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 1972241557   23 PVFYCKATKEVFLTHEEYFNRMILLNSTAWSCSLTRKSNLTYFEAIASEREAEQELC-NFPTALEIPITLIVHkYTNRGR 101
Cdd:pfam10537    1 EVFVIPLTGEIFRDYEEYLERLDLYNQRIWSCEITGKSNLTYFEALESEEKARKKLEeKFPESLREPVLRLVQ-FSTRSR 79

                           90       100
                   ....*....|....*....|..
gi 1972241557  102 FEDLVNDIYHILKDRFFNNEEV 123
Cdd:pfam10537   80 LDDLVDDVYEEFKDRFFPGEEV 101

domain in different transcription and chromosome remodeling factors;

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1972241557   457 NAEFEDYLFIFQFFNSFKQLLPLKEIRGSdevqFSDIIIAIKCNDpQNSSFADLLRVLLSIRTDIADE 524
Cdd:smart00571    1 NEAFGDLLMVYEFLRSFGKVLGLSPFRAT----LEDFIAALKCRD-QNGLLTEVHVVLLRAILKDEGE 63

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 1972241557  795 ISDIRLGSDRAYRRYIVM-ENLSAILVETATFQElgiycdepsiiddplnllenehqevfictgnmdtcrvhgdesnnwt 873
Cdd:pfam15613    1 IRSLPLGRDRRYNRYWWFdPGTGRLFVESPSDGE---------------------------------------------- 34

                           90       100
                   ....*....|....*....|....
gi 1972241557  874 rWSYIRDREQFEQLLKSLNPRGNR 897
Cdd:pfam15613   35 -WGVYSSKEQLDALIASLNPRGVR 57

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 1972241557   23 PVFYCKATKEVFLTHEEYFNRMILLNSTAWSCSLTRKSNLTYFEAIASEREAEQELC-NFPTALEIPITLIVHkYTNRGR 101
Cdd:pfam10537    1 EVFVIPLTGEIFRDYEEYLERLDLYNQRIWSCEITGKSNLTYFEALESEEKARKKLEeKFPESLREPVLRLVQ-FSTRSR 79

                           90       100
                   ....*....|....*....|..
gi 1972241557  102 FEDLVNDIYHILKDRFFNNEEV 123
Cdd:pfam10537   80 LDDLVDDVYEEFKDRFFPGEEV 101

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 1972241557 1312 TLIETLLKEAMRQECSWPFLQPVDSKEVPDYYDVIKRPMNLRTMMNKIKQRIYNKPIEVRNDFQLILSNCETYNEPENEI 1391
Cdd:cd05509      4 TQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEY 83

                           90
                   ....*....|....*...
gi 1972241557 1392 YKLSRELHDFMADRLDEI 1409
Cdd:cd05509     84 YKCANKLEKFFWKKLKEL 101

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972241557 1231 LSLKNRKSNGSMPVTPSERPVRNVSvRIFDVENENVLTDEDDSDGENTRKRKTPTSKKSVTSTPTTNDISRVIIPniKEK 1310
Cdd:COG5076     71 GSMANVNDDLENVGGITYSPFEKNR-PESLRFDEIVFLAIESVTPESGLGSLLMAHLKTSVKKRKTPKIEDELLY--ADN 147

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972241557 1311 MTLIETLLKEAMRQ--ECSWPFLQPVDSKEVPDYYDVIKRPMNLRTMMNKIKQRIYNKPIEVRNDFQLILSNCETYNEPE 1388
Cdd:COG5076    148 KAIAKFKKQLFLRDgrFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPD 227

                          170       180
                   ....*....|....*....|.
gi 1972241557 1389 NEIYKLSRELHDFMADRLDEI 1409
Cdd:COG5076    228 SSVYVDAKELEKYFLKLIEEI 248

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 1972241557  1100 CRSCRRKAAAHDLVLCSECDNCYHLKCAKLDVNSDAPAD-WMCTSC 1144
Cdd:smart00249    2 CSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEEEPDGkWYCPKC 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 1972241557  795 ISDIRLGSDRAYRRYIVM-ENLSAILVETATFQElgiycdepsiiddplnllenehqevfictgnmdtcrvhgdesnnwt 873
Cdd:pfam15613    1 IRSLPLGRDRRYNRYWWFdPGTGRLFVESPSDGE---------------------------------------------- 34

                           90       100
                   ....*....|....*....|....
gi 1972241557  874 rWSYIRDREQFEQLLKSLNPRGNR 897
Cdd:pfam15613   35 -WGVYSSKEQLDALIASLNPRGVR 57

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 1972241557  629 HPGIMEKLRTLTVFDLEAPERLEIVKTLIYQLLTYSKFRGHLE 671
Cdd:pfam15612    4 LPGLLETLKKGGYYELSPEEKLKILKALCDLLLSSSAIRDEIE 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 1972241557   23 PVFYCKATKEVFLTHEEYFNRMILLNSTAWSCSLTRKSNLTYFEAIASEREAEQELC-NFPTALEIPITLIVHkYTNRGR 101
Cdd:pfam10537    1 EVFVIPLTGEIFRDYEEYLERLDLYNQRIWSCEITGKSNLTYFEALESEEKARKKLEeKFPESLREPVLRLVQ-FSTRSR 79

                           90       100
                   ....*....|....*....|..
gi 1972241557  102 FEDLVNDIYHILKDRFFNNEEV 123
Cdd:pfam10537   80 LDDLVDDVYEEFKDRFFPGEEV 101

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 1972241557 1312 TLIETLLKEAMRQECSWPFLQPVDSKEVPDYYDVIKRPMNLRTMMNKIKQRIYNKPIEVRNDFQLILSNCETYNEPENEI 1391
Cdd:cd05509      4 TQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEY 83

                           90
                   ....*....|....*...
gi 1972241557 1392 YKLSRELHDFMADRLDEI 1409
Cdd:cd05509     84 YKCANKLEKFFWKKLKEL 101

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 1972241557 1311 MTLIETLLKEAMRQECSWPFLQPVDSKEVPDYYDVIKRPMNLRTMMNKIKQRIYNKPIEVRNDFQLILSNCETYNEPENE 1390
Cdd:cd05503      2 LALCETILDEMEAHEDAWPFLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSE 81

                           90
                   ....*....|....*
gi 1972241557 1391 IYKLSRELHDFMADR 1405
Cdd:cd05503     82 VGRAGHNMRKFFEKR 96

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        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972241557 1314 IETLLKEAMRQECSWPFLQPVDSKEVPDYYDVIKRPMNLRTMMNKIKQRIYNKPIEVRNDFQLILSNCETYNEPENEIYK 1393
Cdd:pfam00439    1 CLEILDKLMEHPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYK 80

                   ....
gi 1972241557 1394 LSRE 1397
Cdd:pfam00439   81 AAEK 84

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        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972241557 1312 TLIETLLKEAMRQECSWPFLQPVDSKEVPDYYDVIKRPMNLRTMMNKIKQRIYNKPIEVRNDFQLILSNCETYNEPENEI 1391
Cdd:cd05511      3 FILDEIVNELKNLPDSWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSVY 82

                           90
                   ....*....|....*..
gi 1972241557 1392 YKLSRELHDFMADRLDE 1408
Cdd:cd05511     83 TKKAKEMLELAEELLAE 99

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972241557 1316 TLLKEAMRQECS---WPFLQPVD--SKEVPDYYDVIKRPMNLRTMMNKIKQRIYNKPIEVRNDFQLILSNCETYNEPENE 1390
Cdd:cd05498      7 GILKELFSKKHKayaWPFYKPVDpeALGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHP 86

                           90
                   ....*....|....*
gi 1972241557 1391 IYKLSRELHDFMADR 1405
Cdd:cd05498     87 VHAMARKLQDVFEDR 101

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 1972241557 1315 ETLLKEAMRQ---ECSWPFLQPVD--SKEVPDYYDVIKRPMNLRTMMNKIKQRIYNKPIEVRNDFQLILSNCETYNEPEN 1389
Cdd:cd05499      6 EEVLKELMKPkhsAYNWPFLDPVDpvALNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGT 85

                           90
                   ....*....|.
gi 1972241557 1390 EIYKLSRELHD 1400
Cdd:cd05499     86 DVYMMGHQLEE 96

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
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1972241557 1327 SWPFLQPVD--SKEVPDYYDVIKRPMNLRTMMNKIKQRIYNKPIEVRNDFQLILSNCETYNEPENEIYKLSREL 1398
Cdd:cd05500     22 ARPFLVPVDpvKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNGPEHPVSQMGKRL 95

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972241557 1231 LSLKNRKSNGSMPVTPSERPVRNVSvRIFDVENENVLTDEDDSDGENTRKRKTPTSKKSVTSTPTTNDISRVIIPniKEK 1310
Cdd:COG5076     71 GSMANVNDDLENVGGITYSPFEKNR-PESLRFDEIVFLAIESVTPESGLGSLLMAHLKTSVKKRKTPKIEDELLY--ADN 147

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972241557 1311 MTLIETLLKEAMRQ--ECSWPFLQPVDSKEVPDYYDVIKRPMNLRTMMNKIKQRIYNKPIEVRNDFQLILSNCETYNEPE 1388
Cdd:COG5076    148 KAIAKFKKQLFLRDgrFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPD 227

                          170       180
                   ....*....|....*....|.
gi 1972241557 1389 NEIYKLSRELHDFMADRLDEI 1409
Cdd:COG5076    228 SSVYVDAKELEKYFLKLIEEI 248

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972241557 1311 MTLIETLLKEamrQECSWPFLQPVDSK--EVPDYYDVIKRPMNLRTMMNKIKQRIYNKPIEVRNDFQLILSNCETYNEPE 1388
Cdd:cd05495      9 MPTLEKLYKQ---DPESLPFRQPVDPKllGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYNRKT 85

                           90       100
                   ....*....|....*....|.
gi 1972241557 1389 NEIYKLSRELHDFMADRLDEI 1409
Cdd:cd05495     86 SRVYKYCTKLAEVFEQEIDPV 106

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972241557 1329 PFLQPVDSK-EVPDYYDVIKRPMNLRTMMNKIKQRIYNKPIEVRNDFQLILSNCETYNEPENEIYKLSRELhdfmADRLD 1407
Cdd:cd05529     47 YFEYPVDLRaWYPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEPNSEIAKKAKRL----SDWLL 122

                   ...
gi 1972241557 1408 EII 1410
Cdd:cd05529    123 RIL 125

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972241557 1314 IETLLKEAMRQECSWpFLQPVDSKEVPDYYDVIKRPMNLRTMMNKIKQRIYNKPIEVRNDFQLILSNCETYNEPENEIYK 1393
Cdd:cd05519     12 VLNCEDETGRKLSEL-FLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYNQEGSIVYE 90

                           90
                   ....*....|.
gi 1972241557 1394 LSRELHDFMAD 1404
Cdd:cd05519     91 DAVEMEKAFKK 101

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972241557 1313 LIETLLKEAMRQECSWPFLQPVDSKEVPDYYDVIKRPMNLRTMMNKIKQRIYNKPIEVRNDFQLILSNCETYNEPENEIY 1392
Cdd:cd05513      5 ALEQLIRQLQRKDPHGFFAFPVTDFIAPGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDTIYY 84

                   ....*.
gi 1972241557 1393 KLSREL 1398
Cdd:cd05513     85 KAAKKL 90

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972241557 1329 PFLQPVDSKEVPDYYDVIKRPMNLRTMMNKIKQRIYNKPIEVRNDFQLILSNCETYNEPENEIYKLSR----ELHDFMAD 1404
Cdd:cd05528     23 AFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPDRDPADKLIRsracELRDEVHA 102

                   ....*..
gi 1972241557 1405 RLDEIID 1411
Cdd:cd05528    103 MIEAELD 109

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
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1972241557 1329 PFLQPVDSKEVPDYYDVIKRPMNLRTMMNKIKQRIYNKPIEVRNDFQLILSNCETYNEPENEIYKLSRELH 1399
Cdd:cd05516     27 VFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQ 97

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
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1972241557 1335 DSKEVPDYYDVIKRPMNLRTMMNKIKQRIYNKPIEVRNDFQLILSNCETYNEPENEIYKLSREL 1398
Cdd:cd05522     33 DKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYKDAVLL 96

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 1972241557  1100 CRSCRRKAAAHDLVLCSECDNCYHLKCAKLDVNSDAPAD-WMCTSC 1144
Cdd:smart00249    2 CSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEEEPDGkWYCPKC 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.

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                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972241557  795 ISDIRLGSDRAYRRYIVM-ENLSAILVETATFQElgiycdepsiiddplnllenehqevfictgnmdtcrvhgdesnnwt 873
Cdd:pfam15613    1 IRSLPLGRDRRYNRYWWFdPGTGRLFVESPSDGE---------------------------------------------- 34

                           90       100
                   ....*....|....*....|....
gi 1972241557  874 rWSYIRDREQFEQLLKSLNPRGNR 897
Cdd:pfam15613   35 -WGVYSSKEQLDALIASLNPRGVR 57

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.

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                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972241557 1323 RQECSWPFLQPVDSKEVPDYYDVIKRPMNLRTmmnkIKQRIYNKPIEVRNDFQ----LILSNCETYNEPENEIYKLSREL 1398
Cdd:cd05507     17 SHRYASVFLKPVTEDIAPGYHSVVYRPMDLST----IKKNIENGTIRSTAEFQrdvlLMFQNAIMYNSSDHDVYLMAVEM 92

                   ..
gi 1972241557 1399 HD 1400
Cdd:cd05507     93 QR 94

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.

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                   ....*....|....*....|....*....|....*....|....*...
gi 1972241557 1100 CRSCRRKAAAHDLVLCSECDNCYHLKCAK--LDVNSDAPADWMCTSCR 1145
Cdd:pfam00628    2 CAVCGKSDDGGELVQCDGCDDWFHLACLGppLDPAEIPSGEWLCPECK 49

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.

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                   ....*....|....*....|....*....|....*....|....*.
gi 1972241557 1099 KCRSCRRKAAAHDLVLCSECDNCYHLKCAKLDVNSDAPADWMCTSC 1144
Cdd:cd15628      1 KCKVCRKKGEDDKLILCDECNQAFHLFCLRPALYEVPDGEWMCPAC 46

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.

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                   ....*....|....*....|....*....|....*....|....*
gi 1972241557 1100 CRSCRRKAAAHDLVLCSECDNCYHLKCAKLDVNSDAPADWMCTSC 1144
Cdd:cd15543      2 CRKCGLSDHPEWILLCDRCDAGYHTACLRPPLMIIPDGNWFCPPC 46

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

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                   ....*....|....*....|....*....|....*....|....*..
gi 1972241557 1100 CRSCRRK-AAAHDLVLCSECDNCYHLKCAKLDVNSDAP-ADWMCTSC 1144
Cdd:cd15489      2 CIVCGKGgDLGGELLQCDGCGKWFHADCLGPPLSSFVPnGKWICPVC 48

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

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                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1972241557 1340 PDYYDVIKRPMNLRTMMNKIKQRIYNKPIEVRNDFQLILSNCETYNEPENEIYKLSREL 1398
Cdd:cd05524     39 PEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYKPDSPEHKDACKL 97

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

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                   ....*....|....*....|....*....|....*....|....*
gi 1972241557 1100 CRSCRRKAaahDLVLCSECDNCYHLKCAKLDVNSDAPADWMCTSC 1144
Cdd:cd15559      2 CRVCHKLG---DLLCCETCSAVYHLECVDPPLEEVPEEDWQCEVC 43

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.

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                   ....*....|....*....|....*....|....*....|....*.
gi 1972241557 1100 CRSCRRKAAAHDLVLCSECDNCYHLKCAKLDVNSdAPAD-WMCTSC 1144
Cdd:cd15595      2 CQTCRKPGEDSKMLVCEACDKGYHTFCLKPAMES-LPTDsWKCKAC 46

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 1972241557 1099 KCRSCRRKAAAHDLVLCSECDNCYHLKCAKLDVNSDAPADWMCTSC 1144
Cdd:cd15527      1 TCSVCQDSGNADNLLFCDACDKGFHMECHDPPLTRMPKGKWVCQIC 46