557
Cdd:PHA03247  2494 AAPdPGGGGPPDPDAPPAPSRLAPAILPDEPvgePVHPRML--TWIRGLEELASDDAGDPP-PPLPPAAPPAAPDRSVPP 2570

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3558 PQLAPQSPAMlghrlVLGQPLHPPQAPLQHfAQPRVPGqAPSGLQLAQGMQPLAAGKEQPMDGPPAEGTEGPPEPQGAPG 3637
Cdd:PHA03247  2571 PRPAPRPSEP-----AVTSRARRPDAPPQS-ARPRAPV-DDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPP 2643

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3638 LGAAESPAVLGLPTAPK---HPTELGQGQQLLLASPQPGSLGTSARLLHQPLPSpgAARPELPQSHGDVAGSALVTELPP 3714
Cdd:PHA03247  2644 PTVPPPERPRDDPAPGRvsrPRRARRLGRAAQASSPPQRPRRRAARPTVGSLTS--LADPPPPPPTPEPAPHALVSATPL 2721

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3715 APQPPSPEQPGKGLPGSGAlPPPRLQSPGQqKAGPAPQPAPTLPPSILGPVP--APVMGQIRAqlqgvlAKNPQLRHLTP 3792
Cdd:PHA03247  2722 PPGPAAARQASPALPAAPA-PPAVPAGPAT-PGGPARPARPPTTAGPPAPAPpaAPAAGPPRR------LTRPAVASLSE 2793

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3793 QQQQQLQALLVQRHQQSLLQQNQALRQSGPFPGTVPEqglPPGRQPSRPQFPVRPPVLTEAPTGFAADPGTGGRSQPGQQ 3872
Cdd:PHA03247  2794 SRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPP---PTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRS 2870

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3873 PlaelvqAALATRGPQPGFVRLSTPPALSPLDSQPSPEQSPHEPKTptptttgglapspvaplelpqspwgseppalddd 3952
Cdd:PHA03247  2871 P------AAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQ---------------------------------- 2910

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3953 vaetsvngqgvegtpdecPQLPVK-----QEPREETALPAAAREPEPQEPVKPEANGDAVGGALAGSPPGLGGRSEAGHL 4027
Cdd:PHA03247  2911 ------------------PQAPPPpqpqpQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRV 2972

                          570       580       590
                   ....*....|....*....|....*....|.
gi 1443700932 4028 LLQKLL---RAKNVQLAAQSPGELNGHAESR 4055
Cdd:PHA03247  2973 AVPRFRvpqPAPSREAPASSTPPLTGHSLSR 3003
PHD_BAZ2A cd15629
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also ...
 1006-1051 1.57e-09

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. It contains a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277099  Cd Length: 47  Bit Score: 56.40  E-value: 1.57e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932 1006 CEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 1051
Cdd:cd15629      2 CLVCRKGDNDEYLLLCDGCDRGCHMYCHRPKMLQVPEGDWFCPNCV 47
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 270-318 1.93e-09

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 56.35  E-value: 1.93e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1443700932  270 VCQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIET--LPAASWKCKNCRVC 318
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPaeIPSGEWLCPECKPK 51
zf-HC5HC2H_2 pfam13832
PHD-zinc-finger like domain;
4603-4698 2.09e-09

PHD-zinc-finger like domain;


Pssm-ID: 463991 [Multi-domain]  Cd Length: 109  Bit Score: 58.12  E-value: 2.09e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4603 RKCCFCHEEGdGAtdgparLLNLDLDLWVHLNCALWSTEV----YETQggALINVEVALHRGLLTKCSLC-QKTGATNSC 4677
Cdd:pfam13832    1 VRCCLCPLRG-GA------LKQTSDGRWVHVLCAIFVPEVrfgnVATM--EPIDVSRIPPERWKLKCVFCkKRSGACIQC 71

                           90       100
                   ....*....|....*....|.
gi 1443700932 4678 NRIRCPSVYHFACAIRAKCMF 4698
Cdd:pfam13832   72 SKGRCTTAFHVTCAQAAGVYM 92
PHD2_CHD_II cd15532
PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 1005-1050 2.13e-09

PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the second PHD finger.


Pssm-ID: 277007 [Multi-domain]  Cd Length: 43  Bit Score: 55.75  E-value: 2.13e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932 1005 VCEVCGkasDPSRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1050
Cdd:cd15532      1 FCRVCK---DGGELLCCDGCPSSYHLHCLNPPLAEIPDGDWFCPRC 43
SET cd08161
SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily; The Su(var)3-9, ...
 4971-5085 6.30e-09

SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily; The Su(var)3-9, Enhancer-of-zeste, Trithorax (SET) domain superfamily corresponds to SET domain-containing lysine methyltransferases, which catalyze site and state-specific methylation of lysine residues in histones that are fundamental in epigenetic regulation of gene activation and silencing in eukaryotic organisms. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains has been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as N-SET and C-SET. C-SET forms an unusual and conserved knot-like structure of probable functional importance. In addition to N-SET and C-SET, an insert region (I-SET) and flanking regions of high structural variability form part of the overall structure. Some family members contain a pre-SET domain, which is found in a number of histone methyltransferases (HMTase), and a post-SET domain, which harbors a zinc-binding site.


Pssm-ID: 380914 [Multi-domain]  Cd Length: 72  Bit Score: 55.33  E-value: 6.30e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4971 NVYLARSRIQGLGLYAAKDIEKhtmvieyiGTIIrnevanrrekiyeeqnrgiymfrinnehvidatltgGPARYINHSC 5050
Cdd:cd08161      1 EIRPSTIPGAGFGLFATRDIPK--------GEVI------------------------------------GLARFINHSC 36

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1443700932 5051 APNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDY 5085
Cdd:cd08161     37 EPNCEFEEVYVGGKPRVFIVALRDIKAGEELTVDY 71
PHD_PHF21A cd15523
PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC ...
 1005-1050 6.75e-09

PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC complex protein BHC80) along with HDAC1/2, CtBP1, CoREST, and BRAF35, is associated with LSD1, a lysine (K)-specific histone demethylase. It inhibits LSD1-mediated histone demethylation in vitro. PHF21A is predominantly present in the central nervous system and spermatogenic cells and is one of the six components of BRAF-HDAC complex (BHC) involved in REST-dependent transcriptional repression of neuron-specific genes in non-neuronal cells. It acts as a scaffold protein in BHC in neuronal as well as non-neuronal cells and also plays a role in spermatogenesis. PHF21A contains a C-terminal plant homeodomain (PHD) finger that is responsible for the binding directly to each of five other components of BHC, and of organizing BHC mediating transcriptional repression.


Pssm-ID: 276998 [Multi-domain]  Cd Length: 43  Bit Score: 54.32  E-value: 6.75e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932 1005 VCEVCGKASDpsrLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1050
Cdd:cd15523      1 FCSVCRKSGE---LLMCDTCSLVYHLDCLDPPLKTIPKGMWICPKC 43
PHA03247 PHA03247
large tegument protein UL36; Provisional
 2053-2508 7.27e-09

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 63.03  E-value: 7.27e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2053 DPFTPLhkPPRAQLPAAPLSHSPAGSGGFGGAATGEPPAKAPGVPQQPPFARSPGAGIFTTGQPPMRFTFPPAVSEPLKG 2132
Cdd:PHA03247  2550 DPPPPL--PPAAPPAAPDRSVPPPRPAPRPSEPAVTSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPP 2627

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2133 SPSHQLHG--LNSHYVPSKPQSAGYTSSPSFHQAGSPLGPGAGAAETYSLSPLR-------PPSVLPQASPSAPQPQDAS 2203
Cdd:PHA03247  2628 PPSPSPAAnePDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQrprrraaRPTVGSLTSLADPPPPPPT 2707

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2204 VAYVPRAAVLTTPADKREVAATTALSAPlnrdlGELPSAQDGALGAMSQSELEKQRQRQRlrellirqqiqrnslrQEKE 2283
Cdd:PHA03247  2708 PEPAPHALVSATPLPPGPAAARQASPAL-----PAAPAPPAVPAGPATPGGPARPARPPT----------------TAGP 2766

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2284 SAAAAAGPAGWVPEPSGQAFGMAPYQPAQDKSLLGPLAGTAKLPVPVQAAFTQDERIARPPPATTPAALDINSSPLGAPF 2363
Cdd:PHA03247  2767 PAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPP 2846

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2364 IElrhNVQKGPGNVVGSPFVPQPPrprfflpGDEGAPQGICAPVMPVQALSTPTLQPPKMSMVLPPASPQGAKMGNSHQQ 2443
Cdd:PHA03247  2847 PP---SLPLGGSVAPGGDVRRRPP-------SRSPAAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPP 2916

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1443700932 2444 PLAKATVPTPGLelqhvaPRPLPPSAPlRPEGPKDSPAPEPVPAPAPGKSHLSLEGGRLPCEVAV 2508
Cdd:PHA03247  2917 PQPQPQPPPPPQ------PQPPPPPPP-RPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAV 2974
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 3519-3957 7.69e-09

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 62.31  E-value: 7.69e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3519 GHAQTPALQHPSGLGSGAPQRPllltpqqqqqqqrvlgsPQLAPQSPAMLGHRLVLGQPLHPPQAPlqhfAQPRVPGQAP 3598
Cdd:PRK07764   389 GGAGAPAAAAPSAAAAAPAAAP-----------------APAAAAPAAAAAPAPAAAPQPAPAPAP----APAPPSPAGN 447

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3599 SGLQLAQGMQPLAAGKEQPMDGP-PAEGTEGPPEPQGAPGLGAAESPAVLGLPTAPKHPTELGQGQQ------------- 3664
Cdd:PRK07764   448 APAGGAPSPPPAAAPSAQPAPAPaAAPEPTAAPAPAPPAAPAPAAAPAAPAAPAAPAGADDAATLRErwpeilaavpkrs 527

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3665 -----LLLASPQPGSL-GTSARLLHqplPSPGAARPELPQSHGDVAGSALVTELPPAPQPPSPEQPGKGLPGSGALPPPR 3738
Cdd:PRK07764   528 rktwaILLPEATVLGVrGDTLVLGF---STGGLARRFASPGNAEVLVTALAEELGGDWQVEAVVGPAPGAAGGEGPPAPA 604

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3739 LQSPGQQKAGPAPQPAPTLPPsilGPVPAPVMGqiraqlqgvlaknpqlrhlTPQQQQQLQALLVQRHQQSLLQQNQALR 3818
Cdd:PRK07764   605 SSGPPEEAARPAAPAAPAAPA---APAPAGAAA-------------------APAEASAAPAPGVAAPEHHPKHVAVPDA 662

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3819 QSGPFPGTVPEQGLPPGRQPSRPQFPVRPPVLTEAPTGFAADPGTGGRSQPGQQPLAELVQAALATRGPQPGFVRLSTPP 3898
Cdd:PRK07764   663 SDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLP 742

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1443700932 3899 ALSPLDSQPSPEQSPHEPKTPTPTTTGGLAPSPVAPLElpqspwgSEPPALDDDVAETS 3957
Cdd:PRK07764   743 PEPDDPPDPAGAPAQPPPPPAPAPAAAPAAAPPPSPPS-------EEEEMAEDDAPSMD 794
PHD_BAZ2B cd15630
PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also ...
 271-315 8.77e-09

PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A, which is the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP-and histone H4 tail-dependent fashion. BAZ2B contains a TAM (TIP5/ARBP/MBD) domain, an Apolipophorin-III like domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277100  Cd Length: 49  Bit Score: 54.21  E-value: 8.77e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932  271 CQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIETLPAASWKCKNC 315
Cdd:cd15630      3 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPEGDWFCPAC 47
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 1949-2467 1.04e-08

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 62.02  E-value: 1.04e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1949 AHPLAPSPPGHAdlfRQSPYSDPYAQPPLTPRPQPPEGCCTAPPRSLPSEPFSRIPASPQSQSSSQSPLTPRPLSNEAFC 2028
Cdd:PRK10263   337 VEPVTQTPPVAS---VDVPPAQPTVAWQPVPGPQTGEPVIAPAPEGYPQQSQYAQPAVQYNEPLQQPVQPQQPYYAPAAE 413

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2029 QSPVTPRF----QSPDPYSQPPSRPQSRDPFTPLHKPPRAQLPAAPLSHSPagSGGFGGAATGEPPAKAP-GVPQQPPFA 2103
Cdd:PRK10263   414 QPAQQPYYapapEQPAQQPYYAPAPEQPVAGNAWQAEEQQSTFAPQSTYQT--EQTYQQPAAQEPLYQQPqPVEQQPVVE 491

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2104 RSPGAGIFTTGQPPMRF--------------------TFPPAVSEPLKGSPSHQLHGLNShYVPSKPQSAGYTSSPSFHQ 2163
Cdd:PRK10263   492 PEPVVEETKPARPPLYYfeeveekrarereqlaawyqPIPEPVKEPEPIKSSLKAPSVAA-VPPVEAAAAVSPLASGVKK 570

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2164 AGSPLGPGAG-AAETYSLSPLRPPSvlPQAS----PSAPQPQDASVAYVPRAAVLTTPADKREVAATTALSAPLNRDLGE 2238
Cdd:PRK10263   571 ATLATGAAATvAAPVFSLANSGGPR--PQVKegigPQLPRPKRIRVPTRRELASYGIKLPSQRAAEEKAREAQRNQYDSG 648

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2239 LPSAQDGAlGAMSQSELEKQ---RQRQRLREL-------------------LIRQQIQRNSLRQEKEsaaaaagpagwvp 2296
Cdd:PRK10263   649 DQYNDDEI-DAMQQDELARQfaqTQQQRYGEQyqhdvpvnaedadaaaeaeLARQFAQTQQQRYSGE------------- 714

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2297 EPSG-QAFGMAPYQPAQDKSLLG-----PLAGTAKLPV--PVQAAFTQDERIARPPPATTPAALDINSSPLGAPFIELRH 2368
Cdd:PRK10263   715 QPAGaNPFSLDDFEFSPMKALLDdgphePLFTPIVEPVqqPQQPVAPQQQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQP 794

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2369 NVQKGPGNVVGSPFVPQPPRPRFFLPGDEGAPQgicapvMPVQALSTPTLQPPKMSMVLPpaspqgAKMGNSHQQPLAKA 2448
Cdd:PRK10263   795 QQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQ------PQYQQPQQPVAPQPQDTLLHP------LLMRNGDSRPLHKP 862

                          570
                   ....*....|....*....
gi 1443700932 2449 TVPTPGLELQHVAPRPLPP 2467
Cdd:PRK10263   863 TTPLPSLDLLTPPPSEVEP 881
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 1082-1132 1.04e-08

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 53.86  E-value: 1.04e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1443700932 1082 VCPVCREKYVEDDLLIQCRHCERWLHAACDSLFTEEEVEqaaDEGFDCSAC 1132
Cdd:cd15489      1 SCIVCGKGGDLGGELLQCDGCGKWFHADCLGPPLSSFVP---NGKWICPVC 48
PHD_BAZ2B cd15630
PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also ...
 1004-1051 2.00e-08

PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A, which is the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP-and histone H4 tail-dependent fashion. BAZ2B contains a TAM (TIP5/ARBP/MBD) domain, an Apolipophorin-III like domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277100  Cd Length: 49  Bit Score: 53.44  E-value: 2.00e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1443700932 1004 IVCEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWCV 1051
Cdd:cd15630      1 VYCQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPEGDWFCPACI 48
PHD3_PHF14 cd15563
PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 1005-1050 2.04e-08

PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the third PHD finger.


Pssm-ID: 277038  Cd Length: 49  Bit Score: 53.17  E-value: 2.04e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1443700932 1005 VCEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQTVPKG---GWKCKWC 1050
Cdd:cd15563      1 ECCVCKQTGDNSQLVRCDECKLCYHFGCLDPPLKKSPKQrgyGWVCEEC 49
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
 1006-1050 2.08e-08

PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED) protein, functions as a regulator of gene transcription in the thymus. It is essential for prevention of autoimmunity. AIRE plays a critical role in the induction of central tolerance. It promotes self-tolerance through tissue-specific antigen (TSA) expression. It also acts as an active regulator of chondrocyte differentiation. AIRE contains a homogeneously-staining region (HSR) or caspase-recruitment domain (CARD), a nuclear localization signal (NLS), a SAND (for Sp100, AIRE, nuclear phosphoprotein 41/75 or NucP41/75, and deformed epidermal auto regulatory factor 1 or Deaf1) domain, two plant homeodomain (PHD) fingers, and four LXXLL (where L stands for leucine) motifs. This model corresponds to the first PHD finger that recognizes the unmethylated tail of histone H3 and targets AIRE-dependent genes.


Pssm-ID: 277014 [Multi-domain]  Cd Length: 43  Bit Score: 52.84  E-value: 2.08e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932 1006 CEVCGkasDPSRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1050
Cdd:cd15539      2 CAVCG---DGGELLCCDGCPRAFHLACLVPPLTLIPSGTWRCSSC 43
PHD_BAZ1B cd15628
PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also ...
 271-315 2.59e-08

PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. BAZ1B contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277098  Cd Length: 46  Bit Score: 52.82  E-value: 2.59e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932  271 CQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIETLPAASWKCKNC 315
Cdd:cd15628      2 CKVCRKKGEDDKLILCDECNQAFHLFCLRPALYEVPDGEWMCPAC 46
PHD1_KDM5C_5D cd15604
PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family ...
 270-315 3.22e-08

PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family includes KDM5C and KDM5D, both of which belong to the JARID subfamily within the JmjC proteins. KDM5C (also termed Histone demethylase JARID1C, Jumonji/ARID domain-containing protein 1C, SmcX, or Xe169) is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D (also termed Histocompatibility Y antigen (H-Y), Histone demethylase JARID1D, Jumonji/ARID domain-containing protein 1D, or SmcY) is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me3 andH3K4me2), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. Both KDM5C and KDM5D contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277077  Cd Length: 46  Bit Score: 52.54  E-value: 3.22e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932  270 VCQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIETLPAASWKCKNC 315
Cdd:cd15604      1 VCRMCSRGDEDDKLLLCDGCDDNYHTFCLLPPLPEPPKGIWRCPKC 46
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 223-268 3.28e-08

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 52.70  E-value: 3.28e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1443700932  223 RCVVCDGPGDL-RDLLFCTSCGQHYHGACLDV-VLAPHKRAGWQCPEC 268
Cdd:cd15489      1 SCIVCGKGGDLgGELLQCDGCGKWFHADCLGPpLSSFVPNGKWICPVC 48
PHD1_KDM5A_like cd15515
PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar ...
 270-315 5.15e-08

PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar proteins; The JARID subfamily within the JmjC proteins includes Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and a Drosophila homolog, protein little imaginal discs (Lid). KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. KDM5C is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me2 and H3K4me3), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. This family also includes Drosophila melanogaster protein little imaginal discs (Lid) that functions as a JmjC-dependent H3K4me3 demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Members in this family contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two or three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 276990  Cd Length: 46  Bit Score: 52.01  E-value: 5.15e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932  270 VCQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIETLPAASWKCKNC 315
Cdd:cd15515      1 ICQVCGRGDDEDKLLLCDGCDDSYHTFCLIPPLPDIPPGDWRCPKC 46
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 270-315 6.58e-08

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 51.83  E-value: 6.58e-08
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 1443700932   270 VCQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIET-LPAASWKCKNC 315
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47
PHD1_Lid_like cd15605
PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar ...
 270-315 7.47e-08

PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar proteins; Drosophila melanogaster Lid, also termed Retinoblastoma-binding protein 2 homolog, is identified genetically as a trithorax group (trxG) protein that is a Drosophila homolog of the human protein JARID1A/kdm5A, a member of the JARID subfamily within the JmjC proteins. Lid functions as a JmjC-dependent trimethyl histone H3K4 (H3K4me3) demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Lid contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger of Lid.


Pssm-ID: 277078  Cd Length: 46  Bit Score: 51.68  E-value: 7.47e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1443700932  270 VCQTC-RLPGEDSMMLvCEACDKGYHTFCMEPAIETLPAASWKCKNC 315
Cdd:cd15605      1 VCHTCgRGDGEESMLL-CDGCDDSYHTFCLLPPLSEVPKGDWRCPKC 46
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 3610-4016 7.75e-08

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 59.23  E-value: 7.75e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3610 LAAGKEQPMDGPPAEGTEGPPEPQGAPGLGAAESPAVLGLPTAPK-HPTELGQGQQLLLASPQPGslgtsarllHQPLPS 3688
Cdd:PRK07764   374 LLARLERLERRLGVAGGAGAPAAAAPSAAAAAPAAAPAPAAAAPAaAAAPAPAAAPQPAPAPAPA---------PAPPSP 444

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3689 PGAARPELPQSHgDVAGSALVTELPPAPQPPSPEQPGKGLPGSGALPPPRLQSPGQQKAGPAPQPAPTLP---PSILGPV 3765
Cdd:PRK07764   445 AGNAPAGGAPSP-PPAAAPSAQPAPAPAAAPEPTAAPAPAPPAAPAPAAAPAAPAAPAAPAGADDAATLRerwPEILAAV 523

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3766 P------APVMGQiRAQLQGVLAKNPQLRHLTPQqqqqlqallvqrHQQSLLQQN------QALRQ-----------SGP 3822
Cdd:PRK07764   524 PkrsrktWAILLP-EATVLGVRGDTLVLGFSTGG------------LARRFASPGnaevlvTALAEelggdwqveavVGP 590

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3823 FPGTVPEQGLPPGRQPSRPQFPVRPPVlTEAPTGFAADPGTGGRSQPGQQPLAELVQAALATRGPQPGFVrlsTPPALSP 3902
Cdd:PRK07764   591 APGAAGGEGPPAPASSGPPEEAARPAA-PAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAV---PDASDGG 666

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3903 LDSQPSPEQSPHEPKTPTPTTTGGLAPSPVAP-LELPQSPWGSEPPALDDDVAETSVNGQG-VEGTPDECPQLPVKQEPR 3980
Cdd:PRK07764   667 DGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPaQPAPAPAATPPAGQADDPAAQPPQAAQGaSAPSPAADDPVPLPPEPD 746

                          410       420       430
                   ....*....|....*....|....*....|....*.
gi 1443700932 3981 EETALPAAAREPEPQEPVKPEANGDAVGGALAGSPP 4016
Cdd:PRK07764   747 DPPDPAGAPAQPPPPPAPAPAAAPAAAPPPSPPSEE 782
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 955-1003 1.27e-07

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 50.78  E-value: 1.27e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1443700932  955 MCVVCGSfGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVEC 1003
Cdd:cd15489      1 SCIVCGK-GGDLGGELLQCDGCGKWFHADCLGPPLSSFVPNGKWICPVC 48
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 3482-3769 1.31e-07

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 58.63  E-value: 1.31e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3482 AAPPAQGAIGQPVGPKQPALPQSLLVQQLSPQPPALLGHAQTPALQHPSGLGSGAPQRPLLLTPQQQQQQQRVLGSPQLA 3561
Cdd:pfam03154  193 QAATAGPTPSAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQTPTLHPQRLPSPHPPLQPMTQPPPPSQVSPQPLPQPSLH 272

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3562 PQSPAMlGHRLVLGQPLHPPQAPLQHFAQPRVPGQA-------PSGLQLAQGMQPLAAGKEQPMDGPPAEGTEGPPEPQG 3634
Cdd:pfam03154  273 GQMPPM-PHSLQTGPSHMQHPVPPQPFPLTPQSSQSqvppgpsPAAPGQSQQRIHTPPSQSQLQSQQPPREQPLPPAPLS 351

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3635 APGLGAAESPAVLGLPTAP--KHPTELGQGQQLLLAS--PQPGSLGTSARL-----------------LHQPLPSPGAAR 3693
Cdd:pfam03154  352 MPHIKPPPTTPIPQLPNPQshKHPPHLSGPSPFQMNSnlPPPPALKPLSSLsthhppsahppplqlmpQSQQLPPPPAQP 431

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1443700932 3694 PELPQS--HGDVAGSALVTELPPAPQPPSPEQPGKGLPG-SGALPPPRLQSPGQQKAGPAPQPAPTLPPSILGPVPAPV 3769
Cdd:pfam03154  432 PVLTQSqsLPPPAASHPPTSGLHQVPSQSPFPQHPFVPGgPPPITPPSGPPTSTSSAMPGIQPPSSASVSSSGPVPAAV 510
HMG smart00398
high mobility group;
1641-1692 1.62e-07

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 51.16  E-value: 1.62e-07
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....
gi 1443700932  1641 VLYANMNFPNLKQDYPDWSS--RCKQIMKLWRKVPATDKAPYLQKAKDNRAAHR 1692
Cdd:smart00398   10 MLFSQENRAKIKAENPDLSNaeISKKLGERWKLLSEEEKAPYEEKAKKDKERYE 63
SET_SpSET3-like cd19183
SET domain (including post-SET domain) found in Schizosaccharomyces pombe SET ...
 4982-5096 3.21e-07

SET domain (including post-SET domain) found in Schizosaccharomyces pombe SET domain-containing protein 3 (SETD3) and similar proteins; Schizosaccharomyces pombe SETD3 functions as a transcriptional regulator that acts via the formation of large multiprotein complexes that modify and/or remodel the chromatin. It is required for both, gene activation and repression.


Pssm-ID: 380960  Cd Length: 173  Bit Score: 53.56  E-value: 3.21e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4982 LGLYAAKDIEKHTMVIEYIGtiirnEVANRREKIYEEQNRgiY----------MFRINNEHVIDATLTGGPARYINHSCA 5051
Cdd:cd19183     14 FGLFADRPIPAGDPIQELLG-----EIGLQSEYIADPENQ--YqilgapkphvFFHPQSPLYIDTRRSGSVARFIRRSCR 86

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1443700932 5052 PNCVAEVVTFDK--EDKIIIISSRRIPKGEELTYDYQFDFEDDQHKI 5096
Cdd:cd19183     87 PNAELVTVASDSgsVLKFVLYASRDISPGEEITIGWDWDNPHPFRRF 133
PHD_PHRF1 cd15536
PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also ...
 271-315 3.67e-07

PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also termed KIAA1542, or CTD-binding SR-like protein rA9, is a ubiquitin ligase that induces the ubiquitination of TGIF (TG-interacting factor) at lysine 130. It acts as a tumor suppressor that promotes the transforming growth factor (TGF)-beta cytostatic program through selective release of TGIF-driven promyelocytic leukemia protein (PML) inactivation. PHRF1 contains a plant homeodomain (PHD) finger and a RING finger.


Pssm-ID: 277011  Cd Length: 46  Bit Score: 49.72  E-value: 3.67e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932  271 CQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIETLPAASWKCKNC 315
Cdd:cd15536      2 CEVCGRSDREDRLLLCDGCDAGYHMECLTPPLDEVPIEEWFCPEC 46
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 1006-1050 4.23e-07

PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the first PHD finger.


Pssm-ID: 276984  Cd Length: 48  Bit Score: 49.23  E-value: 4.23e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1443700932 1006 CEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQTVP--KGGWKCKWC 1050
Cdd:cd15509      2 CAVCDSPGDLSDLLFCTSCGQHYHGSCLDPAVRPTPlvRAGWQCPEC 48
PHD1_PHF12 cd15533
PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is ...
 1005-1050 4.86e-07

PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is a plant homeodomain (PHD) zinc finger-containing protein that bridges the transducin-like enhancer of split (TLE) corepressor to the mSin3A-histone deacetylase (HDAC)-complex, and further represses transcription at targeted genes. PHF12 also interacts with MRG15 (mortality factor-related genes on chromosome 15), a member of the mortality factor (MORF) family of proteins implicated in regulating cellular senescence. PHF12 contains two plant-homeodomain (PHD) zinc fingers followed by a polybasic region. The PHD fingers function downstream of phosphoinositide signaling triggered by the interaction between polybasic regions and phosphoinositides. This model corresponds to the first PHD finger.


Pssm-ID: 277008 [Multi-domain]  Cd Length: 45  Bit Score: 49.28  E-value: 4.86e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1443700932 1005 VCEVCGKASDpsrLLLCDDCDISYHTYCLDPPL--QTVPKGGWKCKWC 1050
Cdd:cd15533      1 YCDSCGEGGD---LLCCDRCPASFHLQCCNPPLdeEDLPPGEWLCHRC 45
PHD1_KDM5B cd15603
PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
 270-315 4.91e-07

PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis antigen 31 (CT31), Histone demethylase JARID1B, Jumonji/ARID domain-containing protein 1B (JARID1B), PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A)) is a member of the JARID subfamily within the JmjC proteins. It has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of pregnant females and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well as TIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277076  Cd Length: 46  Bit Score: 49.18  E-value: 4.91e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932  270 VCQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIETLPAASWKCKNC 315
Cdd:cd15603      1 VCLVCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 46
PHD_RSF1 cd15543
PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV ...
 271-315 5.03e-07

PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV pX-associated protein 8, or Hepatitis B virus X-associated protein alpha (HBxAPalpha), or p325 subunit of RSF chromatin-remodeling complex, is a novel nuclear protein with histone chaperon function. It is a subunit of an ISWI chromatin remodeling complex, remodeling and spacing factor (RSF), and plays a role in mediating ATPase-dependent chromatin remodeling and conferring tumor aggressiveness in common carcinomas. As an ataxia-telangiectasia mutated (ATM)-dependent chromatin remodeler, Rsf-1 facilitates DNA damage checkpoints and homologous recombination repair. It regulates the mitotic spindle checkpoint and chromosome instability through the association with serine/threonine kinase BubR1 (BubR1) and Hepatitis B virus (HBV) X protein (HBx) in the chromatin fraction during mitosis. It also interacts with cyclin E1 and promotes tumor development. Rsf-1 contains a plant homeodomain (PHD) finger.


Pssm-ID: 277018 [Multi-domain]  Cd Length: 46  Bit Score: 49.19  E-value: 5.03e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932  271 CQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIETLPAASWKCKNC 315
Cdd:cd15543      2 CRKCGLSDHPEWILLCDRCDAGYHTACLRPPLMIIPDGNWFCPPC 46
PHD1_Lid2p_like cd15519
PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
 270-315 5.09e-07

PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar proteins; Lid2p is a trimethyl H3K4 (H3K4me3) demethylase responsible for H3K4 hypomethylation in heterochromatin. It interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, and mediates H3K9 methylation and small RNA production. It also acts cooperatively with the histone modification enzymes Set1 and Lsd1 and plays an essential role in cross-talk between H3K4 and H3K9 methylation in euchromatin. Lid2p contains a JmjC domain, three PHD fingers and a JmjN domain. This model corresponds to the first PHD finger.


Pssm-ID: 276994 [Multi-domain]  Cd Length: 46  Bit Score: 49.00  E-value: 5.09e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932  270 VCQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIETLPAASWKCKNC 315
Cdd:cd15519      1 GCEVCGLDDNEGEVLLCDGCDAEYHTSCLDPPLGEIPPGTWFCPSC 46
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1082-1132 5.68e-07

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 49.13  E-value: 5.68e-07
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|.
gi 1443700932  1082 VCPVCREKYvEDDLLIQCRHCERWLHAACDSLFTEEEVEqaaDEGFDCSAC 1132
Cdd:smart00249    1 YCSVCGKPD-DGGELLQCDGCDRWYHQTCLGPPLLEEEP---DGKWYCPKC 47
PHD2_PHF12_Rco1 cd15534
PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, ...
 1005-1047 7.53e-07

PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, also termed PHD factor 1 (Pf1), is a plant homeodomain (PHD) zinc finger-containing protein that bridges the transducin-like enhancer of split (TLE) corepressor to the mSin3A-histone deacetylase (HDAC)-complex, and further represses transcription at targeted genes. PHF12 also interacts with MRG15 (mortality factor-related genes on chromosome 15), a member of the mortality factor (MORF) family of proteins implicated in regulating cellular senescence. PHF12 contains two plant homeodomain (PHD) zinc fingers followed by a polybasic region. The PHD fingers function downstream of phosphoinositide signaling triggered by the interaction between polybasic regions and phosphoinositides. This subfamily also includes yeast transcriptional regulatory protein Rco1 and similar proteins. Rco1 is a component of the Rpd3S histone deacetylase complex that plays an important role at actively transcribed genes. Rco1 contains two PHD fingers, which are required for the methylation of histone H3 lysine 36 (H3K36) nucleosome recognition by Rpd3S. This model corresponds to the second PHD finger.


Pssm-ID: 277009  Cd Length: 47  Bit Score: 48.50  E-value: 7.53e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1443700932 1005 VCEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQTVPKGG-WKC 1047
Cdd:cd15534      1 VCFKCNRSCRVAPLIQCDYCPLLFHLDCLDPPLTHPPATGrWMC 44
PHD1_MTF2_PHF19_like cd15499
PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ...
 1005-1052 7.80e-07

PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) family proteins MTF2, PHF19, and similar proteins; The family includes two PCL family proteins, metal-response element-binding transcription factor 2 (MTF2/PCL2) and PHF19/PCL3, which are homologs of PHD finger protein1 (PHF1). PCL family proteins are accessory components of the polycomb repressive complex 2 (PRC2) core complex and all contain an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. They specifically recognize tri-methylated H3K36 (H3K36me3) through their N-terminal Tudor domains. The interaction between their Tudor domains and H3K36me3 is critical for both the targeting and spreading of PRC2 into active chromatin regions and for the maintenance of optimal repression of poised developmental genes where PCL proteins, H3K36me3, and H3K27me3 coexist. Moreover, unlike other PHD finger-containing proteins, the first PHD fingers of PCL proteins do not display histone H3K4 binding affinity and they do not affect the Tudor domain binding to histones. This model corresponds to the first PHD finger.


Pssm-ID: 276974  Cd Length: 53  Bit Score: 49.04  E-value: 7.80e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1443700932 1005 VCEVCG--KASDPSRLLLCDDCDISYHTYCLDPPLQTVPK---GGWKCKWCVC 1052
Cdd:cd15499      1 TCSICGgaEARDGNEILICDKCDKGYHQLCHSPKVRTSPLegdEKWFCSRCVF 53
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 1006-1050 8.31e-07

PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the first PHD finger.


Pssm-ID: 277006 [Multi-domain]  Cd Length: 43  Bit Score: 48.37  E-value: 8.31e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932 1006 CEVCGKASDpsrLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1050
Cdd:cd15531      2 CEVCQQGGE---IILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 43
PHD_TIF1_like cd15541
PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar ...
 1005-1050 8.49e-07

PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar proteins; The TIF1 family of transcriptional cofactors includes TIF1alpha (TRIM24), TIF1beta (TRIM28), TIF1gamma (TRIM33), and TIF1delta (TRIM66), which are characterized by an N-terminal RING-finger B-box coiled-coil (RBCC/TRIM) motif and plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region. TIF1 proteins couple chromatin modifications to transcriptional regulation, signaling, and tumor suppression. They exert a deacetylase-dependent silencing effect when tethered to a promoter region. TIF1alpha, TIF1beta, and TIF1delta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. TIF1alpha and TIF1beta bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. In contrast, TIF1delta appears to lack nuclear receptor- and KRAB-binding activity. Moreover, TIF1delta is specifically involved in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. TIF1gamma is structurally closely related to TIF1alpha and TIF1beta, but has very little functional features in common with them. It does not interact with the KRAB silencing domain of KOX1 or the heterochromatinic proteins HP1alpha, beta, and gamma. It cannot bind to nuclear receptors (NRs). This family also includes Sp100/Sp140 family proteins, the nuclear body SP100 and SP140. Sp110 is a leukocyte-specific component of the nuclear body. It may function as a nuclear hormone receptor transcriptional coactivator that may play a role in inducing differentiation of myeloid cells. It is also involved in resisting intracellular pathogens and functions as an important drug target for preventing intracellular pathogen diseases, such as tuberculosis, hepatic veno-occlusive disease, and intracellular cancers. SP140 is an interferon inducible nuclear leukocyte-specific protein involved in primary biliary cirrhosis and a risk factor in chronic lymphocytic leukemia. It is also implicated in innate immune response to human immunodeficiency virus type 1 (HIV-1) by binding to the virus viral infectivity factor (Vif) protein. Both Sp110 and Sp140 contain a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD).


Pssm-ID: 277016 [Multi-domain]  Cd Length: 43  Bit Score: 48.49  E-value: 8.49e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932 1005 VCEVCGkasDPSRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1050
Cdd:cd15541      1 WCAVCQ---NGGELLCCDKCPRVFHLDCHIPPIPEFPSGEWSCSLC 43
SET_AtSUVH-like cd10545
SET domain found in Arabidopsis thaliana histone H3-K9 methyltransferases (SUVHs) and similar ...
 4969-5085 8.72e-07

SET domain found in Arabidopsis thaliana histone H3-K9 methyltransferases (SUVHs) and similar proteins; Arabidopsis thaliana SUVH protein (also termed suppressor of variegation 3-9 homolog protein) is a histone-lysine N-methyltransferase that methylates 'Lys-9' of histone H3. H3 'Lys-9' methylation represents a specific tag for epigenetic transcriptional repression. Some family members contain a post-SET domain which binds a Zn2+ ion. Most family members, except for Arabidopsis thaliana SUVH9, contain a post-SET domain which harbors a zinc-binding site.


Pssm-ID: 380943 [Multi-domain]  Cd Length: 232  Bit Score: 53.56  E-value: 8.72e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4969 KNNVYLARSRIQGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKiyeeqnRGIYMFRINN------------------ 5030
Cdd:cd10545     85 RYRLEVFKTAERGWGVRSWDSIPAGSFICEYVGELLDTSEADTRSG------NDDYLFDIDNrqtnrgwdggqrldvgms 158

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1443700932 5031 -------------EHVIDATLTGGPARYINHSCAPNCVAEVVTFDKEDKIIII----SSRRIPKGEELTYDY 5085
Cdd:cd10545    159 dgerssaedeessEFTIDAGSFGNVARFINHSCSPNLFVQCVLYDHNDLRLPRvmlfAADNIPPLQELTYDY 230
PHD2_d4 cd15530
PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three ...
 271-315 9.79e-07

PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three members of the d4 gene family, DPF1 (neuro-d4), DPF2 (ubi-d4/Requiem), and DPF3 (cer-d4), which function as transcription factors and are involved in transcriptional regulation of genes by changing the condensed/decondensed state of chromatin in the nucleus. DPF2 is ubiquitously expressed and it acts as a transcription factor that may participate in developmentally programmed cell death. DPF1 and DPF3 are expressed predominantly in neural tissues, and they may be involved in the transcription regulation of neuro-specific gene clusters. The d4 family proteins show distinct domain organization with domain 2/3 in the N-terminal region, a Cys2His2 (C2H2) zinc finger or Kruppel-type zinc finger in the central part and two adjacent plant homeodomain (PHD) fingers (d4-domain) in the C-terminal part of the molecule. This model corresponds to the second PHD finger.


Pssm-ID: 277005  Cd Length: 46  Bit Score: 48.15  E-value: 9.79e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932  271 CQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIETLPAASWKCKNC 315
Cdd:cd15530      2 CSLCGTSENDDQLLFCDDCDRGYHMYCLSPPMSEPPEGSWSCHLC 46
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 270-315 1.30e-06

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 48.08  E-value: 1.30e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1443700932  270 VCQTCRLPGED-SMMLVCEACDKGYHTFCMEPAIETL-PAASWKCKNC 315
Cdd:cd15489      1 SCIVCGKGGDLgGELLQCDGCGKWFHADCLGPPLSSFvPNGKWICPVC 48
PHD3_PHF14 cd15563
PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 224-268 1.35e-06

PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the third PHD finger.


Pssm-ID: 277038  Cd Length: 49  Bit Score: 48.16  E-value: 1.35e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1443700932  224 CVVCDGPGDLRDLLFCTSCGQHYHGACLDVVLA--PHKRA-GWQCPEC 268
Cdd:cd15563      2 CCVCKQTGDNSQLVRCDECKLCYHFGCLDPPLKksPKQRGyGWVCEEC 49
PHD1_Snt2p_like cd15497
PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and ...
 1006-1050 1.43e-06

PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and similar proteins; Snt2p is a yeast protein that may function in multiple stress pathways. It coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress through interaction with Ecm5 and the Rpd3 deacetylase. Snt2p contains a bromo adjacent homology (BAH) domain, two canonical Cys4HisCys3 plant homeodomain (PHD) fingers, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domain; this model corresponds to the first canonical Cys4HisCys3 PHD finger.


Pssm-ID: 276972  Cd Length: 48  Bit Score: 48.07  E-value: 1.43e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1443700932 1006 CEVCGKASDPSRLLLCDDCDISYHTYCLDPPLQTVPKGG--WKCKWC 1050
Cdd:cd15497      2 CKVCKEWCASDDSVRCDECKVSYHLLCVDPPLTKKPNRGfvWSCAPC 48
PHD1_BPTF cd15559
PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, ...
 1006-1050 1.53e-06

PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, also termed nucleosome-remodeling factor subunit BPTF, or fetal Alz-50 clone 1 protein (FAC1), or fetal Alzheimer antigen, functions as a transcriptional regulator that exhibits altered expression and subcellular localization during neuronal development and neurodegenerative diseases such as Alzheimer's disease. It interacts with the human orthologue of the Kelch-like Ech-associated protein (Keap1). Its function and subcellular localization can be regulated by Keap1. Moreover, BPTF is a novel DNA-binding protein that recognizes the DNA sequence CACAACAC and represses transcription through this site in a phosphorylation-dependent manner. Furthermore, BPTF interacts with the Myc-associated zinc finger protein (ZF87/MAZ) and alters its transcriptional activity, which has been implicated in gene regulation in neurodegeneration. Some family members contain two or three plant homeodomain (PHD) fingers, which may be involved in complex formation with histone H3 trimethylated at K4 (H3K4me3). This family corresponds to the first PHD finger.


Pssm-ID: 277034 [Multi-domain]  Cd Length: 43  Bit Score: 47.80  E-value: 1.53e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932 1006 CEVCGKASDpsrLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1050
Cdd:cd15559      2 CRVCHKLGD---LLCCETCSAVYHLECVDPPLEEVPEEDWQCEVC 43
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
 224-268 1.69e-06

PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, also termed histone acetyltransferase KAT6A, YBF2/SAS3, SAS2 and TIP60 protein 3 (MYST-3), or runt-related transcription factor-binding protein 2, or zinc finger protein 220, is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ-related factor (MORF), also termed MOZ2, or histone acetyltransferase KAT6B, or MOZ, YBF2/SAS3, SAS2 and TIP60 protein 4 (MYST4), is a ubiquitously expressed transcriptional regulator with intrinsic HAT activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. Both MOZ and MORF are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are also implicated in human leukemias. MOZ is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphomagenesis and bone development, and its homologs. MOZ contains a linker histone 1 and histone 5 domains and two plant homeodomain (PHD) fingers. In contrast, MORF contains an N-terminal region containing two PHD fingers, a putative HAT domain, an acidic region, and a C-terminal Ser/Met-rich domain. The family corresponds to the first PHD finger.


Pssm-ID: 277002  Cd Length: 46  Bit Score: 47.76  E-value: 1.69e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932  224 CVVCDGPGDLRDLLFCTSCGQHYHGACLDVVLaPHKRAG-WQCPEC 268
Cdd:cd15527      2 CSVCQDSGNADNLLFCDACDKGFHMECHDPPL-TRMPKGkWVCQIC 46
PHA03247 PHA03247
large tegument protein UL36; Provisional
 3435-3773 1.73e-06

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 54.94  E-value: 1.73e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3435 PGILPQPSLQPQGL---MAQPAMQPAGSLAQPPLPQQPPMQQPGLGVQQVAAPPAQGAIGQ--PVGPKQPALPQsllvqq 3509
Cdd:PHA03247  2670 LGRAAQASSPPQRPrrrAARPTVGSLTSLADPPPPPPTPEPAPHALVSATPLPPGPAAARQasPALPAAPAPPA------ 2743

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3510 lSPQPPALLGHAQTPAL-QHPSGLGSGAPQRPLLLTPqqqqqqQRVLGSPQLAPQSPAMlghrlvLGQPLHPPQAPLQHF 3588
Cdd:PHA03247  2744 -VPAGPATPGGPARPARpPTTAGPPAPAPPAAPAAGP------PRRLTRPAVASLSESR------ESLPSPWDPADPPAA 2810

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3589 AQPRVPGQAPSGLQLAQGMQPLAAgkeQPMDGPPAEGTEGPPEPQG---APG-----LGAAESPAVlgLPTAPKHPTELG 3660
Cdd:PHA03247  2811 VLAPAAALPPAASPAGPLPPPTSA---QPTAPPPPPGPPPPSLPLGgsvAPGgdvrrRPPSRSPAA--KPAAPARPPVRR 2885

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3661 QGQQLLLASPQPgslgtsarllhQPLPSPGAARPELPQShgdvagsalvtelppapqppSPEQPGKGLPGSGALPPPRLQ 3740
Cdd:PHA03247  2886 LARPAVSRSTES-----------FALPPDQPERPPQPQA--------------------PPPPQPQPQPPPPPQPQPPPP 2934

                          330       340       350
                   ....*....|....*....|....*....|...
gi 1443700932 3741 SPGQQKAGPAPQPAPTLPPSILGPVPAPVMGQI 3773
Cdd:PHA03247  2935 PPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGAL 2967
PHD1_KDM5A cd15602
PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone ...
 270-315 1.77e-06

PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone demethylase JARID1A, Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2)) was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5A functions as a trimethylated histone H3 lysine 4 (H3K4me3) demethylase that belongs to the JARID subfamily within the JmjC proteins. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5A contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277075  Cd Length: 49  Bit Score: 47.64  E-value: 1.77e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932  270 VCQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIETLPAASWKCKNC 315
Cdd:cd15602      1 VCLFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKC 46
PHD_Phf1p_Phf2p_like cd15502
PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 ...
 1003-1050 1.92e-06

PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 (Phf1p) and Phf2 (Phf2p); Phf1p and Phf2p are components of the SWM histone demethylase complex that specifically demethylates histone H3 at lysine 9 (H3K9me2), a specific tag for epigenetic transcriptional activation. They function as corepressors and play roles in regulating heterochromatin propagation and euchromatic transcription. Both Phf1p and Phf2p contain a plant homeodomain (PHD) finger.


Pssm-ID: 276977  Cd Length: 52  Bit Score: 47.82  E-value: 1.92e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1443700932 1003 CIVCEvCGKASDPSRLLLCDDCDISYHTYCLDPPLQT----VPKGGWKCKWC 1050
Cdd:cd15502      2 CIVCQ-RGHSPKSNRIVFCDGCNTPYHQLCHDPSIDDevveDPDAEWFCKKC 52
PHD_Phf1p_Phf2p_like cd15502
PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 ...
 268-315 1.94e-06

PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 (Phf1p) and Phf2 (Phf2p); Phf1p and Phf2p are components of the SWM histone demethylase complex that specifically demethylates histone H3 at lysine 9 (H3K9me2), a specific tag for epigenetic transcriptional activation. They function as corepressors and play roles in regulating heterochromatin propagation and euchromatic transcription. Both Phf1p and Phf2p contain a plant homeodomain (PHD) finger.


Pssm-ID: 276977  Cd Length: 52  Bit Score: 47.82  E-value: 1.94e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1443700932  268 CKVCQTCRLPGEDSMMLvCEACDKGYHTFCMEPAIETLPA----ASWKCKNC 315
Cdd:cd15502      2 CIVCQRGHSPKSNRIVF-CDGCNTPYHQLCHDPSIDDEVVedpdAEWFCKKC 52
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 3508-3917 2.48e-06

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 54.39  E-value: 2.48e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3508 QQLSPQPPALlgHAQTPALQHPS----GLGSGAPQRPLLLTPQQQQQQQRVLGSPQLAPQSPAMLGHRLVLGQPLHPPQA 3583
Cdd:pfam03154  165 QILQTQPPVL--QAQSGAASPPSppppGTTQAATAGPTPSAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQTPTLHPQRL 242

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3584 PLQHFA-QPRVPGQAPSGLQLAQGMQPLAAGKEQPMDGPPAEGTEGPPEPqgapglgaaespavlgLPTAPkHPTELGQG 3662
Cdd:pfam03154  243 PSPHPPlQPMTQPPPPSQVSPQPLPQPSLHGQMPPMPHSLQTGPSHMQHP----------------VPPQP-FPLTPQSS 305

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3663 QQLLLASPQPGSLGTSARLLHQPLPSPGAARPELPQSHgdvagsalvtelppapqppspeqpgkglpgsgALPPPRLQSP 3742
Cdd:pfam03154  306 QSQVPPGPSPAAPGQSQQRIHTPPSQSQLQSQQPPREQ--------------------------------PLPPAPLSMP 353

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3743 GQQKagPAPQPAPTLPPSILGPVPAPVMGQIRAQLQGVLAKNPQLRHLTPQQQQQLQALLVQRHQqsLLQQNQALrQSGP 3822
Cdd:pfam03154  354 HIKP--PPTTPIPQLPNPQSHKHPPHLSGPSPFQMNSNLPPPPALKPLSSLSTHHPPSAHPPPLQ--LMPQSQQL-PPPP 428

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3823 F--PGTVPEQGLPPGRQ-----------PSRPQFPVRPPVLTEAP--TGFAADPGTGGRSQPGQQPLAelvQAALATRGP 3887
Cdd:pfam03154  429 AqpPVLTQSQSLPPPAAshpptsglhqvPSQSPFPQHPFVPGGPPpiTPPSGPPTSTSSAMPGIQPPS---SASVSSSGP 505

                          410       420       430
                   ....*....|....*....|....*....|...
gi 1443700932 3888 QPGFVRLSTPPAL---SPLDSQPSPEQSPHEPK 3917
Cdd:pfam03154  506 VPAAVSCPLPPVQikeEALDEAEEPESPPPPPR 538
PHD_UHRF1_2 cd15525
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and ...
 271-315 2.92e-06

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and UHRF2; UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277000  Cd Length: 47  Bit Score: 46.98  E-value: 2.92e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932  271 CQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIETLPA-ASWKCKNC 315
Cdd:cd15525      2 CHVCGGKQDPEKQLLCDECDMAYHLYCLDPPLTSLPDdDEWYCPDC 47
ePHD_PHF6_like cd15673
Extended PHD finger found in PHD finger protein 6 (PHF6) and PHD finger protein 11 (PHF11); ...
 162-212 3.19e-06

Extended PHD finger found in PHD finger protein 6 (PHF6) and PHD finger protein 11 (PHF11); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the two ePHD fingers of PFH6 and the single ePHD finger of PFH11. PHF6, also termed the X-linked mental retardation disorder Borjeson-Forssman-Lehmann syndrome-associated protein, is a nucleolus, ribosomal RNA promoter-associated protein that regulates cell cycle progression by suppressing ribosomal RNA synthesis. It has been implicated in cell cycle control, genomic maintenance, and tumor suppression. PHF6 shows transcriptional repression activity through directly interacting with the nucleosome remodeling and deacetylation complex component RBBP4. PHF6 contains two non-canonical ePHD fingers. PHF11, also termed BRCA1 C-terminus-associated protein, or renal carcinoma antigen NY-REN-34, is a transcriptional co-activator of the Th1 effector cytokine genes, interleukin-2 (IL2) and interferon-gamma (IFNG), co-operating with nuclear factor kappa B (NF-kappaB). It is involved in T-cell activation and viability. Polymorphisms within PHF11 are associated with total IgE, allergic asthma and eczema.


Pssm-ID: 277143  Cd Length: 116  Bit Score: 49.31  E-value: 3.19e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1443700932  162 GISQKCEHCQRMGATIPCRADGCPRLYHFPCAA-ASGCFQSMK---TLRLLCPEH 212
Cdd:cd15673     62 GRKLKCNLCKKTGATIGCDVKQCKKTYHYHCAKkDDAKIIERNsqgIYRVYCKNH 116
PHD_PRHA_like cd15504
PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and ...
 1005-1050 3.70e-06

PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and similar proteins; PRHA is a homeodomain protein encoded by a single-copy Arabidopsis thaliana homeobox gene, prha. It shows the capacity to bind to TAATTG core sequence elements but requires additional adjacent bases for high-affinity binding. PRHA contains a plant homeodomain (PHD) finger, a homeodomain, peptide repeats and a putative leucine zipper dimerization domain.


Pssm-ID: 276979  Cd Length: 53  Bit Score: 47.04  E-value: 3.70e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1443700932 1005 VCEVCGK--ASDPSRLLLCD-DCDISYHTYCLDPPLQT--VPKG--GWKCKWC 1050
Cdd:cd15504      1 FCAKCQSgeASPDNDILLCDgGCNRAYHQKCLEPPLLTedIPPEdeGWLCPLC 53
PHD2_PHF14 cd15562
PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 224-268 5.76e-06

PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the second PHD finger.


Pssm-ID: 277037  Cd Length: 50  Bit Score: 46.25  E-value: 5.76e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1443700932  224 CVVCDGPGDLRDLLFCTSCGQHYHGACLDVVLA--PHKRA--GWQCPEC 268
Cdd:cd15562      2 CGICKKSNDQHLLALCDTCKLYYHLGCLDPPLTrmPKKTKnsGWQCSEC 50
PHD2_KMT2A_like cd15507
PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 1003-1050 5.97e-06

PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger.


Pssm-ID: 276982  Cd Length: 50  Bit Score: 46.31  E-value: 5.97e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1443700932 1003 CIVCEVCGKASDPsrLLLCDDCDISYHTYCLDPPLQTVP---KGGWKCKWC 1050
Cdd:cd15507      2 CHVCGRKGQAQKQ--LLECEKCQRGYHVDCLGPSYPTKPtrkKKTWICSKC 50
PHD3_KMT2A_like cd15508
PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 1083-1132 6.79e-06

PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the third PHD finger.


Pssm-ID: 276983  Cd Length: 57  Bit Score: 46.28  E-value: 6.79e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1443700932 1083 CPVCREKYVEDDL---LIQCRHCERWLHAACDSLfTEEEVEQAAD----EGFDCSAC 1132
Cdd:cd15508      2 CPLCEKCYDDDDYdskMMQCSQCDHWVHAKCEGL-SDEMYEILSYlpesIEYTCSLC 57
SET_SETD5 cd19181
SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and ...
 4984-5105 7.97e-06

SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins; SETD5 is a probable transcriptional regulator that acts via the formation of large multiprotein complexes that modify and/or remodel the chromatin. SETD5 loss-of-function mutations are a likely cause of a familial syndromic intellectual disability with variable phenotypic expression.


Pssm-ID: 380958  Cd Length: 150  Bit Score: 48.85  E-value: 7.97e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4984 LYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEEQNRGIYMFRINN--EHVIDATLTGGPARYINHSCAPNCVAEVVTF 5061
Cdd:cd19181     21 LRAARDLALDTLIIEYRGKVMLRQQFEVNGHFFKRPYPFVLFYSKFNgvEMCVDARTFGNDARFIRRSCTPNAEVRHMIA 100

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932 5062 DKEDKIIIISSRRIPKGEELTYDYQFDFEDDQHKIPCHC--GAWNC 5105
Cdd:cd19181    101 DGMIHLCIYAVAAIAKDAEVTIAFDYEYSNCNYKVDCAChkGNRNC 146
PHD2_CHD_II cd15532
PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 270-315 1.01e-05

PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the second PHD finger.


Pssm-ID: 277007 [Multi-domain]  Cd Length: 43  Bit Score: 45.35  E-value: 1.01e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932  270 VCQTCRLPGEdsmMLVCEACDKGYHTFCMEPAIETLPAASWKCKNC 315
Cdd:cd15532      1 FCRVCKDGGE---LLCCDGCPSSYHLHCLNPPLAEIPDGDWFCPRC 43
PHD1_MTF2_PHF19_like cd15499
PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ...
 268-315 1.19e-05

PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) family proteins MTF2, PHF19, and similar proteins; The family includes two PCL family proteins, metal-response element-binding transcription factor 2 (MTF2/PCL2) and PHF19/PCL3, which are homologs of PHD finger protein1 (PHF1). PCL family proteins are accessory components of the polycomb repressive complex 2 (PRC2) core complex and all contain an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. They specifically recognize tri-methylated H3K36 (H3K36me3) through their N-terminal Tudor domains. The interaction between their Tudor domains and H3K36me3 is critical for both the targeting and spreading of PRC2 into active chromatin regions and for the maintenance of optimal repression of poised developmental genes where PCL proteins, H3K36me3, and H3K27me3 coexist. Moreover, unlike other PHD finger-containing proteins, the first PHD fingers of PCL proteins do not display histone H3K4 binding affinity and they do not affect the Tudor domain binding to histones. This model corresponds to the first PHD finger.


Pssm-ID: 276974  Cd Length: 53  Bit Score: 45.57  E-value: 1.19e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1443700932  268 CKVCQTCRLPGEDSMmLVCEACDKGYHTFCMEPAIETLPAAS---WKCKNC 315
Cdd:cd15499      2 CSICGGAEARDGNEI-LICDKCDKGYHQLCHSPKVRTSPLEGdekWFCSRC 51
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 271-315 1.55e-05

PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the first PHD finger.


Pssm-ID: 277006 [Multi-domain]  Cd Length: 43  Bit Score: 44.90  E-value: 1.55e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932  271 CQTCRLPGEdsmMLVCEACDKGYHTFCMEPAIETLPAASWKCKNC 315
Cdd:cd15531      2 CEVCQQGGE---IILCDTCPRAYHLVCLDPELEKAPEGKWSCPHC 43
SET_SMYD cd20071
SET domain (including SET domain and post-SET domain) found in SET and MYND domain-containing ...
 4981-5085 1.87e-05

SET domain (including SET domain and post-SET domain) found in SET and MYND domain-containing protein, and similar proteins; The family includes SET and MYND domain-containing proteins, SMYD1-SYMD5. SMYD1 (EC 2.1.1.43; also termed BOP) is a heart and muscle specific SET-MYND domain containing protein, which functions as a histone methyltransferase and regulates downstream gene transcription. It methylates histone H3 at 'Lys-4' (H3K4me), seems able to perform both mono-, di-, and trimethylation. SMYD2 (also termed HSKM-B, or lysine N-methyltransferase 3C (KMT3C)) functions as a histone methyltransferase that methylates both histones and non-histone proteins, including p53/TP53 and RB1. It specifically methylates histone H3 'Lys-4' (H3K4me) and dimethylates histone H3 'Lys-36' (H3K36me2). SMYD3 (also termed zinc finger MYND domain-containing protein 1) functions as a histone methyltransferase that specifically methylates 'Lys-4' of histone H3, inducing di- and tri-methylation, but not monomethylation. It also methylates 'Lys-5' of histone H4. SMYD3 plays an important role in transcriptional activation as a member of an RNA polymerase complex. SMYD4 functions as a potential tumor suppressor that plays a critical role in breast carcinogenesis at least partly through inhibiting the expression of PDGFR-alpha. SMYD5 (also termed protein NN8-4AG, or retinoic acid-induced protein 15) functions as histone lysine methyltransferase that mediates H4K20me3 at heterochromatin regions.


Pssm-ID: 380997 [Multi-domain]  Cd Length: 122  Bit Score: 46.99  E-value: 1.87e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4981 GLGLYAAKDIEKhtmvieyiGTIIRNE------VANRREKIYEEQNRGIYMFRInnehvidatltggpARYINHSCAPNC 5054
Cdd:cd20071     10 GRGLVATRDIEP--------GELILVEkplvsvPSNSFSLTDGLNEIGVGLFPL--------------ASLLNHSCDPNA 67

                           90       100       110
                   ....*....|....*....|....*....|.
gi 1443700932 5055 VaevVTFDKEDKIIIISSRRIPKGEELTYDY 5085
Cdd:cd20071     68 V---VVFDGNGTLRVRALRDIKAGEELTISY 95
PHD1_KMT2A_like cd15506
PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 270-315 2.08e-05

PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the first PHD finger.


Pssm-ID: 276981  Cd Length: 47  Bit Score: 44.66  E-value: 2.08e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1443700932  270 VCQTCRLPGEDSMmLVCEACDKGYHTFCMEPAIETLPAA--SWKCKNC 315
Cdd:cd15506      1 LCFLCGSAGLNEL-LYCSVCCEPYHTFCLEEAERPLNINkdNWCCRRC 47
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 3807-4006 2.15e-05

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 51.31  E-value: 2.15e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3807 QQSLLQQNQALRQSgpfPGTVPEQGLPPGRQPSRPQFPVRPPVLTEAPTgfaadPGTGGRSQPGQQPLAELVQAALATRG 3886
Cdd:pfam03154  163 QQQILQTQPPVLQA---QSGAASPPSPPPPGTTQAATAGPTPSAPSVPP-----QGSPATSQPPNQTQSTAAPHTLIQQT 234

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3887 PQPGFVRLSTP-PALSPLDSQPSPEQSPHEPKTPTP------------TTTGGLAPSPVAPLELPQSPWGSEPPALDDDV 3953
Cdd:pfam03154  235 PTLHPQRLPSPhPPLQPMTQPPPPSQVSPQPLPQPSlhgqmppmphslQTGPSHMQHPVPPQPFPLTPQSSQSQVPPGPS 314

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1443700932 3954 AETSVNGQGVEGTPDECPQLPVKQEPREETALPAAAR----EPEPQEPVKPEANGDA 4006
Cdd:pfam03154  315 PAAPGQSQQRIHTPPSQSQLQSQQPPREQPLPPAPLSmphiKPPPTTPIPQLPNPQS 371
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 1642-1691 2.15e-05

high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenetically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4, and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.


Pssm-ID: 438789 [Multi-domain]  Cd Length: 59  Bit Score: 44.82  E-value: 2.15e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1443700932 1642 LYANMNFPNLKQDYPDWSSrcKQIMKL----WRKVPATDKAPYLQKAKDNRAAH 1691
Cdd:cd00084      8 LFSKEKRPKLKKENPDLSF--TEISKLlgerWKELSEEEKQPYEEKAKEDKERY 59
PHA03379 PHA03379
EBNA-3A; Provisional
 1744-2203 2.45e-05

EBNA-3A; Provisional


Pssm-ID: 223066 [Multi-domain]  Cd Length: 935  Bit Score: 50.83  E-value: 2.45e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1744 EGFLKPPAGTGAGPESPSELFLKLPPQSPAQVPSHDPygaagSYAPEP-----RFPSPL----GQSPTVGAAFQPFPGQP 1814
Cdd:PHA03379   403 EALEKASEPTYGTPRPPVEKPRPEVPQSLETATSHGS-----AQVPEPppvhdLEPGPLhdqhSMAPCPVAQLPPGPLQD 477

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1815 LagartQPPDFHPTPPGTPRhQSGTPDP-----FLKPRCPSLDNLSG-----------PGSPGARPPEALLSPLPFSEQK 1878
Cdd:PHA03379   478 L-----EPGDQLPGVVQDGR-PACAPVPapagpIVRPWEASLSQVPGvafapvmpqpmPVEPVPVPTVALERPVCPAPPL 551

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1879 KGLEVKKEDGGALGVcSPGYVPATGYSDSPGcthiPSTELKVAD---VFKAPLTPRVSQVEPQSPGLGHRPPDAhPLAPS 1955
Cdd:PHA03379   552 IAMQGPGETSGIVRV-RERWRPAPWTPNPPR----SPSQMSVRDrlaRLRAEAQPYQASVEVQPPQLTQVSPQQ-PMEYP 625

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1956 PPGHADLFRQSPYSDPYAQPPLTPRPQPPegcctAPPRSLPSEPFSRIPASPQSQSSSQSPLTPRPLSNEAFCQSPVTpr 2035
Cdd:PHA03379   626 LEPEQQMFPGSPFSQVADVMRAGGVPAMQ-----PQYFDLPLQQPISQGAPLAPLRASMGPVPPVPATQPQYFDIPLT-- 698

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2036 fqspDPYSQPPSRPQSRD--PFTPLHKPPRAQLPAAPLSHS-----------------PAGSGGFGGAATGEPPAKAPGV 2096
Cdd:PHA03379   699 ----EPINQGASAAHFLPqqPMEGPLVPERWMFQGATLSQSvrpgvaqsqyfdlpltqPINHGAPAAHFLHQPPMEGPWV 774

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2097 PQQPPFARSPGAGIFTTGQPPMrftfppavseplkGSPSHQLHGLNSHYVPSKPQSAGY-TSSPSFhqaGSPL-----GP 2170
Cdd:PHA03379   775 PEQWMFQGAPPSQGTDVVQHQL-------------DALGYVLHVLNHPGVPVSPAVNQYhVSQAAF---GLPIdedesGE 838

                          490       500       510
                   ....*....|....*....|....*....|....*..
gi 1443700932 2171 GAGAAETYSLSPL----RPPSVLPQASPSAPQPQDAS 2203
Cdd:PHA03379   839 GSDTSEPCEALDLsihgRPCPQAPEWPVQGEGGQDAT 875
PHD_TCF19_like cd15517
PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and ...
 1082-1132 2.70e-05

PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and KDM5B, and other similar proteins; TCF-19 was identified as a putative trans-activating factor with expression beginning at the late G1-S boundary in dividing cells. It functions as a novel islet factor necessary for proliferation and survival in the INS-1 beta cell line. It plays an important role in susceptibility to both Type 1 Diabetes Mellitus (T1DM) and Type 2 Diabetes Mellitus (T2DM); it has been suggested that it may positively impact beta cell mass under conditions of beta cell stress and increased insulin demand. KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interaction with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK, and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. This family also includes Caenorhabditis elegans Lysine-specific demethylase 7 homolog (ceKDM7A). ceKDM7A (also termed JmjC domain-containing protein 1.2, PHD finger protein 8 homolog, or PHF8 homolog) is a plant homeodomain (PHD)- and JmjC domain-containing protein that functions as a histone demethylase specific for H3K9me2 and H3K27me2. The binding of the PHD finger to H3K4me3 guides H3K9me2- and H3K27me2-specific demethylation by its catalytic JmjC domain in a trans-histone regulation mechanism. In addition, this family includes plant protein OBERON 1 and OBERON 2, Alfin1-like (AL) proteins, histone acetyltransferases (HATs) HAC, and AT-rich interactive domain-containing protein 4 (ARID4).


Pssm-ID: 276992 [Multi-domain]  Cd Length: 49  Bit Score: 44.46  E-value: 2.70e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1443700932 1082 VCPVCR-EKYVEDDLLIQCRHCERWLHAACDSLfteeEVEQAADEG-FDCSAC 1132
Cdd:cd15517      1 VCGICNlETAAVDELWVQCDGCDKWFHQFCLGL----SNERYADEDkFKCPNC 49
PHD1_Rco1 cd15535
PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and ...
 1006-1050 3.07e-05

PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and similar proteins; Rco1 is a component of the Rpd3S histone deacetylase complex that plays an important role at actively transcribed genes. Rco1 contains two plant homeodomain (PHD) fingers, which are required for the methylation of histone H3 lysine 36 (H3K36) nucleosome recognition by Rpd3S. This model corresponds to the first PHD finger.


Pssm-ID: 277010 [Multi-domain]  Cd Length: 45  Bit Score: 43.95  E-value: 3.07e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1443700932 1006 CEVCGKasdPSRLLLCDDCDISYHTYCLDPPL--QTVPKGGWKCKWC 1050
Cdd:cd15535      2 CSACGG---YGSFLCCDGCPRSFHFSCLDPPLeeDNLPDDEWFCNEC 45
ePHD1_PHF6 cd15710
Extended PHD finger 1 found in PHD finger protein 6 (PHF6); The extended plant homeodomain ...
 4632-4695 3.20e-05

Extended PHD finger 1 found in PHD finger protein 6 (PHF6); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. PHF6 contains two non-canonical ePHD fingers, this model corresponds to the first ePHD finger. PHF6, also termed the X-linked mental retardation disorder Borjeson-Forssman-Lehmann syndrome-associated protein, is a nucleolus, ribosomal RNA promoter-associated protein that regulates cell cycle progression by suppressing ribosomal RNA synthesis. It has been implicated in cell cycle control, genomic maintenance, and tumor suppression. PHF6 shows transcriptional repression activity through directly interacting with the nucleosome remodeling and deacetylation complex component RBBP4. .


Pssm-ID: 277180  Cd Length: 115  Bit Score: 46.11  E-value: 3.20e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1443700932 4632 HLNCALWSTEVYETQ------GGALI-NVEVALHRGLLTKCSLCQKTGATNSCNRIRCPSVYHFACAIRAK 4695
Cdd:cd15710     26 HHKCMLFSSALVSSHsdsenlGGFSIeDVQKEIKRGTKLMCSLCHCPGATIGCDVKTCHRTYHYYCALHDK 96
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 3602-4001 3.41e-05

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 50.54  E-value: 3.41e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3602 QLAQGMQPLAagkeQPMDGPPAEGTEGPPEPQGAPGlgAAESPAVLGLPTAPKHPTELGQGQQLLLASPQpgSLGTSARL 3681
Cdd:pfam03154  165 QILQTQPPVL----QAQSGAASPPSPPPPGTTQAAT--AGPTPSAPSVPPQGSPATSQPPNQTQSTAAPH--TLIQQTPT 236

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3682 LHQP-LPSPGAARPELPQSHGDVAGSAlvtelppapqppspeqpgkglpgsGALPPPRLQSPGQqkagPAPQPAPTLPPS 3760
Cdd:pfam03154  237 LHPQrLPSPHPPLQPMTQPPPPSQVSP------------------------QPLPQPSLHGQMP----PMPHSLQTGPSH 288

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3761 ILGPVPAPVMGQIRAQLQGVLAKNPQlrhltPQQQQQLQALLVQRHQQSLLQQNQALRQSG--PFPGTVPEQGLPPGR-- 3836
Cdd:pfam03154  289 MQHPVPPQPFPLTPQSSQSQVPPGPS-----PAAPGQSQQRIHTPPSQSQLQSQQPPREQPlpPAPLSMPHIKPPPTTpi 363

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3837 -QPSRPQFPVRPPVLTeAPTGFAADPGTggRSQPGQQPLAELVQAALATRGPQPGFV-----RLSTPPALSPLDSQ---- 3906
Cdd:pfam03154  364 pQLPNPQSHKHPPHLS-GPSPFQMNSNL--PPPPALKPLSSLSTHHPPSAHPPPLQLmpqsqQLPPPPAQPPVLTQsqsl 440

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3907 --------------PSPEQSPHEPKTPTPTTTGGLAPSPVAPLELPQSPWGSEPPAldddVAETSVNGQGVEGTPDECPQ 3972
Cdd:pfam03154  441 pppaashpptsglhQVPSQSPFPQHPFVPGGPPPITPPSGPPTSTSSAMPGIQPPS----SASVSSSGPVPAAVSCPLPP 516

                          410       420
                   ....*....|....*....|....*....
gi 1443700932 3973 LPVKQEPREETALPAAArePEPQEPVKPE 4001
Cdd:pfam03154  517 VQIKEEALDEAEEPESP--PPPPRSPSPE 543
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 1082-1134 3.85e-05

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 44.02  E-value: 3.85e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1443700932 1082 VCPVCReKYVEDDLLIQCRHCERWLHAACDSLftEEEVEQAADEGFDCSACQP 1134
Cdd:pfam00628    1 YCAVCG-KSDDGGELVQCDGCDDWFHLACLGP--PLDPAEIPSGEWLCPECKP 50
ePHD_PHF11 cd15712
Extended PHD finger found in PHD finger protein 11 (PHF11); The extended plant homeodomain ...
 4628-4709 5.48e-05

Extended PHD finger found in PHD finger protein 11 (PHF11); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of PHF11. PHF11, also termed BRCA1 C-terminus-associated protein, or renal carcinoma antigen NY-REN-34, is a transcriptional co-activator of the Th1 effector cytokine genes, interleukin-2 (IL2) and interferon-gamma (IFNG), co-operating with nuclear factor kappa B (NF-kappaB). It is involved in T-cell activation and viability. Polymorphisms within PHF11 are associated with total IgE, allergic asthma and eczema.


Pssm-ID: 277182 [Multi-domain]  Cd Length: 115  Bit Score: 45.66  E-value: 5.48e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4628 DLWVHLNCALWSTEVYETQGGALINVEVA---------LHRGLLTKCSLCQKTGATNSCNRIRCPSVYHFACAIRAKCMF 4698
Cdd:cd15712     20 NIAAHQNCLLYSSGFVESEEYNPLNLDRRfdvesvlneIKRGKRLKCNFCRKKGATVGCEERACRRSYHYFCALCDDAAI 99

                           90
                   ....*....|....*.
gi 1443700932 4699 FKDKT-----MLCPLH 4709
Cdd:cd15712    100 ETDEVrgiyrVFCQKH 115
PHD2_KMT2B cd15591
PHD domain 2 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed ...
 956-1003 5.91e-05

PHD domain 2 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed trithorax homolog 2 or WW domain-binding protein 7 (WBP-7), is encoded by the gene that was first named myeloid/lymphoid or mixed-lineage leukemia 2 (MLL2), a second human homolog of Drosophila trithorax, located on chromosome 19. It belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2) and is vital for normal mammalian embryonic development. KMT2B functions as the catalytic subunit in the MLL2 complex, which contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL2 complex is highly active and specific for histone 3lysine 4 (H3K4) methylation, which stimulates chromatin transcription in a SAM- and H3K4-dependent manner. Moreover, KMT2B plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. KMT2B contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD), an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger.


Pssm-ID: 277066  Cd Length: 50  Bit Score: 43.39  E-value: 5.91e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1443700932  956 CVVCGSFGRGAEgHLLACSQCSQCYHPYCVNSKITKVMLLK--GWRCVEC 1003
Cdd:cd15591      2 CHVCGRKNKESK-PLLECERCRNCYHPACLGPNYPKPANRKkrPWICSAC 50
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 2780-2926 6.05e-05

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 49.65  E-value: 6.05e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2780 LLEHEKKELQKKQQMSVQLPRGAP-QHLPAAGHPLLHPGAPGQPPEGQGPRLGTPQPTLQLGLMARQQLLQPQQSRLGGP 2858
Cdd:pfam09770  203 MRAQAKKPAQQPAPAPAQPPAAPPaQQAQQQQQFPPQIQQQQQPQQQPQQPQQHPGQGHPVTILQRPQSPQPDPAQPSIQ 282

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1443700932 2859 QQGLPLAGHMGMAPAQP-HVLAAP--HGVQVALPPQQGQQPVLMQKPMGAG-QPPGLGLKPPQLVMQQQLAN 2926
Cdd:pfam09770  283 PQAQQFHQQPPPVPVQPtQILQNPnrLSAARVGYPQNPQPGVQPAPAHQAHrQQGSFGRQAPIITHPQQLAQ 354
PHD_TIF1beta cd15623
PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also ...
 1006-1050 6.51e-05

PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also termed Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), or KRAB-interacting protein 1 (KRIP-1), or nuclear co-repressor KAP-1, or RING finger protein 96, or tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, acts as a nuclear co-repressor that plays a role in transcription and in DNA damage response. Upon DNA damage, the phosphorylation of KAP-1 on serine 824 by the ataxia telangiectasia-mutated (ATM) kinase enhances cell survival and facilitates chromatin relaxation and heterochromatic DNA repair. It also regulates CHD3 nucleosome remodeling during DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. In addition, KAP-1 is a co-activator of the orphan nuclear receptor NGFI-B (or Nur77) and is involved in NGFI-B-dependent transcription. It is also a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase. TIF1-beta contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), which can interact with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and mediates homo- and heterodimerization, a plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region, which interact with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity.


Pssm-ID: 277093  Cd Length: 43  Bit Score: 43.25  E-value: 6.51e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932 1006 CEVCGKASDpsrLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1050
Cdd:cd15623      2 CRVCQKAGA---LVMCDQCEFCFHLDCHLPALQEVPGEDWKCLLC 43
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 2793-2923 8.27e-05

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 49.26  E-value: 8.27e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2793 QMSVQLPRGAPQHLPAAGHPllhpgaPGQPPEGQGPRLGTPQPTLQLGLMARQQLLQPQQSRLGGP-------QQGLPLA 2865
Cdd:pfam09770  202 AMRAQAKKPAQQPAPAPAQP------PAAPPAQQAQQQQQFPPQIQQQQQPQQQPQQPQQHPGQGHpvtilqrPQSPQPD 275

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1443700932 2866 GHMGMAPAQPHVLAAPHGVQVALPPQQGQQPVLM---QKPMGAGQPPGLGLKPPQLVMQQQ 2923
Cdd:pfam09770  276 PAQPSIQPQAQQFHQQPPPVPVQPTQILQNPNRLsaaRVGYPQNPQPGVQPAPAHQAHRQQ 336
PHD_BRPF_JADE_like cd15492
PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; ...
 1005-1050 8.31e-05

PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; The family includes BRPF proteins, Jade proteins, protein AF-10 and AF-17. BRPF proteins are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. Jade proteins are required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6, to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. AF-10, also termed ALL1 (acute lymphoblastic leukemia)-fused gene from chromosome 10 protein, is a transcription factor that has been implicated in the development of leukemia following chromosomal rearrangements between the AF10 gene and one of at least two other genes, MLL and CALM. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is a putative transcription factor that may play a role in multiple signaling pathways. All Jade proteins, AF-10, and AF-17 contain a canonical PHD finger followed by a non-canonical ePHD finger. This model corresponds to the canonical PHD finger.


Pssm-ID: 276967 [Multi-domain]  Cd Length: 46  Bit Score: 42.99  E-value: 8.31e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1443700932 1005 VCEVCGKAS--DPSRLLLCDDCDISYHTYCLDppLQTVPKGGWKCKWC 1050
Cdd:cd15492      1 VCDVCLDGEseDDNEIVFCDGCNVAVHQSCYG--IPLIPEGDWFCRKC 46
PHD_UHRF2 cd15617
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); ...
 271-315 1.05e-04

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); UHRF2 (also termed Np95/ICBP90-like RING finger protein (NIRF), Np95-like RING finger protein, nuclear protein 97, nuclear zinc finger protein Np97, RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2) was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs,p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277089  Cd Length: 47  Bit Score: 42.63  E-value: 1.05e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932  271 CQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIETLPA-ASWKCKNC 315
Cdd:cd15617      2 CYVCGGKQDAHMQLLCDECNMAYHIYCLNPPLDKIPEdEDWYCPSC 47
PHD_PHF21B cd15524
PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) ...
 1006-1050 1.51e-04

PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) finger-containing protein whose biological function remains unclear. It shows high sequence similarity with PHF21A, which is associated with LSD1, a lysine (K)-specific histone demethylase and inhibits LSD1-mediated histone demethylation in vitro. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins.


Pssm-ID: 276999 [Multi-domain]  Cd Length: 43  Bit Score: 42.19  E-value: 1.51e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932 1006 CEVCGKASDpsrLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 1050
Cdd:cd15524      2 CAACKRGGN---LQPCGTCPRAYHLDCLDPPLKTAPKGVWVCPKC 43
EIF4E-T pfam10477
Nucleocytoplasmic shuttling protein for mRNA cap-binding EIF4E; EIF4E-T is the transporter ...
 3285-3441 1.64e-04

Nucleocytoplasmic shuttling protein for mRNA cap-binding EIF4E; EIF4E-T is the transporter protein for shuttling the mRNA cap-binding protein EIF4E protein, targeting it for nuclear import. EIF4E-T contains several key binding domains including two functional leucine-rich NESs (nuclear export signals) between residues 438-447 and 613-638 in the human protein. The other two binding domains are an EIF4E-binding site, between residues 27-42 in Q9EST3, and a bipartite NLS (nuclear localization signals) between 194-211, and these lie in family EIF4E-T_N. EIF4E is the eukaryotic translation initiation factor 4E that is the rate-limiting factor for cap-dependent translation initiation.


Pssm-ID: 371079  Cd Length: 646  Bit Score: 48.08  E-value: 1.64e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3285 MGQASMQQPGVMGQVSMQQTGVMGQMSIQQPSMAGQASMQQTGVLgQVSMQQSGIMGQASMQQPGVLGQVSMQQPGVMGQ 3364
Cdd:pfam10477  462 LGSQGTQHHSVNDSAPTINDSNAGQLANQPVPYHIQENHQDQQAK-FLGVHTPNIFAQPNMEIQHLIQELVRPDISHEFL 540

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3365 TMQQ--PGVMGQTSMQPPGVMGQTS---------MQQTSVMGQVSMQQPGAVGQASMQPQGIMAQASLQQSGVMGQTALQ 3433
Cdd:pfam10477  541 EKELsnPSTLGHTKDVIAAVLRECSngmrntmspKPQQNVMTPQSLHQAQLQPLQQPQQLALQQDLFYQNDGNQNRQQHI 620


                   ....*...
gi 1443700932 3434 QPGILPQP 3441
Cdd:pfam10477  621 RHSNSPTP 628
PHD_TIF1_like cd15541
PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar ...
 267-315 1.80e-04

PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar proteins; The TIF1 family of transcriptional cofactors includes TIF1alpha (TRIM24), TIF1beta (TRIM28), TIF1gamma (TRIM33), and TIF1delta (TRIM66), which are characterized by an N-terminal RING-finger B-box coiled-coil (RBCC/TRIM) motif and plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region. TIF1 proteins couple chromatin modifications to transcriptional regulation, signaling, and tumor suppression. They exert a deacetylase-dependent silencing effect when tethered to a promoter region. TIF1alpha, TIF1beta, and TIF1delta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. TIF1alpha and TIF1beta bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. In contrast, TIF1delta appears to lack nuclear receptor- and KRAB-binding activity. Moreover, TIF1delta is specifically involved in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. TIF1gamma is structurally closely related to TIF1alpha and TIF1beta, but has very little functional features in common with them. It does not interact with the KRAB silencing domain of KOX1 or the heterochromatinic proteins HP1alpha, beta, and gamma. It cannot bind to nuclear receptors (NRs). This family also includes Sp100/Sp140 family proteins, the nuclear body SP100 and SP140. Sp110 is a leukocyte-specific component of the nuclear body. It may function as a nuclear hormone receptor transcriptional coactivator that may play a role in inducing differentiation of myeloid cells. It is also involved in resisting intracellular pathogens and functions as an important drug target for preventing intracellular pathogen diseases, such as tuberculosis, hepatic veno-occlusive disease, and intracellular cancers. SP140 is an interferon inducible nuclear leukocyte-specific protein involved in primary biliary cirrhosis and a risk factor in chronic lymphocytic leukemia. It is also implicated in innate immune response to human immunodeficiency virus type 1 (HIV-1) by binding to the virus viral infectivity factor (Vif) protein. Both Sp110 and Sp140 contain a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD).


Pssm-ID: 277016 [Multi-domain]  Cd Length: 43  Bit Score: 41.95  E-value: 1.80e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1443700932  267 ECKVCQTcrlpGEDSMMlvCEACDKGYHTFCMEPAIETLPAASWKCKNC 315
Cdd:cd15541      1 WCAVCQN----GGELLC--CDKCPRVFHLDCHIPPIPEFPSGEWSCSLC 43
PHD_PRKCBP1 cd15538
PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed ...
 967-1003 2.14e-04

PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed cutaneous T-cell lymphoma-associated antigen se14-3 (CTCL-associated antigen se14-3), or Rack7, or zinc finger MYND domain-containing protein 8 (ZMYND8), is a novel receptor for activated C-kinase (RACK)-like protein that may play an important role in the activation and regulation of PKC-beta I, and the PKC signaling cascade. It also has been identified as a formin homology-2-domain containing protein 1 (FHOD1)-binding protein that may be involved in FHOD1-regulated actin polymerization and transcription. Moreover, PRKCBP1 may function as a REST co-repressor 2 (RCOR2) interacting factor; the RCOR2/ZMYND8 complex which might be involved in the regulation of neural differentiation. PRKCBP1 contains a plant homeodomain (PHD) finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain.


Pssm-ID: 277013  Cd Length: 41  Bit Score: 41.54  E-value: 2.14e-04
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 1443700932  967 EGHLLACSQCSQCYHPYCVNSKItkvMLLKGWRCVEC 1003
Cdd:cd15538      8 EGQVLCCSLCPRVYHKKCLKLTS---EPDEDWVCPEC 41
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 4665-4709 2.36e-04

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 41.81  E-value: 2.36e-04
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 1443700932  4665 CSLCQKTGATN---SCNRirCPSVYHFACAIRAKCMFFKDKTMLCPLH 4709
Cdd:smart00249    2 CSVCGKPDDGGellQCDG--CDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
SET_Suv4-20-like cd10524
SET domain (including post-SET domain) found in Drosophila melanogaster suppressor of ...
 4971-5107 2.36e-04

SET domain (including post-SET domain) found in Drosophila melanogaster suppressor of variegation 4-20 (Suv4-20) and similar proteins; Suv4-20 (also termed Su(var)4-20) is a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-20' of histone H4. It acts as a dominant suppressor of position-effect variegation. The family also includes Suv4-20 homologs, lysine N-methyltransferase 5B (KMT5B) and lysine N-methyltransferase 5C (KMT5C). Both KMT5B (also termed lysine-specific methyltransferase 5B, or suppressor of variegation 4-20 homolog 1, or Su(var)4-20 homolog 1, or Suv4-20h1) and KMT5C (also termed lysine-specific methyltransferase 5C, or suppressor of variegation 4-20 homolog 2, or Su(var)4-20 homolog 2, or Suv4-20h2) are histone methyltransferases that specifically trimethylate 'Lys-20' of histone H4 (H4K20me3). They play central roles in the establishment of constitutive heterochromatin in pericentric heterochromatin regions.


Pssm-ID: 380922 [Multi-domain]  Cd Length: 141  Bit Score: 44.58  E-value: 2.36e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4971 NVYLARSRiQGLGLYAAKDIEKHTMVIEYIGTIIRNEVANRREKIYEEQNRG-IYMFRINNEHVIDatltgGPARYINHS 5049
Cdd:cd10524     10 NRYSLENH-YGAKIIATKPIKKGEKIHELCGCIAELSEEEEALLRPGGNDFSvMYSSRKKCSQLWL-----GPAAFINHD 83

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 5050 CAPNCVaevvtFDKEDKIIIISSRRIP--KGEELTYDYQFDFEDDQHkipCHCGAWNCRK 5107
Cdd:cd10524     84 CRPNCK-----FVPTGKSTACVKVLRDiePGEEITVYYGDNYFGENN---EECECETCER 135
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
 1937-2228 3.27e-04

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 47.38  E-value: 3.27e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1937 PQSPGLGHRPPDAHPLAPSPPGHADLFRQSPYSDPYAQPPLTPrpqppEGCCTAPPRSLPSEPFSRIPASPQSQSSSQSP 2016
Cdd:PTZ00449   511 PEGPEASGLPPKAPGDKEGEEGEHEDSKESDEPKEGGKPGETK-----EGEVGKKPGPAKEHKPSKIPTLSKKPEFPKDP 585

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2017 LTPRPLSNEAFCQSPVTPRfqspDPYSQP-PSRPQSRD-PFTPLH--------KPPRAQLPAAPlshspagsggfggaat 2086
Cdd:PTZ00449   586 KHPKDPEEPKKPKRPRSAQ----RPTRPKsPKLPELLDiPKSPKRpespkspkRPPPPQRPSSP---------------- 645

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2087 gEPPaKAPGVPQQPPFARSPgagifttgQPPmrftFPPAVSEPLKGSPSHQLhglnSHYVPSKPQSAGYTSSPSFHQAGS 2166
Cdd:PTZ00449   646 -ERP-EGPKIIKSPKPPKSP--------KPP----FDPKFKEKFYDDYLDAA----AKSKETKTTVVLDESFESILKETL 707

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1443700932 2167 PLGPGAGAAETYSLSPLRP--PSV--LPQASPSAPQPQDASVAYVP---RAAVLTTPADKREVAATTAL 2228
Cdd:PTZ00449   708 PETPGTPFTTPRPLPPKLPrdEEFpfEPIGDPDAEQPDDIEFFTPPeeeRTFFHETPADTPLPDILAEE 776
PHD_UHRF1 cd15616
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); ...
 271-315 3.37e-04

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); UHRF1 (also termed inverted CCAAT box-binding protein of 90 kDa, nuclear protein 95, nuclear zinc finger protein Np95 (Np95), RING finger protein 106, transcription factor ICBP90, or E3 ubiquitin-protein ligase UHRF1) is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF1 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET and RING finger associated (SRA) domain, and a C-terminal RING-finger domain. It specifically binds to hemimethylated DNA, double-stranded CpG dinucleotides, and recruits the maintenance methyltransferase DNMT1 to its hemimethylated DNA substrate through its SRA domain. UHRF1-dependent H3K23 ubiquitylation has an essential role in maintaining DNA methylation and replication. The tandem Tudor domain directs UHRF1 binding to the heterochromatin mark histone H3K9me3 and the PHD finger targets UHRF1 to unmodified histone H3 in euchromatic regions. The RING-finger domain exhibit both autocatalytic E3 ubiquitin (Ub) ligase activity and activity against histone H3 and DNMT1.


Pssm-ID: 277088  Cd Length: 47  Bit Score: 41.11  E-value: 3.37e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932  271 CQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIETLPA-ASWKCKNC 315
Cdd:cd15616      2 CHVCGGKQDPDKQLMCDECDMAFHIYCLNPPLSSIPDdEDWYCPEC 47
PHD_TAF3 cd15522
PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed ...
 223-268 3.90e-04

PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed 140 kDa TATA box-binding protein-associated factor, TBP-associated factor 3, transcription initiation factor TFIID 140 kDa subunit (TAF140), or TAFII-140, is an integral component of TFIID) is a general initiation factor (GTF) that plays a key role in preinitiation complex (PIC) assembly through core promoter recognition. The interaction of H3K4me3 with TAF3 directs global TFIID recruitment to active genes, which regulates gene-selective functions of p53 in response to genotoxic stress. TAF3 is highly enriched in embryonic stem cells and is required for endoderm lineage differentiation and prevents premature specification of neuroectoderm and mesoderm. Moreover, TAF3, along with TRF3, forms a complex that is essential for myogenic differentiation. TAF3 contains a plant homeodomain (PHD) finger. This family also includes Drosophila melanogaster BIP2 (Bric-a-brac interacting protein 2) protein, which functions as an interacting partner of D. melanogaster p53 (Dmp53).


Pssm-ID: 276997 [Multi-domain]  Cd Length: 46  Bit Score: 41.12  E-value: 3.90e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932  223 RCVVCDGPGDLRDLLFCTSCGQHYHGACLDVVLAPHKRAGWQCPEC 268
Cdd:cd15522      1 ICPICKKPDDGSPMIGCDECDDWYHWECVGITDEPPEEDDWFCPKC 46
HMG_box pfam00505
HMG (high mobility group) box;
1641-1692 3.92e-04

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 41.83  E-value: 3.92e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1443700932 1641 VLYANMNFPNLKQDYPDWSSR--CKQIMKLWRKVPATDKAPYLQKAKDNRAAHR 1692
Cdd:pfam00505    9 FLFSKEQRAKLKAENPGLKNAeiSKILGEKWKALSEEEKKPYEEKAEKEKARYE 62
PHA03247 PHA03247
large tegument protein UL36; Provisional
 3402-3701 3.96e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 47.24  E-value: 3.96e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3402 PGAVGQASMQPQGIMAQASLQ-QSGVMGQTALQQPGILPQPSLQPQGLMAQPAMQPAGSLAQPPLPQQppmqqpglgvqq 3480
Cdd:PHA03247  2741 PPAVPAGPATPGGPARPARPPtTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPP------------ 2808

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3481 VAAPPAQGAIGQPVGPKQPALPQSLLVQQLSPQPPALLGHAQTPAlqhpsglGSGAPQRPLlltpqqqqqqqRVLGSPQL 3560
Cdd:PHA03247  2809 AAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLG-------GSVAPGGDV-----------RRRPPSRS 2870

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3561 APQSPAMLGHRLVLGQPLHPPQAPLQHFAQPRVPGQAPSGLQLAQGMQPLAAGKEQPMDGPPAEgTEGPPEPQGAPGLGA 3640
Cdd:PHA03247  2871 PAAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPP-PPPRPQPPLAPTTDP 2949

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1443700932 3641 AESPAVLGLPTAPKhptelgqgqqllLASPQPGSLGTSARLLHQPLPSPGAARPELPQSHG 3701
Cdd:PHA03247  2950 AGAGEPSGAVPQPW------------LGALVPGRVAVPRFRVPQPAPSREAPASSTPPLTG 2998
ePHD2_PHF6 cd15711
Extended PHD finger 2 found in PHD finger protein 6 (PHF6); The extended plant homeodomain ...
 4605-4701 4.55e-04

Extended PHD finger 2 found in PHD finger protein 6 (PHF6); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. PHF6 contains two non-canonical ePHD fingers, this model corresponds to the second ePHD finger. PHF6, also termed the X-linked mental retardation disorder Borjeson-Forssman-Lehmann syndrome-associated protein, is a nucleolus, ribosomal RNA promoter-associated protein that regulates cell cycle progression by suppressing ribosomal RNA synthesis. It has been implicated in cell cycle control, genomic maintenance, and tumor suppression. PHF6 shows transcriptional repression activity through directly interacting with the nucleosome remodeling and deacetylation complex component RBBP4.


Pssm-ID: 277181  Cd Length: 118  Bit Score: 43.15  E-value: 4.55e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4605 CCFCHE-EGDGATDGPARLLNLDlDLWVHLNCALWST---EVYETQGGALINVEVA-----LHRGLLTKCSLCQKTGATN 4675
Cdd:cd15711      1 CGFCHAgEEENETRGKLHIFNAK-KAAAHYKCMLFSSgtvQLTTTSRAEFGDFDIKtviqeIKRGKRMKCTLCSQLGATI 79

                           90       100
                   ....*....|....*....|....*.
gi 1443700932 4676 SCNRIRCPSVYHFACAIRAKCMFFKD 4701
Cdd:cd15711     80 GCEIKACVKTYHYHCGVQDKAKYIEN 105
PHD1_NSD cd15564
PHD finger 1 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
 224-269 4.66e-04

PHD finger 1 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the first PHD finger.


Pssm-ID: 277039  Cd Length: 43  Bit Score: 40.78  E-value: 4.66e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1443700932  224 CVVCDGPGdlrDLLFCT-SCGQHYHGACLDVVLAPhkRAGWQCPECK 269
Cdd:cd15564      2 CQICEKPG---KLLTCEgPCCGHFHLDCLGLSEQP--DEPFKCDECT 43
ePHD_JADE cd15671
Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins; The extended ...
 4630-4691 4.97e-04

Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-1 (PHF17), Jade-2 (PHF15), and Jade-3 (PHF16); each of these proteins is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, has reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. This family also contains Drosophila melanogaster PHD finger protein rhinoceros (RNO). It is a novel plant homeodomain (PHD)-containing nuclear protein that may function as a transcription factor that antagonizes Ras signaling by regulating transcription of key EGFR/Ras pathway regulators in the Drosophila eye. All Jade proteins contain a canonical PHD finger followed by this non-canonical ePHD finger, both of which are zinc-binding motifs.


Pssm-ID: 277141  Cd Length: 112  Bit Score: 42.82  E-value: 4.97e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1443700932 4630 WVHLNCALWSTEV-------YEtqggALINVE-VALHRGLLTkCSLCQ-KTGATNSCNRIRCPSVYHFACA 4691
Cdd:cd15671     20 WVHVSCALWIPEVsigcpekME----PITKIShIPMSRWALV-CVLCKeKTGACIQCSVKSCKTAFHVTCA 85
PHD4_KMT2C cd15596
PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
 224-268 5.14e-04

PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the fourth PHD finger.


Pssm-ID: 277071  Cd Length: 57  Bit Score: 41.15  E-value: 5.14e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1443700932  224 CVVCD--GPGDLRDLLFCTSCGQHYHGACLDV-VLAPHKRAGWQCPEC 268
Cdd:cd15596      9 CVVCGsfGQGAEGRLLACSQCGQCYHPYCVSIkITKVVLSKGWRCLEC 56
PHD1_KMT2A_like cd15506
PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 224-268 5.21e-04

PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the first PHD finger.


Pssm-ID: 276981  Cd Length: 47  Bit Score: 40.81  E-value: 5.21e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1443700932  224 CVVCdGPGDLRDLLFCTSCGQHYHGACLDVVLAPHKRAG--WQCPEC 268
Cdd:cd15506      2 CFLC-GSAGLNELLYCSVCCEPYHTFCLEEAERPLNINKdnWCCRRC 47
Glutenin_hmw pfam03157
High molecular weight glutenin subunit; Members of this family include high molecular weight ...
 3277-3634 5.24e-04

High molecular weight glutenin subunit; Members of this family include high molecular weight subunits of glutenin. This group of gluten proteins is thought to be largely responsible for the elastic properties of gluten, and hence, doughs. Indeed, glutenin high molecular weight subunits are classified as elastomeric proteins, because the glutenin network can withstand significant deformations without breaking, and return to the original conformation when the stress is removed. Elastomeric proteins differ considerably in amino acid sequence, but they are all polymers whose subunits consist of elastomeric domains, composed of repeated motifs, and non-elastic domains that mediate cross-linking between the subunits. The elastomeric domain motifs are all rich in glycine residues in addition to other hydrophobic residues. High molecular weight glutenin subunits have an extensive central elastomeric domain, flanked by two terminal non-elastic domains that form disulphide cross-links. The central elastomeric domain is characterized by the following three repeated motifs: PGQGQQ, GYYPTS[P/L]QQ, GQQ. It possesses overlapping beta-turns within and between the repeated motifs, and assumes a regular helical secondary structure with a diameter of approx. 1.9 nm and a pitch of approx. 1.5 nm.


Pssm-ID: 367362 [Multi-domain]  Cd Length: 786  Bit Score: 46.48  E-value: 5.24e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3277 TSMQQPGiMGQASMQQPGVMGQVSMQQTGVMGQMSIQQPSMAGQASM-QQTGVLGQVSMQQSGIMGQ-----ASMQQPGV 3350
Cdd:pfam03157  417 TSPQQSG-QGQPGYYPTSPQQSGQGQQPGQGQQPGQEQPGQGQQPGQgQQGQQPGQPEQGQQPGQGQpgyypTSPQQSGQ 495

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3351 LGQVSMQQPGVMGQTMQQPGVMGQTSMQPPGVMGQTSMQ--QTSVMGQVSMQQPGAVGQASMQPQGIMAQASLQQSGVMG 3428
Cdd:pfam03157  496 GQQLGQWQQQGQGQPGYYPTSPLQPGQGQPGYYPTSPQQpgQGQQLGQLQQPTQGQQGQQSGQGQQGQQPGQGQQGQQPG 575

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3429 QTAL-QQPGILPQPSLQPQGLMAQPAMQPAgslaqpplpqqppmqqPGLGVQQVAAPPAQGAIGQPVGPKQPALPQsllv 3507
Cdd:pfam03157  576 QGQQgQQPGQGQQPGQGQPGYYPTSPQQSG----------------QGQQPGQWQQPGQGQPGYYPTSSLQLGQGQ---- 635

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3508 QQLSPQPPALLGHAQTPALQHPSGLGSgapqrpllltpqqqqqQQRVLGSPQLAPQsPAMLGHRLVLGQPLHPPQAplQH 3587
Cdd:pfam03157  636 QGYYPTSPQQPGQGQQPGQWQQSGQGQ----------------QGYYPTSPQQSGQ-AQQPGQGQQPGQWLQPGQG--QQ 696

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*..
gi 1443700932 3588 FAQPRVPGQAPSGLQLAQGMQPlAAGKEQPMDGPPAEGTEGPPEPQG 3634
Cdd:pfam03157  697 GYYPTSPQQPGQGQQLGQGQQS-GQGQQGYYPTSPGQGQQSGQGQQG 742
ePHD_JMJD2A cd15713
Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A); The ...
 4605-4701 5.35e-04

Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2A. JMJD2A, also termed lysine-specific demethylase 4A (KDM4A), or JmjC domain-containing histone demethylation protein 3A (JHDM3A), catalyzes the demethylation of di- and trimethylated H3K9 and H3K36. It is involved in carcinogenesis and functions as a transcription regulator that may either stimulate or repress gene transcription. It associates with nuclear receptor co-repressor complex or histone deacetylases. Moreover, JMJD2A forms complexes with both the androgen and estrogen receptor (ER) and plays an essential role in growth of both ER-positive and -negative breast tumors. It is also involved in prostate, colon, and lung cancer progression. JMJD2A contains jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD finger, this non-canonical ePHD finger, and a Tudor domain.


Pssm-ID: 277183  Cd Length: 110  Bit Score: 42.65  E-value: 5.35e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4605 CCFCHEEGdGAtdgparLLNLDLDLWVHLNCALWSTEVYETQGGALINVEVA---LHRGLLtKCSLCQK-----TGATNS 4676
Cdd:cd15713      1 CCLCSLRG-GA------LQRANDDKWVHVMCAVAVLEARFVNIAERSPVDVSkipLQRFKL-KCIFCKKrrkrtAGCCVQ 72

                           90       100
                   ....*....|....*....|....*
gi 1443700932 4677 CNRIRCPSVYHFACAIRAKCMFFKD 4701
Cdd:cd15713     73 CSHGRCPTSFHASCAQAAGVMMQPD 97
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
 271-315 5.61e-04

PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED) protein, functions as a regulator of gene transcription in the thymus. It is essential for prevention of autoimmunity. AIRE plays a critical role in the induction of central tolerance. It promotes self-tolerance through tissue-specific antigen (TSA) expression. It also acts as an active regulator of chondrocyte differentiation. AIRE contains a homogeneously-staining region (HSR) or caspase-recruitment domain (CARD), a nuclear localization signal (NLS), a SAND (for Sp100, AIRE, nuclear phosphoprotein 41/75 or NucP41/75, and deformed epidermal auto regulatory factor 1 or Deaf1) domain, two plant homeodomain (PHD) fingers, and four LXXLL (where L stands for leucine) motifs. This model corresponds to the first PHD finger that recognizes the unmethylated tail of histone H3 and targets AIRE-dependent genes.


Pssm-ID: 277014 [Multi-domain]  Cd Length: 43  Bit Score: 40.51  E-value: 5.61e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932  271 CQTCRLPGEdsmMLVCEACDKGYHTFCMEPAIETLPAASWKCKNC 315
Cdd:cd15539      2 CAVCGDGGE---LLCCDGCPRAFHLACLVPPLTLIPSGTWRCSSC 43
PHD_PHF21A cd15523
PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC ...
 270-315 5.83e-04

PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC complex protein BHC80) along with HDAC1/2, CtBP1, CoREST, and BRAF35, is associated with LSD1, a lysine (K)-specific histone demethylase. It inhibits LSD1-mediated histone demethylation in vitro. PHF21A is predominantly present in the central nervous system and spermatogenic cells and is one of the six components of BRAF-HDAC complex (BHC) involved in REST-dependent transcriptional repression of neuron-specific genes in non-neuronal cells. It acts as a scaffold protein in BHC in neuronal as well as non-neuronal cells and also plays a role in spermatogenesis. PHF21A contains a C-terminal plant homeodomain (PHD) finger that is responsible for the binding directly to each of five other components of BHC, and of organizing BHC mediating transcriptional repression.


Pssm-ID: 276998 [Multi-domain]  Cd Length: 43  Bit Score: 40.46  E-value: 5.83e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932  270 VCQTCRLPGEdsmMLVCEACDKGYHTFCMEPAIETLPAASWKCKNC 315
Cdd:cd15523      1 FCSVCRKSGE---LLMCDTCSLVYHLDCLDPPLKTIPKGMWICPKC 43
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 2003-2199 6.46e-04

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 46.30  E-value: 6.46e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2003 IPASPQSQSSSQSPLTPRPLSNEAFCQSPVTPRFQSPDPYSQPPSRPQSRDPFTPLHKPPRAQLPAAPLSHSPAGSggfg 2082
Cdd:pfam03154  181 ASPPSPPPPGTTQAATAGPTPSAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQTPTLHPQRLPSPHPPLQPMTQPP---- 256

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2083 gaatgePPAKAPGVPQQPPFARSPGagifttgqPPMrftfppavSEPLKGSPSHQLHGLNSHYVPSKPQSAgytsspsfh 2162
Cdd:pfam03154  257 ------PPSQVSPQPLPQPSLHGQM--------PPM--------PHSLQTGPSHMQHPVPPQPFPLTPQSS--------- 305

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 1443700932 2163 QAGSPLGPGAGAAETYSLSPLRPPsvlPQASPSAPQP 2199
Cdd:pfam03154  306 QSQVPPGPSPAAPGQSQQRIHTPP---SQSQLQSQQP 339
PHA03247 PHA03247
large tegument protein UL36; Provisional
 3571-4094 7.30e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 46.47  E-value: 7.30e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3571 RLVLGQPLHppqapLQHFAQPRVPGqAPSGLQLAQGMQPLAAGkeqpmdGPPAEGTEGPPEPQGAPglgAAESPAVLGLP 3650
Cdd:PHA03247  2457 RTILGAPFS-----LSLLLGELFPG-APVYRRPAEARFPFAAG------AAPDPGGGGPPDPDAPP---APSRLAPAILP 2521

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3651 TAPkhptelgqgqqllLASPQPGSLGTSARLLHQpLPSPGAARPELPqshgdvagsalvtelppAPQPPSPEQPGKGLPG 3730
Cdd:PHA03247  2522 DEP-------------VGEPVHPRMLTWIRGLEE-LASDDAGDPPPP-----------------LPPAAPPAAPDRSVPP 2570

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3731 SGALPPP-------------------RLQSPGQQKAGPAPQPAPT-LPPSILGPVPAPVMGQIRAQLQGVLAKNPQLRHL 3790
Cdd:PHA03247  2571 PRPAPRPsepavtsrarrpdappqsaRPRAPVDDRGDPRGPAPPSpLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPE 2650

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3791 TPQQQQQLQALLVQRHQQSLLQQNQ-----------ALRQS-GPF-----------------PGTVPEQGLPPGRQPSRP 3841
Cdd:PHA03247  2651 RPRDDPAPGRVSRPRRARRLGRAAQassppqrprrrAARPTvGSLtsladpppppptpepapHALVSATPLPPGPAAARQ 2730

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3842 QFPvrPPVLTEAPTGFAADPGT-GGRSQPGQQPLAELVQAALATRGPQPGFVRLSTPPALSPL----DSQPSP-EQSPHE 3915
Cdd:PHA03247  2731 ASP--ALPAAPAPPAVPAGPATpGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLsesrESLPSPwDPADPP 2808

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3916 PKTPTPTTTGGLAPSPVAPLELPQSPWGSEPPALDDDVAETSVNGQGVEGTPDECPQLPVKQEPREETA--LPAAAREPE 3993
Cdd:PHA03247  2809 AAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAApaRPPVRRLAR 2888

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3994 PQEPVKPEANGDAVGGALAGSPPGLGGRSEAGHLLLQKLLRAKNVQLAAQSPGELNGHAESRGTAQQPPALPGREDPSLA 4073
Cdd:PHA03247  2889 PAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALV 2968

                          570       580
                   ....*....|....*....|.
gi 1443700932 4074 KKPVAAKPKRVQKGSERVPVS 4094
Cdd:PHA03247  2969 PGRVAVPRFRVPQPAPSREAP 2989
PHD3_KMT2D cd15597
PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
 224-268 7.75e-04

PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the third PHD finger.


Pssm-ID: 277072  Cd Length: 51  Bit Score: 40.40  E-value: 7.75e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1443700932  224 CVVCD--GPGDLRDLLFCTSCGQHYHGACLDVVLAPHK-RAGWQCPEC 268
Cdd:cd15597      3 CVVCGsfGRGSEGHLLACSQCSQCYHPYCVNSKITKVMlLKGWRCVEC 50
PHD3_KMT2A cd15592
PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, ...
 1082-1116 8.40e-04

PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, CXXC-type zinc finger protein 7, myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), trithorax-like protein (Htrx), or zinc finger protein HRX) is a histone methyltransferase that belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2). It regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex, which also contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL1 complex is highly active and specific for H3K4 methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, a Bromodomain domain, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the third PHD finger.


Pssm-ID: 277067  Cd Length: 57  Bit Score: 40.36  E-value: 8.40e-04
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 1443700932 1082 VCPVCREKYVEDDL---LIQCRHCERWLHAACDSLFTE 1116
Cdd:cd15592      1 FCPLCDKCYDDDDYeskMMQCGKCDRWVHSKCENLSDE 38
PHA03378 PHA03378
EBNA-3B; Provisional
 1728-1880 8.61e-04

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 45.83  E-value: 8.61e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1728 PPGAQPVYMgSPPGVGEGFLKPPAGTGAGPESPSELFLKLPPQSPAQVPSHDPYGAAGSYAPEPRFPSPLGQSPTVGAAF 1807
Cdd:PHA03378   686 PIQWAPGTM-QPPPRAPTPMRPPAAPPGRAQRPAAATGRARPPAAAPGRARPPAAAPGRARPPAAAPGRARPPAAAPGRA 764

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1443700932 1808 QPFPGQPLAGARTQPPDFHPTPPGTPRhqsGTPDPFLKPRC-PSLDNLSGPGSPGAR-PPEALLSPLPFSEQKKG 1880
Cdd:PHA03378   765 RPPAAAPGAPTPQPPPQAPPAPQQRPR---GAPTPQPPPQAgPTSMQLMPRAAPGQQgPTKQILRQLLTGGVKRG 836
PHD2_CHD_II cd15532
PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 224-268 8.66e-04

PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the second PHD finger.


Pssm-ID: 277007 [Multi-domain]  Cd Length: 43  Bit Score: 39.96  E-value: 8.66e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932  224 CVVCDGPGDLrdlLFCTSCGQHYHGACLDVVLAPHKRAGWQCPEC 268
Cdd:cd15532      2 CRVCKDGGEL---LCCDGCPSSYHLHCLNPPLAEIPDGDWFCPRC 43
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 2792-2923 8.70e-04

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 45.77  E-value: 8.70e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2792 QQMSvQLPRGAPQHLPAAGhpllhPGAPGQPPeGQGPRLGTPQPTLQLGLMARQQLLQPQQSRLGGPQQG-LPL------ 2864
Cdd:pfam09606  262 NQMQ-QMPQGVGGGAGQGG-----PGQPMGPP-GQQPGAMPNVMSIGDQNNYQQQQTRQQQQQQGGNHPAaHQQqmnqsv 334

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1443700932 2865 --AGHMGMAPAQPHVLAAPHGVQVAL--PPQQGQQPVLMQKPMGAGQPPGLGLKPPQLVMQQQ 2923
Cdd:pfam09606  335 gqGGQVVALGGLNHLETWNPGNFGGLgaNPMQRGQPGMMSSPSPVPGQQVRQVTPNQFMRQSP 397
DUF4175 pfam13779
Domain of unknown function (DUF4175);
3274-3434 9.22e-04

Domain of unknown function (DUF4175);


Pssm-ID: 463981 [Multi-domain]  Cd Length: 833  Bit Score: 45.75  E-value: 9.22e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3274 MGQTSMQQPGIMGQASMQQPGVMGQVSMQQtgVMGQM--SIQQPSM--AGQASMQ--------QTGVLGQVSMQQSGIMG 3341
Cdd:pfam13779  529 LAEQAQQNPQDLQQPDDPNAQEMTQQDLQR--MLDRIeeLARSGRRaeAQQMLSQlqqmlenlQAGQPQQQQQQGQSEMQ 606

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3342 QAsMQQpgvLGQVSMQQPGVMGQT---MQQPGVMGQTSMQPPGVMGQTSMQqtsvmgqvsMQQPGAVGQASMQPQGIMAQ 3418
Cdd:pfam13779  607 QA-MDE---LGDLLREQQQLLDETfrqLQQQGGQQQGQPGQQGQQGQGQQP---------GQGGQQPGAQMPPQGGAEAL 673

                          170
                   ....*....|....*.
gi 1443700932 3419 ASLQQsgvmGQTALQQ 3434
Cdd:pfam13779  674 GDLAE----RQQALRR 685
PHA03247 PHA03247
large tegument protein UL36; Provisional
 3561-4186 9.71e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 46.08  E-value: 9.71e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3561 APQSPAMLGHRLVLGQPLH--PPQAplqhfAQPRVPGQAPSglqlaqgmqPLAAGKEQPmDGPPAEGTEGPP----EPQG 3634
Cdd:PHA03247  2462 APFSLSLLLGELFPGAPVYrrPAEA-----RFPFAAGAAPD---------PGGGGPPDP-DAPPAPSRLAPAilpdEPVG 2526

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3635 AP----------GLGAAES-----PAVLGLPTAPkhPTELGQGQQLLLASPQPGSLGTSARLlHQPLPSPGAARPELPQS 3699
Cdd:PHA03247  2527 EPvhprmltwirGLEELASddagdPPPPLPPAAP--PAAPDRSVPPPRPAPRPSEPAVTSRA-RRPDAPPQSARPRAPVD 2603

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3700 -HGDVAGSALVTELPpapqppspeqpgkglPGSGALPPPRLQSPGQQKAGPAPQPAPTLPPSILGPVPAPvmGQIRAQLQ 3778
Cdd:PHA03247  2604 dRGDPRGPAPPSPLP---------------PDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAP--GRVSRPRR 2666

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3779 GVLAKNPQLRHLTPQQQQQLQALLVQRHQQSLLQQNQALRQSGPFP-GTVPEQGLPPGRQPSRPQFPvrPPVLTEAPTGF 3857
Cdd:PHA03247  2667 ARRLGRAAQASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAPhALVSATPLPPGPAAARQASP--ALPAAPAPPAV 2744

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3858 AADPGT-GGRSQPGQQPLAELVQAALATRGPQPGFVRLSTPPALSPL----DSQPSP-EQSPHEPKTPTPTTTGGLAPSP 3931
Cdd:PHA03247  2745 PAGPATpGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLsesrESLPSPwDPADPPAAVLAPAAALPPAASP 2824

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3932 VAPLELPQSPWGSEPPALDDDVAETSVNGQGVEGTPDECPQLPVKQEPREETA--LPAAAREPEPQEPVKPEANGDAVGG 4009
Cdd:PHA03247  2825 AGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAApaRPPVRRLARPAVSRSTESFALPPDQ 2904

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4010 ALAGSPPGLGGRSEAGHLLLQKLLRAKNVQLAAQSPGELNGHAESRGTAQQPPALPGREDPSLAKKPVAAKPKRVQKGSE 4089
Cdd:PHA03247  2905 PERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRVPQPAP 2984

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4090 RVPVSRKKLRKddglRSGEALMRqLKQELSLLPLTEPTITANFSLFAPFGSSalngkSQLRGAFGSAVLDSVPDYySQLL 4169
Cdd:PHA03247  2985 SREAPASSTPP----LTGHSLSR-VSSWASSLALHEETDPPPVSLKQTLWPP-----DDTEDSDADSLFDSDSER-SDLE 3053

                          650
                   ....*....|....*..
gi 1443700932 4170 TKNNLSNPPTPPSSLPP 4186
Cdd:PHA03247  3054 ALDPLPPEPHDPFAHEP 3070
PHD_BAZ1A cd15627
PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also ...
 223-268 1.15e-03

PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1A contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277097 [Multi-domain]  Cd Length: 46  Bit Score: 39.68  E-value: 1.15e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932  223 RCVVCDGPGDLRDLLFCTSCGQHYHGACLDVVLAPHKRAGWQCPEC 268
Cdd:cd15627      1 RCRICRRKGDAEKMLLCDGCDRGHHMYCLRPPLKKVPEGDWFCPDC 46
PHD1_MTF2 cd15578
PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also ...
 1005-1051 1.25e-03

PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also termed metal regulatory transcription factor 2, or metal-response element DNA-binding protein M96, or polycomb-like protein 2 (PCL2), complexes with the polycomb repressive complex-2 (PRC2) in embryonic stem cells and regulates the transcriptional networks during embryonic stem cell self-renewal and differentiation. It recruits the PRC2 complex to the inactive X chromosome and target loci in embryonic stem cells. Moreover, MTF2 is required for PRC2-mediated Hox cluster repression. It activates the Cdkn2a gene and promotes cellular senescence, thus suppressing the catalytic activity of PRC2 locally. MTF2 consists of an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. This model corresponds to the first PHD finger.


Pssm-ID: 277053  Cd Length: 53  Bit Score: 39.68  E-value: 1.25e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1443700932 1005 VCEVCGKASD--PSRLLLCDDCDISYHTYCLDPPLQTV---PKGGWKCKWCV 1051
Cdd:cd15578      1 VCTVCQDGSSesPNEIVLCDKCGQGYHQLCHNPKIDSSvldPDVPWLCRQCV 52
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 3494-3685 1.26e-03

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 45.41  E-value: 1.26e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3494 VGPKQPALPQSLLVQQLSPQPP---------------ALLGHAQTPALQHPSglgsgAPQRPLLLTPQQQQQQQRVLGSP 3558
Cdd:pfam09770  165 VAPKKAAAPAPAPQPAAQPASLpapsrkmmsleeveaAMRAQAKKPAQQPAP-----APAQPPAAPPAQQAQQQQQFPPQ 239

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3559 QLAPQSPAMLGHRLVLGQPLHPPQAPLQHFAQPRVPGQAPSGLQLAQGMQPLAAgkeqPMDGPPAEGTEGPPEPqgapgl 3638
Cdd:pfam09770  240 IQQQQQPQQQPQQPQQHPGQGHPVTILQRPQSPQPDPAQPSIQPQAQQFHQQPP----PVPVQPTQILQNPNRL------ 309

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 1443700932 3639 gaaeSPAVLGLPTAPKHPTELGQGQQlllASPQPGSLGTSARLLHQP 3685
Cdd:pfam09770  310 ----SAARVGYPQNPQPGVQPAPAHQ---AHRQQGSFGRQAPIITHP 349
PHD_BRPF2 cd15677
PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar ...
 1005-1051 1.29e-03

PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar proteins; BRPF2, also termed bromodomain-containing protein 1 (BRD1), or BR140-like protein, is encoded by BRL (BR140 Like gene). It is responsible for the bulk of the acetylation of H3K14 and forms a novel monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with HBO1 and ING4. The complex is required for full transcriptional activation of the erythroid-specific regulator genes essential for terminal differentiation and survival of erythroblasts in fetal liver. BRPF2 shows widespread expression and localizes to the nucleus within spermatocytes. It contains a cysteine rich region harboring a canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277147 [Multi-domain]  Cd Length: 54  Bit Score: 40.00  E-value: 1.29e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1443700932 1005 VCEVC--GKASDPSRLLLCDDCDISYHTYCLDPPLqtVPKGGWKCKWCV 1051
Cdd:cd15677      3 VCCICmdGECQNSNVILFCDMCNLAVHQECYGVPY--IPEGQWLCRHCL 49
PHD5_NSD cd15568
PHD finger 5 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
 4665-4709 1.35e-03

PHD finger 5 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the fifth PHD finger.


Pssm-ID: 277043 [Multi-domain]  Cd Length: 43  Bit Score: 39.23  E-value: 1.35e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932 4665 CSLCQKTGATNSCNRIRCPSVYHFACAIRAKcmfFKDKTMLCPLH 4709
Cdd:cd15568      2 CFRCGDGGDLVLCDFKGCPKVYHLSCLGLEK---PPGGKWICPWH 43
PHD2_PHF10 cd15529
PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
 223-268 1.37e-03

PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed BRG1-associated factor 45a (BAF45a), or XAP135, is a ubiquitously expressed transcriptional regulator that is required for maintaining the undifferentiated status of neuroblasts. It contains a SAY (supporter of activation of yellow) domain and two adjacent plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger.


Pssm-ID: 277004  Cd Length: 44  Bit Score: 39.21  E-value: 1.37e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932  223 RCVVCDGPGDLRDLLFCTSCGQHYHGACLDVVLAPHKRagWQCPEC 268
Cdd:cd15529      1 TCTKCGDPHDEDKMMFCDQCDRGYHTFCVGLRSIPDGR--WICPLC 44
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 3411-3568 1.47e-03

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 44.80  E-value: 1.47e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3411 QPQGIMAQASLQQSGVMGQTALQQPGIL----PQPSLQPQGLMAQPAMQPAGSLAQPPLPQQPPMQQPGLGVQQVAAPPA 3486
Cdd:TIGR01628  379 QPRMRQLPMGSPMGGAMGQPPYYGQGPQqqfnGQPLGWPRMSMMPTPMGPGGPLRPNGLAPMNAVRAPSRNAQNAAQKPP 458

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3487 QGAIgqpvgPKQPALPQSLLVQQLsPQPPALLGHaQTPALQHPSGLGSGAPQrpllltpqqqqQQQRVLG---------- 3556
Cdd:TIGR01628  459 MQPV-----MYPPNYQSLPLSQDL-PQPQSTASQ-GGQNKKLAQVLASATPQ-----------MQKQVLGerlfplveai 520

                          170
                   ....*....|..
gi 1443700932 3557 SPQLAPQSPAML 3568
Cdd:TIGR01628  521 EPALAAKITGML 532
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 4665-4709 1.47e-03

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 39.61  E-value: 1.47e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1443700932 4665 CSLCQKTGATN----SCNRirCPSVYHFACAIRAKCMFFKDKTMLCPLH 4709
Cdd:cd15489      2 CIVCGKGGDLGgellQCDG--CGKWFHADCLGPPLSSFVPNGKWICPVC 48
PHD2_KMT2C_like cd15510
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 224-268 1.48e-03

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 276985  Cd Length: 46  Bit Score: 39.34  E-value: 1.48e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932  224 CVVCDGPGDLRDLLFCTSCGQHYHGACLDVVLAPHKRAGWQCPEC 268
Cdd:cd15510      2 CQACRQPGDDTKMLVCETCDKGYHTSCLRPVMSSIPKYGWKCKNC 46
COG5141 COG5141
PHD zinc finger-containing protein [General function prediction only];
1003-1142 1.50e-03

PHD zinc finger-containing protein [General function prediction only];


Pssm-ID: 227470 [Multi-domain]  Cd Length: 669  Bit Score: 44.97  E-value: 1.50e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1003 CIVCEVCGKA--SDPSRLLLCDDCDISYHTYCLDppLQTVPKGGWKCKWCV-------CCVQCGAASPGFHCEWQNNYTH 1073
Cdd:COG5141    193 DDICTKCTSThnENSNAIVFCDGCEICVHQSCYG--IQFLPEGFWLCRKCIygeyqirCCSFCPSSDGAFKQTSDGRWGH 270

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1074 --CA---PCASL---------------------VVCPVCREKYvedDLLIQC--RHCERWLHAAC---DSLFTEEEVeqA 1122
Cdd:COG5141    271 viCAmfnPELSFghllskdpidniasvsssrwkLGCLICKEFG---GTCIQCsyFNCTRAYHVTCarrAGYFDLNIY--S 345

                          170       180
                   ....*....|....*....|
gi 1443700932 1123 ADEGFDCSACQPYVVKPAVP 1142
Cdd:COG5141    346 HNGISYCIDHEPLCRKHYPL 365
SET_KMT2E cd19182
SET domain found in inactive histone-lysine N-methyltransferase 2E (KMT2E) and similar ...
 4984-5089 1.65e-03

SET domain found in inactive histone-lysine N-methyltransferase 2E (KMT2E) and similar proteins; KMT2E (also termed inactive lysine N-methyltransferase 2E, myeloid/lymphoid or mixed-lineage leukemia protein 5 (MLL5)) plays a key role in hematopoiesis, spermatogenesis and cell cycle progression. It associates with chromatin regions downstream of transcriptional start sites of active genes and thus regulates gene transcription. Lack of key residues in the SET domain as well as the presence of an unusually large loop in the SET-I subdomain preclude the interaction of MLL5 SET with its cofactor and substrate thus making MLL5 devoid of any in vitro methyltransferase activity on full-length histones and histone H3 peptide.


Pssm-ID: 380959  Cd Length: 129  Bit Score: 41.80  E-value: 1.65e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4984 LYAAKDIEKHTMVIEYIGTIIRNEV--AN----RREK---IYEEQNRGIYMfrinnehVIDATLTGGPARYINHSCAPNC 5054
Cdd:cd19182     21 LKAAKDLPPDTLIIEYRGKFMLREQfeANgyffKRPYpfvLFYSKFHGLEM-------CVDARTFGNEARFIRRSCTPNA 93

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1443700932 5055 VAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDF 5089
Cdd:cd19182     94 EVRHVIEDGTIHLYIYSIRSIPKGTEITIAFDFDY 128
PHD3_PHF14 cd15563
PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 270-315 1.74e-03

PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the third PHD finger.


Pssm-ID: 277038  Cd Length: 49  Bit Score: 39.30  E-value: 1.74e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1443700932  270 VCQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIETLPAA---SWKCKNC 315
Cdd:cd15563      1 ECCVCKQTGDNSQLVRCDECKLCYHFGCLDPPLKKSPKQrgyGWVCEEC 49
ePHD_PHF11 cd15712
Extended PHD finger found in PHD finger protein 11 (PHF11); The extended plant homeodomain ...
 166-212 1.77e-03

Extended PHD finger found in PHD finger protein 11 (PHF11); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of PHF11. PHF11, also termed BRCA1 C-terminus-associated protein, or renal carcinoma antigen NY-REN-34, is a transcriptional co-activator of the Th1 effector cytokine genes, interleukin-2 (IL2) and interferon-gamma (IFNG), co-operating with nuclear factor kappa B (NF-kappaB). It is involved in T-cell activation and viability. Polymorphisms within PHF11 are associated with total IgE, allergic asthma and eczema.


Pssm-ID: 277182 [Multi-domain]  Cd Length: 115  Bit Score: 41.42  E-value: 1.77e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1443700932  166 KCEHCQRMGATIPCRADGCPRLYHFPCA----AASGCFQSMKTLRLLCPEH 212
Cdd:cd15712     65 KCNFCRKKGATVGCEERACRRSYHYFCAlcddAAIETDEVRGIYRVFCQKH 115
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 3456-3646 1.87e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 44.59  E-value: 1.87e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3456 PAGSLAQPPLPQQPPMQQPGLGVQQVAAPPAQGAIGQPVGPKQPALPQSLLVQQlSPQPPALLGHAQTPALQHPSGLGSG 3535
Cdd:PRK07764   590 PAPGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAP-APGVAAPEHHPKHVAVPDASDGGDG 668

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3536 APQRPLLLTPQQQQQQQRVLGSPQLAPQSPAMLGHRLVLGQPLHPPQAPLQHFAQPRVPGQAPSGlqLAQGMQPLAAGKE 3615
Cdd:PRK07764   669 WPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSP--AADDPVPLPPEPD 746

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1443700932 3616 QPMDGPPAEGTEGPPEPQGAPGLGAAESPAV 3646
Cdd:PRK07764   747 DPPDPAGAPAQPPPPPAPAPAAAPAAAPPPS 777
PHD1_Rco1 cd15535
PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and ...
 271-315 1.91e-03

PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and similar proteins; Rco1 is a component of the Rpd3S histone deacetylase complex that plays an important role at actively transcribed genes. Rco1 contains two plant homeodomain (PHD) fingers, which are required for the methylation of histone H3 lysine 36 (H3K36) nucleosome recognition by Rpd3S. This model corresponds to the first PHD finger.


Pssm-ID: 277010 [Multi-domain]  Cd Length: 45  Bit Score: 38.94  E-value: 1.91e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1443700932  271 CQTCRLPGEdsmMLVCEACDKGYHTFCMEPAIE--TLPAASWKCKNC 315
Cdd:cd15535      2 CSACGGYGS---FLCCDGCPRSFHFSCLDPPLEedNLPDDEWFCNEC 45
PHD_BAZ1A_like cd15544
PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, ...
 223-268 1.93e-03

PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. Both BAZ1A and BAZ1B contain a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277019  Cd Length: 46  Bit Score: 38.93  E-value: 1.93e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932  223 RCVVCDGPGDLRDLLFCTSCGQHYHGACLDVVLAPHKRAGWQCPEC 268
Cdd:cd15544      1 RCKVCRKKGDPDNMILCDGCDKAFHLYCLRPALREVPSGDWFCPAC 46
zf-HC5HC2H_2 pfam13832
PHD-zinc-finger like domain;
133-212 2.13e-03

PHD-zinc-finger like domain;


Pssm-ID: 463991 [Multi-domain]  Cd Length: 109  Bit Score: 40.79  E-value: 2.13e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932  133 WVHRCCAAW--SADVLPGAT-GLTHVDRAVFSGISQKCEHC-QRMGATIPCRADGCPRLYHFPCAAASGCFQSMKTLR-- 206
Cdd:pfam13832   21 WVHVLCAIFvpEVRFGNVATmEPIDVSRIPPERWKLKCVFCkKRSGACIQCSKGRCTTAFHVTCAQAAGVYMEPEDWPnv 100


                   ....*....
gi 1443700932  207 ---LLCPEH 212
Cdd:pfam13832  101 vviAYCQKH 109
PHD2_PHF12_Rco1 cd15534
PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, ...
 270-314 2.15e-03

PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, also termed PHD factor 1 (Pf1), is a plant homeodomain (PHD) zinc finger-containing protein that bridges the transducin-like enhancer of split (TLE) corepressor to the mSin3A-histone deacetylase (HDAC)-complex, and further represses transcription at targeted genes. PHF12 also interacts with MRG15 (mortality factor-related genes on chromosome 15), a member of the mortality factor (MORF) family of proteins implicated in regulating cellular senescence. PHF12 contains two plant homeodomain (PHD) zinc fingers followed by a polybasic region. The PHD fingers function downstream of phosphoinositide signaling triggered by the interaction between polybasic regions and phosphoinositides. This subfamily also includes yeast transcriptional regulatory protein Rco1 and similar proteins. Rco1 is a component of the Rpd3S histone deacetylase complex that plays an important role at actively transcribed genes. Rco1 contains two PHD fingers, which are required for the methylation of histone H3 lysine 36 (H3K36) nucleosome recognition by Rpd3S. This model corresponds to the second PHD finger.


Pssm-ID: 277009  Cd Length: 47  Bit Score: 38.87  E-value: 2.15e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932  270 VCQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIETLPAAS-WKCKN 314
Cdd:cd15534      1 VCFKCNRSCRVAPLIQCDYCPLLFHLDCLDPPLTHPPATGrWMCPN 46
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 1894-2229 2.26e-03

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 44.78  E-value: 2.26e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1894 CSPGYVPATGYSDSPGCTHIPSTELKVADVFKAPLTPRVSQVEPQSPGLGHRPPDAHPLAPSP---PGHADLFRQSPYSD 1970
Cdd:PHA03307    66 EPPTGPPPGPGTEAPANESRSTPTWSLSTLAPASPAREGSPTPPGPSSPDPPPPTPPPASPPPspaPDLSEMLRPVGSPG 145

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1971 PYAQPPLTPRPQPPEGCCTAPPRSLPSEPFSRIPASpqsqsssqsplTPRPLSNEAFCQSPVTPRFqSPDPYSQPPSRPQ 2050
Cdd:PHA03307   146 PPPAASPPAAGASPAAVASDAASSRQAALPLSSPEE-----------TARAPSSPPAEPPPSTPPA-AASPRPPRRSSPI 213

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2051 SRDPFTPLHKPPRAQ---LPAAPLSHSPAGSGGFGGAATGEPPAKAPGVPQQPPFARSPGAGI---FTTGQPPMRFTFPP 2124
Cdd:PHA03307   214 SASASSPAPAPGRSAaddAGASSSDSSSSESSGCGWGPENECPLPRPAPITLPTRIWEASGWNgpsSRPGPASSSSSPRE 293

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2125 AVSEPLKGSPSHQLHGLNSHYVP--SKPQSAGYTSSPSFHQAGSPLGPGAGAAETYSLSPLRPPSVLPQASPSAPQPQDA 2202
Cdd:PHA03307   294 RSPSPSPSSPGSGPAPSSPRASSssSSSRESSSSSTSSSSESSRGAAVSPGPSPSRSPSPSRPPPPADPSSPRKRPRPSR 373

                          330       340
                   ....*....|....*....|....*..
gi 1443700932 2203 SVAYVPRAAVLTTPADKREVAATTALS 2229
Cdd:PHA03307   374 APSSPAASAGRPTRRRARAAVAGRARR 400
ePHD_BRPF3 cd15703
Extended PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and ...
 4630-4694 2.35e-03

Extended PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of BRPF3. BRF3 is a homolog of BRPF1 and BRPF2. It is a scaffold protein that forms a novel monocytic leukemic zinc finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with other regulatory subunits. BRPF3 contains a plant homeodomain (PHD) finger followed by this non-canonical ePHD finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain.


Pssm-ID: 277173 [Multi-domain]  Cd Length: 118  Bit Score: 41.19  E-value: 2.35e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1443700932 4630 WVHLNCALWSTEVYETQGGALINVE----VALHRGLLTkCSLCQKT--GATNSCNRIRCPSVYHFACAIRA 4694
Cdd:cd15703     19 WAHVVCAIWIPEVCFANTVFLEPVEgvnnIPPARWKLT-CYLCKQKgrGAAIQCHKVNCYTAFHVTCAQRA 88
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 1791-2217 2.41e-03

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 44.37  E-value: 2.41e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1791 PRFPSPLGQSPTV--GAAFQPFPGQPLAGARTQPPDFHPTPPGTPRHQSGTPDPflKPRCPSLD-NLSGPGSPGARPPEA 1867
Cdd:pfam03154  146 PSIPSPQDNESDSdsSAQQQILQTQPPVLQAQSGAASPPSPPPPGTTQAATAGP--TPSAPSVPpQGSPATSQPPNQTQS 223

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1868 LLSPLPFSEQKKGLEVKKedggalgvcspgyvpatgysdspgcthIPSTELKVADVFKAPLTPRVSQVEPQSPGL-GHRP 1946
Cdd:pfam03154  224 TAAPHTLIQQTPTLHPQR---------------------------LPSPHPPLQPMTQPPPPSQVSPQPLPQPSLhGQMP 276

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 1947 PDAHPLAPSPPGHADLFRQSPYSDPyaqppltprPQPPEGCCTAPPRSLPSEPFSRIPASPQSQSSSQSPLTPRplsnea 2026
Cdd:pfam03154  277 PMPHSLQTGPSHMQHPVPPQPFPLT---------PQSSQSQVPPGPSPAAPGQSQQRIHTPPSQSQLQSQQPPR------ 341

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2027 fcQSPVTPRfQSPDPYSQPPsrpqsrdPFTPLHKPPRAQLPAAPlSHSPAGSGGFGGAATGEPPAKAPGVP---QQPPFA 2103
Cdd:pfam03154  342 --EQPLPPA-PLSMPHIKPP-------PTTPIPQLPNPQSHKHP-PHLSGPSPFQMNSNLPPPPALKPLSSlstHHPPSA 410

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 2104 RSPGAGIFTTGQPpmrFTFPPAVSEPLKGSPSHQLHGlnshyvPSKPQSAGYTSSPSfhQAGSPLGPGAGAAETYSLSPL 2183
Cdd:pfam03154  411 HPPPLQLMPQSQQ---LPPPPAQPPVLTQSQSLPPPA------ASHPPTSGLHQVPS--QSPFPQHPFVPGGPPPITPPS 479

                          410       420       430
                   ....*....|....*....|....*....|....*..
gi 1443700932 2184 RPPSVLPQASPSAPQPQDASVAY---VPRAAVLTTPA 2217
Cdd:pfam03154  480 GPPTSTSSAMPGIQPPSSASVSSsgpVPAAVSCPLPP 516
PHD3_KMT2B cd15593
PHD finger 3 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed ...
 1083-1120 2.50e-03

PHD finger 3 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed trithorax homolog 2 or WW domain-binding protein 7 (WBP-7), is encoded by the gene that was first named myeloid/lymphoid or mixed-lineage leukemia 2 (MLL2), a second human homolog of Drosophila trithorax, located on chromosome 19. It belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2) and is vital for normal mammalian embryonic development. KMT2B functions as the catalytic subunit in the MLL2 complex, which contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL2 complex is highly active and specific for histone 3 lysine 4 (H3K4) methylation, which stimulates chromatin transcription in a SAM- and H3K4-dependent manner. Moreover, KMT2B plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. KMT2B contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the third PHD finger.


Pssm-ID: 277068  Cd Length: 57  Bit Score: 39.06  E-value: 2.50e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1443700932 1083 CPVCREKYVEDDL---LIQCRHCERWLHAACDSLfTEEEVE 1120
Cdd:cd15593      2 CPICLKCYEDNDYeskMMQCAKCDHWVHAKCEGL-SDELYE 41
PHD_JADE1 cd15679
PHD finger found in protein Jade-1 and similar proteins; Jade-1, also termed PHD finger ...
 1005-1050 2.56e-03

PHD finger found in protein Jade-1 and similar proteins; Jade-1, also termed PHD finger protein 17 (PHF17), is a novel binding partner of von Hippel-Lindau (VHL) tumor suppressor Pvhl, a key regulator of the cellular oxygen sensing pathway. It is highly expressed in renal proximal tubules. Jade-1 functions as an essential regulator of multiple cell signaling pathways. It may be involved in the serine/threonine kinase AKT/AKT1 pathway during renal cancer pathogenesis and normally prevents renal epithelial cell proliferation and transformation. It also acts as a pro-apoptotic and growth suppressive ubiquitin ligase to inhibit canonical Wnt downstream effector beta-catenin for proteasomal degradation, and as a transcription factor associated with histone acetyltransferase activity and with increased abundance of cyclin-dependent kinase inhibitor p21. Moreover, Jade-1 is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and Eaf6 to form a HBO1 complex, and plays a role in epithelial cell regeneration. It has also been identified as a novel component of the nephrocystin protein (NPHP) complex and interacts with the ciliary protein nephrocystin-4 (NPHP4). Jade-1 contains a canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277149 [Multi-domain]  Cd Length: 46  Bit Score: 38.90  E-value: 2.56e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1443700932 1005 VCEVCGK--ASDPSRLLLCDDCDISYHTYCLDppLQTVPKGGWKCKWC 1050
Cdd:cd15679      1 VCDVCQSpdGEDGNEMVFCDKCNICVHQACYG--ILKVPEGSWLCRTC 46
PHD_JADE2 cd15680
PHD finger found in protein Jade-2 and similar proteins; Jade-2, also termed PHD finger ...
 1005-1050 2.82e-03

PHD finger found in protein Jade-2 and similar proteins; Jade-2, also termed PHD finger protein 15 (PHF15), is a plant homeodomain (PHD) zinc finger protein that is closely related to Jade-1, which functions as an essential regulator of multiple cell signaling pathways. Like Jade-1, Jade-2 is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and Eaf6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. Jade-2 contains a canonical Cys4HisCys3 PHD finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277150 [Multi-domain]  Cd Length: 46  Bit Score: 38.45  E-value: 2.82e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1443700932 1005 VCEVC--GKASDPSRLLLCDDCDISYHTYCLDppLQTVPKGGWKCKWC 1050
Cdd:cd15680      1 VCDVCrsPEGEDGNEMVFCDKCNVCVHQACYG--ILKVPTGSWLCRTC 46
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 3738-3872 2.82e-03

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 44.26  E-value: 2.82e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3738 RLQSPGqqkagPAPQPAPTLPPSILGPVPAPVMGQIRAQLQGVLAKNPQLRHLTPqqqqqlQALLVQRHQQSLLQQNQAL 3817
Cdd:pfam09770  204 RAQAKK-----PAQQPAPAPAQPPAAPPAQQAQQQQQFPPQIQQQQQPQQQPQQP------QQHPGQGHPVTILQRPQSP 272

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1443700932 3818 RQSGPFPGTVPEQGLPPGRQPSRPQFPV----RPPVLTEAPTGFAADPGTGGRSQPGQQ 3872
Cdd:pfam09770  273 QPDPAQPSIQPQAQQFHQQPPPVPVQPTqilqNPNRLSAARVGYPQNPQPGVQPAPAHQ 331
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
 224-268 2.85e-03

PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED) protein, functions as a regulator of gene transcription in the thymus. It is essential for prevention of autoimmunity. AIRE plays a critical role in the induction of central tolerance. It promotes self-tolerance through tissue-specific antigen (TSA) expression. It also acts as an active regulator of chondrocyte differentiation. AIRE contains a homogeneously-staining region (HSR) or caspase-recruitment domain (CARD), a nuclear localization signal (NLS), a SAND (for Sp100, AIRE, nuclear phosphoprotein 41/75 or NucP41/75, and deformed epidermal auto regulatory factor 1 or Deaf1) domain, two plant homeodomain (PHD) fingers, and four LXXLL (where L stands for leucine) motifs. This model corresponds to the first PHD finger that recognizes the unmethylated tail of histone H3 and targets AIRE-dependent genes.


Pssm-ID: 277014 [Multi-domain]  Cd Length: 43  Bit Score: 38.59  E-value: 2.85e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932  224 CVVCdgpGDLRDLLFCTSCGQHYHGACLDVVLAPHKRAGWQCPEC 268
Cdd:cd15539      2 CAVC---GDGGELLCCDGCPRAFHLACLVPPLTLIPSGTWRCSSC 43
PHD_TAF3 cd15522
PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed ...
 270-315 2.88e-03

PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed 140 kDa TATA box-binding protein-associated factor, TBP-associated factor 3, transcription initiation factor TFIID 140 kDa subunit (TAF140), or TAFII-140, is an integral component of TFIID) is a general initiation factor (GTF) that plays a key role in preinitiation complex (PIC) assembly through core promoter recognition. The interaction of H3K4me3 with TAF3 directs global TFIID recruitment to active genes, which regulates gene-selective functions of p53 in response to genotoxic stress. TAF3 is highly enriched in embryonic stem cells and is required for endoderm lineage differentiation and prevents premature specification of neuroectoderm and mesoderm. Moreover, TAF3, along with TRF3, forms a complex that is essential for myogenic differentiation. TAF3 contains a plant homeodomain (PHD) finger. This family also includes Drosophila melanogaster BIP2 (Bric-a-brac interacting protein 2) protein, which functions as an interacting partner of D. melanogaster p53 (Dmp53).


Pssm-ID: 276997 [Multi-domain]  Cd Length: 46  Bit Score: 38.42  E-value: 2.88e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932  270 VCQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIETLPAASWKCKNC 315
Cdd:cd15522      1 ICPICKKPDDGSPMIGCDECDDWYHWECVGITDEPPEEDDWFCPKC 46
PHD2_KMT2A cd15590
PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, ...
 1006-1050 2.90e-03

PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, CXXC-type zinc finger protein 7, myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), trithorax-like protein (Htrx), or zinc finger protein HRX) is a histone methyltransferase that belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2). It regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex, which also contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL1 complex is highly active and specific for H3K4 methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, a Bromodomain domain, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger.


Pssm-ID: 277065  Cd Length: 50  Bit Score: 38.86  E-value: 2.90e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1443700932 1006 CEVCGKASDPSRLLL-CDDCDISYHTYCLDPPLQTVP---KGGWKCKWC 1050
Cdd:cd15590      2 CHVCGRQHQATKQLLeCNKCRNSYHPECLGPNYPTKPtkkKRVWICTKC 50
PHD2_KMT2C_like cd15510
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 956-1003 2.98e-03

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 276985  Cd Length: 46  Bit Score: 38.57  E-value: 2.98e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1443700932  956 CVVCGSfgRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLkGWRCVEC 1003
Cdd:cd15510      2 CQACRQ--PGDDTKMLVCETCDKGYHTSCLRPVMSSIPKY-GWKCKNC 46
PHD_KDM7 cd15640
PHD finger found in lysine-specific demethylase 7 (KDM7); KDM7, also termed JmjC ...
 1085-1134 3.07e-03

PHD finger found in lysine-specific demethylase 7 (KDM7); KDM7, also termed JmjC domain-containing histone demethylation protein 1D (JHDM1D), or KIAA1718, is a dual histone demethylase that catalyzes demethylation of monomethylated and dimethylated H3K9 (H3K9me2/me1) and H3K27 (H3K27me2/me1), which functions as an eraser of silencing marks on chromatin during brain development. It also plays a tumor-suppressive role by regulating angiogenesis. KDM7 contains a plant homeodomain (PHD) that binds Lys4-trimethylated histone 3 (H3K4me3) and a jumonji domain that demethylates either H3K9me2 or H3K27me2.


Pssm-ID: 277110  Cd Length: 50  Bit Score: 38.82  E-value: 3.07e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1443700932 1085 VCREKYVEDDLLIQCRHCERWLHAACdslfTEEEVEQAAD-EGFDCSACQP 1134
Cdd:cd15640      3 VCRQPYDVNRFMIECDICKDWFHGSC----VQVEEHHAADiDLYHCPNCEV 49
PHD1_KMT2A_like cd15506
PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 955-1003 3.16e-03

PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the first PHD finger.


Pssm-ID: 276981  Cd Length: 47  Bit Score: 38.49  E-value: 3.16e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1443700932  955 MCVVCGSFGRGaegHLLACSQCSQCYHPYCVNSKITKVMLLKG-WRCVEC 1003
Cdd:cd15506      1 LCFLCGSAGLN---ELLYCSVCCEPYHTFCLEEAERPLNINKDnWCCRRC 47
ePHD_JADE cd15671
Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins; The extended ...
 130-212 3.39e-03

Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-1 (PHF17), Jade-2 (PHF15), and Jade-3 (PHF16); each of these proteins is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, has reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. This family also contains Drosophila melanogaster PHD finger protein rhinoceros (RNO). It is a novel plant homeodomain (PHD)-containing nuclear protein that may function as a transcription factor that antagonizes Ras signaling by regulating transcription of key EGFR/Ras pathway regulators in the Drosophila eye. All Jade proteins contain a canonical PHD finger followed by this non-canonical ePHD finger, both of which are zinc-binding motifs.


Pssm-ID: 277141  Cd Length: 112  Bit Score: 40.50  E-value: 3.39e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932  130 GHCWVHRCCAAWSADVlpgatGLTHVDRAV----FSGISQK-----CEHCQ-RMGATIPCRADGCPRLYHFPCAAASGCf 199
Cdd:cd15671     17 GTKWVHVSCALWIPEV-----SIGCPEKMEpitkISHIPMSrwalvCVLCKeKTGACIQCSVKSCKTAFHVTCAFQHGL- 90

                           90       100
                   ....*....|....*....|...
gi 1443700932  200 qSMKT----------LRLLCPEH 212
Cdd:cd15671     91 -EMKTilededdevkFKSYCPKH 112
PHD_UHRF1_2 cd15525
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and ...
 956-1003 3.39e-03

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and UHRF2; UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277000  Cd Length: 47  Bit Score: 38.50  E-value: 3.39e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1443700932  956 CVVCGsfGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVEC 1003
Cdd:cd15525      2 CHVCG--GKQDPEKQLLCDECDMAYHLYCLDPPLTSLPDDDEWYCPDC 47
ePHD_RNO cd15707
Extended PHD finger found in Drosophila melanogaster PHD finger protein rhinoceros (RNO) and ...
 129-212 3.57e-03

Extended PHD finger found in Drosophila melanogaster PHD finger protein rhinoceros (RNO) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Drosophila melanogaster RNO. RNO is a novel plant homeodomain (PHD)-containing nuclear protein that may function as a transcription factor that antagonizes Ras signaling by regulating the transcription of key EGFR/Ras pathway regulators in the Drosophila eye. RNO contains a canonical PHD domain followed by this non-canonical ePHD domain, both of which are zinc-binding motifs.


Pssm-ID: 277177 [Multi-domain]  Cd Length: 113  Bit Score: 40.27  E-value: 3.57e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932  129 AGHCWVHRCCAAWSADVLPGATG----LTHVDRAVFSGISQKCEHC-QRMGATIPCRADGCPRLYHFPCAAASGCfqSMK 203
Cdd:cd15707     16 SGTKWAHVSCALWIPEVSIGCVEkmepITKISSIPASRWALICVLCrERTGACIQCSVKTCKTAYHVTCGFQHGL--EMK 93

                           90       100
                   ....*....|....*....|
gi 1443700932  204 T-----------LRLLCPEH 212
Cdd:cd15707     94 TildeesedgvkLRSYCQKH 113
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
 956-1003 3.77e-03

PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the first PHD finger.


Pssm-ID: 276984  Cd Length: 48  Bit Score: 38.44  E-value: 3.77e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1443700932  956 CVVCGSFGRGAEghLLACSQCSQCYHPYCVNSKITKVMLL-KGWRCVEC 1003
Cdd:cd15509      2 CAVCDSPGDLSD--LLFCTSCGQHYHGSCLDPAVRPTPLVrAGWQCPEC 48
PHD_BAZ1B cd15628
PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also ...
 223-268 4.08e-03

PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. BAZ1B contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277098  Cd Length: 46  Bit Score: 38.19  E-value: 4.08e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932  223 RCVVCDGPGDLRDLLFCTSCGQHYHGACLDVVLAPHKRAGWQCPEC 268
Cdd:cd15628      1 KCKVCRKKGEDDKLILCDECNQAFHLFCLRPALYEVPDGEWMCPAC 46
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 3353-3699 4.13e-03

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 43.60  E-value: 4.13e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3353 QVSMQQPGVMgqtMQQPGVMGQTSMQPPGVMGQTSMQQTSVMGQVSMQQPGAVGQASMQPQGIMAQASLQQSGVMGQ--- 3429
Cdd:pfam03154  165 QILQTQPPVL---QAQSGAASPPSPPPPGTTQAATAGPTPSAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQTPTLHpqr 241

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3430 -----TALQQ-----------PGILPQPSLQPQGLMAQPAMQPAGSLAQPPLPQQPPMQQPGLGVQQVAAPPAQGAIGQP 3493
Cdd:pfam03154  242 lpsphPPLQPmtqppppsqvsPQPLPQPSLHGQMPPMPHSLQTGPSHMQHPVPPQPFPLTPQSSQSQVPPGPSPAAPGQS 321

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3494 VGPKQPALPQSLLVQQLSPQ----PPALLGhaqTPALQHPsglgsgaPQRPLLLTPQQQQQQQrvlgSPQLAPQSPAMLG 3569
Cdd:pfam03154  322 QQRIHTPPSQSQLQSQQPPReqplPPAPLS---MPHIKPP-------PTTPIPQLPNPQSHKH----PPHLSGPSPFQMN 387

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3570 HRLvlgqPLHPPQAPLQHFAQPRVPGQAPSGLQLAQGMQPLAAGKEQPmDGPPAEGTEGPPEPQGAPGLGAAESPAvlgL 3649
Cdd:pfam03154  388 SNL----PPPPALKPLSSLSTHHPPSAHPPPLQLMPQSQQLPPPPAQP-PVLTQSQSLPPPAASHPPTSGLHQVPS---Q 459

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3650 PTAPKHPTELGQGQQLLLASPQPGSLGTSARLLHQPLPSPGAARPELPQS 3699
Cdd:pfam03154  460 SPFPQHPFVPGGPPPITPPSGPPTSTSSAMPGIQPPSSASVSSSGPVPAA 509
PHD1_MOZ_d4 cd15526
PHD finger 1 found in monocytic leukemia zinc-finger protein (MOZ), its factor (MORF), and d4 ...
 970-1003 4.23e-03

PHD finger 1 found in monocytic leukemia zinc-finger protein (MOZ), its factor (MORF), and d4 gene family proteins; MOZ is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity and to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ-related factor (MORF) is a ubiquitously expressed transcriptional regulator with intrinsic HAT activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. Both MOZ and MORF are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are implicated in human leukemias. MOZ is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphoma genesis and bone development, and its homologs. This family also includes three members of the d4 gene family, DPF1 (neuro-d4), DPF2 (ubi-d4/Requiem), and DPF3 (cer-d4), which function as transcription factors and are involved in transcriptional regulation of genes via changing the condensed/decondensed state of chromatin in nucleus. DPF2 is ubiquitously expressed and it acts as a transcription factor that may participate in developmentally programmed cell death. DPF1 and DPF3 are expressed predominantly in neural tissues, and they may be involved in the transcription regulation of neuro specific gene clusters. All family members contain two plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277001  Cd Length: 56  Bit Score: 38.49  E-value: 4.23e-03
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1443700932  970 LLACSQCSQCYHPYCVN--SKITKVMLLKGWRCVEC 1003
Cdd:cd15526     21 LISCADCGSSGHPSCLKfsPGLTDAVKSYRWQCIEC 56
PHD_ARID4_like cd15615
PHD finger found in Arabidopsis thaliana AT-rich interactive domain-containing protein 4 ...
 1083-1132 4.31e-03

PHD finger found in Arabidopsis thaliana AT-rich interactive domain-containing protein 4 (ARID4) and similar proteins; This family includes A. thaliana ARID4 (ARID domain-containing protein 4) and similar proteins. Their biological roles remain unclear, but they all contain an AT-rich interactive domain (ARID) and a plant homeodomain (PHD) finger at the C-terminus. ARID is a helix-turn-helix motif-based DNA-binding domain conserved in all eukaryotes. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins.


Pssm-ID: 277087  Cd Length: 57  Bit Score: 38.23  E-value: 4.31e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1443700932 1083 CPVCREKYVEDDLL----IQCRHCERWLHAACDSLFTEEEVEQAADEG--FDCSAC 1132
Cdd:cd15615      2 CILCGQVYEENEGDekewVQCDSCSEWVHFECDGRTGLGAFKYAKSDGlqYVCPRC 57
PHD_BRPF cd15572
PHD finger found in bromodomain and PHD finger-containing (BRPF) proteins; The family of BRPF ...
 1005-1051 4.64e-03

PHD finger found in bromodomain and PHD finger-containing (BRPF) proteins; The family of BRPF proteins includes BRPF1, BRD1/BRPF2, and BRPF3. They are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277047 [Multi-domain]  Cd Length: 54  Bit Score: 38.37  E-value: 4.64e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1443700932 1005 VCEVC--GKASDPSRLLLCDDCDISYHTYCLDPPLqtVPKGGWKCKWCV 1051
Cdd:cd15572      3 VCCICldGECQNSNVILFCDMCNLAVHQECYGVPY--IPEGQWLCRRCL 49
ePHD_JMJD2 cd15675
Extended PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone ...
 4605-4698 4.71e-03

Extended PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone demethylases; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2 proteins. JMJD2 proteins, also termed lysine-specific demethylase 4 histone demethylases (KDM4), have been implicated in various cellular processes including DNA damage response, transcription, cell cycle regulation, cellular differentiation, senescence, and carcinogenesis. They selectively catalyze the demethylation of di- and trimethylated H3K9 and H3K36. This model contains three JMJD2 proteins, JMJD2A-C, which all contain jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD finger, this non-canonical ePHD finger, and a Tudor domain. JMJD2D is not included in this family, since it lacks both PHD and Tudor domains and has a different substrate specificity. JMJD2A-C are required for efficient cancer cell growth.


Pssm-ID: 277145 [Multi-domain]  Cd Length: 112  Bit Score: 40.04  E-value: 4.71e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4605 CCFCHEEGdGA----TDGparllnldldLWVHLNCALWSTEVYETQGGALINVEVA---LHRGLLtKCSLCQK------- 4670
Cdd:cd15675      1 CCLCCLRG-GAlkptTDG----------RWAHVVCAIAIPEVRFSNVPERGPIDISkipPARLKL-KCIYCSKitksmsh 68

                           90       100
                   ....*....|....*....|....*...
gi 1443700932 4671 TGATNSCNRIRCPSVYHFACAIRAKCMF 4698
Cdd:cd15675     69 MGACIQCSTGKCTTSFHVTCAHAAGVQM 96
PHD_UHRF2 cd15617
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); ...
 956-1003 4.86e-03

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); UHRF2 (also termed Np95/ICBP90-like RING finger protein (NIRF), Np95-like RING finger protein, nuclear protein 97, nuclear zinc finger protein Np97, RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2) was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs,p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277089  Cd Length: 47  Bit Score: 38.01  E-value: 4.86e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1443700932  956 CVVCGsfGRGAEGHLLACSQCSQCYHPYCVNSKITKVMLLKGWRCVEC 1003
Cdd:cd15617      2 CYVCG--GKQDAHMQLLCDECNMAYHIYCLNPPLDKIPEDEDWYCPSC 47
PHD1_KDM5B cd15603
PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
 224-268 5.29e-03

PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis antigen 31 (CT31), Histone demethylase JARID1B, Jumonji/ARID domain-containing protein 1B (JARID1B), PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A)) is a member of the JARID subfamily within the JmjC proteins. It has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of pregnant females and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well as TIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277076  Cd Length: 46  Bit Score: 38.01  E-value: 5.29e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932  224 CVVCDGPGDLRDLLFCTSCGQHYHGACLDVVLAPHKRAGWQCPEC 268
Cdd:cd15603      2 CLVCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 46
PHD_TIF1delta cd15625
PHD finger found in transcriptional intermediary factor 1 delta (TIF1delta); TIF1delta, also ...
 271-316 5.35e-03

PHD finger found in transcriptional intermediary factor 1 delta (TIF1delta); TIF1delta, also termed tripartite motif-containing protein 66 (TRIM66), is a novel heterochromatin protein 1 (HP1)-interacting member of the transcriptional intermediary factor1 (TIF1) family expressed by elongating spermatids. Like other TIF1 proteins, TIF1delta displays a potent trichostatin A (TSA)-sensitive repression function; TSA is a specific inhibitor of histone deacetylases. Moreover, TIF1delta plays an important role in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. It functions as a negative regulator of postmeiotic genes acting through HP1 isotype gamma (HP1gamma) complex formation and centromere association. TIF1delta contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region.


Pssm-ID: 277095 [Multi-domain]  Cd Length: 49  Bit Score: 38.02  E-value: 5.35e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1443700932  271 CQTCRLPGEdsmMLVCEACDKGYHTFCMEPAIETLPAASWKCKNCR 316
Cdd:cd15625      5 CAVCLNGGE---LLCCDRCPKVFHLSCHVPALLSFPVGEWVCTLCR 47
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 3815-4096 5.53e-03

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 43.15  E-value: 5.53e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3815 QALRQSGPFPGTVPEQGLPPGRQPSRPQFPVRPPVLTEAPTGFAADPGTGGRSQPGQQPLAELVQAALATRGPQ------ 3888
Cdd:PRK10263   338 EPVTQTPPVASVDVPPAQPTVAWQPVPGPQTGEPVIAPAPEGYPQQSQYAQPAVQYNEPLQQPVQPQQPYYAPAaeqpaq 417

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3889 -----PGFVRLSTPPALSPLDSQPSPEQS-PHEPKTPTPTTTGGLAPSPVAPLELPQSPWGSEPPALDDDVAETSVngQG 3962
Cdd:PRK10263   418 qpyyaPAPEQPAQQPYYAPAPEQPVAGNAwQAEEQQSTFAPQSTYQTEQTYQQPAAQEPLYQQPQPVEQQPVVEPE--PV 495

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3963 VEGTPDECPQLPVKQEPREETALP----AAAREPEPqEPVK-PEANGDAVGGALAGSPPGLGGRSEAGHLllqkllrAKN 4037
Cdd:PRK10263   496 VEETKPARPPLYYFEEVEEKRAREreqlAAWYQPIP-EPVKePEPIKSSLKAPSVAAVPPVEAAAAVSPL-------ASG 567

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1443700932 4038 VQLAAQSPGELNGHAESRGTaqqpPALPGREDPSLAK--KPVAAKPKRVqkgseRVPVSRK 4096
Cdd:PRK10263   568 VKKATLATGAAATVAAPVFS----LANSGGPRPQVKEgiGPQLPRPKRI-----RVPTRRE 619
PHD2_PHF14 cd15562
PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 270-315 5.72e-03

PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the second PHD finger.


Pssm-ID: 277037  Cd Length: 50  Bit Score: 37.77  E-value: 5.72e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1443700932  270 VCQTCRLPGEDSMMLVCEACDKGYHTFCMEPAIETLPAAS----WKCKNC 315
Cdd:cd15562      1 SCGICKKSNDQHLLALCDTCKLYYHLGCLDPPLTRMPKKTknsgWQCSEC 50
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 3809-4090 5.80e-03

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 43.24  E-value: 5.80e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3809 SLLQQNQALRQSGPFPGTVPEQGLPPGRQPSRPQFPVRPPVLTEAPTGFAADPGTGGR--SQPGQQPLAELVQAALATRG 3886
Cdd:PHA03307     9 DLIEAAAEGGEFFPRPPATPGDAADDLLSGSQGQLVSDSAELAAVTVVAGAAACDRFEppTGPPPGPGTEAPANESRSTP 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3887 PQPGFVRLSTPPALSPLDSQPSPEQSPHEPKTPTPTTTgglAPSPVAPLELPQSPWGSEPPALDDDVAETSVNGQGVEGT 3966
Cdd:PHA03307    89 TWSLSTLAPASPAREGSPTPPGPSSPDPPPPTPPPASP---PPSPAPDLSEMLRPVGSPGPPPAASPPAAGASPAAVASD 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3967 PDECPQ--LPVKQEPREETALPAAAREPEPQEPVKPEANGDAVGG----ALAGSPPGLGGRSEAGhlllqKLLRAKNVQL 4040
Cdd:PHA03307   166 AASSRQaaLPLSSPEETARAPSSPPAEPPPSTPPAAASPRPPRRSspisASASSPAPAPGRSAAD-----DAGASSSDSS 240

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|
gi 1443700932 4041 AAQSPGELNGhaeSRGTAQQPPALPGReDPSLAKKPVAAKPKRVQKGSER 4090
Cdd:PHA03307   241 SSESSGCGWG---PENECPLPRPAPIT-LPTRIWEASGWNGPSSRPGPAS 286
PHD2_KMT2A_like cd15507
PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
 956-1003 6.05e-03

PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger.


Pssm-ID: 276982  Cd Length: 50  Bit Score: 37.83  E-value: 6.05e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1443700932  956 CVVCGSFGRGAEgHLLACSQCSQCYHPYCVN----SKITKVMllKGWRCVEC 1003
Cdd:cd15507      2 CHVCGRKGQAQK-QLLECEKCQRGYHVDCLGpsypTKPTRKK--KTWICSKC 50
PHD_TIF1beta cd15623
PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also ...
 268-315 6.18e-03

PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also termed Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), or KRAB-interacting protein 1 (KRIP-1), or nuclear co-repressor KAP-1, or RING finger protein 96, or tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, acts as a nuclear co-repressor that plays a role in transcription and in DNA damage response. Upon DNA damage, the phosphorylation of KAP-1 on serine 824 by the ataxia telangiectasia-mutated (ATM) kinase enhances cell survival and facilitates chromatin relaxation and heterochromatic DNA repair. It also regulates CHD3 nucleosome remodeling during DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. In addition, KAP-1 is a co-activator of the orphan nuclear receptor NGFI-B (or Nur77) and is involved in NGFI-B-dependent transcription. It is also a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase. TIF1-beta contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), which can interact with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and mediates homo- and heterodimerization, a plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region, which interact with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity.


Pssm-ID: 277093  Cd Length: 43  Bit Score: 37.48  E-value: 6.18e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1443700932  268 CKVCQtcrlpgEDSMMLVCEACDKGYHTFCMEPAIETLPAASWKCKNC 315
Cdd:cd15623      2 CRVCQ------KAGALVMCDQCEFCFHLDCHLPALQEVPGEDWKCLLC 43
ePHD1_PHF6 cd15710
Extended PHD finger 1 found in PHD finger protein 6 (PHF6); The extended plant homeodomain ...
 123-193 6.27e-03

Extended PHD finger 1 found in PHD finger protein 6 (PHF6); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. PHF6 contains two non-canonical ePHD fingers, this model corresponds to the first ePHD finger. PHF6, also termed the X-linked mental retardation disorder Borjeson-Forssman-Lehmann syndrome-associated protein, is a nucleolus, ribosomal RNA promoter-associated protein that regulates cell cycle progression by suppressing ribosomal RNA synthesis. It has been implicated in cell cycle control, genomic maintenance, and tumor suppression. PHF6 shows transcriptional repression activity through directly interacting with the nucleosome remodeling and deacetylation complex component RBBP4. .


Pssm-ID: 277180  Cd Length: 115  Bit Score: 39.56  E-value: 6.27e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1443700932  123 SRCQLPAGHcwvHRCCAAWSADVLP-------GATGLTHVDRAVFSGISQKCEHCQRMGATIPCRADGCPRLYHFPCA 193
Cdd:cd15710     18 SENQKVAAH---HKCMLFSSALVSShsdsenlGGFSIEDVQKEIKRGTKLMCSLCHCPGATIGCDVKTCHRTYHYYCA 92
PHD1_Snt2p_like cd15497
PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and ...
 268-315 6.55e-03

PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and similar proteins; Snt2p is a yeast protein that may function in multiple stress pathways. It coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress through interaction with Ecm5 and the Rpd3 deacetylase. Snt2p contains a bromo adjacent homology (BAH) domain, two canonical Cys4HisCys3 plant homeodomain (PHD) fingers, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domain; this model corresponds to the first canonical Cys4HisCys3 PHD finger.


Pssm-ID: 276972  Cd Length: 48  Bit Score: 37.67  E-value: 6.55e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1443700932  268 CKVC-QTCrlPGEDSmmLVCEACDKGYHTFCMEPAIETLPAA--SWKCKNC 315
Cdd:cd15497      2 CKVCkEWC--ASDDS--VRCDECKVSYHLLCVDPPLTKKPNRgfVWSCAPC 48
PHD4_NSD cd15567
PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
 1006-1050 7.15e-03

PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the fourth PHD finger.


Pssm-ID: 277042 [Multi-domain]  Cd Length: 41  Bit Score: 37.23  E-value: 7.15e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932 1006 CEVCGKASDpsrLLLCDDCDISYHTYCLDppLQTVPKGGWKCKWC 1050
Cdd:cd15567      2 CFICSEGGS---LICCESCPASFHPECLG--LEPPPEGKFYCEDC 41
PHD_TIF1gamma cd15624
PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also ...
 268-316 7.41e-03

PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also termed tripartite motif-containing 33 (trim33), or ectodermin, or RFG7, or PTC7, is an E3-ubiquitin ligase that functions as a regulator of transforming growth factor beta (TGFbeta) signaling; it inhibits the Smad4-mediated TGFbeta response by interaction with Smad2/3 or ubiquitylation of Smad4. Moreover, TIF1gamma is an important regulator of transcription during hematopoiesis, as well as a key factor of tumorigenesis. Like other TIF1 family members, TIF1gamma also contains an intrinsic transcriptional silencing function. It can control erythroid cell fate by regulating transcription elongation. It can bind to the anaphase-promoting complex/cyclosome (APC/C) and promotes mitosis. TIF1gamma contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region.


Pssm-ID: 277094  Cd Length: 46  Bit Score: 37.33  E-value: 7.41e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1443700932  268 CKVCQTcrlpGEDsmMLVCEACDKGYHTFCMEPAIETLPAASWKCKNCR 316
Cdd:cd15624      2 CAVCQN----GGD--LLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCR 44
SP1-4_arthropods_N cd22553
N-terminal domain of transcription factor Specificity Protein (SP) 1-4 from arthropods; ...
 3273-3619 7.45e-03

N-terminal domain of transcription factor Specificity Protein (SP) 1-4 from arthropods; Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. There are many SPs in vertebrates (9 SPs in humans and mice, 7 SPs in the chicken, and 11 SPs in teleost fish), but arthropods only have 3 SPs. One SP is clade SP1-4, which is expressed ubiquitously throughout development. SP1-4 belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. This model represents the N-terminal domain of SP1-4 from arthropods.


Pssm-ID: 411778 [Multi-domain]  Cd Length: 384  Bit Score: 42.32  E-value: 7.45e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3273 IMGQTSMQQPGIMGQASMQQPGVMGQVSMQQTGVMGQMSIQQPSMAGQASMQQTGVLGQVsmQQSGIMGQAS--MQQPGV 3350
Cdd:cd22553     14 QVATTASNIGGQQKQAQSDSSETHDPLILSPPLSQPQQIITAQSSGSAAGGVAYSVSPAV--QTVTVDGHEAifIPANSG 91

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3351 LGQVSMQQPGVM--GQTMQQPgVMGQTSMQPPGVMGQTsmQQTSVMGQVSmqQPGAVGQASMQPQGIMAQASLQQ---SG 3425
Cdd:cd22553     92 LLQTNNQQAIQLapGGTQAIL-ANQQTLIRPNTVQGQA--NASNVLQNIA--QIASGGNAVQLPLNNMTQTIPVQvpvST 166

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3426 VMGQTALQ------QPGILPQPSLQPQGLMAQ--PAMQPAGSLAQpplpqqppmqqpglgvQQVAAPPAQGAIGQPVGPK 3497
Cdd:cd22553    167 ANGQTVYQtiqvpiQAIQSGNAGGGNQALQAQviPQLAQAAQLQP----------------QQLAQVSSQGYIQQIPANA 230

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3498 QPALPQslLVQQLSPQPPALLGhaqtpalQHPSGLGSGAPQRPllLTPQQQQQQQRVLGSPQLAPQSPAMLGHRLVLGQP 3577
Cdd:cd22553    231 SQQQPQ--MVQQGPNQSGQIIG-------QVASASSIQAAAIP--LTVYTGALAGQNGSNQQQVGQIVTSPIQGMTQGLT 299

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|..
gi 1443700932 3578 LHPPQAPLQHFAQprvpgQAPSGLQLAQGMQPLAAGKEQPMD 3619
Cdd:cd22553    300 APASSSIPTVVQQ-----QAIQGNPLPPGTQIIAAGQQLQQD 336
PRK14971 PRK14971
DNA polymerase III subunit gamma/tau;
3358-3456 7.68e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237874 [Multi-domain]  Cd Length: 614  Bit Score: 42.46  E-value: 7.68e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1443700932 3358 QPGVMGQTMQQPGVMGQTSMQPPGVMGQTSMQQTSVMGQVSMQQPGAVGQASMQPQGIMAQASLQQSGVMGQTALQQPGI 3437
Cdd:PRK14971   370 SGGRGPKQHIKPVFTQPAAAPQPSAAAAASPSPSQSSAAAQPSAPQSATQPAGTPPTVSVDPPAAVPVNPPSTAPQAVRP 449

                           90
                   ....*....|....*....
gi 1443700932 3438 LPQPSLQPQGLMAQPAMQP 3456
Cdd:PRK14971   450 AQFKEEKKIPVSKVSSLGP 468
PHD2_KMT2B cd15591
PHD domain 2 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed ...
 1006-1050 7.78e-03

PHD domain 2 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed trithorax homolog 2 or WW domain-binding protein 7 (WBP-7), is encoded by the gene that was first named myeloid/lymphoid or mixed-lineage leukemia 2 (MLL2), a second human homolog of Drosophila trithorax, located on chromosome 19. It belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2) and is vital for normal mammalian embryonic development. KMT2B functions as the catalytic subunit in the MLL2 complex, which contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL2 complex is highly active and specific for histone 3lysine 4 (H3K4) methylation, which stimulates chromatin transcription in a SAM- and H3K4-dependent manner. Moreover, KMT2B plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. KMT2B contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD), an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger.


Pssm-ID: 277066  Cd Length: 50  Bit Score: 37.61  E-value: 7.78e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1443700932 1006 CEVCGKASDPSRLLL-CDDCDISYHTYCLDPPLQTVP---KGGWKCKWC 1050
Cdd:cd15591      2 CHVCGRKNKESKPLLeCERCRNCYHPACLGPNYPKPAnrkKRPWICSAC 50
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
 224-268 7.79e-03

PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger of KMT2C and the fourth PHD finger of KMT2D.


Pssm-ID: 276988  Cd Length: 47  Bit Score: 37.46  E-value: 7.79e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1443700932  224 CVVCDGPGDLRDLLFCTSCGQHYHGACLDVVLAPHKRAGWQCPEC 268
Cdd:cd15513      2 CEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGGWKCKWC 46
HMG-box_SSRP1-like cd21994
high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and ...
 1641-1689 8.60e-03

high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and similar proteins; SSRP1, also called FACT complex subunit SSRP1, chromatin-specific transcription elongation factor 80 kDa subunit, facilitates chromatin transcription complex 80 kDa subunit (FACT 80 kDa subunit or FACTp80), facilitates chromatin transcription complex subunit SSRP1, recombination signal sequence recognition protein 1, or T160, is a factor that facilitates transcript elongation through nucleosomes. It is a component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication, and DNA repair.


Pssm-ID: 438810 [Multi-domain]  Cd Length: 67  Bit Score: 38.05  E-value: 8.60e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1443700932 1641 VLYANMNFPNLKQDYPDWSSrcKQIMK----LWRKVPATDKAPYLQKAKDNRA 1689
Cdd:cd21994      7 MLWLNENREKIKKENPGISV--TEISKkageIWKELDEEDKEKWEQKAEKAKE 57
PostSET smart00508
Cysteine-rich motif following a subset of SET domains;
5094-5110 9.01e-03

Cysteine-rich motif following a subset of SET domains;


Pssm-ID: 214703  Cd Length: 17  Bit Score: 36.61  E-value: 9.01e-03
                            10
                    ....*....|....*..
gi 1443700932  5094 HKIPCHCGAWNCRKWMN 5110
Cdd:smart00508    1 KKQPCLCGAPNCRGFLG 17
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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