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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1111745847 1371 ELQKCEEILQKIMKFRHSWPFREPVSAEEAEDYQDVITSPMDLTTMQGKFKSSEYHSASDFIEDMKLIFSNAEEYNQPSS 1450
Cdd:cd05505      1 ELQKCEEILSKILKYRFSWPFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGS 80

                           90
                   ....*....|....*..
gi 1111745847 1451 NVLTCMSRTEEAFVELL 1467
Cdd:cd05505     81 YVLSCMRKTEQCCVNLL 97

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

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1111745847 1204 RCKVCRRKGEDDKLILCDECNKAFHLFCLRPALYRIPAGEWLCPAC 1249
Cdd:cd15628      1 KCKVCRKKGEDDKLILCDECNQAFHLFCLRPALYEVPDGEWMCPAC 46

WSTF, HB1, Itc1p, MBD9 motif 1; A conserved alpha helical motif that along with the WHIM2 and WHIM3 motifs, and the DDT domain comprise an alpha helical module found in diverse eukaryotic chromatin proteins.Based on the Ioc3 structure, this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. The conserved basic residue in WHIM1 is involved in packing with the DDT motif. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognising and DNA binding domains, some of which discriminate methylated DNA.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1111745847  724 SEFLEKLETAEVFELDPQEKVSLLLALCHRILMTYSVEDHVE 765
Cdd:pfam15612    5 PGLLETLKKGGYYELSPEEKLKILKALCDLLLSSSAIRDEIE 46

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1111745847  761 EDHVEAVHQKSAEMWKERVATLKEANDRKRAEKQKRKE-QMETKTDGDVLIKAEKKKestvkketpKVLPKEEPEPEDMI 839
Cdd:pfam17380  459 QQQVERLRQQEEERKRKKLELEKEKRDRKRAEEQRRKIlEKELEERKQAMIEEERKR---------KLLEKEMEERQKAI 529

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1111745847  840 STVKSRRLMSIQAKKEKEEQERLNKVRMEKEAEEERIRRQKAATEK 885
Cdd:pfam17380  530 YEEERRREAEEERRKQQEMEERRRIQEQMRKATEERSRLEAMERER 575

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1111745847 1371 ELQKCEEILQKIMKFRHSWPFREPVSAEEAEDYQDVITSPMDLTTMQGKFKSSEYHSASDFIEDMKLIFSNAEEYNQPSS 1450
Cdd:cd05505      1 ELQKCEEILSKILKYRFSWPFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGS 80

                           90
                   ....*....|....*..
gi 1111745847 1451 NVLTCMSRTEEAFVELL 1467
Cdd:cd05505     81 YVLSCMRKTEQCCVNLL 97

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

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1111745847 1204 RCKVCRRKGEDDKLILCDECNKAFHLFCLRPALYRIPAGEWLCPAC 1249
Cdd:cd15628      1 KCKVCRKKGEDDKLILCDECNQAFHLFCLRPALYEVPDGEWMCPAC 46

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

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1111745847 1375 CEEILQKIMKFRHSWPFREPVSAEEAEDYQDVITSPMDLTTMQGKFKSSEYHSASDFIEDMKLIFSNAEEYNQPSS 1450
Cdd:pfam00439    1 CLEILDKLMEHPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGS 76

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

                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 1111745847  1204 RCKVCRRKGEDDKLILCDECNKAFHLFCLRPAL-YRIPAGEWLCPAC 1249
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLlEEEPDGKWYCPKC 47

Williams-Beuren syndrome DDT (WSD), D-TOX E motif; This family represents the combined alpha-helical module found in diverse eukaryotic chromatin proteins. Based on the Ioc3 structure, the N-terminus of this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. The acidic residue from the GxD signature at the N-terminus is a major determinant of the interaction between the ISWI and WHIM motifs. The N-terminal portion also contacts the inter-nucleosomal linker DNA. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognizing and DNA binding domains, some of which discriminate methylated DNA. The WSD module constitutes the inter-nucleosomal linker DNA binding site in the major groove of DNA, and was first identified as WSD, the D-TOX E motif of plant homeodomains homologous with the mutant transcription factor causing Williams-Beuren syndrome in association with the DDT-domain.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1111745847  898 LRRTPLGTDRNHNRYWLFSDVVPGLYIEKGWvhesidysftlppeeepvlteeeeeeeevkkeeetedgekedegsiisa 977
Cdd:pfam15613    1 IRSLPLGRDRRYNRYWWFDPGTGRLFVESPS------------------------------------------------- 31

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1111745847  978 sndisqqgapshessiettvpkqgQNLWFVCDTPKDFDELLESLHPQGVRESELKIRLQ 1036
Cdd:pfam15613   32 ------------------------DGEWGVYSSKEQLDALIASLNPRGVRESALKEALE 66

MAEBL; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1111745847 1519 SKRKVDNSRRKNAKRNKDDSESEEDEDEDDEEEDDERSRKQRNGKQS-KKASSRRKEDNSRRKNTKRNKDDSESEEEEDD 1597
Cdd:PTZ00121  1403 DKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAkKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEA 1482

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1111745847 1598 DEEDEEEEEDDEGSKK----QKNGKQDKKNSSRKKGNSRQRNTKRNKDESEDDEDDDDDEEEEERSKKQKNGKRSKKASS 1673
Cdd:PTZ00121  1483 KKADEAKKKAEEAKKKadeaKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEE 1562

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1111745847 1674 RRKEDNSRRKNTKRNKD-----------DSESEEDDDEEEEDEKMKKQKNRKQTTNRRKQDNSR---QKKTKQNKDDSES 1739
Cdd:PTZ00121  1563 KKKAEEAKKAEEDKNMAlrkaeeakkaeEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKkaeEEKKKVEQLKKKE 1642

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1111745847 1740 EEDDDEDEPVRKSRRTNRKDYHEQDSDSEQDSRRTGLRRTSRGVTDNKEASSDEDSGGQRHSKRLKR 1806
Cdd:PTZ00121  1643 AEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKK 1709

MAEBL; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1111745847  765 EAVHQKSAEMWK--ERVATLKEANDRKRAEKQKRKEQMETKTDGDVLIKAEK-KKESTVKKETPKVLPKEEPE---PEDM 838
Cdd:PTZ00121  1642 EAEEKKKAEELKkaEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEAlKKEAEEAKKAEELKKKEAEEkkkAEEL 1721

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1111745847  839 ISTVKSRRLMSIQAKKEKEEQERLNKVRMEKEAEEERIRRQKAATEKAFQDAVTKAKLVLR 899
Cdd:PTZ00121  1722 KKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIE 1782

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1111745847 1371 ELQKCEEILQKIMKFRHSWPFREPVSAEEAEDYQDVITSPMDLTTMQGKFKSSEYHSASDFIEDMKLIFSNAEEYNQPSS 1450
Cdd:cd05505      1 ELQKCEEILSKILKYRFSWPFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGS 80

                           90
                   ....*....|....*..
gi 1111745847 1451 NVLTCMSRTEEAFVELL 1467
Cdd:cd05505     81 YVLSCMRKTEQCCVNLL 97

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1111745847 1374 KCEEILQKIMKFRHSWPFREPVSAEEAEDYQDVITSPMDLTTMQGKFKSSEYHSASDFIEDMKLIFSNAEEYNQPSSNVL 1453
Cdd:cd05509      5 QLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEYY 84

                           90
                   ....*....|....*.
gi 1111745847 1454 TCMSRTEEAFVELLQK 1469
Cdd:cd05509     85 KCANKLEKFFWKKLKE 100

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1111745847 1371 ELQKCEEILQKIMKFRH--SWPFREPVSAEEAEDYQDVITSPMDLTTMQGKFKSSEYHSASDFIEDMKLIFSNAEEYNQP 1448
Cdd:cd04369      1 LKKKLRSLLDALKKLKRdlSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGP 80

                           90
                   ....*....|....*....
gi 1111745847 1449 SSNVLTCMSRTEEAFVELL 1467
Cdd:cd04369     81 GSPIYKDAKKLEKLFEKLL 99

bromo domain;

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1111745847  1373 QKCEEILQKIMKFRHSWPFREPVSAEEAEDYQDVITSPMDLTTMQGKFKSSEYHSASDFIEDMKLIFSNAEEYNQPSSNV 1452
Cdd:smart00297   10 ELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYNGPDSEV 89

                            90
                    ....*....|....*..
gi 1111745847  1453 LTCMSRTEEAFVELLQK 1469
Cdd:smart00297   90 YKDAKKLEKFFEKKLRE 106

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

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1111745847 1204 RCKVCRRKGEDDKLILCDECNKAFHLFCLRPALYRIPAGEWLCPAC 1249
Cdd:cd15627      1 RCRICRRKGDAEKMLLCDGCDRGHHMYCLRPPLKKVPEGDWFCPDC 46

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1111745847 1375 CEEILQKIMKFRHSWPFREPV--SAEEAEDYQDVITSPMDLTTMQGKFKSSEYHSASDFIEDMKLIFSNAEEYNQPSSNV 1452
Cdd:cd05506      5 CGTLLRKLMKHKWGWVFNAPVdvVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDV 84

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1111745847 1371 ELQKCEEILQKIMKFRHS---WPFREPVS--AEEAEDYQDVITSPMDLTTMQGKFKSSEYHSASDFIEDMKLIFSNAEEY 1445
Cdd:cd05499      1 ELKFCEEVLKELMKPKHSaynWPFLDPVDpvALNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTF 80

                           90
                   ....*....|....*...
gi 1111745847 1446 NQPSSNVLTCMSRTEEAF 1463
Cdd:cd05499     81 NPEGTDVYMMGHQLEEVF 98

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1111745847 1371 ELQKCEEILQKIMKFRHSWPFREPVSAEEAEDYQDVITSPMDLTTMQGKFKSSEYHSASDFIEDMKLIFSNAEEYNQPSS 1450
Cdd:cd05503      1 DLALCETILDEMEAHEDAWPFLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDS 80

                   ..
gi 1111745847 1451 NV 1452
Cdd:cd05503     81 EV 82

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1111745847 1386 RHSWPFREPVSAEEAEDYQDVITSPMDLTTMQGKFKSSEYHSASDFIEDMKLIFSNAEEYNQPSSNVLTCMSRTEEAFVE 1465
Cdd:cd05510     24 EHSTPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYNSDPSHPLRRHANFMKKKAE 103

                   ....*..
gi 1111745847 1466 LLQKSLP 1472
Cdd:cd05510    104 HLLKLIP 110

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1111745847 1372 LQKceEILQKIMKFRHSWPFREPVSAEEAE--DYQDVITSPMDLTTMQGKFKSSEYHSASDFIEDMKLIFSNAEEYNQPS 1449
Cdd:cd05497      9 LLK--VVLKALWKHKFAWPFQQPVDAVKLNlpDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKPG 86

                           90
                   ....*....|....*.
gi 1111745847 1450 SNVLTCMSRTEEAFVE 1465
Cdd:cd05497     87 DDVVLMAQTLEKLFLQ 102

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1111745847 1375 CEEILQKIMKFRHSWPFREPVS--AEEAEDYQDVITSPMDLTTMQGKFKSSEYHSASDFIEDMKLIFSNAEEYNQPSSNV 1452
Cdd:cd05500      9 LLSSIRSLKRLKDARPFLVPVDpvKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNGPEHPV 88

                           90
                   ....*....|.
gi 1111745847 1453 LTCMSRTEEAF 1463
Cdd:cd05500     89 SQMGKRLQAAF 99

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

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1111745847 1204 RCKVCRRKGEDDKLILCDECNKAFHLFCLRPALYRIPAGEWLCPAC 1249
Cdd:cd15515      1 ICQVCGRGDDEDKLLLCDGCDDSYHTFCLIPPLPDIPPGDWRCPKC 46

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

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                   ....*....|....*....|....*....|....*....|....*
gi 1111745847 1205 CKVCRRKGEDDKLILCDECNKAFHLFCLRPALYRIPAGEWLCPAC 1249
Cdd:cd15545      2 CQICRSGDNEDQLLLCDGCDRGYHTYCFKPKMTNVPEGDWFCPEC 46

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

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                   ....*....|....*....|....*....|....*....|....*
gi 1111745847 1205 CKVCRRKGEDDKLILCDECNKAFHLFCLRPALYRIPAGEWLCPAC 1249
Cdd:cd15604      2 CRMCSRGDEDDKLLLCDGCDDNYHTFCLLPPLPEPPKGIWRCPKC 46

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.

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                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1111745847 1373 QKCEEILQKIMKFRHSWPFREPVSAEEAEDYQDVITSPMDLTTMQGKFKSSEYHSASDFIEDMKLIFSNAEEYN 1446
Cdd:cd05496      8 KQCKELVNLMWDCEDSEPFRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYT 81

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

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                   ....*....|....*....|....*....|....*....|....*
gi 1111745847 1205 CKVCRRKGEDDKLILCDECNKAFHLFCLRPALYRIPAGEWLCPAC 1249
Cdd:cd15594      2 CQTCRQPGDDNKMLVCDTCDKGYHTFCLQPVMTTIPKNGWKCKNC 46

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

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                   ....*....|....*....|....*....|....*....|....*.
gi 1111745847 1204 RCKVCRRKGEDDKLILCDECNKAFHLFCLRPALYRIPAGEWLCPAC 1249
Cdd:cd15536      1 YCEVCGRSDREDRLLLCDGCDAGYHMECLTPPLDEVPIEEWFCPEC 46

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

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                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1111745847 1355 ELVRQSSKPPSRKKDVELQKCEEILQKIMKFR----------HSWPFREPVSAEEAEDYQDVITSPMDLTTMQGKFKSSE 1424
Cdd:COG5076    123 MAHLKTSVKKRKTPKIEDELLYADNKAIAKFKkqlflrdgrfLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGR 202

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 1111745847 1425 YHSASDFIEDMKLIFSNAEEYNQPSSNVLTCMSRTEEAFVELLQK 1469
Cdd:COG5076    203 YKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLIEE 247

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.

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                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1111745847 1391 FREPVSAEEAEDYQDVITSPMDLTTMQGKFKSSEYHSASDFIEDMKLIFSNAEEYN 1446
Cdd:cd05512     22 FSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYN 77

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

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                   ....*....|....*....|....*....|....*....|....*
gi 1111745847 1205 CKVCRRKGEDDKLILCDECNKAFHLFCLRPALYRIPAGEWLCPAC 1249
Cdd:cd15527      2 CSVCQDSGNADNLLFCDACDKGFHMECHDPPLTRMPKGKWVCQIC 46

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

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                   ....*....|....*....|....*....|....*....|....*
gi 1111745847 1205 CKVCRRKGEDDKLILCDECNKAFHLFCLRPALYRIPAGEWLCPAC 1249
Cdd:cd15602      2 CLFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGDWRCPKC 46

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

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                   ....*....|....*....|....*....|....*....|....*
gi 1111745847 1205 CKVCRRKGEDDKLILCDECNKAFHLFCLRPALYRIPAGEWLCPAC 1249
Cdd:cd15603      2 CLVCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKC 46

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

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                   ....*....|....*....|....*....|....*....|....*.
gi 1111745847 1205 CKVCRRKGEDDKLILCDECNKAFHLFCLRPALYRIPA-GEWLCPAC 1249
Cdd:cd15616      2 CHVCGGKQDPDKQLMCDECDMAFHIYCLNPPLSSIPDdEDWYCPEC 47

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

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1111745847 1205 CKVCRRKGEDDKLILCDECNKAFHLFCLRPALYRIPAGEWLCPAC 1249
Cdd:cd15630      3 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPEGDWFCPAC 47