ATP-utilizing chromatin assembly and remodelling N-terminal; ACF (for ATP-utilizing chromatin assembly and remodelling factor) is a chromatin-remodelling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. The WAC (WSTF/Acf1/cbp146) domain is an approximately 110-residue module present at the N-termini of Acf1-related proteins in a variety of organizms. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440885175   23 EVFLCKYTHEIFRTYDEFFERTILCNSLVWSCAVTGKPGLTYQEALESEKKARLSLQ-NFPNALAVPLLHLTALTHRSRL 101
Cdd:pfam10537    1 EVFVIPLTGEIFRDYEEYLERLDLYNQRIWSCEITGKSNLTYFEALESEEKARKKLEeKFPESLREPVLRLVQFSTRSRL 80

                           90       100
                   ....*....|....*....|.
gi 1440885175  102 HEICDDVYAYVKDRFFPGEMV 122
Cdd:pfam10537   81 DDLVDDVYEEFKDRFFPGEEV 101

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 1440885175  759 TYILPLGRDRLYRRYWIF-PSAGALFVEDDFFGltedmleprptpepkieevlsaespvktdgateelvlvqntsppvnr 837
Cdd:pfam15613    1 IRSLPLGRDRRYNRYWWFdPGTGRLFVESPSDG----------------------------------------------- 33

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1440885175  838 pnQWYFYSTTEEVEQLIEALNPRGLRESSLKETLTLER 875
Cdd:pfam15613   34 --EWGVYSSKEQLDALIASLNPRGVRESALKEALEKIK 69

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 1440885175  570 RLSNHGLLKKLSCTSVYDLLPGEKLKILHSMCGKLLTLVSTRDFIE 615
Cdd:pfam15612    1 REDLPGLLETLKKGGYYELSPEEKLKILKALCDLLLSSSAIRDEIE 46

ATP-utilizing chromatin assembly and remodelling N-terminal; ACF (for ATP-utilizing chromatin assembly and remodelling factor) is a chromatin-remodelling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. The WAC (WSTF/Acf1/cbp146) domain is an approximately 110-residue module present at the N-termini of Acf1-related proteins in a variety of organizms. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440885175   23 EVFLCKYTHEIFRTYDEFFERTILCNSLVWSCAVTGKPGLTYQEALESEKKARLSLQ-NFPNALAVPLLHLTALTHRSRL 101
Cdd:pfam10537    1 EVFVIPLTGEIFRDYEEYLERLDLYNQRIWSCEITGKSNLTYFEALESEEKARKKLEeKFPESLREPVLRLVQFSTRSRL 80

                           90       100
                   ....*....|....*....|.
gi 1440885175  102 HEICDDVYAYVKDRFFPGEMV 122
Cdd:pfam10537   81 DDLVDDVYEEFKDRFFPGEEV 101

bromo domain;

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440885175  1366 LVRHEDSWPFMKLVSRTQVPDYYDIIKKPIALSTIREKVNNCEYQTAAEYIEDVELMFSNCLEYNPHNTNEAKAGLRLQA 1445
Cdd:smart00297   19 LDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYNGPDSEVYKDAKKLEK 98

                    ....*....
gi 1440885175  1446 FFHSELQRL 1454
Cdd:smart00297   99 FFEKKLREL 107

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 1440885175  759 TYILPLGRDRLYRRYWIF-PSAGALFVEDDFFGltedmleprptpepkieevlsaespvktdgateelvlvqntsppvnr 837
Cdd:pfam15613    1 IRSLPLGRDRRYNRYWWFdPGTGRLFVESPSDG----------------------------------------------- 33

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1440885175  838 pnQWYFYSTTEEVEQLIEALNPRGLRESSLKETLTLER 875
Cdd:pfam15613   34 --EWGVYSSKEQLDALIASLNPRGVRESALKEALEKIK 69

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440885175 1369 HEDSWPFMKLVSRTQVPDYYDIIKKPIALSTIREKVNNCEYQTAAEYIEDVELMFSNCLEYNPHNTNEAKAGLRLQAFFH 1448
Cdd:COG5076    163 RFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFL 242

                           90       100
                   ....*....|....*....|
gi 1440885175 1449 SELQRlgLADRMTPPQKRPR 1468
Cdd:COG5076    243 KLIEE--IPEEMLELSIKPG 260

domain in different transcription and chromosome remodeling factors;

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1440885175   406 PELFGDALMVLEFLHAFGELFDLKDEFPdgvTLEVLEEAVVGSDPEGPLCELLFFFLSAIFQ 467
Cdd:smart00571    1 NEAFGDLLMVYEFLRSFGKVLGLSPFRA---TLEDFIAALKCRDQNGLLTEVHVVLLRAILK 59

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 1440885175  570 RLSNHGLLKKLSCTSVYDLLPGEKLKILHSMCGKLLTLVSTRDFIE 615
Cdd:pfam15612    1 REDLPGLLETLKKGGYYELSPEEKLKILKALCDLLLSSSAIRDEIE 46

Borrelia P83/100 protein; This family consists of several Borrelia P83/P100 antigen proteins.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440885175  612 DFIEDNADEQRAAKQElrELKAEQHRREREEAAERVRKRK--EEKLREQElKLKEKHERLKEEAKNGGQLAGEEMDTSTE 689
Cdd:pfam05262  237 DFAQDNADKQRDEVRQ--KQQEAKNLPKPADTSSPKEDKQvaENQKREIE-KAQIEIKKNDEEALKAKDHKAFDLKQESK 313

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1440885175  690 SQEGHAEQHTEDeeeqpAKSKKVKKTNGTTKEKPSGEVEMK 730
Cdd:pfam05262  314 ASEKEAEDKELE-----AQKKREPVAEDLQKTKPQVEAQPT 349

ATP-utilizing chromatin assembly and remodelling N-terminal; ACF (for ATP-utilizing chromatin assembly and remodelling factor) is a chromatin-remodelling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. The WAC (WSTF/Acf1/cbp146) domain is an approximately 110-residue module present at the N-termini of Acf1-related proteins in a variety of organizms. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440885175   23 EVFLCKYTHEIFRTYDEFFERTILCNSLVWSCAVTGKPGLTYQEALESEKKARLSLQ-NFPNALAVPLLHLTALTHRSRL 101
Cdd:pfam10537    1 EVFVIPLTGEIFRDYEEYLERLDLYNQRIWSCEITGKSNLTYFEALESEEKARKKLEeKFPESLREPVLRLVQFSTRSRL 80

                           90       100
                   ....*....|....*....|.
gi 1440885175  102 HEICDDVYAYVKDRFFPGEMV 122
Cdd:pfam10537   81 DDLVDDVYEEFKDRFFPGEEV 101

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 1440885175 1118 RCKVCRRKGDAENMLLCDGCGRGYHIFCVRPKLKAVPSEDWFCPEC 1163
Cdd:cd15627      1 RCRICRRKGDAEKMLLCDGCDRGHHMYCLRPPLKKVPEGDWFCPDC 46

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 1440885175 1361 LLSVDLVRHEDSWPFMKLVSRTQVPDYYDIIKKPIALSTIREKVNNCEYQTAAEYIEDVELMFSNCLEYNPHNTNEAKAG 1440
Cdd:cd04369      9 LDALKKLKRDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGPGSPIYKDA 88

                           90
                   ....*....|.
gi 1440885175 1441 LRLQAFFHSEL 1451
Cdd:cd04369     89 KKLEKLFEKLL 99

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

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1440885175 1118 RCKVCRRKGDAENMLLCDGCGRGYHIFCVRPKLKAVPSEDWFCPEC 1163
Cdd:cd15544      1 RCKVCRKKGDPDNMILCDGCDKAFHLYCLRPALREVPSGDWFCPAC 46

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440885175 1355 ELSACELLSVDLVRHEDSWPFMKLVSRTqVPDYYDIIKKPIALSTIREKV---NNCEYQTAAEYIEDVELMFSNCLEYNP 1431
Cdd:cd05502      5 DQRKCERLLLELYCHELSLPFHEPVSPS-VPNYYKIIKTPMDLSLIRKKLqpkSPQHYSSPEEFVADVRLMFKNCYKFNE 83

                           90       100
                   ....*....|....*....|...
gi 1440885175 1432 HNTNEAKAGLRLQAFFHSELQRL 1454
Cdd:cd05502     84 EDSEVAQAGKELELFFEEQLKEI 106

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.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440885175 1371 DSWPFMKLVSRTQVPDYYDIIKKPIALSTIREKVNNCEYQTAAEYIEDVELMFSNCLEYN 1430
Cdd:cd05511     17 DSWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYN 76

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 1440885175 1355 ELSACELLSVDLVR---HEDSWPFMKLVS--RTQVPDYYDIIKKPIALSTIREKVNNCEYQTAAEYIEDVELMFSNCLEY 1429
Cdd:cd05499      1 ELKFCEEVLKELMKpkhSAYNWPFLDPVDpvALNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTF 80

                           90       100
                   ....*....|....*....|..
gi 1440885175 1430 NPHNTNEAKAGLRLQAFFHSEL 1451
Cdd:cd05499     81 NPEGTDVYMMGHQLEEVFNDKW 102

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
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1440885175 1358 ACELLSVDLVRH-EDSWPFMKLVSRTQVPDYYDIIKKPIALSTIREKVNNCEYQTAAEYIEDVELMFSNCLEYNPHNTN 1435
Cdd:cd05510     11 SLDKVLNELKTYtEHSTPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYNSDPSH 89

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

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1440885175 1119 CKVCRRKGDAENMLLCDGCGRGYHIFCVRPKLKAVPSEDWFCPEC 1163
Cdd:cd15543      2 CRKCGLSDHPEWILLCDRCDAGYHTACLRPPLMIIPDGNWFCPPC 46

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

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1440885175 1118 RCKVCRRKGDAENMLLCDGCGRGYHIFCVRPKL--KAVPSEDWFCPECRPK 1166
Cdd:pfam00628    1 YCAVCGKSDDGGELVQCDGCDDWFHLACLGPPLdpAEIPSGEWLCPECKPK 51

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

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1440885175 1119 CKVCRRKGDAENMLLCDGCGRGYHIFCVRPKLKAVPSEDWFCPEC 1163
Cdd:cd15629      2 CLVCRKGDNDEYLLLCDGCDRGCHMYCHRPKMLQVPEGDWFCPNC 46

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 1440885175 1118 RCKVCRRKGDAENMLLCDGCGRGYHIFCVRPKLKAVPSEDWFCPEC 1163
Cdd:cd15628      1 KCKVCRKKGEDDKLILCDECNQAFHLFCLRPALYEVPDGEWMCPAC 46

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

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1440885175 1369 HEDSWPFMKLVSRTQVPDYYDIIKKPIALSTIREKVNNCEYQTAAEYIEDVELMFSNCLEYN 1430
Cdd:cd05515     21 RRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYN 82

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

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1440885175 1119 CKVCRRKGDAENMLLCDGCGRGYHIFCVRPKLKAVPSEDWFCPEC 1163
Cdd:cd15519      2 CEVCGLDDNEGEVLLCDGCDAEYHTSCLDPPLGEIPPGTWFCPSC 46

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 1440885175 1355 ELSACELLSVDLVRHEDSWPFMKLVSRTQVPDYYDIIKKPIALSTIREKVNNCEYQTAAEYIEDVELMFSNCLEYNPHNT 1434
Cdd:cd05505      1 ELQKCEEILSKILKYRFSWPFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGS 80

                   .
gi 1440885175 1435 N 1435
Cdd:cd05505     81 Y 81

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.

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                    ....*....|....*....|....*....|....*....|....*..
gi 1440885175  1118 RCKVCRRKGDAENMLLCDGCGRGYHIFCVRPKLK-AVPSEDWFCPEC 1163
Cdd:smart00249    1 YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLeEEPDGKWYCPKC 47

domain in different transcription and chromosome remodeling factors;

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1440885175   406 PELFGDALMVLEFLHAFGELFDLKDEFPdgvTLEVLEEAVVGSDPEGPLCELLFFFLSAIFQ 467
Cdd:smart00571    1 NEAFGDLLMVYEFLRSFGKVLGLSPFRA---TLEDFIAALKCRDQNGLLTEVHVVLLRAILK 59

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

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1440885175 1119 CKVCRRKGDAENMLLCDGCGRGYHIFCVRPKLKAVP-SEDWFCPEC 1163
Cdd:cd15525      2 CHVCGGKQDPEKQLLCDECDMAYHLYCLDPPLTSLPdDDEWYCPDC 47

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.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1440885175 1375 FMKLVSRTQVPDYYDIIKKPIALSTIREKVNNCEYQTAAEYIEDVELMFSNCLEYN 1430
Cdd:cd05518     27 FMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYN 82

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1440885175 1360 ELLSVdLVRHED------SWPFMKLVSRTQVPDYYDIIKKPIALSTIREKVNNCEYQTAAEYIEDVELMFSNCLEYNPHN 1433
Cdd:cd05516      8 KIVDV-VIKYKDsdgrqlAEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTFNLEG 86

                           90       100
                   ....*....|....*....|.
gi 1440885175 1434 TNEAKAGLRLQAFFHSELQRL 1454
Cdd:cd05516     87 SLIYEDSIVLQSVFKSARQKI 107

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 1440885175 1357 SACELLSVDLVRHEDSWPFMKLVSRTQVPDYYDIIKKPIALSTIREKVNNCEYQTAAEYIEDVELMFSNCLEYNPHNTNE 1436
Cdd:cd05496      8 KQCKELVNLMWDCEDSEPFRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYTPNKRSR 87

                           90
                   ....*....|....*....
gi 1440885175 1437 AKA-GLRLQAFFHSELQRL 1454
Cdd:cd05496     88 IYSmTLRLSALFEEHIKKI 106

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

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1440885175 1374 PFMKLVSRTQVPDYYDIIKKPIALSTIREKVNNCEYQTAAEYIEDVELMFSNCLEYNPHNTNEAKAGLRLQAFFH 1448
Cdd:cd05522     27 HFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYKDAVLLEKEAR 101

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

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1440885175 1118 RCKVCRRKGDAENMLLCDGCGRGYHIFCVrpKLKAVPSEDWFCPEC 1163
Cdd:cd15529      1 TCTKCGDPHDEDKMMFCDQCDRGYHTFCV--GLRSIPDGRWICPLC 44

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

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1440885175 1119 CKVCRRKGDAENMLLCDGCGRGYHIFCVRPKLKAVPS-EDWFCPEC 1163
Cdd:cd15617      2 CYVCGGKQDAHMQLLCDECNMAYHIYCLNPPLDKIPEdEDWYCPSC 47

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

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1440885175 1119 CKVCRRKGDAENMLLCDGCGRGYHIFCVRPKLKAVPSEDWFCPEC 1163
Cdd:cd15605      2 CHTCGRGDGEESMLLCDGCDDSYHTFCLLPPLSEVPKGDWRCPKC 46

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

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1440885175 1119 CKVCRRKGDAENMLLCDGCGRGYHIFCVRPKLKAVPSEDWFCPEC 1163
Cdd:cd15595      2 CQTCRKPGEDSKMLVCEACDKGYHTFCLKPAMESLPTDSWKCKAC 46