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Conserved domains on  [gi|2029300282|ref|NP_001381477|]
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bromodomain-containing protein 1 isoform 6 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ePHD_BRPF2 cd15702
Extended PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and ...
 271-388 1.41e-85

Extended PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of BRPF2. BRPF2 also termed bromodomain-containing protein 1 (BRD1), or BR140-likeprotein, 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 plant homeodomain (PHD) finger followed by a non-canonical ePHD finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain.


:

Pssm-ID: 277172  Cd Length: 118  Bit Score: 272.69  E-value: 1.41e-85
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  271 CVLCPNKGGAFKKTDDDRWGHVVCALWIPEVGFANTVFIEPIDGVRNIPPARWKLTCYLCKQKGVGACIQCHKANCYTAF 350
Cdd:cd15702      1 CVLCPNKGGAFKKTDDDRWGHVVCALWIPEVGFANTVFIEPIDGVRNIPPARWKLTCYLCKQKGVGACIQCHKANCYTAF 80

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 2029300282  351 HVTCAQKAGLYMKMEPVKELTGGGTTFSVRKTAYCDVH 388
Cdd:cd15702     81 HVTCAQKAGLYMKMEPVKEVTGGGTTFSVRKTAYCDAH 118
PWWP_BRPF2 cd20157
PWWP domain found in bromodomain and PHD finger-containing protein 2 (BRPF2); BRPF2, also ...
 1056-1175 3.93e-83

PWWP domain found in bromodomain and PHD finger-containing protein 2 (BRPF2); BRPF2, also called bromodomain-containing protein 1 (BRD1), or BR140-likeprotein, 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 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, C2HC5HC2H, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The PHD finger binds to lysine 4 of histone H3 (K4H3), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties.


:

Pssm-ID: 438985  Cd Length: 120  Bit Score: 266.03  E-value: 3.93e-83
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282 1056 LEPLKVVWAKCSGYPSYPALIIDPKMPRVPGHHNGVTIPAPPLDVLKIGEHMQTKSDEKLFLVLFFDNKRSWQWLPKSKM 1135
Cdd:cd20157      1 LEPLKVVWAKCSGYPSYPALIIDPKMPRVGCHHNGVTIPVPPLDVLKIGEQMQTKSDEKLFLVLFFDNKRSWQWLPKSKM 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 2029300282 1136 VPLGIDETIDKLKMMEGRNSSIRKAVRIAFDRAMNHLSRV 1175
Cdd:cd20157     81 VPLGIDETIDKLKMMEGRNSSIRKAVRIAFDRAMNHLSRV 120
COG5141 super family cl34917
PHD zinc finger-containing protein [General function prediction only];
139-549 5.08e-79

PHD zinc finger-containing protein [General function prediction only];


The actual alignment was detected with superfamily member COG5141:

Pssm-ID: 227470 [Multi-domain]  Cd Length: 669  Bit Score: 274.17  E-value: 5.08e-79
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  139 YYKFIEKSAEELDNE-VEYDMDEEDYAWLEIVNEKRKGDcvpAVSQSMFEFLMDRFEKE----SHCENQKQGEQQSLIDE 213
Cdd:COG5141    115 GKKFIDIEPPRGLFFsVIYDLDEYDTMWLRYLNESAIDE---NVSEEAFEIIVTRLEKEwfffEHGLPDKHVEPIEPSDE 191

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  214 -DAVCCICMDGECQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSRARPADCVLCPNKGGAFKKTDDDRWGHV 292
Cdd:COG5141    192 fDDICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQFLPEGFWLCRKCIYGEYQIRCCSFCPSSDGAFKQTSDGRWGHV 271

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  293 VCALWIPEVGFANTVFIEPIDGVRNIPPARWKLTCYLCKQKGvGACIQCHKANCYTAFHVTCAQKAGLYMKmepvKELTG 372
Cdd:COG5141    272 ICAMFNPELSFGHLLSKDPIDNIASVSSSRWKLGCLICKEFG-GTCIQCSYFNCTRAYHVTCARRAGYFDL----NIYSH 346

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  373 GGTTFSVRKTAYCDVHTPPGctrrplniYGDVEMKNGVCRKESSVKTVRSTSKVRKKAKKAKKALAEPCAVLPTVCAPYI 452
Cdd:COG5141    347 NGISYCIDHEPLCRKHYPLG--------YGRMNGLRYFGYEKLRYKNPPTAIPRKVRAARPRATLFMKLCWKQPPATPSV 418

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  453 PPQRLNRIANQVAIQRKKQFVERAHSYWLLKRLSRNGAPllrrlqsSLQSQRSSQQRENDEEmKAAKEKLKYWQRLRHDL 532
Cdd:COG5141    419 LSRVEACDLKEKDRQDLPVNIFDICKYWEMKRKSEIGGP-------LVILPDIVYSLKTLED-WMSKRRMREVAKALQDQ 490

                          410
                   ....*....|....*..
gi 2029300282  533 ERARLLIELLRKREKLK 549
Cdd:COG5141    491 YQLLTLVESTAKRQLLK 507
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
 564-661 7.02e-60

Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


:

Pssm-ID: 99944  Cd Length: 98  Bit Score: 199.93  E-value: 7.02e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  564 PLTVLLRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARD 643
Cdd:cd05512      1 PLEVLLRKTLDQLQEKDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKD 80

                           90
                   ....*....|....*...
gi 2029300282  644 TVFYRAAVRLRDQGGVVL 661
Cdd:cd05512     81 TIFYRAAVRLRDQGGAIL 98
EPL1 pfam10513
Enhancer of polycomb-like; This is a family of EPL1 (Enhancer of polycomb-like) proteins. The ...
 47-196 6.71e-42

Enhancer of polycomb-like; This is a family of EPL1 (Enhancer of polycomb-like) proteins. The EPL1 protein is a member of a histone acetyltransferase complex which is involved in transcriptional activation of selected genes.


:

Pssm-ID: 463128  Cd Length: 168  Bit Score: 151.10  E-value: 6.71e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282   47 RLHRISIFDPLEIILEDDL-------TAQEMSECNSNKENS-----------ERPPVCLRTKrhknNRVKKKNEALPSAH 108
Cdd:pfam10513    1 RHRRISIKQPLPIISEDEVdgldtspDEDEPSECNSNKENSlhavetgvdkeEEDEVHLKVI----NAAKKALSSSKKSQ 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  109 GTPASASA--------LPEP---KVRIVEYSPPsaprrppVYYKFIEKSAEELDNEVEYDMDEEDYAWLEIVNEKRKGDC 177
Cdd:pfam10513   77 NTSESSVPapnkerlyLPTPdagKFREFERPPA-------SYIRFSETVEEELDEGVEYDMDEEDEAWLEELNEKRKSEG 149

                          170
                   ....*....|....*....
gi 2029300282  178 VPAVSQSMFEFLMDRFEKE 196
Cdd:pfam10513  150 VEKISEDEFEILMDRFEKE 168
 
Name Accession Description Interval E-value
ePHD_BRPF2 cd15702
Extended PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and ...
 271-388 1.41e-85

Extended PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of BRPF2. BRPF2 also termed bromodomain-containing protein 1 (BRD1), or BR140-likeprotein, 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 plant homeodomain (PHD) finger followed by a non-canonical ePHD finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain.


Pssm-ID: 277172  Cd Length: 118  Bit Score: 272.69  E-value: 1.41e-85
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  271 CVLCPNKGGAFKKTDDDRWGHVVCALWIPEVGFANTVFIEPIDGVRNIPPARWKLTCYLCKQKGVGACIQCHKANCYTAF 350
Cdd:cd15702      1 CVLCPNKGGAFKKTDDDRWGHVVCALWIPEVGFANTVFIEPIDGVRNIPPARWKLTCYLCKQKGVGACIQCHKANCYTAF 80

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 2029300282  351 HVTCAQKAGLYMKMEPVKELTGGGTTFSVRKTAYCDVH 388
Cdd:cd15702     81 HVTCAQKAGLYMKMEPVKEVTGGGTTFSVRKTAYCDAH 118
PWWP_BRPF2 cd20157
PWWP domain found in bromodomain and PHD finger-containing protein 2 (BRPF2); BRPF2, also ...
 1056-1175 3.93e-83

PWWP domain found in bromodomain and PHD finger-containing protein 2 (BRPF2); BRPF2, also called bromodomain-containing protein 1 (BRD1), or BR140-likeprotein, 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 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, C2HC5HC2H, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The PHD finger binds to lysine 4 of histone H3 (K4H3), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties.


Pssm-ID: 438985  Cd Length: 120  Bit Score: 266.03  E-value: 3.93e-83
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282 1056 LEPLKVVWAKCSGYPSYPALIIDPKMPRVPGHHNGVTIPAPPLDVLKIGEHMQTKSDEKLFLVLFFDNKRSWQWLPKSKM 1135
Cdd:cd20157      1 LEPLKVVWAKCSGYPSYPALIIDPKMPRVGCHHNGVTIPVPPLDVLKIGEQMQTKSDEKLFLVLFFDNKRSWQWLPKSKM 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 2029300282 1136 VPLGIDETIDKLKMMEGRNSSIRKAVRIAFDRAMNHLSRV 1175
Cdd:cd20157     81 VPLGIDETIDKLKMMEGRNSSIRKAVRIAFDRAMNHLSRV 120
COG5141 COG5141
PHD zinc finger-containing protein [General function prediction only];
139-549 5.08e-79

PHD zinc finger-containing protein [General function prediction only];


Pssm-ID: 227470 [Multi-domain]  Cd Length: 669  Bit Score: 274.17  E-value: 5.08e-79
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  139 YYKFIEKSAEELDNE-VEYDMDEEDYAWLEIVNEKRKGDcvpAVSQSMFEFLMDRFEKE----SHCENQKQGEQQSLIDE 213
Cdd:COG5141    115 GKKFIDIEPPRGLFFsVIYDLDEYDTMWLRYLNESAIDE---NVSEEAFEIIVTRLEKEwfffEHGLPDKHVEPIEPSDE 191

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  214 -DAVCCICMDGECQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSRARPADCVLCPNKGGAFKKTDDDRWGHV 292
Cdd:COG5141    192 fDDICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQFLPEGFWLCRKCIYGEYQIRCCSFCPSSDGAFKQTSDGRWGHV 271

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  293 VCALWIPEVGFANTVFIEPIDGVRNIPPARWKLTCYLCKQKGvGACIQCHKANCYTAFHVTCAQKAGLYMKmepvKELTG 372
Cdd:COG5141    272 ICAMFNPELSFGHLLSKDPIDNIASVSSSRWKLGCLICKEFG-GTCIQCSYFNCTRAYHVTCARRAGYFDL----NIYSH 346

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  373 GGTTFSVRKTAYCDVHTPPGctrrplniYGDVEMKNGVCRKESSVKTVRSTSKVRKKAKKAKKALAEPCAVLPTVCAPYI 452
Cdd:COG5141    347 NGISYCIDHEPLCRKHYPLG--------YGRMNGLRYFGYEKLRYKNPPTAIPRKVRAARPRATLFMKLCWKQPPATPSV 418

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  453 PPQRLNRIANQVAIQRKKQFVERAHSYWLLKRLSRNGAPllrrlqsSLQSQRSSQQRENDEEmKAAKEKLKYWQRLRHDL 532
Cdd:COG5141    419 LSRVEACDLKEKDRQDLPVNIFDICKYWEMKRKSEIGGP-------LVILPDIVYSLKTLED-WMSKRRMREVAKALQDQ 490

                          410
                   ....*....|....*..
gi 2029300282  533 ERARLLIELLRKREKLK 549
Cdd:COG5141    491 YQLLTLVESTAKRQLLK 507
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
 564-661 7.02e-60

Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99944  Cd Length: 98  Bit Score: 199.93  E-value: 7.02e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  564 PLTVLLRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARD 643
Cdd:cd05512      1 PLEVLLRKTLDQLQEKDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKD 80

                           90
                   ....*....|....*...
gi 2029300282  644 TVFYRAAVRLRDQGGVVL 661
Cdd:cd05512     81 TIFYRAAVRLRDQGGAIL 98
zf-HC5HC2H_2 pfam13832
PHD-zinc-finger like domain;
269-388 2.18e-50

PHD-zinc-finger like domain;


Pssm-ID: 463991 [Multi-domain]  Cd Length: 109  Bit Score: 173.30  E-value: 2.18e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  269 ADCVLCPNKGGAFKKTDDDRWGHVVCALWIPEVGFANTVFIEPIDgVRNIPPARWKLTCYLCKQKGvGACIQCHKANCYT 348
Cdd:pfam13832    1 VRCCLCPLRGGALKQTSDGRWVHVLCAIFVPEVRFGNVATMEPID-VSRIPPERWKLKCVFCKKRS-GACIQCSKGRCTT 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 2029300282  349 AFHVTCAQKAGLYMKMEPVKeltgggttfSVRKTAYCDVH 388
Cdd:pfam13832   79 AFHVTCAQAAGVYMEPEDWP---------NVVVIAYCQKH 109
EPL1 pfam10513
Enhancer of polycomb-like; This is a family of EPL1 (Enhancer of polycomb-like) proteins. The ...
 47-196 6.71e-42

Enhancer of polycomb-like; This is a family of EPL1 (Enhancer of polycomb-like) proteins. The EPL1 protein is a member of a histone acetyltransferase complex which is involved in transcriptional activation of selected genes.


Pssm-ID: 463128  Cd Length: 168  Bit Score: 151.10  E-value: 6.71e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282   47 RLHRISIFDPLEIILEDDL-------TAQEMSECNSNKENS-----------ERPPVCLRTKrhknNRVKKKNEALPSAH 108
Cdd:pfam10513    1 RHRRISIKQPLPIISEDEVdgldtspDEDEPSECNSNKENSlhavetgvdkeEEDEVHLKVI----NAAKKALSSSKKSQ 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  109 GTPASASA--------LPEP---KVRIVEYSPPsaprrppVYYKFIEKSAEELDNEVEYDMDEEDYAWLEIVNEKRKGDC 177
Cdd:pfam10513   77 NTSESSVPapnkerlyLPTPdagKFREFERPPA-------SYIRFSETVEEELDEGVEYDMDEEDEAWLEELNEKRKSEG 149

                          170
                   ....*....|....*....
gi 2029300282  178 VPAVSQSMFEFLMDRFEKE 196
Cdd:pfam10513  150 VEKISEDEFEILMDRFEKE 168
PHD_BRPF2 cd15677
PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar ...
 214-267 3.80e-37

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: 133.21  E-value: 3.80e-37
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2029300282  214 DAVCCICMDGECQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSRAR 267
Cdd:cd15677      1 DAVCCICMDGECQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSRSR 54
BROMO smart00297
bromo domain;
558-655 1.77e-33

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 124.70  E-value: 1.77e-33
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282   558 MELRLTPLTVLLRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCM 637
Cdd:smart00297    1 DPKLQKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNAR 80

                            90
                    ....*....|....*...
gi 2029300282   638 KYNARDTVFYRAAVRLRD 655
Cdd:smart00297   81 TYNGPDSEVYKDAKKLEK 98
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 569-652 2.15e-25

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 100.85  E-value: 2.15e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  569 LRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYR 648
Cdd:pfam00439    1 CLEILDKLMEHPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYK 80


                   ....
gi 2029300282  649 AAVR 652
Cdd:pfam00439   81 AAEK 84
PWWP smart00293
domain with conserved PWWP motif; conservation of Pro-Trp-Trp-Pro residues
 1056-1139 1.33e-18

domain with conserved PWWP motif; conservation of Pro-Trp-Trp-Pro residues


Pssm-ID: 214603 [Multi-domain]  Cd Length: 63  Bit Score: 80.85  E-value: 1.33e-18
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  1056 LEPLKVVWAKCSGYPSYPALIIDPKMPRVPghhngvtipappldvlkigeHMQTKSDEKLFLVLFFDNKRSwQWLPKSKM 1135
Cdd:smart00293    1 FKPGDLVWAKMKGFPWWPALVISPKMTPDN--------------------IMKRKSDENLYPVLFFGDKDT-AWIPSSKL 59


                    ....
gi 2029300282  1136 VPLG 1139
Cdd:smart00293   60 FPLT 63
PWWP pfam00855
PWWP domain; The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain ...
 1061-1173 3.21e-14

PWWP domain; The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain binds to Histone-4 methylated at lysine-20, H4K20me, suggesting that it is methyl-lysine recognition motif. Removal of two conserved aromatic residues in a hydrophobic cavity created by this domain within the full-length protein, Pdp1, abolishes the interaction o f the protein with H4K20me3. In fission yeast, Set9 is the sole enzyme that catalyzes all three states of H4K20me, and Set9-mediated H4K20me is required for efficient recruitment of checkpoint protein Crb2 to sites of DNA damage. The methylation of H4K20 is involved in a diverse array of cellular processes, such as organizing higher-order chromatin, maintaining genome stability, and regulating cell-cycle progression.


Pssm-ID: 459964 [Multi-domain]  Cd Length: 92  Bit Score: 69.38  E-value: 3.21e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282 1061 VVWAKCSGYPSYPALIIDPKMPRVPGHHNgvtipappldvlkigehmqtKSDEKLFLVLFFDNKRSwQWLPKSKMVPLGI 1140
Cdd:pfam00855    3 LVWAKLKGYPWWPARVVDPEELPENVLKP--------------------KKKDGEYLVRFFGDSEF-AWVKPKDLKPFDE 61

                           90       100       110
                   ....*....|....*....|....*....|...
gi 2029300282 1141 DETIDKLKMMegRNSSIRKAVRIAFDRAMNHLS 1173
Cdd:pfam00855   62 GDEFEYLKKK--KKKKKKKAFKKALEEAEEALK 92
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 584-650 8.37e-13

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 71.38  E-value: 8.37e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2029300282  584 IFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYRAA 650
Cdd:COG5076    168 IFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDA 234
PHD_2 pfam13831
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 228-261 2.19e-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: 463990 [Multi-domain]  Cd Length: 35  Bit Score: 56.58  E-value: 2.19e-10
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 2029300282  228 SNVILFCDMCNLAVHQECYGVPYIPEG-QWLCRHC 261
Cdd:pfam13831    1 TSPLVYCSKCSVQVHASCYGVPPIPDGdGWKCRRC 35
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 216-261 9.92e-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: 52.21  E-value: 9.92e-09
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*....
gi 2029300282   216 VCCICmdGECQNSNVILFCDMCNLAVHQECYGVPY---IPEGQWLCRHC 261
Cdd:smart00249    1 YCSVC--GKPDDGGELLQCDGCDRWYHQTCLGPPLleeEPDGKWYCPKC 47
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 326-360 5.42e-03

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: 36.04  E-value: 5.42e-03
                            10        20        30
                    ....*....|....*....|....*....|....*.
gi 2029300282   326 TCYLCKQKGV-GACIQCHKanCYTAFHVTCAQKAGL 360
Cdd:smart00249    1 YCSVCGKPDDgGELLQCDG--CDRWYHQTCLGPPLL 34
 
Name Accession Description Interval E-value
ePHD_BRPF2 cd15702
Extended PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and ...
 271-388 1.41e-85

Extended PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of BRPF2. BRPF2 also termed bromodomain-containing protein 1 (BRD1), or BR140-likeprotein, 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 plant homeodomain (PHD) finger followed by a non-canonical ePHD finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain.


Pssm-ID: 277172  Cd Length: 118  Bit Score: 272.69  E-value: 1.41e-85
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  271 CVLCPNKGGAFKKTDDDRWGHVVCALWIPEVGFANTVFIEPIDGVRNIPPARWKLTCYLCKQKGVGACIQCHKANCYTAF 350
Cdd:cd15702      1 CVLCPNKGGAFKKTDDDRWGHVVCALWIPEVGFANTVFIEPIDGVRNIPPARWKLTCYLCKQKGVGACIQCHKANCYTAF 80

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 2029300282  351 HVTCAQKAGLYMKMEPVKELTGGGTTFSVRKTAYCDVH 388
Cdd:cd15702     81 HVTCAQKAGLYMKMEPVKEVTGGGTTFSVRKTAYCDAH 118
PWWP_BRPF2 cd20157
PWWP domain found in bromodomain and PHD finger-containing protein 2 (BRPF2); BRPF2, also ...
 1056-1175 3.93e-83

PWWP domain found in bromodomain and PHD finger-containing protein 2 (BRPF2); BRPF2, also called bromodomain-containing protein 1 (BRD1), or BR140-likeprotein, 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 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, C2HC5HC2H, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The PHD finger binds to lysine 4 of histone H3 (K4H3), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties.


Pssm-ID: 438985  Cd Length: 120  Bit Score: 266.03  E-value: 3.93e-83
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282 1056 LEPLKVVWAKCSGYPSYPALIIDPKMPRVPGHHNGVTIPAPPLDVLKIGEHMQTKSDEKLFLVLFFDNKRSWQWLPKSKM 1135
Cdd:cd20157      1 LEPLKVVWAKCSGYPSYPALIIDPKMPRVGCHHNGVTIPVPPLDVLKIGEQMQTKSDEKLFLVLFFDNKRSWQWLPKSKM 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 2029300282 1136 VPLGIDETIDKLKMMEGRNSSIRKAVRIAFDRAMNHLSRV 1175
Cdd:cd20157     81 VPLGIDETIDKLKMMEGRNSSIRKAVRIAFDRAMNHLSRV 120
COG5141 COG5141
PHD zinc finger-containing protein [General function prediction only];
139-549 5.08e-79

PHD zinc finger-containing protein [General function prediction only];


Pssm-ID: 227470 [Multi-domain]  Cd Length: 669  Bit Score: 274.17  E-value: 5.08e-79
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  139 YYKFIEKSAEELDNE-VEYDMDEEDYAWLEIVNEKRKGDcvpAVSQSMFEFLMDRFEKE----SHCENQKQGEQQSLIDE 213
Cdd:COG5141    115 GKKFIDIEPPRGLFFsVIYDLDEYDTMWLRYLNESAIDE---NVSEEAFEIIVTRLEKEwfffEHGLPDKHVEPIEPSDE 191

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  214 -DAVCCICMDGECQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSRARPADCVLCPNKGGAFKKTDDDRWGHV 292
Cdd:COG5141    192 fDDICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQFLPEGFWLCRKCIYGEYQIRCCSFCPSSDGAFKQTSDGRWGHV 271

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  293 VCALWIPEVGFANTVFIEPIDGVRNIPPARWKLTCYLCKQKGvGACIQCHKANCYTAFHVTCAQKAGLYMKmepvKELTG 372
Cdd:COG5141    272 ICAMFNPELSFGHLLSKDPIDNIASVSSSRWKLGCLICKEFG-GTCIQCSYFNCTRAYHVTCARRAGYFDL----NIYSH 346

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  373 GGTTFSVRKTAYCDVHTPPGctrrplniYGDVEMKNGVCRKESSVKTVRSTSKVRKKAKKAKKALAEPCAVLPTVCAPYI 452
Cdd:COG5141    347 NGISYCIDHEPLCRKHYPLG--------YGRMNGLRYFGYEKLRYKNPPTAIPRKVRAARPRATLFMKLCWKQPPATPSV 418

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  453 PPQRLNRIANQVAIQRKKQFVERAHSYWLLKRLSRNGAPllrrlqsSLQSQRSSQQRENDEEmKAAKEKLKYWQRLRHDL 532
Cdd:COG5141    419 LSRVEACDLKEKDRQDLPVNIFDICKYWEMKRKSEIGGP-------LVILPDIVYSLKTLED-WMSKRRMREVAKALQDQ 490

                          410
                   ....*....|....*..
gi 2029300282  533 ERARLLIELLRKREKLK 549
Cdd:COG5141    491 YQLLTLVESTAKRQLLK 507
ePHD_BRPF cd15670
Extended PHD finger found in BRPF proteins; The extended plant homeodomain (ePHD) zinc finger ...
 271-388 8.60e-79

Extended PHD finger found in BRPF proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the ePHD finger of the family of BRPF proteins, which includes BRPF1, BRD1/BRPF2, and BRPF3. These 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 plant homeodomain (PHD) zinc finger followed by a non-canonical ePHD finger, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. This PHD finger binds to lysine 4 of histone H3 (K4H3), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties.


Pssm-ID: 277140  Cd Length: 116  Bit Score: 253.80  E-value: 8.60e-79
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  271 CVLCPNKGGAFKKTDDDRWGHVVCALWIPEVGFANTVFIEPIDGVRNIPPARWKLTCYLCKQKGvGACIQCHKANCYTAF 350
Cdd:cd15670      1 CVLCPNKGGAFKQTDDGRWAHVVCALWIPEVSFANTVFLEPIDGIQNIPKARWKLTCYICKKRM-GACIQCHKKNCYTAF 79

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 2029300282  351 HVTCAQKAGLYMKMEPVKElTGGGTTFSVRKTAYCDVH 388
Cdd:cd15670     80 HVTCAQQAGLYMKIEPVKD-PGNGTSDSVRKEAYCDKH 116
ePHD_BRPF1 cd15701
Extended PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and ...
 271-391 7.64e-78

Extended PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of BRPF1. BRPF1, also termed peregrin, or protein Br140, is a multi-domain protein that binds histones, mediates monocytic leukemic zinc-finger protein (MOZ) -dependent histone acetylation, and is required for Hox gene expression and segmental identity. It is a close partner of the MOZ histone acetyltransferase (HAT) complex and a novel Trithorax group (TrxG) member with a central role during development. BRPF1 is primarily a nuclear protein that has a broad tissue distribution and is abundant in testes and spermatogonia. It contains a plant homeodomain (PHD) zinc finger followed by a non-canonical ePHD finger, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. This PHD finger binds to methylated lysine 4 of histone H3 (H3K4me), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties. BRPF1 may be involved in chromatin remodeling.


Pssm-ID: 277171 [Multi-domain]  Cd Length: 121  Bit Score: 251.54  E-value: 7.64e-78
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  271 CVLCPNKGGAFKKTDDDRWGHVVCALWIPEVGFANTVFIEPIDGVRNIPPARWKLTCYLCKQKGVGACIQCHKANCYTAF 350
Cdd:cd15701      1 CALCPNKGGAFKQTDDGRWAHVVCALWIPEVCFANTVFLEPIDSIEHIPPARWKLTCYICKQRGSGACIQCHKANCYTAF 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 2029300282  351 HVTCAQKAGLYMKMEPVKELTGGGTTFSVRKTAYCDVHTPP 391
Cdd:cd15701     81 HVTCAQQAGLYMKMEPVRETGANGTSFSVRKTAYCDIHTPP 121
ePHD_BRPF3 cd15703
Extended PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and ...
 271-388 1.16e-73

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: 239.57  E-value: 1.16e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  271 CVLCPNKGGAFKKTDDDRWGHVVCALWIPEVGFANTVFIEPIDGVRNIPPARWKLTCYLCKQKGVGACIQCHKANCYTAF 350
Cdd:cd15703      1 CVLCPNKGGAFKQTSDGRWAHVVCAIWIPEVCFANTVFLEPVEGVNNIPPARWKLTCYLCKQKGRGAAIQCHKVNCYTAF 80

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 2029300282  351 HVTCAQKAGLYMKMEPVKELTGGGTTFSVRKTAYCDVH 388
Cdd:cd15703     81 HVTCAQRAGLFMKIEPVRETGLNGTTFTVRKTAYCENH 118
PWWP_BRPF3 cd20158
PWWP domain found in bromodomain and PHD finger-containing protein 3 (BRPF3); BRPF3 is a ...
 1056-1173 5.19e-66

PWWP domain found in bromodomain and PHD finger-containing protein 3 (BRPF3); BRPF3 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 a non-canonical extended PHD (ePHD) finger, C2HC5HC2H, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The PHD finger binds to lysine 4 of histone H3 (K4H3), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties.


Pssm-ID: 438986  Cd Length: 118  Bit Score: 217.89  E-value: 5.19e-66
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282 1056 LEPLKVVWAKCSGYPSYPALIIDPKMPRVPGHHNGVTIPAPPLDVLKIGEHMQTKSDEKLFLVLFFDNKRSWQWLPKSKM 1135
Cdd:cd20158      1 LEPLELVWAKCRGYPSYPALIIDPKMPREGLLHNGVPIPVPPLDVLKLGEQKQAEAGEKLFLVLFFDNKRTWQWLPRDKV 80

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 2029300282 1136 VPLGIDETIDKLKMMEGRNSSIRKAVRIAFDRAMNHLS 1173
Cdd:cd20158     81 LPLGVDDTVDKLKMMEGRKTSIRKSVQVAYDRAMIHLS 118
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
 564-661 7.02e-60

Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99944  Cd Length: 98  Bit Score: 199.93  E-value: 7.02e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  564 PLTVLLRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARD 643
Cdd:cd05512      1 PLEVLLRKTLDQLQEKDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKD 80

                           90
                   ....*....|....*...
gi 2029300282  644 TVFYRAAVRLRDQGGVVL 661
Cdd:cd05512     81 TIFYRAAVRLRDQGGAIL 98
PWWP_BRPF1 cd20156
PWWP domain found in bromodomain and PHD finger-containing protein 1 (BRPF1); BRPF1, also ...
 1056-1175 5.56e-57

PWWP domain found in bromodomain and PHD finger-containing protein 1 (BRPF1); BRPF1, also called peregrin, or protein Br140, is a multi-domain protein that binds histones, mediates monocytic leukemic zinc-finger protein (MOZ)-dependent histone acetylation, and is required for Hox gene expression and segmental identity. It is a close partner of the MOZ histone acetyltransferase (HAT) complex and a novel Trithorax group (TrxG) member with a central role during development. BRPF1 is primarily a nuclear protein that has a broad tissue distribution and is abundant in testes and spermatogonia. It may be involved in chromatin remodeling. It contains a plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, C2HC5HC2H, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The PHD finger binds to methylated lysine 4 of histone H3 (K4H3), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties.


Pssm-ID: 438984  Cd Length: 120  Bit Score: 192.54  E-value: 5.56e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282 1056 LEPLKVVWAKCSGYPSYPALIIDPKMPRVPGHHNGVTIPAPPLDVLKIGEHMQTKSDEKLFLVLFFDNKRSWQWLPKSKM 1135
Cdd:cd20156      1 LDALDLVWAKCRGYPSYPALIIDPKMPREGMFHHGVPIPVPPLEVLKLGEQMTQEAREHLYLVLFFDNKRTWQWLPRTKL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 2029300282 1136 VPLGIDETIDKLKMMEGRNSSIRKAVRIAFDRAMNHLSRV 1175
Cdd:cd20156     81 VPLGVNQDLDKEKMLEGRKSNIRKSVQIAYHRAMQHRNKV 120
zf-HC5HC2H_2 pfam13832
PHD-zinc-finger like domain;
269-388 2.18e-50

PHD-zinc-finger like domain;


Pssm-ID: 463991 [Multi-domain]  Cd Length: 109  Bit Score: 173.30  E-value: 2.18e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  269 ADCVLCPNKGGAFKKTDDDRWGHVVCALWIPEVGFANTVFIEPIDgVRNIPPARWKLTCYLCKQKGvGACIQCHKANCYT 348
Cdd:pfam13832    1 VRCCLCPLRGGALKQTSDGRWVHVLCAIFVPEVRFGNVATMEPID-VSRIPPERWKLKCVFCKKRS-GACIQCSKGRCTT 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 2029300282  349 AFHVTCAQKAGLYMKMEPVKeltgggttfSVRKTAYCDVH 388
Cdd:pfam13832   79 AFHVTCAQAAGVYMEPEDWP---------NVVVIAYCQKH 109
PWWP_BRPF cd05839
PWWP domain found in the bromodomain and PHD finger-containing (BRPF) protein family; The BRPF ...
 1056-1171 1.11e-47

PWWP domain found in the bromodomain and PHD finger-containing (BRPF) protein family; The BRPF family of 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 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, C2HC5HC2H, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The PHD finger binds to lysine 4 of histone H3 (K4H3), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties.


Pssm-ID: 438964  Cd Length: 106  Bit Score: 165.13  E-value: 1.11e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282 1056 LEPLKVVWAKCSGYPSYPALIIDPKMPRVPghhNGVTIPAPPLDVLKigehmqtKSDEKLFLVLFFDNKRSWQWLPKSKM 1135
Cdd:cd05839      1 LEPGDLVWAKCRGYPWYPAEIVDPKDPKEG---NGVPIPVPPDRVLK-------KSNEKLYLVLFFDAKRTWGWLPRNKL 70

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 2029300282 1136 VPLGIDETIDKLKMMEGRNSSIRKAVRIAFDRAMNH 1171
Cdd:cd05839     71 RPLGVDEELDKLKLSEAKKSKRRKEVRKAYERACKH 106
EPL1 pfam10513
Enhancer of polycomb-like; This is a family of EPL1 (Enhancer of polycomb-like) proteins. The ...
 47-196 6.71e-42

Enhancer of polycomb-like; This is a family of EPL1 (Enhancer of polycomb-like) proteins. The EPL1 protein is a member of a histone acetyltransferase complex which is involved in transcriptional activation of selected genes.


Pssm-ID: 463128  Cd Length: 168  Bit Score: 151.10  E-value: 6.71e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282   47 RLHRISIFDPLEIILEDDL-------TAQEMSECNSNKENS-----------ERPPVCLRTKrhknNRVKKKNEALPSAH 108
Cdd:pfam10513    1 RHRRISIKQPLPIISEDEVdgldtspDEDEPSECNSNKENSlhavetgvdkeEEDEVHLKVI----NAAKKALSSSKKSQ 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  109 GTPASASA--------LPEP---KVRIVEYSPPsaprrppVYYKFIEKSAEELDNEVEYDMDEEDYAWLEIVNEKRKGDC 177
Cdd:pfam10513   77 NTSESSVPapnkerlyLPTPdagKFREFERPPA-------SYIRFSETVEEELDEGVEYDMDEEDEAWLEELNEKRKSEG 149

                          170
                   ....*....|....*....
gi 2029300282  178 VPAVSQSMFEFLMDRFEKE 196
Cdd:pfam10513  150 VEKISEDEFEILMDRFEKE 168
ePHD_JADE cd15671
Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins; The extended ...
 271-388 4.43e-41

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: 146.82  E-value: 4.43e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  271 CVLCPNKGGAFKKTDD-DRWGHVVCALWIPEVGFANTVFIEPIDGVRNIPPARWKLTCYLCKQKgVGACIQCHKANCYTA 349
Cdd:cd15671      1 CVLCPKKGGAMKSTKSgTKWVHVSCALWIPEVSIGCPEKMEPITKISHIPMSRWALVCVLCKEK-TGACIQCSVKSCKTA 79

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 2029300282  350 FHVTCAQKAGLYMKMEPVKEltgggtTFSVRKTAYCDVH 388
Cdd:cd15671     80 FHVTCAFQHGLEMKTILEDE------DDEVKFKSYCPKH 112
PHD_BRPF2 cd15677
PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar ...
 214-267 3.80e-37

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: 133.21  E-value: 3.80e-37
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2029300282  214 DAVCCICMDGECQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSRAR 267
Cdd:cd15677      1 DAVCCICMDGECQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSRSR 54
PHD_BRPF cd15572
PHD finger found in bromodomain and PHD finger-containing (BRPF) proteins; The family of BRPF ...
 214-267 3.05e-36

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: 130.81  E-value: 3.05e-36
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2029300282  214 DAVCCICMDGECQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSRAR 267
Cdd:cd15572      1 DAVCCICLDGECQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRRCLQSPSR 54
ePHD cd15571
Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is ...
 271-388 3.99e-36

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: 132.71  E-value: 3.99e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  271 CVLCPNKGGAFKK------TDDDRWGHVVCALWIPEVGFANTVFIEpIDGVRNIPPARWKLTCYLCKQKGvGACIQCHKA 344
Cdd:cd15571      1 CALCPRSGGALKGggalktTSDGLWVHVVCALWSPEVYFDDGTLLE-VEGVSKIPKRRKKLKCSICGKRG-GACIQCSYP 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 2029300282  345 NCYTAFHVTCAQKAGLYMKMepvkeltgggTTFSVRKTAYCDVH 388
Cdd:cd15571     79 GCPRSFHVSCAIRAGCLFEF----------EDGPGNFVVYCPKH 112
ePHD_JMJD2 cd15675
Extended PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone ...
 271-366 5.11e-34

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: 126.32  E-value: 5.11e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  271 CVLCPNKGGAFKKTDDDRWGHVVCALWIPEVGFANTVFIEPIDgVRNIPPARWKLTCYLCKQ-----KGVGACIQCHKAN 345
Cdd:cd15675      1 CCLCCLRGGALKPTTDGRWAHVVCAIAIPEVRFSNVPERGPID-ISKIPPARLKLKCIYCSKitksmSHMGACIQCSTGK 79

                           90       100
                   ....*....|....*....|.
gi 2029300282  346 CYTAFHVTCAQKAGlyMKMEP 366
Cdd:cd15675     80 CTTSFHVTCAHAAG--VQMEP 98
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 291-388 1.26e-33

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: 124.36  E-value: 1.26e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  291 HVVCALWIPEVGFANTVF-IEPIDGVRNIPPARWKLTCYLCKQKGvGACIQCHKANCYTAFHVTCAQKAGLYMKMEPVke 369
Cdd:pfam13771    1 HVVCALWSPELVQRGNDSmGFPIEDIEKIPKRRWKLKCYLCKKKG-GACIQCSKKNCRRAFHVTCALEAGLLMQFDED-- 77

                           90
                   ....*....|....*....
gi 2029300282  370 ltgggttfSVRKTAYCDVH 388
Cdd:pfam13771   78 --------NGTFKSYCKKH 88
BROMO smart00297
bromo domain;
558-655 1.77e-33

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 124.70  E-value: 1.77e-33
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282   558 MELRLTPLTVLLRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCM 637
Cdd:smart00297    1 DPKLQKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNAR 80

                            90
                    ....*....|....*...
gi 2029300282   638 KYNARDTVFYRAAVRLRD 655
Cdd:smart00297   81 TYNGPDSEVYKDAKKLEK 98
PHD_BRPF1 cd15676
PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar ...
 208-267 2.47e-33

PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar proteins; BRPF1, also termed peregrin or protein Br140, is a multi-domain protein that binds histones, mediates monocytic leukemic zinc-finger protein (MOZ)-dependent histone acetylation, and is required for Hox gene expression and segmental identity. It is a close partner of the MOZ histone acetyltransferase (HAT) complex and a novel Trithorax group (TrxG) member with a central role during development. BRPF1 is primarily a nuclear protein that has a broad tissue distribution and is abundant in testes and spermatogonia. It contains 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. BRPF1 may be involved in chromatin remodeling. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277146 [Multi-domain]  Cd Length: 62  Bit Score: 122.86  E-value: 2.47e-33
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  208 QSLIDEDAVCCICMDGECQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSRAR 267
Cdd:cd15676      1 NALIDEDAVCCICNDGECQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRRCLQSPSR 60
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
 564-653 1.32e-32

Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99941 [Multi-domain]  Cd Length: 101  Bit Score: 121.89  E-value: 1.32e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  564 PLTVLLRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARD 643
Cdd:cd05509      1 PLYTQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPD 80

                           90
                   ....*....|
gi 2029300282  644 TVFYRAAVRL 653
Cdd:cd05509     81 TEYYKCANKL 90
ePHD_JADE3 cd15706
Extended PHD finger found in protein Jade-3 and similar proteins; The extended plant ...
 271-363 1.01e-31

Extended PHD finger found in protein Jade-3 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-3. Jade-3, also termed PHD finger protein 16 (PHF16), is a plant homeodomain (PHD) zinc finger protein that is close related to Jade-1, which functions as an essential regulator of multiple cell signaling pathways. Like Jade-1, Jade-3 is required for ING4 and ING5 to associate with histone acetyl transferase (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-3 contains a canonical PHD domain followed by this non-canonical ePHD domain, both of which are zinc-binding motifs.


Pssm-ID: 277176  Cd Length: 111  Bit Score: 119.83  E-value: 1.01e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  271 CVLCPNKGGAFKKTDD-DRWGHVVCALWIPEVGFANTVFIEPIDGVRNIPPARWKLTCYLCKQKgVGACIQCHKANCYTA 349
Cdd:cd15706      1 CLLCPKTGGAMKATRTgTKWAHVSCALWIPEVSIACPERMEPITKVSHIPPSRWALVCSLCKLK-TGACIQCSVKSCITA 79

                           90
                   ....*....|....
gi 2029300282  350 FHVTCAQKAGLYMK 363
Cdd:cd15706     80 FHVTCAFEHSLEMK 93
ePHD_ATX1_2_like cd15662
Extended PHD finger found in Arabidopsis thaliana ATX1, -2, and similar proteins; The extended ...
 271-388 1.87e-31

Extended PHD finger found in Arabidopsis thaliana ATX1, -2, and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of A. thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like proteins ATX1, -2, and similar proteins. ATX1 and -2 are sister paralogs originating from a segmental chromosomal duplication; they are plant counterparts of the Drosophila melanogaster trithorax (TRX) and mammalian mixed-lineage leukemia (MLL1) proteins. ATX1 (also known as protein SET domain group 27, or trithorax-homolog protein 1/TRX-homolog protein 1), is a methyltransferase that trimethylates histone H3 at lysine 4 (H3K4me3). It also acts as a histone modifier and as a positive effector of gene expression. ATX1 regulates transcription from diverse classes of genes implicated in biotic and abiotic stress responses. It is involved in dehydration stress signaling in both abscisic acid (ABA)-dependent and ABA-independent pathways. ATX2 (also known as protein SET domain group 30, or trithorax-homolog protein 2/TRX-homolog protein 2), is involved in dimethylating histone H3 at lysine 4 (H3K4me2). ATX1 and ATX2 are multi-domain proteins that consist of an N-terminal PWWP domain, FYRN- and FYRC (DAST, domain associated with SET in trithorax) domains, a canonical PHD finger, this non-canonical ePHD finger, and a C-terminal SET domain.


Pssm-ID: 277132  Cd Length: 115  Bit Score: 119.12  E-value: 1.87e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  271 CVLCPNKGGAFKKTDDDRWGHVVCALWIPEVGFANTVFIEPIDGVRNIPPARWKLTCYLCKQKgVGACIQCHKANCYTAF 350
Cdd:cd15662      1 CCLCPVVGGALKPTTDGRWAHLACAIWIPETCLLDVKTMEPVDGINAISKERWELSCTICKQR-YGACIQCSNNSCRVAY 79

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 2029300282  351 HVTCAQKAGLYMKMEPVKELTGGGTTfsVRKTAYCDVH 388
Cdd:cd15662     80 HPLCARAAGLCMEVADEGGEDPGDQG--LRLLSYCPRH 115
ePHD_RNO cd15707
Extended PHD finger found in Drosophila melanogaster PHD finger protein rhinoceros (RNO) and ...
 271-388 4.45e-31

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: 118.08  E-value: 4.45e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  271 CVLCPNKGGAFKKT-DDDRWGHVVCALWIPEVGFANTVFIEPIDGVRNIPPARWKLTCYLCKQKgVGACIQCHKANCYTA 349
Cdd:cd15707      1 CILCPNKGGAMKSTrSGTKWAHVSCALWIPEVSIGCVEKMEPITKISSIPASRWALICVLCRER-TGACIQCSVKTCKTA 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 2029300282  350 FHVTCAQKAGLYMK--MEPVKELtgggttfSVRKTAYCDVH 388
Cdd:cd15707     80 YHVTCGFQHGLEMKtiLDEESED-------GVKLRSYCQKH 113
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
 565-656 5.34e-31

Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.


Pssm-ID: 99922 [Multi-domain]  Cd Length: 99  Bit Score: 117.47  E-value: 5.34e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  565 LTVLLRSVLDQLQDK--DPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNAR 642
Cdd:cd04369      1 LKKKLRSLLDALKKLkrDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGP 80

                           90
                   ....*....|....
gi 2029300282  643 DTVFYRAAVRLRDQ 656
Cdd:cd04369     81 GSPIYKDAKKLEKL 94
ePHD_AF10_like cd15672
Extended PHD finger found in protein AF-10 and AF-17; The extended plant homeodomain (ePHD) ...
 271-388 5.89e-31

Extended PHD finger found in protein AF-10 and AF-17; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of AF-10 and AF-17. AF-10, also termed ALL1 (acute lymphoblastic leukaemia)-fused gene from chromosome 10 protein, is a transcription factor encoded by gene AF10, a translocation partner of the MLL (mixed-lineage leukaemia) oncogene in leukaemia. AF-10 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. It plays a key role in the survival of uncommitted hematopoietic cells. Moreover, AF-10 functions as a follistatin-related gene (FLRG)-interacting protein. The interaction with FLRG enhances AF10-dependent transcription. It interacts with the human counterpart of yeast Dot1, hDOT1L, and may act as a bridge for the recruitment of hDOT1L to the genes targeted by MLL-AF10. It also interacts with the synovial sarcoma associated protein SYT protein and may play a role in synovial sarcomas and acute leukemias. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is encoded by gene AF17 that has been identified in hematological malignancies as translocation partners of the mixed lineage leukemia gene MLL. It is a putative transcription factor that may play a role in multiple signaling pathways. It is involved in chromatin-mediated gene regulation mechanisms. It functions as a component of the multi-subunit Dot1 complex (Dotcom) and plays a role in the Wnt/Wingless signaling pathway. It also seems to be a downstream target of the beta-catenin/T-cell factor pathway, and participates in G2-M progression. Moreover, it may function as an important regulator of ENaC-mediated Na+ transport and thus blood pressure. Both AF-10 and AF-17 contain an N-terminal plant homeodomain (PHD) finger followed by this non-canonical ePHD finger. The PHD finger is involved in their homo-oligomerization. In the C-terminal region, they possess a leucine zipper domain and a glutamine-rich region. This family also includes ZFP-1, the Caenorhabditis elegans AF10 homolog. It was originally identified as a factor promoting RNAi interference in C. elegans. It also acts as Dot1-interacting protein that opposes H2B ubiquitination to reduce polymerase II (Pol II) transcription.


Pssm-ID: 277142  Cd Length: 116  Bit Score: 117.95  E-value: 5.89e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  271 CVLCPNKGGAFKKTDDDRWGHVVCALWIPEVGFANTVFIEPIdGVRNIPPARWKLTCYLCKQKG------VGACIQCHKA 344
Cdd:cd15672      1 CELCPHKDGALKRTDNGGWAHVVCALYIPEVRFGNVATMEPI-ILQDVPQDRFNKTCYICEEQGreskasTGACMQCNKS 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 2029300282  345 NCYTAFHVTCAQKAGLYMKmepvkelTGGGTTFSVRKTAYCDVH 388
Cdd:cd15672     80 GCKQSFHVTCAQMAGLLCE-------EAGNYSDNVKYCGYCSYH 116
ePHD_JMJD2B cd15714
Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B); The extended plant ...
 271-363 5.60e-30

Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2B. JMJD2B, also termed lysine-specific demethylase 4B (KDM4B), or JmjC domain-containing histone demethylation protein 3B (JHDM3B), specifically antagonizes the trimethyl group from H3K9 in pericentric heterochromatin and reduces H3K36 methylation in mammalian cells. It plays an essential role in the growth regulation of cancer cells by modulating the G1-S transition and promotes cell-cycle progression through the regulation of cyclin-dependent kinase 6 (CDK6). It interacts with heat shock protein 90 (Hsp90) and its stability can be regulated by Hsp90. JMJD2B also functions as a direct transcriptional target of p53, which induces its expression through promoter binding. Moreover, JMJD2B expression can be controlled by hypoxia-inducible factor 1alpha (HIF1alpha) in colorectal cancer and estrogen receptor alpha (ERalpha) in breast cancer. It is also involved in bladder, lung, and gastric cancer. JMJD2B 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: 277184  Cd Length: 110  Bit Score: 115.03  E-value: 5.60e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  271 CVLCPNKGGAFKKTDDDRWGHVVCALWIPEVGFANTVFIEPIDgVRNIPPARWKLTCYLCK---QKGVGACIQCHKANCY 347
Cdd:cd15714      1 CCLCNLRGGALQMTTDERWVHVICAIAVPEARFLNVIERHPVD-VSAIPEQRWKLKCVYCRkrmKKVSGACIQCSYDHCS 79

                           90
                   ....*....|....*.
gi 2029300282  348 TAFHVTCAQKAGLYMK 363
Cdd:cd15714     80 TSFHVTCAHAAGVVME 95
ePHD_AF10 cd15708
Extended PHD finger found in protein AF-10 and similar proteins; The extended plant ...
 271-388 8.09e-29

Extended PHD finger found in protein AF-10 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of AF-10. AF-10, also termed ALL1 (acute lymphoblastic leukaemia)-fused gene from chromosome 10 protein, is a transcription factor encoded by gene AF10, a translocation partner of the MLL (mixed-lineage leukaemia) oncogene in leukaemia. AF-10 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. It plays a key role in the survival of uncommitted hematopoietic cells. Moreover, AF-10 functions as a follistatin-related gene (FLRG)-interacting protein. The interaction with FLRG enhances AF10-dependent transcription. It interacts with human counterpart of the yeast Dot1, hDOT1L, and may act as a bridge for the recruitment of hDOT1L to the genes targeted by MLL-AF10. It also interacts with the synovial sarcoma associated protein SYT protein and may play a role in synovial sarcomas and acute leukemias. AF-10 contains an N-terminal plant homeodomain (PHD) finger followed by this non-canonical ePHD finger.


Pssm-ID: 277178  Cd Length: 129  Bit Score: 112.48  E-value: 8.09e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  271 CVLCPNKGGAFKKTDDDRWGHVVCALWIPEVGFANTVFIEPIdGVRNIPPARWKLTCYLCKQKG------VGACIQCHKA 344
Cdd:cd15708      5 CELCPHKDGALKRTDNGGWAHVVCALYIPEVQFANVSTMEPI-VLQSVPHERYNKTCYICDEQGreskaaTGACMTCNKH 83

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 2029300282  345 NCYTAFHVTCAQKAGLYMKMEpvkeltgGGTTFSVRKTAYCDVH 388
Cdd:cd15708     84 GCRQAFHVTCAQLAGLLCEEE-------GNGADNVQYCGYCKYH 120
PHD_BRPF3 cd15678
PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and similar ...
 214-268 1.22e-28

PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and similar proteins; BRPF3 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 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: 277148 [Multi-domain]  Cd Length: 55  Bit Score: 108.95  E-value: 1.22e-28
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2029300282  214 DAVCCICMDGECQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSRARP 268
Cdd:cd15678      1 DAFCCVCLDDECHNSNVILFCDICNLAVHQECYGVPYIPEGQWLCRCCLQSPSRP 55
ePHD_JADE2 cd15705
Extended PHD finger found in protein Jade-2 and similar proteins; The extended plant ...
 271-363 4.05e-28

Extended PHD finger found in protein Jade-2 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-2. 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 PHD finger followed by this non-canonical ePHD finger, both of which are zinc-binding motifs.


Pssm-ID: 277175  Cd Length: 111  Bit Score: 109.80  E-value: 4.05e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  271 CVLCPNKGGAFKKT-DDDRWGHVVCALWIPEVGFANTVFIEPIDGVRNIPPARWKLTCYLCKQKgVGACIQCHKANCYTA 349
Cdd:cd15705      1 CLLCPKRGGALKPTrSGTKWVHVSCALWIPEVSIGCPEKMEPITKISHIPASRWALSCSLCKEC-TGTCIQCSMPSCITA 79

                           90
                   ....*....|....
gi 2029300282  350 FHVTCAQKAGLYMK 363
Cdd:cd15705     80 FHVTCAFDHGLEMR 93
PHD_BRPF_JADE_like cd15492
PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; ...
 216-261 1.35e-27

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: 105.78  E-value: 1.35e-27
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 2029300282  216 VCCICMDGECQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHC 261
Cdd:cd15492      1 VCDVCLDGESEDDNEIVFCDGCNVAVHQSCYGIPLIPEGDWFCRKC 46
ePHD_PHF14 cd15674
Extended PHD finger found in PHD finger protein 14 (PHF14) and similar proteins; The extended ...
 271-360 3.27e-27

Extended PHD finger found in PHD finger protein 14 (PHF14) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of PHF14. 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 this non-canonical ePHD finger. It can interact with histones through its PHD fingers.


Pssm-ID: 277144  Cd Length: 114  Bit Score: 107.08  E-value: 3.27e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  271 CVLCPNKGGAFKKTDDDRWGHVVCALWIPEVGFANTVFIEPIDgVRNIPPARW-KLTCYLCKQK---GVGACIQCHKANC 346
Cdd:cd15674      1 CELCPNRGGIFKETDTGRWVHLVCALYTPGVAFGDVDKLSPVT-LTEMNYSKWgARECSLCEDPrfaRTGVCISCDAGMC 79

                           90
                   ....*....|....
gi 2029300282  347 YTAFHVTCAQKAGL 360
Cdd:cd15674     80 KSYFHVTCAQREGL 93
ePHD_JADE1 cd15704
Extended PHD finger found in protein Jade-1 and similar proteins; The extended plant ...
 271-363 7.26e-27

Extended PHD finger found in protein Jade-1 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-1. 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 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 ASA 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 plant homeodomain (PHD) finger followed by this non-canonical ePHD finger, both of which are zinc-binding motifs.


Pssm-ID: 277174  Cd Length: 118  Bit Score: 106.31  E-value: 7.26e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  271 CVLCPNKGGAFKKT-DDDRWGHVVCALWIPEVGFANTVFIEPIDGVRNIPPARWKLTCYLCKQKgVGACIQCHKANCYTA 349
Cdd:cd15704      4 CLLCPKKGGAMKPTrSGTKWVHVSCALWIPEVSIGSPEKMEPITKVSHIPSSRWALVCSLCNEK-VGASIQCSVKNCRTA 82

                           90
                   ....*....|....
gi 2029300282  350 FHVTCAQKAGLYMK 363
Cdd:cd15704     83 FHVTCAFDRGLEMK 96
Bromo_brd7_like cd05513
Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ...
 564-657 8.36e-27

Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99945  Cd Length: 98  Bit Score: 105.18  E-value: 8.36e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  564 PLTVLLRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARD 643
Cdd:cd05513      1 PLQKALEQLIRQLQRKDPHGFFAFPVTDFIAPGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPD 80

                           90
                   ....*....|....
gi 2029300282  644 TVFYRAAVRLRDQG 657
Cdd:cd05513     81 TIYYKAAKKLLHSG 94
ePHD_JMJD2C cd15715
Extended PHD finger found in Jumonji domain-containing protein 2C (JMJD2C); The extended plant ...
 271-363 5.88e-26

Extended PHD finger found in Jumonji domain-containing protein 2C (JMJD2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2C. JMJD2C, also termed lysine-specific demethylase 4C (KDM4C), or gene amplified in squamous cell carcinoma 1 protein (GASC-1 protein), or JmjC domain-containing histone demethylation protein 3C (JHDM3C), is an epigenetic factor that catalyzes the demethylation of di- and trimethylated H3K9 and H3K36, and may be involved in the development and/or progression of various types of cancer including esophageal squamous cell carcinoma (ESC) and breast cancer. It selectively interacts with hypoxia-inducible factor 1alpha (HIF1alpha) and plays a role in breast cancer progression. Moreover, JMJD2C may play an important role in the treatment of obesity and its complications by modulating the regulation of adipogenesis by nuclear receptor peroxisome proliferator-activated receptor gamma (PPARgamma). JMJD2C contains jmjN and jmjC domains in the N-terminal region, followed by a canonical plant homeodomain (PHD) finger, this non-canonical ePHD finger, and a Tudor domain.


Pssm-ID: 277185  Cd Length: 110  Bit Score: 103.50  E-value: 5.88e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  271 CVLCPNKGGAFKKTDDDRWGHVVCALWIPEVGFANTVFIEPIDgVRNIPPARWKLTCYLCKQ---KGVGACIQCHKANCY 347
Cdd:cd15715      1 CCLCNLRGGALKQTSDDKWAHVMCAVALPEVRFINVVERTPID-ISRIPLQRLKLKCIFCRNrikRVSGACIQCSYGRCP 79

                           90
                   ....*....|....*.
gi 2029300282  348 TAFHVTCAQKAGLYMK 363
Cdd:cd15715     80 ASFHVTCAHAAGVLME 95
ePHD_ATX3_4_5_like cd15663
Extended PHD finger found in Arabidopsis thaliana ATX3, -4, -5, and similar proteins; The ...
 271-388 6.46e-26

Extended PHD finger found in Arabidopsis thaliana ATX3, -4, -5, and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of A. thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like proteins ATX3 (also termed protein SET domain group 14, or trithorax-homolog protein 3), ATX4 (also termed protein SET domain group 16, or trithorax-homolog protein 4) and ATX5 (also termed protein SET domain group 29, or trithorax-homolog protein 5), which belong to the histone-lysine methyltransferase family. These proteins show distinct phylogenetic origins from the family of ATX1 and ATX2. They are multi-domain proteins that consist of an N-terminal PWWP domain, a canonical PHD finger, this non-canonical extended PHD finger, and a C-terminal SET domain.


Pssm-ID: 277133  Cd Length: 112  Bit Score: 103.36  E-value: 6.46e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  271 CVLCPNKGGAFKKTD-DDRWGHVVCALWIPEVGFANTVFIEPIDGVRNIPPARWKLTCYLCKQKGvGACIQChkANCYTA 349
Cdd:cd15663      1 CCLCPVKGGALKPTDvEGLWVHVTCAWFRPEVCFKNEEKMEPAVGLLRIPLSTFLKACVICKQIH-GSCTQC--CKCATY 77

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 2029300282  350 FHVTCAQKAGLYMKMEPVKEltggGTTFSVRKTAYCDVH 388
Cdd:cd15663     78 FHAMCASRAGYHMELHCLEK----NGVQITRMVSYCSFH 112
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 569-652 2.15e-25

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 100.85  E-value: 2.15e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  569 LRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYR 648
Cdd:pfam00439    1 CLEILDKLMEHPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYK 80


                   ....
gi 2029300282  649 AAVR 652
Cdd:pfam00439   81 AAEK 84
ePHD_AF17 cd15709
Extended PHD finger found in protein AF-17 and similar proteins; The extended plant ...
 271-388 4.71e-25

Extended PHD finger found in protein AF-17 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of AF-17. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is encoded by gene AF17 that has been identified in hematological malignancies as a translocation partner of the mixed lineage leukemia gene MLL. It is a putative transcription factor that may play a role in multiple signaling pathways. It is involved in chromatin-mediated gene regulation mechanisms. It functions as a component of the multi-subunit Dot1 complex (Dotcom) and plays a role in the Wnt/Wingless signaling pathway. It also seems to be a downstream target of the beta-catenin/T-cell factor pathway, and participates in G2-M progression. Moreover, it may function as an important regulator of ENaC-mediated Na+ transport and thus blood pressure. AF-17 contains an N-terminal plant homeodomain (PHD) finger followed by a non-canonical ePHD finger.


Pssm-ID: 277179  Cd Length: 125  Bit Score: 101.29  E-value: 4.71e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  271 CVLCPNKGGAFKKTDDDRWGHVVCALWIPEVGFANTVFIEPIdGVRNIPPARWKLTCYLCKQKG------VGACIQCHKA 344
Cdd:cd15709      5 CELCPHKDGALKRTDNGGWAHVVCALYIPEVQFANVLTMEPI-VLQYVPHDRFNKTCYICEEQGreskaaSGACMTCNRH 83

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 2029300282  345 NCYTAFHVTCAQKAGLYMKmEPVKELTgggttfSVRKTAYCDVH 388
Cdd:cd15709     84 GCRQAFHVTCAQMAGLLCE-EEVLEVD------NVKYCGYCKYH 120
ePHD_JMJD2A cd15713
Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A); The ...
 271-363 7.69e-23

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: 94.65  E-value: 7.69e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  271 CVLCPNKGGAFKKTDDDRWGHVVCALWIPEVGFANTVFIEPIDgVRNIPPARWKLTCYLCK---QKGVGACIQCHKANCY 347
Cdd:cd15713      1 CCLCSLRGGALQRANDDKWVHVMCAVAVLEARFVNIAERSPVD-VSKIPLQRFKLKCIFCKkrrKRTAGCCVQCSHGRCP 79

                           90
                   ....*....|....*.
gi 2029300282  348 TAFHVTCAQKAGLYMK 363
Cdd:cd15713     80 TSFHASCAQAAGVMMQ 95
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
 569-652 1.43e-19

Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99942 [Multi-domain]  Cd Length: 112  Bit Score: 85.19  E-value: 1.43e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  569 LRSVLDQLQDKDPARI-FAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFY 647
Cdd:cd05510     12 LDKVLNELKTYTEHSTpFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYNSDPSHPL 91


                   ....*
gi 2029300282  648 RAAVR 652
Cdd:cd05510     92 RRHAN 96
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
 568-654 6.66e-19

Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99935  Cd Length: 97  Bit Score: 82.81  E-value: 6.66e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  568 LLRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFY 647
Cdd:cd05503      4 LCETILDEMEAHEDAWPFLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSEVG 83


                   ....*..
gi 2029300282  648 RAAVRLR 654
Cdd:cd05503     84 RAGHNMR 90
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
 567-653 1.04e-18

Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99936  Cd Length: 115  Bit Score: 82.83  E-value: 1.04e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  567 VLLRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVF 646
Cdd:cd05504     15 SALEQLLVEIVKHKDSWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHTSV 94


                   ....*..
gi 2029300282  647 YRAAVRL 653
Cdd:cd05504     95 YKAGTRL 101
Bromo_Brdt_II_like cd05498
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...
 582-655 1.06e-18

Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99930  Cd Length: 102  Bit Score: 82.33  E-value: 1.06e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2029300282  582 ARIFAQPV--SLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYRAAVRLRD 655
Cdd:cd05498     21 AWPFYKPVdpEALGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKLQD 96
PWWP smart00293
domain with conserved PWWP motif; conservation of Pro-Trp-Trp-Pro residues
 1056-1139 1.33e-18

domain with conserved PWWP motif; conservation of Pro-Trp-Trp-Pro residues


Pssm-ID: 214603 [Multi-domain]  Cd Length: 63  Bit Score: 80.85  E-value: 1.33e-18
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  1056 LEPLKVVWAKCSGYPSYPALIIDPKMPRVPghhngvtipappldvlkigeHMQTKSDEKLFLVLFFDNKRSwQWLPKSKM 1135
Cdd:smart00293    1 FKPGDLVWAKMKGFPWWPALVISPKMTPDN--------------------IMKRKSDENLYPVLFFGDKDT-AWIPSSKL 59


                    ....
gi 2029300282  1136 VPLG 1139
Cdd:smart00293   60 FPLT 63
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
 568-655 2.13e-17

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99932  Cd Length: 103  Bit Score: 78.89  E-value: 2.13e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  568 LLRSV--LDQLQDKDPARIFAQPVSLkEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTV 645
Cdd:cd05500      9 LLSSIrsLKRLKDARPFLVPVDPVKL-NIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNGPEHP 87

                           90
                   ....*....|
gi 2029300282  646 FYRAAVRLRD 655
Cdd:cd05500     88 VSQMGKRLQA 97
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
 565-676 8.94e-17

Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99943 [Multi-domain]  Cd Length: 112  Bit Score: 77.30  E-value: 8.94e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  565 LTVLLRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDT 644
Cdd:cd05511      1 LSFILDEIVNELKNLPDSWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDS 80

                           90       100       110
                   ....*....|....*....|....*....|..
gi 2029300282  645 VFYRAAVRLRDQGGVVLrqARREVDSIGLEEA 676
Cdd:cd05511     81 VYTKKAKEMLELAEELL--AEREEKLTQLEKN 110
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
 581-667 1.70e-15

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99946  Cd Length: 105  Bit Score: 73.49  E-value: 1.70e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  581 PARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYRAAVRLRDqggvV 660
Cdd:cd05515     23 LSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYNEPDSQIYKDALTLQK----V 98


                   ....*..
gi 2029300282  661 LRQARRE 667
Cdd:cd05515     99 LLETKRE 105
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
 571-653 4.71e-15

Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99938  Cd Length: 99  Bit Score: 71.98  E-value: 4.71e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  571 SVLDQLQDKDPARIFAQPVSLK--EVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYR 648
Cdd:cd05506      7 TLLRKLMKHKWGWVFNAPVDVValGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVHT 86


                   ....*
gi 2029300282  649 AAVRL 653
Cdd:cd05506     87 MAKEL 91
PWWP pfam00855
PWWP domain; The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain ...
 1061-1173 3.21e-14

PWWP domain; The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain binds to Histone-4 methylated at lysine-20, H4K20me, suggesting that it is methyl-lysine recognition motif. Removal of two conserved aromatic residues in a hydrophobic cavity created by this domain within the full-length protein, Pdp1, abolishes the interaction o f the protein with H4K20me3. In fission yeast, Set9 is the sole enzyme that catalyzes all three states of H4K20me, and Set9-mediated H4K20me is required for efficient recruitment of checkpoint protein Crb2 to sites of DNA damage. The methylation of H4K20 is involved in a diverse array of cellular processes, such as organizing higher-order chromatin, maintaining genome stability, and regulating cell-cycle progression.


Pssm-ID: 459964 [Multi-domain]  Cd Length: 92  Bit Score: 69.38  E-value: 3.21e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282 1061 VVWAKCSGYPSYPALIIDPKMPRVPGHHNgvtipappldvlkigehmqtKSDEKLFLVLFFDNKRSwQWLPKSKMVPLGI 1140
Cdd:pfam00855    3 LVWAKLKGYPWWPARVVDPEELPENVLKP--------------------KKKDGEYLVRFFGDSEF-AWVKPKDLKPFDE 61

                           90       100       110
                   ....*....|....*....|....*....|...
gi 2029300282 1141 DETIDKLKMMegRNSSIRKAVRIAFDRAMNHLS 1173
Cdd:pfam00855   62 GDEFEYLKKK--KKKKKKKAFKKALEEAEEALK 92
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 559-655 4.09e-14

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver


Pssm-ID: 99957  Cd Length: 112  Bit Score: 69.69  E-value: 4.09e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  559 ELRLtpltvLLRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMK 638
Cdd:cd05528      3 ELRL-----FLRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALE 77

                           90       100
                   ....*....|....*....|..
gi 2029300282  639 YNARD-----TVFYRAAvRLRD 655
Cdd:cd05528     78 YNPDRdpadkLIRSRAC-ELRD 98
ePHD_Snt2p_like cd15667
Extended PHD finger found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) ...
 271-388 4.93e-14

Extended PHD finger found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Snt2p. Sntp2 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 PHD fingers, a non-canonical ePHD finger, and a SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domain.


Pssm-ID: 277137  Cd Length: 141  Bit Score: 70.49  E-value: 4.93e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  271 CVLCPNKGG---------------AFKKTDDDRWGHVVCALWIPEVGFANTVFIEPIDGVRNIPPARWKLTCYLCKQKGv 335
Cdd:cd15667      1 CSLCNAKESnyelakkqsprtrpdALKCTSNGTWCHVLCALFNEDIKFGNSKSLQPILNTESVLLKGSRQKCEICKVSG- 79

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2029300282  336 GACIQCHKanCYTAFHVTCAQ---KAGLYMKMEPVKELTG--------GGTTFSVRKTAYCDVH 388
Cdd:cd15667     80 GGLVKCEV--CDDRFHVSCAQdtpGFKLGFKKEYLSDDTEnpfitdkvDNESYTLKPIIVCPKH 141
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
 571-655 5.90e-14

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99931  Cd Length: 102  Bit Score: 68.85  E-value: 5.90e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  571 SVLDQLQDK---DPARIFAQPVS--LKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTV 645
Cdd:cd05499      7 EVLKELMKPkhsAYNWPFLDPVDpvALNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTD 86

                           90
                   ....*....|
gi 2029300282  646 FYRAAVRLRD 655
Cdd:cd05499     87 VYMMGHQLEE 96
PHD_JADE cd15573
PHD finger found in proteins Jade-1, Jade-2, Jade-3, and similar proteins; This family ...
 216-261 8.45e-14

PHD finger found in proteins Jade-1, Jade-2, Jade-3, and similar proteins; This family includes proteins Jade-1 (PHF17), Jade-2 (PHF15), and Jade-3 (PHF16), each of which 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. 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 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: 277048 [Multi-domain]  Cd Length: 46  Bit Score: 66.66  E-value: 8.45e-14
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 2029300282  216 VCCICMDGECQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHC 261
Cdd:cd15573      1 VCDVCRSPDSEEGNEMVFCDKCNICVHQACYGIQKIPEGSWLCRTC 46
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 569-656 3.31e-13

Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99958  Cd Length: 128  Bit Score: 67.75  E-value: 3.31e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  569 LRSVLDQLQDKDP---ARIFAQPVSLK-EVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDT 644
Cdd:cd05529     29 LISGLDKLLLSLQleiAEYFEYPVDLRaWYPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEPNS 108

                           90
                   ....*....|..
gi 2029300282  645 VFYRAAVRLRDQ 656
Cdd:cd05529    109 EIAKKAKRLSDW 120
PHD_JADE1 cd15679
PHD finger found in protein Jade-1 and similar proteins; Jade-1, also termed PHD finger ...
 216-261 3.47e-13

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: 64.71  E-value: 3.47e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 2029300282  216 VCCICMDGECQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHC 261
Cdd:cd15679      1 VCDVCQSPDGEDGNEMVFCDKCNICVHQACYGILKVPEGSWLCRTC 46
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 584-650 8.37e-13

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 71.38  E-value: 8.37e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2029300282  584 IFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYRAA 650
Cdd:COG5076    168 IFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDA 234
Bromo_cbp_like cd05495
Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ...
 559-653 1.53e-12

Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99927  Cd Length: 108  Bit Score: 65.16  E-value: 1.53e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  559 ELRLTPLTVLLRsVLDQLQDKDPARIFAQPVSLkEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMK 638
Cdd:cd05495      3 ELRQALMPTLEK-LYKQDPESLPFRQPVDPKLL-GIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWL 80

                           90
                   ....*....|....*
gi 2029300282  639 YNARDTVFYRAAVRL 653
Cdd:cd05495     81 YNRKTSRVYKYCTKL 95
PHD_JADE3 cd15681
PHD finger found in protein Jade-3 and similar proteins; Jade-3, also termed PHD finger ...
 216-262 3.66e-12

PHD finger found in protein Jade-3 and similar proteins; Jade-3, also termed PHD finger protein 16 (PHF16), 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-3 is required for ING4 and ING5 to associate with histone acetyl transferase (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-3 contains a canonical Cys4HisCys3 PHD domain followed by a non-canonical extended PHD (ePHD) domain, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277151 [Multi-domain]  Cd Length: 50  Bit Score: 61.91  E-value: 3.66e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 2029300282  216 VCCICMDGECQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCL 262
Cdd:cd15681      1 ICDVCRSPDSEEGNDMVFCDKCNICVHQACYGILKVPEGSWLCRTCV 47
PHD_JADE2 cd15680
PHD finger found in protein Jade-2 and similar proteins; Jade-2, also termed PHD finger ...
 216-261 4.26e-12

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: 61.95  E-value: 4.26e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 2029300282  216 VCCICMDGECQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHC 261
Cdd:cd15680      1 VCDVCRSPEGEDGNEMVFCDKCNVCVHQACYGILKVPTGSWLCRTC 46
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
 580-653 8.04e-12

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99934 [Multi-domain]  Cd Length: 109  Bit Score: 63.08  E-value: 8.04e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2029300282  580 DPARIFAQPVSlKEVPDYLDHIKHPMDFATMRKRLE---AQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYRAAVRL 653
Cdd:cd05502     20 ELSLPFHEPVS-PSVPNYYKIIKTPMDLSLIRKKLQpksPQHYSSPEEFVADVRLMFKNCYKFNEEDSEVAQAGKEL 95
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
 585-644 1.22e-11

Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99937  Cd Length: 97  Bit Score: 62.17  E-value: 1.22e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  585 FAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDT 644
Cdd:cd05505     21 FREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGS 80
PHD_AF10_AF17 cd15574
PHD finger found in protein AF-10 and AF-17; This family includes protein AF-10 and AF-17. ...
 217-261 1.47e-11

PHD finger found in protein AF-10 and AF-17; This family includes protein AF-10 and AF-17. AF-10, also termed ALL1 (acute lymphoblastic leukemia)-fused gene from chromosome 10 protein, is a transcription factor encoded by gene AF10, a translocation partner of the MLL (mixed-lineage leukemia) oncogene in leukemia. AF-10 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. It plays a key role in the survival of uncommitted hematopoietic cells. Moreover, AF-10 functions as a follistatin-related gene (FLRG)-interacting protein. The interaction with FLRG enhances AF10-dependent transcription. It interacts with the human counterpart of the yeast Dot1, hDOT1L, and may act as a bridge for the recruitment of hDOT1L to the genes targeted by MLL-AF10. It also interacts with the synovial sarcoma associated SYT protein and may play a role in synovial sarcomas and acute leukemias. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is encoded by gene AF17 that has been identified in hematological malignancies as translocation partners of the mixed lineage leukemia gene MLL. It is a putative transcription factor that may play a role in multiple signaling pathways. It is involved in chromatin-mediated gene regulation mechanisms. It functions as a component of the multi-subunit Dot1 complex (Dotcom) and plays a role in the Wnt/Wingless signaling pathway. It also seems to be a downstream target of the beta-catenin/T-cell factor pathway, and participates in G2-M progression. Moreover, it may function as an important regulator of ENaC-mediated Na+ transport and thus blood pressure. Both AF-10 and AF-17 contain an N-terminal canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. The PHD finger is involved in their homo-oligomerization. In the C-terminal region, they possess a leucine zipper domain and a glutamine-rich region. This family also includes ZFP-1, the Caenorhabditis elegans AF10 homolog. It was originally identified as a factor promoting RNAi interference in C. elegans. It also acts as a Dot1-interacting protein that opposes H2B ubiquitination to reduce polymerase II (Pol II) transcription. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277049 [Multi-domain]  Cd Length: 48  Bit Score: 60.22  E-value: 1.47e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 2029300282  217 CCICMDGECQNSNVILFCD--MCNLAVHQECYGVPYIPEGQWLCRHC 261
Cdd:cd15574      2 CCVCSDERGWAENPLVYCDghGCNVAVHQACYGIVQVPTGPWFCRKC 48
Bromo_RACK7 cd05508
Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) ...
 565-650 3.96e-11

Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) was identified as a potential tumor suppressor genes, it shares domain architecture with BS69/ZMYND11; both have been implicated in the regulation of cellular proliferation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99940  Cd Length: 99  Bit Score: 60.86  E-value: 3.96e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  565 LTVLLRSVLDQLqdKDP-ARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARD 643
Cdd:cd05508      4 LSKLLKFALERM--KQPgAEPFLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYNGGD 81


                   ....*..
gi 2029300282  644 TVFYRAA 650
Cdd:cd05508     82 HKLTQAA 88
Bromo_WDR9_II cd05496
Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 575-640 2.00e-10

Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99928  Cd Length: 119  Bit Score: 59.39  E-value: 2.00e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2029300282  575 QLQDKDPariFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYN 640
Cdd:cd05496     19 DCEDSEP---FRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYT 81
PHD_2 pfam13831
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 228-261 2.19e-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: 463990 [Multi-domain]  Cd Length: 35  Bit Score: 56.58  E-value: 2.19e-10
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 2029300282  228 SNVILFCDMCNLAVHQECYGVPYIPEG-QWLCRHC 261
Cdd:pfam13831    1 TSPLVYCSKCSVQVHASCYGVPPIPDGdGWKCRRC 35
Bromo_Brdt_I_like cd05497
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...
 565-640 3.00e-10

Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99929  Cd Length: 107  Bit Score: 58.59  E-value: 3.00e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2029300282  565 LTVLLRSVLDQLQDKDPARIFAQPVSLK--EVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYN 640
Cdd:cd05497      6 LQYLLKVVLKALWKHKFAWPFQQPVDAVklNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYN 83
PHD_ATX3_4_5_like cd15495
PHD finger found in Arabidopsis thaliana histone-lysine N-methyltransferase arabidopsis ...
 217-261 3.22e-10

PHD finger found in Arabidopsis thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like protein ATX3, ATX4, ATX5, and similar proteins; The family includes A. thaliana ATX3 (also termed protein SET domain group 14, or trithorax-homolog protein 3), ATX4 (also termed protein SET domain group 16, or trithorax-homolog protein 4) and ATX5 (also termed protein SET domain group 29, or trithorax-homolog protein 5), which belong to the histone-lysine methyltransferase family. They show distinct phylogenetic origins from the ATX1 and ATX2 family. They are multi-domain containing proteins that consist of an N-terminal PWWP domain, a canonical Cys4HisCys3 plant homeodomain (PHD) finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a C-terminal SET domain; this model corresponds to the Cys4HisCys3 canonical PHD finger.


Pssm-ID: 276970 [Multi-domain]  Cd Length: 47  Bit Score: 56.61  E-value: 3.22e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 2029300282  217 CCICMDGECQNSNVILFCDMCNLAVHQECYGVPYI-PEGQWLCRHC 261
Cdd:cd15495      2 CAVCNEGEDDDNNPLITCNRCQISVHQKCYGIREVdPDGSWVCRAC 47
Bromo_SNF2 cd05519
Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in ...
 584-655 3.72e-10

Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99950  Cd Length: 103  Bit Score: 58.12  E-value: 3.72e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2029300282  584 IFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYRAAVRLRD 655
Cdd:cd05519     26 LFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYNQEGSIVYEDAVEMEK 97
ePHD2_KMT2C_like cd15666
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
 271-388 8.11e-10

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: 57.31  E-value: 8.11e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  271 CVLCPNKG-------GAFKKTDDDRWGHVVCALWIPEVgfantvfIEPIDG-VRNIPPA---RWKLTCYLCKQkgVGACI 339
Cdd:cd15666      1 CVLCGGEGdgdtdgpGRLLNLDVDKWVHLNCALWSYEV-------YETQNGaLMNVEEAlrrALTTTCSHCGR--TGATV 71

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 2029300282  340 QCHKANCYTAFHVTCAQKAglymkmepvkeltggGTTFSVRKTAYCDVH 388
Cdd:cd15666     72 PCFKPRCANVYHLPCAIKD---------------GCMFFKDKTMLCPSH 105
Bromo_SNF2L2 cd05516
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ...
 582-647 2.33e-09

Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99947  Cd Length: 107  Bit Score: 55.90  E-value: 2.33e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2029300282  582 ARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFY 647
Cdd:cd05516     25 AEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTFNLEGSLIY 90
PHD1_MTF2_PHF19_like cd15499
PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ...
 216-262 3.41e-09

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: 53.66  E-value: 3.41e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2029300282  216 VCCICMDGECQNSNVILFCDMCNLAVHQECY-----GVPYIPEGQWLCRHCL 262
Cdd:cd15499      1 TCSICGGAEARDGNEILICDKCDKGYHQLCHspkvrTSPLEGDEKWFCSRCV 52
Bromo_Rsc1_2_I cd05521
Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 592-653 4.50e-09

Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99952  Cd Length: 106  Bit Score: 55.02  E-value: 4.50e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2029300282  592 KEVPDYLDHIKHPMDFATMRKRLeaQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYRAAVRL 653
Cdd:cd05521     35 KDYPDYYKIIKNPLSLNTVKKRL--PHYTNAQEFVNDLAQIPWNARLYNTKGSVIYKYALIL 94
PWWP cd05162
PWWP (Pro-Trp-Trp-Pro) domain; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, ...
 1061-1164 4.62e-09

PWWP (Pro-Trp-Trp-Pro) domain; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids and is composed of a five-stranded antiparallel beta-barrel followed by a helical region. It is found in numerous proteins that are involved in cell division, growth, and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes. PWWP domains specifically recognize DNA and histone methylated lysines at the level of the nucleosome. Based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes. Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors.


Pssm-ID: 438958 [Multi-domain]  Cd Length: 86  Bit Score: 54.43  E-value: 4.62e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282 1061 VVWAKCSGYPSYPALIIDPKmprvpghhngvtipappldvlKIGEHMQTKSDEKLFLVLFFDNkRSWQWLPKSKMVPLgi 1140
Cdd:cd05162      3 LVWAKLKGYPWWPARVVDPE---------------------ELPEEVGKKKKKGGVLVQFFGD-NDYAWVKSKNIKPF-- 58

                           90       100
                   ....*....|....*....|....*
gi 2029300282 1141 DETIDKLKMMEGRNS-SIRKAVRIA 1164
Cdd:cd05162     59 EEGFKKEFKKKKKKSkKFKKAVEEA 83
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
 590-655 5.25e-09

Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99951  Cd Length: 103  Bit Score: 54.65  E-value: 5.25e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2029300282  590 SLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYRAAVRLRD 655
Cdd:cd05520     32 SKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPNSRIYKDAEKLQK 97
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
 581-650 5.76e-09

Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99949 [Multi-domain]  Cd Length: 103  Bit Score: 54.76  E-value: 5.76e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  581 PARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYRAA 650
Cdd:cd05518     23 LCDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYNEEGSQVYEDA 92
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 216-261 9.92e-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: 52.21  E-value: 9.92e-09
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*....
gi 2029300282   216 VCCICmdGECQNSNVILFCDMCNLAVHQECYGVPY---IPEGQWLCRHC 261
Cdd:smart00249    1 YCSVC--GKPDDGGELLQCDGCDRWYHQTCLGPPLleeEPDGKWYCPKC 47
Bromo_ASH1 cd05525
Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the ...
 590-655 1.31e-08

Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99955 [Multi-domain]  Cd Length: 106  Bit Score: 53.93  E-value: 1.31e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2029300282  590 SLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYRAAVRLRD 655
Cdd:cd05525     34 SKKKNPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYYGRKSPIGRDVCRLRK 99
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
 595-670 1.73e-08

Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99954 [Multi-domain]  Cd Length: 113  Bit Score: 53.49  E-value: 1.73e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2029300282  595 PDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYRAAVRLRDqggvVLRQARREVDS 670
Cdd:cd05524     39 PEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYKPDSPEHKDACKLWE----LFLSARNEVLS 110
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 592-653 8.55e-08

Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99953 [Multi-domain]  Cd Length: 104  Bit Score: 51.47  E-value: 8.55e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2029300282  592 KEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYRAAVRL 653
Cdd:cd05522     35 AREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYKDAVLL 96
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 216-261 8.56e-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: 49.62  E-value: 8.56e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 2029300282  216 VCCICMDGeCQNSNVILFCDMCNLAVHQECYGVPY---IPEGQWLCRHC 261
Cdd:cd15489      1 SCIVCGKG-GDLGGELLQCDGCGKWFHADCLGPPLssfVPNGKWICPVC 48
Bromo_brd8_like cd05507
Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with ...
 568-655 8.57e-08

Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99939  Cd Length: 104  Bit Score: 51.21  E-value: 8.57e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  568 LLRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFY 647
Cdd:cd05507      7 AILLVYRTLASHRYASVFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNSSDHDVY 86


                   ....*...
gi 2029300282  648 RAAVRLRD 655
Cdd:cd05507     87 LMAVEMQR 94
PHD_Phf1p_Phf2p_like cd15502
PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 ...
 216-261 9.25e-08

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: 49.74  E-value: 9.25e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2029300282  216 VCCICMDGECQNSNVILFCDMCNLAVHQECYGvPYI-------PEGQWLCRHC 261
Cdd:cd15502      1 VCIVCQRGHSPKSNRIVFCDGCNTPYHQLCHD-PSIddevvedPDAEWFCKKC 52
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 216-264 1.01e-07

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: 49.41  E-value: 1.01e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2029300282  216 VCCICmdGECQNSNVILFCDMCNLAVHQECYGVPY----IPEGQWLCRHCLQS 264
Cdd:pfam00628    1 YCAVC--GKSDDGGELVQCDGCDDWFHLACLGPPLdpaeIPSGEWLCPECKPK 51
PHD1_MTF2 cd15578
PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also ...
 216-263 1.56e-07

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: 48.93  E-value: 1.56e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2029300282  216 VCCICMDGECQNSNVILFCDMCNLAVHQECYgVPYI------PEGQWLCRHCLQ 263
Cdd:cd15578      1 VCTVCQDGSSESPNEIVLCDKCGQGYHQLCH-NPKIdssvldPDVPWLCRQCVF 53
PHD2_PHF10 cd15529
PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
 216-261 3.07e-07

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: 48.07  E-value: 3.07e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 2029300282  216 VCCICMDGecQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHC 261
Cdd:cd15529      1 TCTKCGDP--HDEDKMMFCDQCDRGYHTFCVGLRSIPDGRWICPLC 44
Bromo_ZMYND11 cd05492
Bromodomain; ZMYND11_like sub-family. ZMYND11 or BS69 is a ubiquitously expressed nuclear ...
 565-650 2.35e-06

Bromodomain; ZMYND11_like sub-family. ZMYND11 or BS69 is a ubiquitously expressed nuclear protein that has been shown to associate with chromatin. It interacts with chromatin remodeling factors and might play a role in chromatin remodeling and gene expression. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99924  Cd Length: 109  Bit Score: 47.38  E-value: 2.35e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  565 LTVLLRSVLDQLQDKDPARIFAQPVSLKEVPDYLDHIK------HPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMK 638
Cdd:cd05492      1 LNCLLKFIVSRMKSWLPPDTTNRAIVLNKRGKATKLPKrrrlihTHLDVADIQEKINSEKYTSLEEFKADALLLLHNTAI 80

                           90
                   ....*....|..
gi 2029300282  639 YNARDTVFYRAA 650
Cdd:cd05492     81 FHGADSEQYDAA 92
ePHD_KMT2A_like cd15664
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); The ...
 271-358 2.75e-06

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: 47.01  E-value: 2.75e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  271 CVLC-------PNKGGAFKKTDDDRWGHVVCALWIPEVgfantvfIEPIDGV-RNIPPA--RWK-LTCYLCKQKG--VGA 337
Cdd:cd15664      1 CALCgvygddePNDAGRLLYCGQDEWVHINCALWSAEV-------FEEDDGSlQNVHSAvsRGRmMKCELCGKPGatVGC 73

                           90       100
                   ....*....|....*....|.
gi 2029300282  338 CIQchkaNCYTAFHVTCAQKA 358
Cdd:cd15664     74 CLK----SCPANYHFMCARKA 90
PHD_PRHA_like cd15504
PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and ...
 216-261 3.80e-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: 45.12  E-value: 3.80e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2029300282  216 VCCICMDGECQNSNVILFCD-MCNLAVHQECYGVPYIPE------GQWLCRHC 261
Cdd:cd15504      1 FCAKCQSGEASPDNDILLCDgGCNRAYHQKCLEPPLLTEdippedEGWLCPLC 53
PWWP_ScIOC4-like cd05840
PWWP domain found in Saccharomyces cerevisiae ISWI one complex protein 4 (ScIOC4) and similar ...
 1061-1166 4.21e-06

PWWP domain found in Saccharomyces cerevisiae ISWI one complex protein 4 (ScIOC4) and similar proteins; ScIOC4 functions as a component of the ISW1B complex, which acts in remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA. The ISW1B complex acts within coding regions to control the amount of RNA polymerase II released into productive elongation and to coordinate elongation with termination and pre-mRNA processing. The family also includes Schizosaccharomyces pombe PWWP domain-containing proteins 1 and 2 (SpPDP1 and SpPDP2). SpPDP1 associates with Set9 to regulate its chromatin localization and methyltransferase activity towards H4K20. Members of this family contain a PWWP domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438965  Cd Length: 94  Bit Score: 46.14  E-value: 4.21e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282 1061 VVWAKCSGYPSYPALIIDPKMprvpghhngvtIPAPPLDVLKigehMQTKSDEKLFLVLFFDNKrSWQWLPKSKMVPLGI 1140
Cdd:cd05840      3 LVLAKVKGYPPWPAMVLPEEL-----------LPKNVLKAKK----RKPKSKKTVYPVQFFPDN-EYYWVSPSSLKPLTK 66

                           90       100
                   ....*....|....*....|....*.
gi 2029300282 1141 DETIDKLKMMEGRNSSIRKAVRIAFD 1166
Cdd:cd05840     67 EEIDKFLSKSKRKNKDLIEAYEVALE 92
PHD_ATX1_2_like cd15494
PHD finger found in Arabidopsis thaliana histone-lysine N-methyltransferase arabidopsis ...
 216-261 4.39e-06

PHD finger found in Arabidopsis thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like protein ATX1, ATX2, and similar proteins; The family includes A. thaliana ATX1 and ATX2, both of which are sister paralogs originating from a segmental chromosomal duplication. They are plant counterparts of the Drosophila melanogaster trithorax (TRX) and mammalian mixed-lineage leukemia (MLL1) proteins. ATX1, also termed protein SET domain group 27, or trithorax-homolog protein 1 (TRX-homolog protein 1), is a methyltransferase that trimethylates histone H3 at lysine 4 (H3K4me3). It also acts as a histone modifier and as a positive effector of gene expression. ATX1regulates transcription from diverse classes of genes implicated in biotic and abiotic stress responses. It is involved in dehydration stress signaling in both abscisic acid (ABA)-dependent and ABA-independent pathways. ATX2, also termed protein SET domain group 30, or trithorax-homolog protein 2 (TRX-homolog protein 2), is involved in dimethylating histone H3 at lysine 4 (H3K4me2). Both ATX1 and ATX2 are multi-domain containing proteins that consist of an N-terminal PWWP domain, FYRN- and FYRC (DAST, domain associated with SET in trithorax) domains, a canonical Cys4HisCys3 plant homeodomain (PHD) finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a C-terminal SET domain; this model corresponds to the Cys4HisCys3 canonical PHD finger.


Pssm-ID: 276969  Cd Length: 47  Bit Score: 44.75  E-value: 4.39e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 2029300282  216 VCCICMDGECQNSNVILFCDMCNLAVHQECYGVPYIPEGQ-WLCRHC 261
Cdd:cd15494      1 KCSVCGEDEEYEDNLLLQCDKCRMMVHMRCYGVLEPPPGAlWLCNLC 47
PHD2_Snt2p_like cd15498
PHD finger 2 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and ...
 216-261 8.12e-06

PHD finger 2 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and similar proteins; This group corresponds to 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 second canonical Cys4HisCys3 PHD finger.


Pssm-ID: 276973  Cd Length: 55  Bit Score: 44.39  E-value: 8.12e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2029300282  216 VCCICMDGECQNSNVILFCDMCNLAVHQECYGVpYIPE----------GQWLCRHC 261
Cdd:cd15498      1 KCSVCSEQFASNFNTSLSCYNCGLNVHASCYGI-TVPGkmnkvknlksYKWLCDPC 55
ePHD_KMT2A cd15693
Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A); The extended plant ...
 271-357 8.39e-06

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: 46.15  E-value: 8.39e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  271 CVLCPNKGGafKKTDD---------DRWGHVVCALWIPEVgfantvfIEPIDG-VRNIPPA--RWK-LTCYLCKQkgVGA 337
Cdd:cd15693      3 CALCLKYGD--DSANDagrllyigqNEWTHVNCALWSAEV-------FEDDDGsLKNVHMAviRGKqLRCEFCQK--PGA 71

                           90       100
                   ....*....|....*....|
gi 2029300282  338 CIQCHKANCYTAFHVTCAQK 357
Cdd:cd15693     72 TVGCCLTSCTSNYHFMCSRA 91
PHD_RSF1 cd15543
PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV ...
 217-261 1.12e-05

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: 43.41  E-value: 1.12e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 2029300282  217 CCICmdGECQNSNVILFCDMCNLAVHQECYGVP--YIPEGQWLCRHC 261
Cdd:cd15543      2 CRKC--GLSDHPEWILLCDRCDAGYHTACLRPPlmIIPDGNWFCPPC 46
ePHD_RAI1_like cd15668
Extended PHD finger found in retinoic acid-induced protein 1 (RAI1), transcription factor 20 ...
 271-362 1.53e-05

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: 44.99  E-value: 1.53e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  271 CVLCpnKGGAFKKTDDD-------RWGHVVCALWIPEVGFANTVFIEPIDGVRNippARwKLTCYLCKQKGvgACIQCHK 343
Cdd:cd15668      1 CVFC--KRGPHYKGLGDlfgpyyeVWVHEDCAVWAPGVYLVGGKLYGLEEAVWV---AK-QSVCSSCQQTG--ATIGCLH 72

                           90
                   ....*....|....*....
gi 2029300282  344 ANCYTAFHVTCAQKAGLYM 362
Cdd:cd15668     73 KGCKAKYHYPCAVESGCQL 91
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
 217-261 2.53e-05

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: 42.36  E-value: 2.53e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 2029300282  217 CCICmdGECQNSNVILFCDMCNLAVHQECYG--VPYIPEGQWLCRHC 261
Cdd:cd15527      2 CSVC--QDSGNADNLLFCDACDKGFHMECHDppLTRMPKGKWVCQIC 46
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
 583-640 3.58e-05

Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99948  Cd Length: 103  Bit Score: 43.97  E-value: 3.58e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2029300282  583 RIFAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYN 640
Cdd:cd05517     25 ELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFN 82
PHD4_NSD cd15567
PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
 217-261 8.51e-05

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: 41.08  E-value: 8.51e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 2029300282  217 CCICMDGecqnsNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHC 261
Cdd:cd15567      2 CFICSEG-----GSLICCESCPASFHPECLGLEPPPEGKFYCEDC 41
PHD1_PHF14 cd15561
PHD finger 1 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
 216-248 1.15e-04

PHD finger 1 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 first PHD finger.


Pssm-ID: 277036  Cd Length: 56  Bit Score: 40.88  E-value: 1.15e-04
                           10        20        30
                   ....*....|....*....|....*....|...
gi 2029300282  216 VCCICMDGECQNSNVILFCDMCNLAVHQECYGV 248
Cdd:cd15561      1 ICCVCLGDRSNDADEIIECDKCGISVHEGCYGV 33
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
 217-261 1.53e-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: 40.13  E-value: 1.53e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 2029300282  217 CCICMDGecqnsNVILFCDMCNLAVHQECYGVP--YIPEGQWLCRHC 261
Cdd:cd15539      2 CAVCGDG-----GELLCCDGCPRAFHLACLVPPltLIPSGTWRCSSC 43
PHD_UHRF2 cd15617
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); ...
 217-261 2.33e-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: 39.94  E-value: 2.33e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 2029300282  217 CCICmdGECQNSNVILFCDMCNLAVHQECYGVPY--IPEGQ-WLCRHC 261
Cdd:cd15617      2 CYVC--GGKQDAHMQLLCDECNMAYHIYCLNPPLdkIPEDEdWYCPSC 47
ePHD_KMT2B cd15694
Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B); The extended plant ...
 271-356 3.03e-04

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: 41.18  E-value: 3.03e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282  271 CVLC-------PNKGGAFKKTDDDRWGHVVCALWIPEvgfantVFIEPIDGVRNIPPARWK---LTCYLCKQkgVGACIQ 340
Cdd:cd15694      1 CALClkygdadSKDAGRLLYIGQNEWTHVNCAIWSAE------VFEENDGSLKNVHAAVARgrqMRCEHCQK--IGATVG 72

                           90
                   ....*....|....*.
gi 2029300282  341 CHKANCYTAFHVTCAQ 356
Cdd:cd15694     73 CCLSACLSNFHFMCAR 88
PHD_BAZ2A_like cd15545
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B ...
 217-261 3.46e-04

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: 39.22  E-value: 3.46e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 2029300282  217 CCICMDGEcqNSNVILFCDMCNLAVHQECYG--VPYIPEGQWLCRHC 261
Cdd:cd15545      2 CQICRSGD--NEDQLLLCDGCDRGYHTYCFKpkMTNVPEGDWFCPEC 46
PWWP_MSH6 cd05837
PWWP domain found in DNA mismatch repair protein MSH6 and similar proteins; MSH6, also called ...
 1057-1170 7.81e-04

PWWP domain found in DNA mismatch repair protein MSH6 and similar proteins; MSH6, also called G/T mismatch-binding protein (GTBP or GTMBP), MutS protein homolog 6, or MutS-alpha 160 kDa subunit (p160), is a mismatch repair protein homologous to bacterial MutS. It is a component of the post-replicative DNA mismatch repair system (MMR). It heterodimerizes with MSH2 to form MutS alpha, which binds to DNA mismatches thereby initiating DNA repair. When bound, MutS alpha bends the DNA helix and shields approximately 20 base pairs, and recognizes single base mismatches and dinucleotide insertion-deletion loops (IDL) in the DNA. After mismatch binding, it forms a ternary complex with the MutL alpha heterodimer, which is thought to be responsible for directing the downstream MMR events, including strand discrimination, excision, and resynthesis. Mutations in MSH6 have been linked to increased cancer susceptibility, particularly in hereditary nonpolyposis colorectal cancer in humans. MSH6 contains a PWWP domain, but its role in MSH6 remains unclear. MSH6 orthologs found in Saccharomyces cerevisiae, Caenorhabditis elegans, and Arabidopsis thaliana lack the PWWP domain. PWWP domains typically recognize DNA and histone methylated lysines.


Pssm-ID: 438962  Cd Length: 103  Bit Score: 39.96  E-value: 7.81e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2029300282 1057 EPLKVVWAKCSGYPSYPALIID-PKMprvpGHHNGvtipapPLDVLKIgeHMQtksdeklflvlFFDNKRSWQWLPKS-- 1133
Cdd:cd05837      2 SPGDLVWAKLEGYPWWPSLVCNhPTT----GFHKK------FGKKGEV--HVQ-----------FFDDPPSRAWVKAKnv 58

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 2029300282 1134 KMVPLGIDETIDKLKMMEGRNSSIRKAVRIAfDRAMN 1170
Cdd:cd05837     59 KPFTGSDDKEFQKGGMFFSKDPKWKKAVKEA-DKALK 94
PHD_PHRF1 cd15536
PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also ...
 217-261 7.96e-04

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: 38.16  E-value: 7.96e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 2029300282  217 CCICmdGECQNSNVILFCDMCNLAVHQECYGVP--YIPEGQWLCRHC 261
Cdd:cd15536      2 CEVC--GRSDREDRLLLCDGCDAGYHMECLTPPldEVPIEEWFCPEC 46
PHD1_PHF1 cd15500
PHD finger 1 found in PHD finger protein1 (PHF1); PHF1, also termed polycomb-like protein 1 ...
 216-261 8.10e-04

PHD finger 1 found in PHD finger protein1 (PHF1); PHF1, also termed polycomb-like protein 1 (PCL1), together with JARID2 and AEBP2, associates with the polycomb repressive complex 2 (PRC2), which is the major H3K27 methyltransferase that regulates pluripotency, differentiation, and tumorigenesis through catalysis of histone H3 lysine 27 trimethylation (H3K27me3) on chromatin. PHF1 is essential in epigenetic regulation and genome maintenance. It acts as a dual reader of Lysine trimethylation at Lysine 36 of Histone H3 and Lysine 27 of Histone variant H3t. PHF1 consists of an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. Its Tudor domain selectively binds to histone H3K36me3. Moreover, PHF1 is required for efficient H3K27me3 and Hox gene silencing. It can mediate deposition of the repressive H3K27me3 mark and acts as a cofactor in early DNA-damage response. This model corresponds to the first PHD finger.


Pssm-ID: 276975  Cd Length: 51  Bit Score: 38.66  E-value: 8.10e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2029300282  216 VCCICMDGECQNSNVILFCDMCNLAVHQECYgVPYIPE------GQWLCRHC 261
Cdd:cd15500      1 ICCVCDSETVSPKNPLVNCEKCHHAYHQECH-VPRVPLesagdgDSWMCRQC 51
PHD1_Lid2p_like cd15519
PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
 216-261 1.67e-03

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: 37.45  E-value: 1.67e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 2029300282  216 VCCICmdGECQNSNVILFCDMCNLAVHQECYGVP--YIPEGQWLCRHC 261
Cdd:cd15519      1 GCEVC--GLDDNEGEVLLCDGCDAEYHTSCLDPPlgEIPPGTWFCPSC 46
PHD2_d4 cd15530
PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three ...
 217-261 2.01e-03

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: 37.36  E-value: 2.01e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 2029300282  217 CCICmdGECQNSNVILFCDMCNLAVHQECYGVPYI--PEGQWLCRHC 261
Cdd:cd15530      2 CSLC--GTSENDDQLLFCDDCDRGYHMYCLSPPMSepPEGSWSCHLC 46
PHD1_PHF19 cd15579
PHD finger 1 found in PHD finger protein 19 (PHF19); PHF19, also termed Polycomb-like protein ...
 217-262 2.23e-03

PHD finger 1 found in PHD finger protein 19 (PHF19); PHF19, also termed Polycomb-like protein 3 (PCL3), is a component of the polycomb repressive complex 2 (PRC2), which is the major H3K27 methyltransferase that regulates pluripotency, differentiation, and tumorigenesis through catalysis of histone H3 lysine 27 trimethylation (H3K27me3) on chromatin. PHF19 consists of an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. It binds trimethylated histone H3 Lys36 (H3K36me3) through its Tudor domain and recruits the PRC2 complex and the H3K36me3 demethylase NO66 to embryonic stem cell genes during differentiation. Moreover, PHF19 and its upstream regulator, Akt, play roles in the phenotype switch of melanoma cells from proliferative to invasive states. This model corresponds to the first PHD finger.


Pssm-ID: 277054  Cd Length: 53  Bit Score: 37.17  E-value: 2.23e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2029300282  217 CCICMDGECQNSNVILFCDMCNLAVHQECYgVPYIPEGQ------WLCRHCL 262
Cdd:cd15579      2 CNVCLGKSSGPLNEILICGKCGLGYHQQCH-IPVVDSSDdppltpWFCRRCI 52
PHD_Int12 cd15501
PHD finger found in integrator complex subunit 12 (Int12) and similar proteins; Int12, also ...
 216-261 2.28e-03

PHD finger found in integrator complex subunit 12 (Int12) and similar proteins; Int12, also termed IntS12, or PHD finger protein 22, is a component of integrator, a multi-protein mediator of small nuclear RNA processing. The integrator complex directly interacts with the C-terminal domain of RNA polymerase II (RNAPII) largest subunit and mediates the 3' end processing of small nuclear RNAs (snRNAs) U1 and U2. Different from other components of integrator, Int12 contains a PHD finger, which is not required for snRNA 3' end cleavage. Instead, Int12 harbors a small microdomain at its N-terminus which is necessary and sufficient for Int12 function; this microdomain facilitates Int12 binding to Int1 and promotes snRNA 3' end formation.


Pssm-ID: 276976  Cd Length: 52  Bit Score: 37.32  E-value: 2.28e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2029300282  216 VCCICMDGECQNSNVILFCDMCNLAVHQECYgVPYIPEGQ-------WLCRHC 261
Cdd:cd15501      1 SCVVCKQMDVTSGNQLVECQECHNLYHQECH-KPPVTDKDvndprlvWYCSRC 52
PHD1_KDM5A_like cd15515
PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar ...
 216-261 2.79e-03

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: 36.99  E-value: 2.79e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 2029300282  216 VCCICMDGEcqNSNVILFCDMCNLAVHQECY--GVPYIPEGQWLCRHC 261
Cdd:cd15515      1 ICQVCGRGD--DEDKLLLCDGCDDSYHTFCLipPLPDIPPGDWRCPKC 46
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 585-655 3.04e-03

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 41.33  E-value: 3.04e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2029300282  585 FAQPVSLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARDTVFYRAAVRLRD 655
Cdd:COG5076    284 FLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVRDAKLFFDNCVMYNGEVTDYYKNANVLED 354
PHD_BAZ2A cd15629
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also ...
 217-262 4.14e-03

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: 36.37  E-value: 4.14e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 2029300282  217 CCICMDGEcqNSNVILFCDMCNLAVHQECY--GVPYIPEGQWLCRHCL 262
Cdd:cd15629      2 CLVCRKGD--NDEYLLLCDGCDRGCHMYCHrpKMLQVPEGDWFCPNCV 47
PHD_BAZ2B cd15630
PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also ...
 217-262 4.77e-03

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: 36.10  E-value: 4.77e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 2029300282  217 CCICMDGEcqNSNVILFCDMCNLAVHQECY--GVPYIPEGQWLCRHCL 262
Cdd:cd15630      3 CQICRKGD--NEELLLLCDGCDKGCHTYCHrpKITTIPEGDWFCPACI 48
Bromo_SP100C_like cd05501
Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major ...
 596-643 4.85e-03

Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major component of PML-SP100 nuclear bodies (NBs), which are poorly understood. It is covalently modified by SUMO-1 and may play a role in processes at the chromatin level. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99933  Cd Length: 102  Bit Score: 37.79  E-value: 4.85e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 2029300282  596 DYLDHIKHPMDFATMRKRLEAQGYKNLHEFEEDFDLIIDNCMKYNARD 643
Cdd:cd05501     32 DYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKDD 79
PHD_JMJD2 cd15493
PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone demethylases; ...
 217-261 5.09e-03

PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone demethylases; 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 only three JMJD2 proteins, JMJD2A-C, which all contain jmjN and jmjC domains in the N-terminal region, followed by a Cys4HisCys3 canonical PHD finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, 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. This model corresponds to the Cys4HisCys3 canonical PHD finger.


Pssm-ID: 276968  Cd Length: 42  Bit Score: 35.75  E-value: 5.09e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 2029300282  217 CCICMDGEcqnsnvILFCDMCNLAVHQECYGVPYIPE--GQWLCRHC 261
Cdd:cd15493      2 CAICSLFR------LLVCSRCCVCVHASCYGVPDIPGdgEGWKCDRC 42
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
 225-261 5.30e-03

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: 36.04  E-value: 5.30e-03
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 2029300282  225 CQNSNVILFCDMCNLAVHQECYG--VPYIPEGQWLCRHC 261
Cdd:cd15531      5 CQQGGEIILCDTCPRAYHLVCLDpeLEKAPEGKWSCPHC 43
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 326-360 5.42e-03

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: 36.04  E-value: 5.42e-03
                            10        20        30
                    ....*....|....*....|....*....|....*.
gi 2029300282   326 TCYLCKQKGV-GACIQCHKanCYTAFHVTCAQKAGL 360
Cdd:smart00249    1 YCSVCGKPDDgGELLQCDG--CDRWYHQTCLGPPLL 34
PHD_PHF21A cd15523
PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC ...
 224-261 5.54e-03

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: 35.83  E-value: 5.54e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 2029300282  224 ECQNSNVILFCDMCNLAVHQECYGVP--YIPEGQWLCRHC 261
Cdd:cd15523      4 VCRKSGELLMCDTCSLVYHLDCLDPPlkTIPKGMWICPKC 43
ePHD2_KMT2C cd15697
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 285-358 6.20e-03

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: 37.72  E-value: 6.20e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2029300282  285 DDDRWGHVVCALWIPEVgfantvFIEPIDGVRNIPPARWK---LTCYLCKQkgVGACIQCHKANCYTAFHVTCAQKA 358
Cdd:cd15697     22 DLDLWVHLNCALWSTEV------YETQAGALINVELALRRglqMKCVFCHK--TGATSGCHRLRCTNVYHFTCAIKA 90
Bromodomain_1 cd05494
Bromodomain; uncharacterized subfamily. Bromodomains are found in many chromatin-associated ...
 578-625 6.64e-03

Bromodomain; uncharacterized subfamily. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.


Pssm-ID: 99926 [Multi-domain]  Cd Length: 114  Bit Score: 37.81  E-value: 6.64e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 2029300282  578 DKDPariFAQPV--SLKEVPDYLDHIKHPMDFATMRKRLEAQGYKNLHEF 625
Cdd:cd05494     20 DAWP---FLEPVnpPRRGAPDYRDVIKRPMSFGTKVNNIVETGARDLEDL 66
PHD1_KDM5A cd15602
PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone ...
 216-262 7.19e-03

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: 35.70  E-value: 7.19e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 2029300282  216 VCCICMDGECQNSnvILFCDMCNLAVHQECY--GVPYIPEGQWLCRHCL 262
Cdd:cd15602      1 VCLFCGRGNNEDK--LLLCDGCDDSYHTFCLipPLPDVPKGDWRCPKCV 47
PHD4_NSD1 cd15656
PHD finger 4 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1); NSD1, ...
 225-261 7.45e-03

PHD finger 4 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1); NSD1, also termed H3 Lysine-36 and H4 Lysine-20 specific histone-lysine N-methyltransferase, or androgen receptor coactivator 267 kDa protein, or androgen receptor-associated protein of 267 kDa, or H3-K36-HMTase H4-K20-HMTase, or Lysine N-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein, is a lysine methyltransferase that preferentially methylates H3 on Lysine36 (H3-K36) and H4 on Lysine20 (H4-K20), which is primarily associated with active transcription. It plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. It can alter transcription by interacting with the protein NSD1-interacting zinc finger protein 1 (NIZP1). It also mitigates caspase-1 activation by listeriolysin o (LLO) in macrophages, and requires functional LLO for the regulation of IL-1beta secretion. Moreover, NSD1 regulates RNA polymerase II (RNAP II) recruitment to bone morphogenetic protein 4 (BMP4). NSD1 contains 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). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the fourth PHD finger.


Pssm-ID: 277126  Cd Length: 40  Bit Score: 35.38  E-value: 7.45e-03
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 2029300282  225 CQNSNVILFCDMCNLAVHQECYGVPyIPEGQWLCRHC 261
Cdd:cd15656      5 CSEGGSLLCCESCPAAFHRECLNID-MPEGSWYCNDC 40
PHD_JMJD2B cd15576
PHD finger found in Jumonji domain-containing protein 2B (JMJD2B); JMJD2B, also termed ...
 228-261 9.22e-03

PHD finger found in Jumonji domain-containing protein 2B (JMJD2B); JMJD2B, also termed lysine-specific demethylase 4B (KDM4B), or JmjC domain-containing histone demethylation protein 3B (JHDM3B), specifically antagonizes the trimethyl group from H3K9 in pericentric heterochromatin and reduces H3K36 methylation in mammalian cells. It plays an essential role in the growth regulation of cancer cells by modulating the G1-S transition and promotes cell-cycle progression through the regulation of cyclin-dependent kinase 6 (CDK6). It interacts with heat shock protein 90 (Hsp90) and its stability can be regulated by Hsp90. JMJD2B also functions as a direct transcriptional target of p53, which induces its expression through promoter binding. Moreover, JMJD2B expression can be controlled by hypoxia-inducible factor 1alpha (HIF1alpha) in colorectal cancer and estrogen receptor alpha (ERalpha) in breast cancer. It is also involved in bladder, lung, and gastric cancer. JMJD2B contains jmjN and jmjC domains in the N-terminal region, followed by a canonical Cys4HisCys3 PHD finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a Tudor domain. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277051  Cd Length: 99  Bit Score: 36.81  E-value: 9.22e-03
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 2029300282  228 SNVILFCDMCNLAVHQECYGV-PYIPEGQWLCRHC 261
Cdd:cd15576     65 TSVLLSCAKCCLQVHASCYGVnPDLVNEGWTCSRC 99
 
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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