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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4BHW_A       19 PEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNAWL 98
Cdd:cd05495   1 PEELRQALMPTLEKLYKQDPESLPFRQPVDPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWL 80

                        90       100
                ....*....|....*....|....*...
4BHW_A       99 YNRKTSRVYKYCSKLSEVFEQEIDPVMQ 126
Cdd:cd05495  81 YNRKTSRVYKYCTKLAEVFEQEIDPVMQ 108

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.

                        10        20        30
                ....*....|....*....|....*....|....*
4BHW_A      211 LFVECTECGRKMHQICVLHHEIIWPAGFVCDGCLK 245
Cdd:cd15646   6 LFVECLECGRKMHQICVLHNETIWPSGFVCEGCLK 40

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4BHW_A       19 PEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNAWL 98
Cdd:cd05495   1 PEELRQALMPTLEKLYKQDPESLPFRQPVDPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWL 80

                        90       100
                ....*....|....*....|....*...
4BHW_A       99 YNRKTSRVYKYCSKLSEVFEQEIDPVMQ 126
Cdd:cd05495  81 YNRKTSRVYKYCTKLAEVFEQEIDPVMQ 108

atypical RING domain found in CREB-binding protein and p300 histone acetyltransferases; CBP and p300 (also known as CREBBP or KAT3A and EP300 or KAT3B, respectively) are two histone acetyltransferases (HATs) that associate with and acetylate transcriptional regulators and chromatin. The catalytic core of animal CBP-p300 contains a bromodomain, a CH2 region containing a discontinuous PHD domain interrupted by this RING domain, and a HAT domain. Bromodomain-RING-PHD forms a compact module in which the RING domain is juxtaposed with the HAT substrate-binding site. This ring domain contains only a single zinc ion-binding cluster instead of two; instead of a second zinc atom, a network of hydrophobic interactions stabilizes the domain. The RING domain has an inhibitory role. Disease mutations that disrupt RING attachment lead to upregulation of HAT activity. HAT regulation may require repositioning of the RING domain to facilitate access to an otherwise partially occluded HAT active site. Plant CBP-p300 type HATs lack a bromodomain whose role in the animal animal CBP-p300's is to bind acetylated histones; it has been suggested that these plant proteins may utilize a different domain or another bromodomain protein to perform this function. This RING domain has also been referred to as DUF902.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
4BHW_A      138 FSPQTLCCYGKqlCTIPRD--ATYYSYQ---NRYHFCEKCFNEIQGESVSLGDDpsqPQTTINKEQFSKRKNDTLDPE 210
Cdd:cd15802   1 FEPQVLYCSGK--CTIPRKrnAVYYSYQnldNRYHFCEKCFNEIRGDEITLGDD---QGTSISKSQFEKKKNDELDEE 73

PHD finger found in histone acetyltransferase p300; p300, also termed KAT3B, or E1A-associated protein p300 (EP300), is a paralog of CREB-binding protein (CBP). It is involved in E1A function in cell cycle progression and cellular differentiation. It functions as an intrinsic HAT, as well as a factor acetyltransferase (FAT) for many transcription regulators. And thus, p300 serves as a scaffold or bridge for transcription factors and other components of the basal transcription machinery to facilitate chromatin remodeling and to activate gene transcription. p300 contains a cysteine-histidine rich region, KIX (CREB interaction) domain, a plant homeodomain (PHD) finger, a HAT domain, followed by a SRC interaction domain.

                        10        20        30
                ....*....|....*....|....*....|....*
4BHW_A      211 LFVECTECGRKMHQICVLHHEIIWPAGFVCDGCLK 245
Cdd:cd15646   6 LFVECLECGRKMHQICVLHNETIWPSGFVCEGCLK 40

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4BHW_A        6 KAVPMQSKKKI---FKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLlgIPDYFDIVKSPMDLSTIKRKLDTGQYQEP 82
Cdd:COG5076 129 SVKKRKTPKIEdelLYADNKAIAKFKKQLFLRDGRFLSSIFLGLPSKRE--YPDYYEIIKSPMDLLTIQKKLKNGRYKSF 206

                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
4BHW_A       83 WQYVDDIWLMFNNAWLYNRKTSRVYKYCSKLSEVFEQEIDPVM 125
Cdd:COG5076 207 EEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLIEEIP 249

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4BHW_A       19 PEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNAWL 98
Cdd:cd05495   1 PEELRQALMPTLEKLYKQDPESLPFRQPVDPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWL 80

                        90       100
                ....*....|....*....|....*...
4BHW_A       99 YNRKTSRVYKYCSKLSEVFEQEIDPVMQ 126
Cdd:cd05495  81 YNRKTSRVYKYCTKLAEVFEQEIDPVMQ 108

atypical RING domain found in CREB-binding protein and p300 histone acetyltransferases; CBP and p300 (also known as CREBBP or KAT3A and EP300 or KAT3B, respectively) are two histone acetyltransferases (HATs) that associate with and acetylate transcriptional regulators and chromatin. The catalytic core of animal CBP-p300 contains a bromodomain, a CH2 region containing a discontinuous PHD domain interrupted by this RING domain, and a HAT domain. Bromodomain-RING-PHD forms a compact module in which the RING domain is juxtaposed with the HAT substrate-binding site. This ring domain contains only a single zinc ion-binding cluster instead of two; instead of a second zinc atom, a network of hydrophobic interactions stabilizes the domain. The RING domain has an inhibitory role. Disease mutations that disrupt RING attachment lead to upregulation of HAT activity. HAT regulation may require repositioning of the RING domain to facilitate access to an otherwise partially occluded HAT active site. Plant CBP-p300 type HATs lack a bromodomain whose role in the animal animal CBP-p300's is to bind acetylated histones; it has been suggested that these plant proteins may utilize a different domain or another bromodomain protein to perform this function. This RING domain has also been referred to as DUF902.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
4BHW_A      138 FSPQTLCCYGKqlCTIPRD--ATYYSYQ---NRYHFCEKCFNEIQGESVSLGDDpsqPQTTINKEQFSKRKNDTLDPE 210
Cdd:cd15802   1 FEPQVLYCSGK--CTIPRKrnAVYYSYQnldNRYHFCEKCFNEIRGDEITLGDD---QGTSISKSQFEKKKNDELDEE 73

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
4BHW_A       42 PFRQPVDPQLLGIPDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNAWLYNRKTSRVYKYCSKLSEVFEQ 119
Cdd:cd05498  23 PFYKPVDPEALGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKLQDVFED 100

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4BHW_A       21 ELRQALMPTLEALyRQDPESLPFRQPVDPQLlgIPDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNAWLYN 100
Cdd:cd05509   1 PLYTQLKKVLDSL-KNHKSAWPFLEPVDKEE--APDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYN 77

                        90       100
                ....*....|....*....|.
4BHW_A      101 RKTSRVYKYCSKLSEVFEQEI 121
Cdd:cd05509  78 GPDTEYYKCANKLEKFFWKKL 98

CREB-binding protein/p300, atypical RING domain; CBP (CREB-binding protein) and p300 (also known as CREBBP or KAT3A and EP300 or KAT3B, respectively) are two histone acetyltransferases (HATs) that associate with and acetylate transcriptional regulators and chromatin. The catalytic core of animal CBP-p300 contains a bromodomain, a CH2 region containing a discontinuous PHD domain interrupted by this RING domain, and a HAT domain. Bromodomain-RING-PHD forms a compact module in which the RING domain is juxtaposed with the HAT substrate-binding site. This RING domain contains only a single zinc ion-binding cluster instead of two; instead of a second zinc atom, a network of hydrophobic interactions stabilizes the domain. The RING domain has an inhibitory role. Disease mutations that disrupt RING attachment lead to upregulation of HAT activity. HAT regulation may require repositioning of the RING domain to facilitate access to an otherwise partially occluded HAT active site. Plant CBP-p300 type HATs lack a bromodomain whose role in the animal animal CBP-p300's is to bind acetylated histones; it has been suggested that these plant proteins may utilize a different domain or another bromodomain protein to perform this function. This RING domain has also been referred to as DUF902.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
4BHW_A        124 VMQSLGYCCGRKLEFSPQTLCCYGKQLCTIPRDATYYSYQ 163
Cdd:pfam06001   1 VMKSLGYCCGRKLVFNPQVLCCYGKQLCTIPRDAVYYTYQ 40

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4BHW_A       39 ESLPFRQPVDpqLLGIPDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNAWLYN-RKTSRVYKYCSKLSEVF 117
Cdd:cd05496  22 DSEPFRQPVD--LLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYTpNKRSRIYSMTLRLSALF 99

                        90
                ....*....|
4BHW_A      118 EQEIDPVMQS 127
Cdd:cd05496 100 EEHIKKIISD 109

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
4BHW_A       42 PFRQPVDPQLLGIPDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNAWLYNRKTSRVYKYCSKLSEVFE 118
Cdd:cd05499  23 PFLDPVDPVALNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTDVYMMGHQLEEVFN 99

PHD finger found in histone acetyltransferase p300; p300, also termed KAT3B, or E1A-associated protein p300 (EP300), is a paralog of CREB-binding protein (CBP). It is involved in E1A function in cell cycle progression and cellular differentiation. It functions as an intrinsic HAT, as well as a factor acetyltransferase (FAT) for many transcription regulators. And thus, p300 serves as a scaffold or bridge for transcription factors and other components of the basal transcription machinery to facilitate chromatin remodeling and to activate gene transcription. p300 contains a cysteine-histidine rich region, KIX (CREB interaction) domain, a plant homeodomain (PHD) finger, a HAT domain, followed by a SRC interaction domain.

                        10        20        30
                ....*....|....*....|....*....|....*
4BHW_A      211 LFVECTECGRKMHQICVLHHEIIWPAGFVCDGCLK 245
Cdd:cd15646   6 LFVECLECGRKMHQICVLHNETIWPSGFVCEGCLK 40

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4BHW_A       20 EELRQALMPTLEALYRQDPESLPFRQPVDPQllGIPDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNAWLY 99
Cdd:cd05510   6 EEFYESLDKVLNELKTYTEHSTPFLTKVSKR--EAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLY 83

                        90
                ....*....|.
4BHW_A      100 NRKTSRVYKYC 110
Cdd:cd05510  84 NSDPSHPLRRH 94

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4BHW_A       25 ALMPTLEALYRQDPESLpFRQPVDpqLLGIPDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNAWLYNRKTS 104
Cdd:cd05512   5 LLRKTLDQLQEKDTAEI-FSEPVD--LSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKDT 81

                        90
                ....*....|.
4BHW_A      105 RVYKYCSKLSE 115
Cdd:cd05512  82 IFYRAAVRLRD 92

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4BHW_A       38 PESLPFRQPVDPQLlgIPDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNAWLYNRKTSRVYKYCSKLSEVF 117
Cdd:cd05503  16 EDAWPFLEPVNTKL--VPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSEVGRAGHNMRKFF 93

                .
4BHW_A      118 E 118
Cdd:cd05503  94 E 94

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4BHW_A       35 RQDPESLPFRQPVDPQLlgIPDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNAWLYNRKTSR-------VY 107
Cdd:cd05511  13 KNLPDSWPFHTPVNKKK--VPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSVytkkakeML 90

                        90
                ....*....|...
4BHW_A      108 KYCSKLSEVFEQE 120
Cdd:cd05511  91 ELAEELLAEREEK 103

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4BHW_A       23 RQALMPTLEALYRQdPESLPFRQPVdpQLLGIPDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNAWLYNR- 101
Cdd:cd05507   5 KKAILLVYRTLASH-RYASVFLKPV--TEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNSs 81

                        90       100
                ....*....|....*....|..
4BHW_A      102 ----KTSRVYKYCSKLSEVFEQ 119
Cdd:cd05507  82 dhdvYLMAVEMQREVMSQIQQL 103

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.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
4BHW_A       55 PDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNAWLYNRKTSRVYKYCSKLSEVFEQEIDPVMQ 126
Cdd:cd05524  39 PEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYKPDSPEHKDACKLWELFLSARNEVLS 110

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4BHW_A       22 LRQALMPTLEALYRQDPESLpFRQPVDPQLlgIPDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNAWLYNR 101
Cdd:cd05513   2 LQKALEQLIRQLQRKDPHGF-FAFPVTDFI--APGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNK 78

                        90
                ....*....|..
4BHW_A      102 KTSRVYKYCSKL 113
Cdd:cd05513  79 PDTIYYKAAKKL 90

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

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
4BHW_A       55 PDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNAWLYNRKTSRVYKYCSKL 113
Cdd:cd05520  37 PDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPNSRIYKDAEKL 95

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4BHW_A       22 LRQALMPTLEALYRQDPE-----SLPFRQPVDPQLLgiPDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNA 96
Cdd:cd05519   1 LKAAMLEIYDAVLNCEDEtgrklSELFLEKPSKKLY--PDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANA 78

                        90       100
                ....*....|....*....|....*
4BHW_A       97 WLYNRKTSRVYKYCSKLSEVFEQEI 121
Cdd:cd05519  79 RTYNQEGSIVYEDAVEMEKAFKKKY 103

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
                ....*....|....*....|....*....|....*....|....*....|....*....
4BHW_A       55 PDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNAWLYNRKTSRVYKYCSKL 113
Cdd:cd05522  38 PEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYKDAVLL 96

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4BHW_A       20 EELRQALMPTLEALYRQDPESL--PFRQPVDpQLLGIPDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNAW 97
Cdd:cd05529  23 DEERERLISGLDKLLLSLQLEIaeYFEYPVD-LRAWYPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAE 101

                        90       100
                ....*....|....*....|....
4BHW_A       98 LYNRKTSRVYKYCSKLSEVFEQEI 121
Cdd:cd05529 102 TFNEPNSEIAKKAKRLSDWLLRIL 125

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

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4BHW_A       55 PDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNAWLYNRKTSRVYKYCSKLSEVFEQ 119
Cdd:cd05517  37 PDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFNEPGSQVYKDANAIKKIFTA 101

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

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4BHW_A       54 IPDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNAWLYNRKTSRVyKYCSKLSEVFEQ 119
Cdd:cd05501  30 IRDYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKDDDFG-QVGITLEKKFEK 94