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Conserved domains on  [gi|1907139267|ref|XP_036017584|]
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MYND-type zinc finger-containing chromatin reader ZMYND8 isoform X27 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DUF3544 pfam12064
Protein kinase C-binding protein 1; This is a domain found predominantly in eukaryotes and ...
 277-477 5.27e-82

Protein kinase C-binding protein 1; This is a domain found predominantly in eukaryotes and associated with pfam00628 pfam01753 pfam00439 pfam00855. Family members include protein kinase C-binding protein 1 (also known as ZMYND8) which acts as a transcriptional corepressor of the H3K4 demethylase JARID1D. ZMYND8 (zinc finger and MYND [myeloid, Nervy, and DEAF-1] domain containing 8) binds acetylated damaged chromatin, including actively transcribed regions, as a means of recruiting the nucleosome remodeling and histone deacetylation (NuRD) chromatin remodeling complex for transcriptional repression and DNA double-strand break (DSB) repair by homologous recombination (HR).


:

Pssm-ID: 463452  Cd Length: 195  Bit Score: 264.46  E-value: 5.27e-82
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  277 RRISLSDMPRSPTSTNSSVHTGSDVEQDP----EKKAPSSHFSASEESMDFldksTASPASTKtgqAGSLSGSPKPFSPQ 352
Cdd:pfam12064    1 RRISLTDMPRSPMSTNSSAHTGSDGEQDTaekgQAKAPSSHYSTGEESMDC----TASPASPK---AGSSLDSPKPFHSQ 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  353 APTPimTKPDKTSTstTGSILNLNLDRSKAEMDLKELSESVQQ-QSAPVPLISPKRQIRSRFQLNLDKTIESCKAQLGIN 431
Cdd:pfam12064   74 APGT--PKQEKTPT--TGSILNLNLDRSKAEMDLKELSETVQQqQGATVVLTSPKRQIRSRFQLNLDKTIESCKAQLGID 149

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 1907139267  432 EISEDVYTAVEHSDSEDSEKSESSDSEYVSDEEQKPKNEPEDPEDK 477
Cdd:pfam12064  150 EISVDVYKGVEHSDSEDSDKSDSSDSEYASDEEQKPKNSQDDASDK 195
Bromo_RACK7 cd05508
Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) ...
 6-104 3.14e-59

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: 197.61  E-value: 3.14e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267    6 IEQLSYLLKFAIQKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGG 85
Cdd:cd05508      1 VDQLSKLLKFALERMKQPGAEPFLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYNGG 80

                           90
                   ....*....|....*....
gi 1907139267   86 NHKLTQIAKVVIKICEHEM 104
Cdd:cd05508     81 DHKLTQAAKAIVKICEQEM 99
PWWP_PRKCBP1 cd20160
PWWP domain found in protein kinase C-binding protein 1 (PRKCBP1) and similar proteins; ...
 127-217 5.29e-57

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


:

Pssm-ID: 438988  Cd Length: 91  Bit Score: 190.85  E-value: 5.29e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  127 EPCSNPHPLVWAKLKGFPFWPAKALRDKDGQVDARFFGQHDRAWVPVNNCYLMSKEIPFSVKKTKSIFNSAMQEMEVYVE 206
Cdd:cd20160      1 EPCRKPHLLVWAKLKGFPFWPAKALRVNNGQVDVRFFGAHDRAWVPVKDCYLYSKEPPTSVKKKKSGLDEAMEELEIHIE 80

                           90
                   ....*....|.
gi 1907139267  207 NIRRKFGVFNY 217
Cdd:cd20160     81 KLREKFGKFNY 91
zf-MYND pfam01753
MYND finger;
843-877 2.64e-08

MYND finger;


:

Pssm-ID: 460312  Cd Length: 39  Bit Score: 50.50  E-value: 2.64e-08
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 1907139267  843 CANCKKEA--IFYC--CWNTSYCDYPCQQAHWPEHMKSC 877
Cdd:pfam01753    1 CAVCGKEAlkLLRCsrCKSVYYCSKECQKADWPYHKKEC 39
AtpF super family cl34015
FoF1-type ATP synthase, membrane subunit b or b' [Energy production and conversion]; FoF1-type ...
 772-839 6.00e-05

FoF1-type ATP synthase, membrane subunit b or b' [Energy production and conversion]; FoF1-type ATP synthase, membrane subunit b or b' is part of the Pathway/BioSystem: FoF1-type ATP synthase


The actual alignment was detected with superfamily member COG0711:

Pssm-ID: 440475 [Multi-domain]  Cd Length: 152  Bit Score: 44.39  E-value: 6.00e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907139267  772 IAEIRRLRIEIEKLQWLHQQELAEMKH-----------NLELTMAEMRQSLEQERDRLIAEVKKQLELEKQQAVDETKK 839
Cdd:COG0711     40 LAEAERAKEEAEAALAEYEEKLAEARAeaaeiiaearkEAEAIAEEAKAEAEAEAERIIAQAEAEIEQERAKALAELRA 118
PRK12323 super family cl46901
DNA polymerase III subunit gamma/tau;
575-839 1.12e-03

DNA polymerase III subunit gamma/tau;


The actual alignment was detected with superfamily member PRK14971:

Pssm-ID: 481241 [Multi-domain]  Cd Length: 614  Bit Score: 42.84  E-value: 1.12e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  575 GEDPSGREGRKNKKDPKVPSPkqdaIGKPPPSSTSAGNQSPPETPVLTRSATqapaagvtvaaattstmstvtvTAPATA 654
Cdd:PRK14971   366 GDDASGGRGPKQHIKPVFTQP----AAAPQPSAAAAASPSPSQSSAAAQPSA----------------------PQSATQ 419

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  655 VTGSPVkkQRPLLPKETVPAVQRV-VWNASTVQQKEVTQSPSTSTI-TLVTSTQPAALVSSSGSASTLASAINADLPIAT 732
Cdd:PRK14971   420 PAGTPP--TVSVDPPAAVPVNPPStAPQAVRPAQFKEEKKIPVSKVsSLGPSTLRPIQEKAEQATGNIKEAPTGTQKEIF 497

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  733 ASADVAADIAKYTSKMM---DAIKGTMTEIYNDLSKNTTgstiaeirrlrIEIEKLQWLHQQELAEMK-----------H 798
Cdd:PRK14971   498 TEEDLQYYWQEFAGTRPqeeKALKETMINCRPKLLNGTT-----------FEVAVDNELQEKELTNLIpdllgflrgrlK 566

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|..
gi 1907139267  799 NLELTMaEMRQSLEQERDRLIAEVKK-QLELEKQQAVDETKK 839
Cdd:PRK14971   567 NSKITM-TVRVSEPTEVNRAYSSVEKfQYLAQKNPALLELRE 607
PTZ00449 super family cl33186
104 kDa microneme/rhoptry antigen; Provisional
 465-620 6.07e-03

104 kDa microneme/rhoptry antigen; Provisional


The actual alignment was detected with superfamily member PTZ00449:

Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 40.83  E-value: 6.07e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  465 QKPKNePEDPEDKEGSR--VDKEAPAIKRKPKPTNQVEV-KEEAKSNSPVSEKPDPTPAKDKASPEPEKDFVEKAKPSPH 541
Cdd:PTZ00449   583 KDPKH-PKDPEEPKKPKrpRSAQRPTRPKSPKLPELLDIpKSPKRPESPKSPKRPPPPQRPSSPERPEGPKIIKSPKPPK 661

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  542 PTK-------------DKLKGKDETDSPTVHLGLDSDSESELVIDLGEDPSGREGRKNK----------------KDPKV 592
Cdd:PTZ00449   662 SPKppfdpkfkekfydDYLDAAAKSKETKTTVVLDESFESILKETLPETPGTPFTTPRPlppklprdeefpfepiGDPDA 741

                          170       180
                   ....*....|....*....|....*...
gi 1907139267  593 PSPKQDAIGKPPPSSTSAGNQSPPETPV 620
Cdd:PTZ00449   742 EQPDDIEFFTPPEEERTFFHETPADTPL 769
 
Name Accession Description Interval E-value
DUF3544 pfam12064
Protein kinase C-binding protein 1; This is a domain found predominantly in eukaryotes and ...
 277-477 5.27e-82

Protein kinase C-binding protein 1; This is a domain found predominantly in eukaryotes and associated with pfam00628 pfam01753 pfam00439 pfam00855. Family members include protein kinase C-binding protein 1 (also known as ZMYND8) which acts as a transcriptional corepressor of the H3K4 demethylase JARID1D. ZMYND8 (zinc finger and MYND [myeloid, Nervy, and DEAF-1] domain containing 8) binds acetylated damaged chromatin, including actively transcribed regions, as a means of recruiting the nucleosome remodeling and histone deacetylation (NuRD) chromatin remodeling complex for transcriptional repression and DNA double-strand break (DSB) repair by homologous recombination (HR).


Pssm-ID: 463452  Cd Length: 195  Bit Score: 264.46  E-value: 5.27e-82
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  277 RRISLSDMPRSPTSTNSSVHTGSDVEQDP----EKKAPSSHFSASEESMDFldksTASPASTKtgqAGSLSGSPKPFSPQ 352
Cdd:pfam12064    1 RRISLTDMPRSPMSTNSSAHTGSDGEQDTaekgQAKAPSSHYSTGEESMDC----TASPASPK---AGSSLDSPKPFHSQ 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  353 APTPimTKPDKTSTstTGSILNLNLDRSKAEMDLKELSESVQQ-QSAPVPLISPKRQIRSRFQLNLDKTIESCKAQLGIN 431
Cdd:pfam12064   74 APGT--PKQEKTPT--TGSILNLNLDRSKAEMDLKELSETVQQqQGATVVLTSPKRQIRSRFQLNLDKTIESCKAQLGID 149

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 1907139267  432 EISEDVYTAVEHSDSEDSEKSESSDSEYVSDEEQKPKNEPEDPEDK 477
Cdd:pfam12064  150 EISVDVYKGVEHSDSEDSDKSDSSDSEYASDEEQKPKNSQDDASDK 195
Bromo_RACK7 cd05508
Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) ...
 6-104 3.14e-59

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: 197.61  E-value: 3.14e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267    6 IEQLSYLLKFAIQKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGG 85
Cdd:cd05508      1 VDQLSKLLKFALERMKQPGAEPFLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYNGG 80

                           90
                   ....*....|....*....
gi 1907139267   86 NHKLTQIAKVVIKICEHEM 104
Cdd:cd05508     81 DHKLTQAAKAIVKICEQEM 99
PWWP_PRKCBP1 cd20160
PWWP domain found in protein kinase C-binding protein 1 (PRKCBP1) and similar proteins; ...
 127-217 5.29e-57

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


Pssm-ID: 438988  Cd Length: 91  Bit Score: 190.85  E-value: 5.29e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  127 EPCSNPHPLVWAKLKGFPFWPAKALRDKDGQVDARFFGQHDRAWVPVNNCYLMSKEIPFSVKKTKSIFNSAMQEMEVYVE 206
Cdd:cd20160      1 EPCRKPHLLVWAKLKGFPFWPAKALRVNNGQVDVRFFGAHDRAWVPVKDCYLYSKEPPTSVKKKKSGLDEAMEELEIHIE 80

                           90
                   ....*....|.
gi 1907139267  207 NIRRKFGVFNY 217
Cdd:cd20160     81 KLREKFGKFNY 91
BROMO smart00297
bromo domain;
7-107 4.91e-18

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 80.40  E-value: 4.91e-18
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267     7 EQLSYLLKFAI-QKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGG 85
Cdd:smart00297    6 KKLQELLKAVLdKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYNGP 85

                            90       100
                    ....*....|....*....|..
gi 1907139267    86 NHKLTQIAKVVIKICEHEMNEI 107
Cdd:smart00297   86 DSEVYKDAKKLEKFFEKKLREL 107
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 18-94 3.47e-16

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: 74.27  E-value: 3.47e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907139267   18 QKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGGNHKLTQIAK 94
Cdd:pfam00439    7 KLMEHPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYKAAE 83
PWWP pfam00855
PWWP domain; The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain ...
 135-206 5.66e-10

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: 57.05  E-value: 5.66e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  135 LVWAKLKGFPFWPAK---------ALRDKDGQVDA---RFFGQHDRAWVPVNNCYLMSKEIPFSV------KKTKSIFNS 196
Cdd:pfam00855    3 LVWAKLKGYPWWPARvvdpeelpeNVLKPKKKDGEylvRFFGDSEFAWVKPKDLKPFDEGDEFEYlkkkkkKKKKKAFKK 82

                           90
                   ....*....|
gi 1907139267  197 AMQEMEVYVE 206
Cdd:pfam00855   83 ALEEAEEALK 92
PWWP smart00293
domain with conserved PWWP motif; conservation of Pro-Trp-Trp-Pro residues
 131-175 6.12e-10

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


Pssm-ID: 214603 [Multi-domain]  Cd Length: 63  Bit Score: 55.81  E-value: 6.12e-10
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*..
gi 1907139267   131 NPHPLVWAKLKGFPFWPA-----KALRD-------KDGQVDARFFGQHDRAWVPVNN 175
Cdd:smart00293    2 KPGDLVWAKMKGFPWWPAlvispKMTPDnimkrksDENLYPVLFFGDKDTAWIPSSK 58
zf-MYND pfam01753
MYND finger;
843-877 2.64e-08

MYND finger;


Pssm-ID: 460312  Cd Length: 39  Bit Score: 50.50  E-value: 2.64e-08
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 1907139267  843 CANCKKEA--IFYC--CWNTSYCDYPCQQAHWPEHMKSC 877
Cdd:pfam01753    1 CAVCGKEAlkLLRCsrCKSVYYCSKECQKADWPYHKKEC 39
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 3-128 3.71e-07

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


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 53.66  E-value: 3.71e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267    3 MLTIEQLSYLLKFAIQKMKQ---PGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNC 79
Cdd:COG5076    141 ELLYADNKAIAKFKKQLFLRdgrFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNC 220

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 1907139267   80 IIYNGGNHKLTQIAKVVIKICEHEMNEIevcPECYLAACQKRDNWFCEP 128
Cdd:COG5076    221 KLYNGPDSSVYVDAKELEKYFLKLIEEI---PEEMLELSIKPGREEREE 266
AtpF COG0711
FoF1-type ATP synthase, membrane subunit b or b' [Energy production and conversion]; FoF1-type ...
 772-839 6.00e-05

FoF1-type ATP synthase, membrane subunit b or b' [Energy production and conversion]; FoF1-type ATP synthase, membrane subunit b or b' is part of the Pathway/BioSystem: FoF1-type ATP synthase


Pssm-ID: 440475 [Multi-domain]  Cd Length: 152  Bit Score: 44.39  E-value: 6.00e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907139267  772 IAEIRRLRIEIEKLQWLHQQELAEMKH-----------NLELTMAEMRQSLEQERDRLIAEVKKQLELEKQQAVDETKK 839
Cdd:COG0711     40 LAEAERAKEEAEAALAEYEEKLAEARAeaaeiiaearkEAEAIAEEAKAEAEAEAERIIAQAEAEIEQERAKALAELRA 118
ATP-synt_Fo_b cd06503
F-type ATP synthase, membrane subunit b; Membrane subunit b is a component of the Fo complex ...
 770-839 3.17e-04

F-type ATP synthase, membrane subunit b; Membrane subunit b is a component of the Fo complex of FoF1-ATP synthase. The F-type ATP synthases (FoF1-ATPase) consist of two structural domains: the F1 (assembly factor one) complex containing the soluble catalytic core, and the Fo (oligomycin sensitive factor) complex containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. F1 is composed of alpha (or A), beta (B), gamma (C), delta (D) and epsilon (E) subunits with a stoichiometry of 3:3:1:1:1, while Fo consists of the three subunits a, b, and c (1:2:10-14). An oligomeric ring of 10-14 c subunits (c-ring) make up the Fo rotor. The flux of protons through the ATPase channel (Fo) drives the rotation of the c-ring, which in turn is coupled to the rotation of the F1 complex gamma subunit rotor due to the permanent binding between the gamma and epsilon subunits of F1 and the c-ring of Fo. The F-ATP synthases are primarily found in the inner membranes of eukaryotic mitochondria, in the thylakoid membranes of chloroplasts or in the plasma membranes of bacteria. The F-ATP synthases are the primary producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). Alternatively, under conditions of low driving force, ATP synthases function as ATPases, thus generating a transmembrane proton or Na(+) gradient at the expense of energy derived from ATP hydrolysis. This group also includes F-ATP synthase that has also been found in the archaea Candidatus Methanoperedens.


Pssm-ID: 349951 [Multi-domain]  Cd Length: 132  Bit Score: 41.65  E-value: 3.17e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  770 STIAEIRRLRIEIEKLQWLHQQELAE-----------MKHNLELTMAEMRQSLEQERDRLIAEVKKQLELEKQQAVDETK 838
Cdd:cd06503     37 ESLEEAEKAKEEAEELLAEYEEKLAEaraeaqeiieeARKEAEKIKEEILAEAKEEAERILEQAKAEIEQEKEKALAELR 116


                   .
gi 1907139267  839 K 839
Cdd:cd06503    117 K 117
PRK05759 PRK05759
F0F1 ATP synthase subunit B; Validated
 771-840 7.77e-04

F0F1 ATP synthase subunit B; Validated


Pssm-ID: 180240 [Multi-domain]  Cd Length: 156  Bit Score: 41.30  E-value: 7.77e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  771 TIAEIRRLRIEIEKLQWLHQQELAEMKH-----------NLELTMAEMRQSLEQERDRLIAEVKKQLELEKQQAVDETKK 839
Cdd:PRK05759    43 GLAAAERAKKELELAQAKYEAQLAEARAeaaeiieqakkRAAQIIEEAKAEAEAEAARIKAQAQAEIEQERKRAREELRK 122


                   .
gi 1907139267  840 K 840
Cdd:PRK05759   123 Q 123
PRK14971 PRK14971
DNA polymerase III subunit gamma/tau;
575-839 1.12e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237874 [Multi-domain]  Cd Length: 614  Bit Score: 42.84  E-value: 1.12e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  575 GEDPSGREGRKNKKDPKVPSPkqdaIGKPPPSSTSAGNQSPPETPVLTRSATqapaagvtvaaattstmstvtvTAPATA 654
Cdd:PRK14971   366 GDDASGGRGPKQHIKPVFTQP----AAAPQPSAAAAASPSPSQSSAAAQPSA----------------------PQSATQ 419

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  655 VTGSPVkkQRPLLPKETVPAVQRV-VWNASTVQQKEVTQSPSTSTI-TLVTSTQPAALVSSSGSASTLASAINADLPIAT 732
Cdd:PRK14971   420 PAGTPP--TVSVDPPAAVPVNPPStAPQAVRPAQFKEEKKIPVSKVsSLGPSTLRPIQEKAEQATGNIKEAPTGTQKEIF 497

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  733 ASADVAADIAKYTSKMM---DAIKGTMTEIYNDLSKNTTgstiaeirrlrIEIEKLQWLHQQELAEMK-----------H 798
Cdd:PRK14971   498 TEEDLQYYWQEFAGTRPqeeKALKETMINCRPKLLNGTT-----------FEVAVDNELQEKELTNLIpdllgflrgrlK 566

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|..
gi 1907139267  799 NLELTMaEMRQSLEQERDRLIAEVKK-QLELEKQQAVDETKK 839
Cdd:PRK14971   567 NSKITM-TVRVSEPTEVNRAYSSVEKfQYLAQKNPALLELRE 607
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
 465-620 6.07e-03

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 40.83  E-value: 6.07e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  465 QKPKNePEDPEDKEGSR--VDKEAPAIKRKPKPTNQVEV-KEEAKSNSPVSEKPDPTPAKDKASPEPEKDFVEKAKPSPH 541
Cdd:PTZ00449   583 KDPKH-PKDPEEPKKPKrpRSAQRPTRPKSPKLPELLDIpKSPKRPESPKSPKRPPPPQRPSSPERPEGPKIIKSPKPPK 661

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  542 PTK-------------DKLKGKDETDSPTVHLGLDSDSESELVIDLGEDPSGREGRKNK----------------KDPKV 592
Cdd:PTZ00449   662 SPKppfdpkfkekfydDYLDAAAKSKETKTTVVLDESFESILKETLPETPGTPFTTPRPlppklprdeefpfepiGDPDA 741

                          170       180
                   ....*....|....*....|....*...
gi 1907139267  593 PSPKQDAIGKPPPSSTSAGNQSPPETPV 620
Cdd:PTZ00449   742 EQPDDIEFFTPPEEERTFFHETPADTPL 769
CCDC90-like pfam07798
Coiled-coil domain-containing protein 90-like; This entry includes coiled-coil ...
 748-839 7.14e-03

Coiled-coil domain-containing protein 90-like; This entry includes coiled-coil domain-containing proteins 90 (CCDC90) and related proteins. CCDC90A is a key regulator of the mitochondrial calcium uniporter (MCU) and hence was renamed MCUR1. A study in mammals and in yeast homolog fmp32 has reported that MCUR1 is a cytochrome c oxidase assembly factor and that it has an indirect role as a regulator of MCU, however, subsequent publications confirmed the function of MCUR1 as a regulator of MCU. The role of CCDC90B proteins is still not known.


Pssm-ID: 462268 [Multi-domain]  Cd Length: 175  Bit Score: 38.65  E-value: 7.14e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  748 MMDAIKGTMTEIYNDL-SK----NTTGSTIAEIRRLRIEIeklQWLHQQELAEMKHNLELTMAE---MRQSLEQERDRLI 819
Cdd:pfam07798   27 LRDLLNDSLENVSKDLvTKedleNETYLQKADLAELRSEL---QILEKSEFAALRSENEKLRRElekLKQRLREEITKLK 103

                           90       100
                   ....*....|....*....|
gi 1907139267  820 AEVKKQLELEKQQAVDETKK 839
Cdd:pfam07798  104 ADVRLDLNLEKGRIREELKA 123
 
Name Accession Description Interval E-value
DUF3544 pfam12064
Protein kinase C-binding protein 1; This is a domain found predominantly in eukaryotes and ...
 277-477 5.27e-82

Protein kinase C-binding protein 1; This is a domain found predominantly in eukaryotes and associated with pfam00628 pfam01753 pfam00439 pfam00855. Family members include protein kinase C-binding protein 1 (also known as ZMYND8) which acts as a transcriptional corepressor of the H3K4 demethylase JARID1D. ZMYND8 (zinc finger and MYND [myeloid, Nervy, and DEAF-1] domain containing 8) binds acetylated damaged chromatin, including actively transcribed regions, as a means of recruiting the nucleosome remodeling and histone deacetylation (NuRD) chromatin remodeling complex for transcriptional repression and DNA double-strand break (DSB) repair by homologous recombination (HR).


Pssm-ID: 463452  Cd Length: 195  Bit Score: 264.46  E-value: 5.27e-82
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  277 RRISLSDMPRSPTSTNSSVHTGSDVEQDP----EKKAPSSHFSASEESMDFldksTASPASTKtgqAGSLSGSPKPFSPQ 352
Cdd:pfam12064    1 RRISLTDMPRSPMSTNSSAHTGSDGEQDTaekgQAKAPSSHYSTGEESMDC----TASPASPK---AGSSLDSPKPFHSQ 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  353 APTPimTKPDKTSTstTGSILNLNLDRSKAEMDLKELSESVQQ-QSAPVPLISPKRQIRSRFQLNLDKTIESCKAQLGIN 431
Cdd:pfam12064   74 APGT--PKQEKTPT--TGSILNLNLDRSKAEMDLKELSETVQQqQGATVVLTSPKRQIRSRFQLNLDKTIESCKAQLGID 149

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 1907139267  432 EISEDVYTAVEHSDSEDSEKSESSDSEYVSDEEQKPKNEPEDPEDK 477
Cdd:pfam12064  150 EISVDVYKGVEHSDSEDSDKSDSSDSEYASDEEQKPKNSQDDASDK 195
Bromo_RACK7 cd05508
Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) ...
 6-104 3.14e-59

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: 197.61  E-value: 3.14e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267    6 IEQLSYLLKFAIQKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGG 85
Cdd:cd05508      1 VDQLSKLLKFALERMKQPGAEPFLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYNGG 80

                           90
                   ....*....|....*....
gi 1907139267   86 NHKLTQIAKVVIKICEHEM 104
Cdd:cd05508     81 DHKLTQAAKAIVKICEQEM 99
PWWP_PRKCBP1 cd20160
PWWP domain found in protein kinase C-binding protein 1 (PRKCBP1) and similar proteins; ...
 127-217 5.29e-57

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


Pssm-ID: 438988  Cd Length: 91  Bit Score: 190.85  E-value: 5.29e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  127 EPCSNPHPLVWAKLKGFPFWPAKALRDKDGQVDARFFGQHDRAWVPVNNCYLMSKEIPFSVKKTKSIFNSAMQEMEVYVE 206
Cdd:cd20160      1 EPCRKPHLLVWAKLKGFPFWPAKALRVNNGQVDVRFFGAHDRAWVPVKDCYLYSKEPPTSVKKKKSGLDEAMEELEIHIE 80

                           90
                   ....*....|.
gi 1907139267  207 NIRRKFGVFNY 217
Cdd:cd20160     81 KLREKFGKFNY 91
PWWP_BS69-like cd05841
PWWP domain found in protein BS69, protein kinase C-binding protein 1 (PRKCBP1) and similar ...
 127-210 6.27e-40

PWWP domain found in protein BS69, protein kinase C-binding protein 1 (PRKCBP1) and similar proteins; Protein BS69, also called zinc finger MYND domain-containing protein 11 (ZMYND11 or ZMY11), is a ubiquitously expressed nuclear protein acting as a transcriptional co-repressor in association with various transcription factors. It was originally identified as an adenovirus 5 E1A-binding protein that inhibits E1A transactivation, as well as c-Myb transcription. BS69 is a multi-domain protein, containing bromo, plant homeodomain (PHD), proline-tryptophan-tryptophan-proline (PWWP), and MYeloid translocation protein 8, Nervy and DEAF-1 (MYND) domains. The specific role of the PWWP domain within BS69 is not clearly identified, but BS69 functions in chromatin remodeling, consistent with other PWWP-containing proteins. PRKCBP1, also called cutaneous T-cell lymphoma-associated antigen se14-3 (CTCL-associated antigen se14-3), Rack7, or zinc finger MYND domain-containing protein 8 (ZMYND8), is a novel receptor for activated C-kinase (RACK)-like protein that may play an important role in the activation and regulation of PKC-beta I, and the PKC signaling cascade. It also has been identified as a formin homology-2-domain containing protein 1 (FHOD1)-binding protein that may be involved in FHOD1-regulated actin polymerization and transcription. Moreover, PRKCBP1 may function as a REST co-repressor 2 (RCOR2) interacting factor. They form a RCOR2/ZMYND8 complex which might be involved in the regulation of neural differentiation. PRKCBP1 contains a PHD finger, a bromodomain, and a PWWP domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438966  Cd Length: 89  Bit Score: 142.15  E-value: 6.27e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  127 EPCSNPHPLVWAKLKGFPFWPAKALRDKDGQVDARFFGQHDRAWVPVNNCYLMSKEIP-----FSVKKTKSIFNSAMQEM 201
Cdd:cd05841      1 KPCPVVHPLVWVKLDGFPFWPAKVMGTKDGQVDVRFFGDYDRAWLPSKNVTLHTREIVstlpdSSESKDKRTLKKAIKEL 80


                   ....*....
gi 1907139267  202 EVYVENIRR 210
Cdd:cd05841     81 ERHIALLRQ 89
PWWP_BS69 cd20159
PWWP domain found in protein BS69 and similar proteins; Protein BS69, also called zinc finger ...
 128-210 5.04e-26

PWWP domain found in protein BS69 and similar proteins; Protein BS69, also called zinc finger MYND domain-containing protein 11 (ZMYND11 or ZMY11), is a ubiquitously expressed nuclear protein acting as a transcriptional co-repressor in association with various transcription factors. It was originally identified as an adenovirus 5 E1A-binding protein that inhibits E1A transactivation, as well as c-Myb transcription. It also mediates repression, at least in part, through interaction with the co-repressor N-CoR. Moreover, it interacts with Toll-interleukin 1 receptor domain (TIR)-containing adaptor molecule-1 (TICAM-1, also named TRIF) to facilitate NF-kappaB activation and type I IFN induction. It associates with PIAS1, a SUMO E3 enzyme, and Ubc9, a SUMO E2 enzyme, and plays an inhibitory role in muscle and neuronal differentiation. Moreover, BS69 regulates Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1)/C-terminal activation region 2 (CTAR2)-mediated NF-kappaB activation by interfering with the complex formation between TNFR-associated death domain protein (TRADD) and LMP1/CTAR2. It also cooperates with tumor necrosis factor receptor (TNFR)-associated factor 3 (TRAF3) in the regulation of EBV-derived LMP1/CTAR1-induced NF-kappaB activation. Furthermore, BS69 is involved in the p53-p21Cip1-mediated senescence pathway. BS69 contains a plant homeodomain (PHD) finger, a bromodomain, a proline-tryptophan-tryptophan-proline (PWWP) domain, and a MYeloid translocation protein 8, Nervy and DEAF-1 (MYND) domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438987  Cd Length: 85  Bit Score: 102.29  E-value: 5.04e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  128 PCSNPHPLVWAKLKGFPFWPAKALRDKDGQVDARFFG-QHDRAWVPVNNCYLMSKEIPFSVKKTKSIFNSAMQEMEVYVE 206
Cdd:cd20159      2 PCRPPHELVWAKQKGFPYWPAKVIQKEDNQYDVRFFGgHHQRAWIPKENIKPITTSPKQLKVKRTAGWNKACEELKKHQE 81


                   ....
gi 1907139267  207 NIRR 210
Cdd:cd20159     82 LLEE 85
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
 9-108 1.33e-21

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: 90.79  E-value: 1.33e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267    9 LSYLLKFAIQKMKQ-PGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGGNH 87
Cdd:cd05511      1 LSFILDEIVNELKNlPDSWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDS 80

                           90       100
                   ....*....|....*....|.
gi 1907139267   88 KLTQIAKVVIKICEHEMNEIE 108
Cdd:cd05511     81 VYTKKAKEMLELAEELLAERE 101
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
 5-104 1.49e-20

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: 87.43  E-value: 1.49e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267    5 TIEQLSYLLKfAIQKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNG 84
Cdd:cd04369      1 LKKKLRSLLD-ALKKLKRDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNG 79

                           90       100
                   ....*....|....*....|
gi 1907139267   85 GNHKLTQIAKVVIKICEHEM 104
Cdd:cd04369     80 PGSPIYKDAKKLEKLFEKLL 99
BROMO smart00297
bromo domain;
7-107 4.91e-18

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 80.40  E-value: 4.91e-18
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267     7 EQLSYLLKFAI-QKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGG 85
Cdd:smart00297    6 KKLQELLKAVLdKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYNGP 85

                            90       100
                    ....*....|....*....|..
gi 1907139267    86 NHKLTQIAKVVIKICEHEMNEI 107
Cdd:smart00297   86 DSEVYKDAKKLEKFFEKKLREL 107
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 18-94 3.47e-16

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: 74.27  E-value: 3.47e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907139267   18 QKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGGNHKLTQIAK 94
Cdd:pfam00439    7 KLMEHPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYKAAE 83
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
 8-86 6.96e-16

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: 74.13  E-value: 6.96e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267    8 QLSYLLKFAIQKMKQpGTDA--FQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGG 85
Cdd:cd05509      1 PLYTQLKKVLDSLKN-HKSAwpFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGP 79


                   .
gi 1907139267   86 N 86
Cdd:cd05509     80 D 80
Bromo_ZMYND11 cd05492
Bromodomain; ZMYND11_like sub-family. ZMYND11 or BS69 is a ubiquitously expressed nuclear ...
 9-110 2.19e-14

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: 70.10  E-value: 2.19e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267    9 LSYLLKFAIQKMKQ--PGTDAFQKPVPLE-----QHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCII 81
Cdd:cd05492      1 LNCLLKFIVSRMKSwlPPDTTNRAIVLNKrgkatKLPKRRRLIHTHLDVADIQEKINSEKYTSLEEFKADALLLLHNTAI 80

                           90       100
                   ....*....|....*....|....*....
gi 1907139267   82 YNGGNHKLTQIAKVVIKICEHEMNEIEVC 110
Cdd:cd05492     81 FHGADSEQYDAARWLYRDTCHDLRELRLC 109
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
 4-104 2.67e-13

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: 66.95  E-value: 2.67e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267    4 LTIEQLSYLLKfAIQKMKQpGTDA--FQKPV-PLEQH-PDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNC 79
Cdd:cd05500      1 MTKHQHKFLLS-SIRSLKR-LKDArpFLVPVdPVKLNiPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNC 78

                           90       100
                   ....*....|....*....|....*
gi 1907139267   80 IIYNGGNHKLTQIAKVVIKICEHEM 104
Cdd:cd05500     79 LTFNGPEHPVSQMGKRLQAAFEKHL 103
PWWP cd05162
PWWP (Pro-Trp-Trp-Pro) domain; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, ...
 135-204 4.86e-12

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: 62.90  E-value: 4.86e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  135 LVWAKLKGFPFWPAKALRDKDGQVDA-----------RFFGQHDRAWVPVNNCYL----MSKEIPFSVKKTKSiFNSAMQ 199
Cdd:cd05162      3 LVWAKLKGYPWWPARVVDPEELPEEVgkkkkkggvlvQFFGDNDYAWVKSKNIKPfeegFKKEFKKKKKKSKK-FKKAVE 81


                   ....*
gi 1907139267  200 EMEVY 204
Cdd:cd05162     82 EAEEA 86
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
 19-84 6.30e-12

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: 62.80  E-value: 6.30e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907139267   19 KMKQPGtDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNG 84
Cdd:cd05512     14 QEKDTA-EIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNA 78
PWWP_GLYR1 cd05836
PWWP domain found in glyoxylate reductase 1 (GLYR1) and similar proteins; GLYR1, also called ...
 135-205 1.04e-11

PWWP domain found in glyoxylate reductase 1 (GLYR1) and similar proteins; GLYR1, also called 3-hydroxyisobutyrate dehydrogenase-like protein, cytokine-like nuclear factor N-PAC, nuclear protein NP60, or nuclear protein of 60 kDa, is a putative oxidoreductase that is recruited on chromatin and promotes KDM1B demethylase activity. It recognizes and binds trimethylated 'Lys-36' of histone H3 (H3K36me3). GLYR1 enhances the activity of MAP2K4 and MAP2K6 kinases to phosphorylate p38-alpha. In addition to the PWWP domain, GLYR1 also contains an AT-hook and a C-terminal NAD-binding domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438961 [Multi-domain]  Cd Length: 86  Bit Score: 61.85  E-value: 1.04e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  135 LVWAKLKGFPFWPAKALR-DKDGQVDAR--------FFGQHDRAWVPVNNC--YLMSKEIPFSVKKTKSiFNSAMQEMEV 203
Cdd:cd05836      6 LVWAKMKGFPPWPGKIVNpPPDLKKPPRkkkmhcvyFFGSENYAWIEDENIkpYEEFKEEMLKSKKSAG-FKDAVEAIEE 84


                   ..
gi 1907139267  204 YV 205
Cdd:cd05836     85 YI 86
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
 27-107 4.05e-11

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: 60.92  E-value: 4.05e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267   27 AFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGG-NHKLTQIAKVVIKICEHEMN 105
Cdd:cd05510     28 PFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYNSDpSHPLRRHANFMKKKAEHLLK 107


                   ..
gi 1907139267  106 EI 107
Cdd:cd05510    108 LI 109
Bromo_brd8_like cd05507
Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with ...
 27-109 5.92e-11

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: 60.07  E-value: 5.92e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267   27 AFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGGNHKLTQIAKVVIkicEHEMNE 106
Cdd:cd05507     23 VFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNSSDHDVYLMAVEMQ---REVMSQ 99


                   ...
gi 1907139267  107 IEV 109
Cdd:cd05507    100 IQQ 102
PWWP_HRP cd05834
PWWP domain found in hepatoma-derived growth factor (HDGF)-related protein (HRP) family; The ...
 135-202 1.99e-10

PWWP domain found in hepatoma-derived growth factor (HDGF)-related protein (HRP) family; The HRP family includes hepatoma-derived growth factor (HDGF), and HDGF-related proteins (HRPs). HDGF, also called high mobility group protein 1-like 2 (HMG-1L2), is a heparin-binding protein that acts as a transcriptional repressor with mitogenic activity for fibroblasts. It is a prognostic factor in several types of cancer. HDGFL1 is also called PWWP domain-containing protein 1 (PWWP1). Its biological function remains unclear. HDGFL2, also called HDGF-related protein 2 (HRP-2), or hepatoma-derived growth factor 2 (HDGF-2), is involved in cellular growth control, through the regulation of cyclin D1 expression. HDGFL3, also called HDGF-related protein 3 (HRP-3), enhances DNA synthesis and may play a role in cell proliferation. The family also includes PC4 and SFRS1-interacting protein (PSIP) and similar proteins. PSIP, also called CLL-associated antigen KW-7, dense fine speckles 70 kDa protein (DFS 70), lens epithelium-derived growth factor (LEDGF), or transcriptional coactivator p75/p52, acts as a transcriptional coactivator involved in neuroepithelial stem cell differentiation and neurogenesis. Members of the HRP family contains a PWWP domain, which is necessary for DNA binding.


Pssm-ID: 438959 [Multi-domain]  Cd Length: 82  Bit Score: 57.95  E-value: 1.99e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907139267  135 LVWAKLKGFPFWPAKALRDKDGQVDAR------FFGQHDRAWVPVNNCYLMSKE-IPFSVKKTKSIFNSAMQEME 202
Cdd:cd05834      6 LVFAKVKGYPPWPARIDEIPEGAKIPKnkypvfFYGTHETAFLKPKDLFPYEENkEKYGKPRKRKGFNEGLWEIE 80
PWWP pfam00855
PWWP domain; The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain ...
 135-206 5.66e-10

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: 57.05  E-value: 5.66e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  135 LVWAKLKGFPFWPAK---------ALRDKDGQVDA---RFFGQHDRAWVPVNNCYLMSKEIPFSV------KKTKSIFNS 196
Cdd:pfam00855    3 LVWAKLKGYPWWPARvvdpeelpeNVLKPKKKDGEylvRFFGDSEFAWVKPKDLKPFDEGDEFEYlkkkkkKKKKKAFKK 82

                           90
                   ....*....|
gi 1907139267  197 AMQEMEVYVE 206
Cdd:pfam00855   83 ALEEAEEALK 92
PWWP smart00293
domain with conserved PWWP motif; conservation of Pro-Trp-Trp-Pro residues
 131-175 6.12e-10

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


Pssm-ID: 214603 [Multi-domain]  Cd Length: 63  Bit Score: 55.81  E-value: 6.12e-10
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*..
gi 1907139267   131 NPHPLVWAKLKGFPFWPA-----KALRD-------KDGQVDARFFGQHDRAWVPVNN 175
Cdd:smart00293    2 KPGDLVWAKMKGFPWWPAlvispKMTPDnimkrksDENLYPVLFFGDKDTAWIPSSK 58
Bromo_Brdt_I_like cd05497
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...
 8-99 2.08e-09

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: 55.89  E-value: 2.08e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267    8 QLSYLLKFAIQKM-KQPGTDAFQKPVPLE--QHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNG 84
Cdd:cd05497      5 QLQYLLKVVLKALwKHKFAWPFQQPVDAVklNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNK 84

                           90
                   ....*....|....*
gi 1907139267   85 GNHKLTQIAKVVIKI 99
Cdd:cd05497     85 PGDDVVLMAQTLEKL 99
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 27-88 6.46e-09

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: 54.67  E-value: 6.46e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907139267   27 AFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGGNHK 88
Cdd:cd05528     23 AFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPDRDP 84
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
 8-99 7.62e-09

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: 54.71  E-value: 7.62e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267    8 QLSYLLKFAIQKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYnggNH 87
Cdd:cd05504     13 NLSALEQLLVEIVKHKDSWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLY---NP 89

                           90
                   ....*....|..
gi 1907139267   88 KLTQIAKVVIKI 99
Cdd:cd05504     90 EHTSVYKAGTRL 101
zf-MYND pfam01753
MYND finger;
843-877 2.64e-08

MYND finger;


Pssm-ID: 460312  Cd Length: 39  Bit Score: 50.50  E-value: 2.64e-08
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 1907139267  843 CANCKKEA--IFYC--CWNTSYCDYPCQQAHWPEHMKSC 877
Cdd:pfam01753    1 CAVCGKEAlkLLRCsrCKSVYYCSKECQKADWPYHKKEC 39
PWWP_NSD_rpt2 cd05838
second PWWP domain found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
 136-206 1.23e-07

second PWWP domain found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein family consists 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 in suppressing cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play nonredundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (C5HCH). This model corresponds to the second PWWP domain. The family also includes Drosophila melanogaster maternal-effect sterile 4 (dMes4) that may act as a histone-lysine N-methyltransferase required for wing morphogenesis. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438963 [Multi-domain]  Cd Length: 96  Bit Score: 50.32  E-value: 1.23e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  136 VWAKLKGFPFWPAKAL------------RDKDGQVDARFFGQHDRAWVPVNNCYLMSKE----IPFSVKKTKSIFNSAMQ 199
Cdd:cd05838      6 VWVKLGNYRWWPAEILhprevpdniqslPHPPGEFPVRFFGSHDYYWVHRGRVFLFEEGdkgsKEKSKKSLDKSFKRALK 85


                   ....*...
gi 1907139267  200 E-MEVYVE 206
Cdd:cd05838     86 EaNEAFRE 93
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
 20-101 1.50e-07

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: 50.41  E-value: 1.50e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267   20 MKQPGTDAFQKPVPLEQH--PDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGGNHKLTQIAKVVI 97
Cdd:cd05506     13 MKHKWGWVFNAPVDVVALglPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVHTMAKELL 92


                   ....
gi 1907139267   98 KICE 101
Cdd:cd05506     93 KIFE 96
Bromo_brd7_like cd05513
Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ...
 28-83 1.97e-07

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: 50.10  E-value: 1.97e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907139267   28 FQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYN 83
Cdd:cd05513     22 FAFPVTDFIAPGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYN 77
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 7-96 2.63e-07

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: 50.41  E-value: 2.63e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267    7 EQLSYLLKfAIQKMKQPG----TDAFQKPVPL-EQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCII 81
Cdd:cd05529     24 EERERLIS-GLDKLLLSLqleiAEYFEYPVDLrAWYPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAET 102

                           90
                   ....*....|....*
gi 1907139267   82 YNGGNHKLTQIAKVV 96
Cdd:cd05529    103 FNEPNSEIAKKAKRL 117
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 3-128 3.71e-07

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


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 53.66  E-value: 3.71e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267    3 MLTIEQLSYLLKFAIQKMKQ---PGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNC 79
Cdd:COG5076    141 ELLYADNKAIAKFKKQLFLRdgrFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNC 220

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 1907139267   80 IIYNGGNHKLTQIAKVVIKICEHEMNEIevcPECYLAACQKRDNWFCEP 128
Cdd:COG5076    221 KLYNGPDSSVYVDAKELEKYFLKLIEEI---PEEMLELSIKPGREEREE 266
Bromo_Brdt_II_like cd05498
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...
 28-94 4.62e-07

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: 49.20  E-value: 4.62e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907139267   28 FQKPVPLEQH--PDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGGNHKLTQIAK 94
Cdd:cd05498     24 FYKPVDPEALglHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPVHAMAR 92
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
 28-83 5.37e-07

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: 48.91  E-value: 5.37e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907139267   28 FQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYN 83
Cdd:cd05503     21 FLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFN 76
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
 11-83 5.54e-07

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: 48.98  E-value: 5.54e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907139267   11 YLLKFAIQKMKQPgTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYN 83
Cdd:cd05518     11 YVLEYREGSGRRL-CDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYN 82
PWWP_AtATX1-like cd20142
PWWP domain found in Arabidopsis thaliana histone-lysine N-methyltransferase trithorax-like ...
 135-204 1.09e-06

PWWP domain found in Arabidopsis thaliana histone-lysine N-methyltransferase trithorax-like proteins ATX1, ATX2, and similar proteins; This family includes A. thaliana ATX1 and ATX2, 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 called 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 called 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 plant homeodomain (PHD) domain, a non-canonical extended PHD (ePHD) domain, and a C-terminal SET domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438970 [Multi-domain]  Cd Length: 97  Bit Score: 47.73  E-value: 1.09e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  135 LVWAKLKGFPFWPA--------------KALRDKDGQVDARFFGQHDRAWVPVNNCYLMSKEI--PFSVKKTKSIFNSAM 198
Cdd:cd20142      5 VVWAKVKGYPMWPAlvideehaercgleANRPGKKGTVPVQFFGTYEVARLNPKKVVGFSKGLdlKYHSKCKAPVFRQAL 84


                   ....*.
gi 1907139267  199 QEMEVY 204
Cdd:cd20142     85 EEAERY 90
PWWP_ZCWPW2 cd20146
PWWP domain found in zinc finger CW-type PWWP domain protein 2 (ZCWPW2) and similar proteins; ...
 135-200 1.25e-06

PWWP domain found in zinc finger CW-type PWWP domain protein 2 (ZCWPW2) and similar proteins; ZCWPW2 is a histone H3K4me3 reader. In addition to the PWWP domain, ZCWPW2 contains a zinc finger CW (zf-CW) domain that is a histone modification reader for the histone H3 tail with trimethylated K4. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438974  Cd Length: 113  Bit Score: 48.06  E-value: 1.25e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  135 LVWAKLKGFPFWPA----------KALRDKDGQVD---ARFFGQ-HDRAWVPV-------NNCYLMSKEIPFSVKKTKSI 193
Cdd:cd20146     14 LVWAKMTGYPRWPAiltpdpicgeYVDYDEDGEVEkyhVEFLGKpHSHAWISAksvepynSNTKTPKCKTKKSKKRKKSY 93


                   ....*..
gi 1907139267  194 fNSAMQE 200
Cdd:cd20146     94 -ESALEE 99
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
 28-107 2.47e-06

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: 47.29  E-value: 2.47e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267   28 FQKPVPLEQhPDYAEYIFHPMDLCTLEKNAKKK---MYGCTEAFLADAKWILHNCIIYNGGNHKLTQIAKVVIKICEHEM 104
Cdd:cd05502     25 FHEPVSPSV-PNYYKIIKTPMDLSLIRKKLQPKspqHYSSPEEFVADVRLMFKNCYKFNEEDSEVAQAGKELELFFEEQL 103


                   ...
gi 1907139267  105 NEI 107
Cdd:cd05502    104 KEI 106
PWWP_AtATX3-like cd20143
PWWP domain found in Arabidopsis thaliana histone-lysine N-methyltransferase trithorax-like ...
 135-207 2.71e-06

PWWP domain found in Arabidopsis thaliana histone-lysine N-methyltransferase trithorax-like protein ATX3, ATX4, ATX5, and similar proteins; The family includes A. thaliana ATX3 (also called protein SET domain group 14, or trithorax-homolog protein 3), ATX4 (also called protein SET domain group 16, or trithorax-homolog protein 4) and ATX5 (also called 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 family of ATX1 and ATX2. They are multi-domain containing protein that consists of an N-terminal PWWP domain, a canonical plant homeodomain (PHD) domain, a non-canonical extended PHD (ePHD) domain, and a C-terminal SET domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438971 [Multi-domain]  Cd Length: 100  Bit Score: 46.98  E-value: 2.71e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  135 LVWAKLKGFPFWPAK-----------ALRDKDGQVDARFFG---QHDRAWVPVNNCYLMSKEIP-FSVKKTK-----SIF 194
Cdd:cd20143      5 LVWAKVGTHPFWPARvvepaeqaeevRRRCVPGSLCVYFFGpggSRDYGWVRRSMIFPFTDDLArFQTQKIKnkkrpQEF 84

                           90
                   ....*....|....
gi 1907139267  195 NSAMQE-MEVYVEN 207
Cdd:cd20143     85 QEALEEaKLADAGF 98
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
 28-94 3.68e-06

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: 46.38  E-value: 3.68e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907139267   28 FQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYN-GGNHKLTQIAK 94
Cdd:cd05505     21 FREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYeNGSYVLSCMRK 88
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
 27-84 1.01e-05

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: 45.35  E-value: 1.01e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267   27 AFQKPVPLE--QHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNG 84
Cdd:cd05499     23 PFLDPVDPValNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNP 82
PWWP_MSH6 cd05837
PWWP domain found in DNA mismatch repair protein MSH6 and similar proteins; MSH6, also called ...
 135-200 1.06e-05

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: 45.35  E-value: 1.06e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  135 LVWAKLKGFPFWPA----------KALRDKDGQVDARFFGQ-HDRAWVPVNN--------CYLMSKEIPFSVKKTKsiFN 195
Cdd:cd05837      6 LVWAKLEGYPWWPSlvcnhpttgfHKKFGKKGEVHVQFFDDpPSRAWVKAKNvkpftgsdDKEFQKGGMFFSKDPK--WK 83


                   ....*
gi 1907139267  196 SAMQE 200
Cdd:cd05837     84 KAVKE 88
PWWP_HULK cd20147
PWWP domain found in Arabidopsis thaliana protein HUA2-LIKE (HULK) family; The HULK family ...
 135-202 2.54e-05

PWWP domain found in Arabidopsis thaliana protein HUA2-LIKE (HULK) family; The HULK family includes HUA2-like proteins 1-3 (HULK1-3), which are probable transcription factors that act with partial redundancy with each other. They may play diverse and essential roles in the control of plant development, physiology and flowering time. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438975 [Multi-domain]  Cd Length: 92  Bit Score: 44.02  E-value: 2.54e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  135 LVWAKLKGFPFWPAKALRDKD-------GQVDARFFGQHDRAWVPVNNCYLMSKEIPFSV------KKTKSIFNSAMQEM 201
Cdd:cd20147      3 LVLAKVKGFPAWPAQVSEPEDwgsapdpKKVFVHFFGTQQIGFCNPGELSEFTEEIKQSLlartlkKKKGSDFSRAVKEI 82


                   .
gi 1907139267  202 E 202
Cdd:cd20147     83 C 83
AtpF COG0711
FoF1-type ATP synthase, membrane subunit b or b' [Energy production and conversion]; FoF1-type ...
 772-839 6.00e-05

FoF1-type ATP synthase, membrane subunit b or b' [Energy production and conversion]; FoF1-type ATP synthase, membrane subunit b or b' is part of the Pathway/BioSystem: FoF1-type ATP synthase


Pssm-ID: 440475 [Multi-domain]  Cd Length: 152  Bit Score: 44.39  E-value: 6.00e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907139267  772 IAEIRRLRIEIEKLQWLHQQELAEMKH-----------NLELTMAEMRQSLEQERDRLIAEVKKQLELEKQQAVDETKK 839
Cdd:COG0711     40 LAEAERAKEEAEAALAEYEEKLAEARAeaaeiiaearkEAEAIAEEAKAEAEAEAERIIAQAEAEIEQERAKALAELRA 118
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 7-86 1.01e-04

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


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 45.95  E-value: 1.01e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267    7 EQLSYLLKFAIQKmkQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGGN 86
Cdd:COG5076    265 EERESVLITNSQA--HVGAWPFLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVRDAKLFFDNCVMYNGEV 342
PWWP_PSIP cd20151
PWWP domain found in PC4 and SFRS1-interacting protein (PSIP); PSIP, also called ...
 132-212 1.95e-04

PWWP domain found in PC4 and SFRS1-interacting protein (PSIP); PSIP, also called CLL-associated antigen KW-7, dense fine speckles 70 kDa protein (DFS 70), lens epithelium-derived growth factor (LEDGF), or transcriptional coactivator p75/p52, acts as a transcriptional coactivator involved in neuroepithelial stem cell differentiation and neurogenesis. It contains a PWWP domain, which is necessary for DNA binding.


Pssm-ID: 438979 [Multi-domain]  Cd Length: 88  Bit Score: 41.12  E-value: 1.95e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  132 PHPLVWAKLKGFPFWPAKALRDKDGQVDAR-------FFGQHDRAwvpvnncYLMSKEI-PFSVKKTK-------SIFNS 196
Cdd:cd20151      3 PGDLIFAKMKGYPHWPARVDEVPDGAVKPPtnklpifFFGTHETA-------FLGPKDIfPYSENKEKygkpnkrKGFNE 75

                           90
                   ....*....|....*.
gi 1907139267  197 AMQEMEvyvENIRRKF 212
Cdd:cd20151     76 GLWEID---NNPKVKF 88
PWWP_DNMT3 cd05835
PWWP domain found in the DNA (cytosine-5)-methyltransferase 3 (DNMT3) family; The DNMT3 family ...
 135-171 2.07e-04

PWWP domain found in the DNA (cytosine-5)-methyltransferase 3 (DNMT3) family; The DNMT3 family includes DNMT3A and DNMT3B, which are required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNMT3A, also called DNA methyltransferase HsaIIIA, DNA MTase HsaIIIA, or M.HsaIIIA, modifies DNA in a non-processive manner and also methylates non-CpG sites. It may preferentially methylate DNA linker between 2 nucleosomal cores and is inhibited by histone H1. DNMT3A is recruited to trimethylated 'Lys-36' of histone H3 (H3K36me3) sites. DNMT3B, also called DNA methyltransferase HsaIIIB, DNA MTase HsaIIIB, or M.HsaIIIB, may preferentially methylate nucleosomal DNA within the nucleosome core region. DNMT3B may function as a transcriptional co-repressor by associating with CBX4 and independently of DNA methylation. Members of this family contains a PWWP domain that is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by DNMT3B is known to play a role in the inactivation of tumor suppressor genes. In addition, a point mutation in the PWWP domain of DNMT3B has been identified in patients with ICF (immunodeficiency, centromeric instability, and facial anomalie) syndrome , a rare autosomal recessive disorder characterized by hypomethylation of classical satellite DNA.


Pssm-ID: 438960 [Multi-domain]  Cd Length: 89  Bit Score: 41.09  E-value: 2.07e-04
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 1907139267  135 LVWAKLKGFPFWPAKALRDKDGQVDARFFGQHdraWV 171
Cdd:cd05835      5 LVWAKLKGSPWWPGIVVSHKDCGQKPPAEGSV---WV 38
ATP-synt_Fo_b cd06503
F-type ATP synthase, membrane subunit b; Membrane subunit b is a component of the Fo complex ...
 770-839 3.17e-04

F-type ATP synthase, membrane subunit b; Membrane subunit b is a component of the Fo complex of FoF1-ATP synthase. The F-type ATP synthases (FoF1-ATPase) consist of two structural domains: the F1 (assembly factor one) complex containing the soluble catalytic core, and the Fo (oligomycin sensitive factor) complex containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. F1 is composed of alpha (or A), beta (B), gamma (C), delta (D) and epsilon (E) subunits with a stoichiometry of 3:3:1:1:1, while Fo consists of the three subunits a, b, and c (1:2:10-14). An oligomeric ring of 10-14 c subunits (c-ring) make up the Fo rotor. The flux of protons through the ATPase channel (Fo) drives the rotation of the c-ring, which in turn is coupled to the rotation of the F1 complex gamma subunit rotor due to the permanent binding between the gamma and epsilon subunits of F1 and the c-ring of Fo. The F-ATP synthases are primarily found in the inner membranes of eukaryotic mitochondria, in the thylakoid membranes of chloroplasts or in the plasma membranes of bacteria. The F-ATP synthases are the primary producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). Alternatively, under conditions of low driving force, ATP synthases function as ATPases, thus generating a transmembrane proton or Na(+) gradient at the expense of energy derived from ATP hydrolysis. This group also includes F-ATP synthase that has also been found in the archaea Candidatus Methanoperedens.


Pssm-ID: 349951 [Multi-domain]  Cd Length: 132  Bit Score: 41.65  E-value: 3.17e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  770 STIAEIRRLRIEIEKLQWLHQQELAE-----------MKHNLELTMAEMRQSLEQERDRLIAEVKKQLELEKQQAVDETK 838
Cdd:cd06503     37 ESLEEAEKAKEEAEELLAEYEEKLAEaraeaqeiieeARKEAEKIKEEILAEAKEEAERILEQAKAEIEQEKEKALAELR 116


                   .
gi 1907139267  839 K 839
Cdd:cd06503    117 K 117
PWWP_HDGFL2 cd20149
PWWP domain found in Hepatoma-derived growth factor-related protein 2 (HDGFL2); HDGFL2, also ...
 132-202 5.77e-04

PWWP domain found in Hepatoma-derived growth factor-related protein 2 (HDGFL2); HDGFL2, also called HDGF-related protein 2 (HRP-2), or Hepatoma-derived growth factor 2 (HDGF-2), is involved in cellular growth control, through the regulation of cyclin D1 expression. It contains a PWWP domain, which is necessary for DNA binding.


Pssm-ID: 438977 [Multi-domain]  Cd Length: 84  Bit Score: 39.89  E-value: 5.77e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907139267  132 PHPLVWAKLKGFPFWPAKALRDKDGQVDAR-------FFGQHDRAWVPVNNCYLMSK-EIPFSVKKTKSIFNSAMQEME 202
Cdd:cd20149      3 PGDLVFAKMKGYPHWPARIDDIADGAVKPPpnkypifFFGTHETAFLGPKDLFPYDKyKDKYGKPNKRKGFNEGLWEIQ 81
PWWP_HDGF cd20148
PWWP domain found in Hepatoma-derived growth factor (HDGF); HDGF, also called high mobility ...
 132-194 6.73e-04

PWWP domain found in Hepatoma-derived growth factor (HDGF); HDGF, also called high mobility group protein 1-like 2 (HMG-1L2), is a heparin-binding protein that acts as a transcriptional repressor with mitogenic activity for fibroblasts. It contains a PWWP domain, which is necessary for DNA binding.


Pssm-ID: 438976 [Multi-domain]  Cd Length: 87  Bit Score: 39.62  E-value: 6.73e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  132 PHPLVWAKLKGFPFWPAK-------ALRDKDGQVDARFFGQHDRAwvpvnncYLMSKEIpFSVKKTKSIF 194
Cdd:cd20148      3 CGDLVFAKMKGYPHWPARidempeaAVKSTANKYQVFFFGTHETA-------FLGPKDL-FPYEESKEKF 64
PRK05759 PRK05759
F0F1 ATP synthase subunit B; Validated
 771-840 7.77e-04

F0F1 ATP synthase subunit B; Validated


Pssm-ID: 180240 [Multi-domain]  Cd Length: 156  Bit Score: 41.30  E-value: 7.77e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  771 TIAEIRRLRIEIEKLQWLHQQELAEMKH-----------NLELTMAEMRQSLEQERDRLIAEVKKQLELEKQQAVDETKK 839
Cdd:PRK05759    43 GLAAAERAKKELELAQAKYEAQLAEARAeaaeiieqakkRAAQIIEEAKAEAEAEAARIKAQAQAEIEQERKRAREELRK 122


                   .
gi 1907139267  840 K 840
Cdd:PRK05759   123 Q 123
PRK14971 PRK14971
DNA polymerase III subunit gamma/tau;
575-839 1.12e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237874 [Multi-domain]  Cd Length: 614  Bit Score: 42.84  E-value: 1.12e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  575 GEDPSGREGRKNKKDPKVPSPkqdaIGKPPPSSTSAGNQSPPETPVLTRSATqapaagvtvaaattstmstvtvTAPATA 654
Cdd:PRK14971   366 GDDASGGRGPKQHIKPVFTQP----AAAPQPSAAAAASPSPSQSSAAAQPSA----------------------PQSATQ 419

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  655 VTGSPVkkQRPLLPKETVPAVQRV-VWNASTVQQKEVTQSPSTSTI-TLVTSTQPAALVSSSGSASTLASAINADLPIAT 732
Cdd:PRK14971   420 PAGTPP--TVSVDPPAAVPVNPPStAPQAVRPAQFKEEKKIPVSKVsSLGPSTLRPIQEKAEQATGNIKEAPTGTQKEIF 497

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  733 ASADVAADIAKYTSKMM---DAIKGTMTEIYNDLSKNTTgstiaeirrlrIEIEKLQWLHQQELAEMK-----------H 798
Cdd:PRK14971   498 TEEDLQYYWQEFAGTRPqeeKALKETMINCRPKLLNGTT-----------FEVAVDNELQEKELTNLIpdllgflrgrlK 566

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|..
gi 1907139267  799 NLELTMaEMRQSLEQERDRLIAEVKK-QLELEKQQAVDETKK 839
Cdd:PRK14971   567 NSKITM-TVRVSEPTEVNRAYSSVEKfQYLAQKNPALLELRE 607
PWWP_NSD_rpt1 cd20144
first PWWP domain found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
 135-189 1.97e-03

first PWWP domain found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein family consists of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1 that are critical in maintaining the chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising in suppressing cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and play nonredundant 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, through mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (C5HCH). This model corresponds to the first PWWP domain. This family also includes Drosophila melanogaster maternal-effect sterile 4 (dMes4) that may act as a histone-lysine N-methyltransferase required for wing morphogenesis. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438972  Cd Length: 114  Bit Score: 39.22  E-value: 1.97e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907139267  135 LVWAKLKGFPFWPA------------KALRDKDG---QVDARFFGqhD---RAWVPVNNCylmskeIPFSVKK 189
Cdd:cd20144      4 LVWAKVSGHPWWPCmvtydpesglytKIKGSGGRtyrQYHVQFFG--DngeRGWVSEKSL------MPFEGKE 68
PWWP_MBD5 cd20141
PWWP domain found in methyl-CpG-binding domain protein 5 (MBD5) and similar proteins; MBD5, is ...
 135-174 2.87e-03

PWWP domain found in methyl-CpG-binding domain protein 5 (MBD5) and similar proteins; MBD5, is a methyl-CpG-binding protein that binds to heterochromatin. It does not interact with either methylated or unmethylated DNA. MBD5 acts as a transcriptional regulator responsible for 2q23.1 deletion syndrome. It belongs to the MBD family proteins, which play central roles in transcriptional regulation and development. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438969  Cd Length: 92  Bit Score: 38.07  E-value: 2.87e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1907139267  135 LVWAKLKGFPFWPAKALR------DKDGQVDARFFGQHDRAWVPVN 174
Cdd:cd20141      6 LVWGQIRGFPSWPGKLVSendvgkTNEGKVWVSWFGDHSFGQVEPD 51
Bromo_WDR9_II cd05496
Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 28-83 4.60e-03

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: 38.21  E-value: 4.60e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907139267   28 FQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYN 83
Cdd:cd05496     26 FRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYT 81
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
 465-620 6.07e-03

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 40.83  E-value: 6.07e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  465 QKPKNePEDPEDKEGSR--VDKEAPAIKRKPKPTNQVEV-KEEAKSNSPVSEKPDPTPAKDKASPEPEKDFVEKAKPSPH 541
Cdd:PTZ00449   583 KDPKH-PKDPEEPKKPKrpRSAQRPTRPKSPKLPELLDIpKSPKRPESPKSPKRPPPPQRPSSPERPEGPKIIKSPKPPK 661

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  542 PTK-------------DKLKGKDETDSPTVHLGLDSDSESELVIDLGEDPSGREGRKNK----------------KDPKV 592
Cdd:PTZ00449   662 SPKppfdpkfkekfydDYLDAAAKSKETKTTVVLDESFESILKETLPETPGTPFTTPRPlppklprdeefpfepiGDPDA 741

                          170       180
                   ....*....|....*....|....*...
gi 1907139267  593 PSPKQDAIGKPPPSSTSAGNQSPPETPV 620
Cdd:PTZ00449   742 EQPDDIEFFTPPEEERTFFHETPADTPL 769
PWWP_PWWP2 cd20140
PWWP domain found in the PWWP domain-containing protein 2 (PWWP2) family; The PWWP2 family ...
 136-149 6.20e-03

PWWP domain found in the PWWP domain-containing protein 2 (PWWP2) family; The PWWP2 family includes PWWP2A and its paralog PWWP2B. PWWP2A is a H2A.Z-specific chromatin binding protein which may play an important role in the neural crest stem cell migration and differentiation during early development. It is also required for proper mitosis progression. PWWP2A and PWWP2B form a stable complex with NuRD subunits MTA1/2/3:HDAC1/2:RBBP4/7, but not with MBD2/3, p66alpha/beta, and CHD3/4. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438968  Cd Length: 92  Bit Score: 36.86  E-value: 6.20e-03
                           10
                   ....*....|....
gi 1907139267  136 VWAKLKGFPFWPAK 149
Cdd:cd20140     10 VWGKIHGFPWWPGR 23
CCDC90-like pfam07798
Coiled-coil domain-containing protein 90-like; This entry includes coiled-coil ...
 748-839 7.14e-03

Coiled-coil domain-containing protein 90-like; This entry includes coiled-coil domain-containing proteins 90 (CCDC90) and related proteins. CCDC90A is a key regulator of the mitochondrial calcium uniporter (MCU) and hence was renamed MCUR1. A study in mammals and in yeast homolog fmp32 has reported that MCUR1 is a cytochrome c oxidase assembly factor and that it has an indirect role as a regulator of MCU, however, subsequent publications confirmed the function of MCUR1 as a regulator of MCU. The role of CCDC90B proteins is still not known.


Pssm-ID: 462268 [Multi-domain]  Cd Length: 175  Bit Score: 38.65  E-value: 7.14e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  748 MMDAIKGTMTEIYNDL-SK----NTTGSTIAEIRRLRIEIeklQWLHQQELAEMKHNLELTMAE---MRQSLEQERDRLI 819
Cdd:pfam07798   27 LRDLLNDSLENVSKDLvTKedleNETYLQKADLAELRSEL---QILEKSEFAALRSENEKLRRElekLKQRLREEITKLK 103

                           90       100
                   ....*....|....*....|
gi 1907139267  820 AEVKKQLELEKQQAVDETKK 839
Cdd:pfam07798  104 ADVRLDLNLEKGRIREELKA 123
PLN03209 PLN03209
translocon at the inner envelope of chloroplast subunit 62; Provisional
 481-695 7.98e-03

translocon at the inner envelope of chloroplast subunit 62; Provisional


Pssm-ID: 178748 [Multi-domain]  Cd Length: 576  Bit Score: 39.91  E-value: 7.98e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  481 RVDKEAPAIKRKPKPTNQVEVKEEAksnspvsekpdPTPAKDKASPEPE-------------KDFVEKAKPSPHPTKDKL 547
Cdd:PLN03209   327 RVPPKESDAADGPKPVPTKPVTPEA-----------PSPPIEEEPPQPKavvprplspytayEDLKPPTSPIPTPPSSSP 395

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  548 KGKDETDSPTVHLGLDSDSESELVIDLGEDPSGREGRK------------NKKDPKVPSPKQDAIGKPPPSSTSAGNQSp 615
Cdd:PLN03209   396 ASSKSVDAVAKPAEPDVVPSPGSASNVPEVEPAQVEAKktrplspyaryeDLKPPTSPSPTAPTGVSPSVSSTSSVPAV- 474

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907139267  616 PETPVLTrSATQAPAAGVTVAAATTSTMSTVTVTAPATAVTGSPVKKQRPLLPKETVPAVQRVVWNASTVQQKEVTQSPS 695
Cdd:PLN03209   475 PDTAPAT-AATDAAAPPPANMRPLSPYAVYDDLKPPTSPSPAAPVGKVAPSSTNEVVKVGNSAPPTALADEQHHAQPKPR 553
PWWP_ZCWPW1 cd20145
PWWP domain found in zinc finger CW-type PWWP domain protein 1 (ZCWPW1) and similar proteins; ...
 135-148 9.05e-03

PWWP domain found in zinc finger CW-type PWWP domain protein 1 (ZCWPW1) and similar proteins; ZCWPW1 is a histone H3K4me3 reader. It is associated with late-onset Alzheimer's disease (LOAD). In addition to the PWWP domain, ZCWPW1 contains a zinc finger CW (zf-CW) domain that is a histone modification reader for the histone H3 tail with trimethylated K4. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438973  Cd Length: 115  Bit Score: 37.14  E-value: 9.05e-03
                           10
                   ....*....|....
gi 1907139267  135 LVWAKLKGFPFWPA 148
Cdd:cd20145     11 LVWAKMPGYPWWPA 24
 
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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