Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244640 315 AFKKSMSLLSRLMKHKFGWVFNKPVDAVALGLHDYFAIIKHPMDLGTIKTRLTHGQYRNPREFADDVRLTFHNAMTYNPK 394
Cdd:cd05506     1 VMKQCGTLLRKLMKHKWGWVFNAPVDVVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPP 80

                          90
                  ....*....|....*....
gi 1002244640 395 GQDVHFMAEQLLGIFEAQW 413
Cdd:cd05506    81 GNDVHTMAKELLKIFETRW 99

Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244640 315 AFKKSMSLLSRLMKHKFGWVFNKPVDAVALGLHDYFAIIKHPMDLGTIKTRLTHGQYRNPREFADDVRLTFHNAMTYNPK 394
Cdd:cd05506     1 VMKQCGTLLRKLMKHKWGWVFNAPVDVVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPP 80

                          90
                  ....*....|....*....
gi 1002244640 395 GQDVHFMAEQLLGIFEAQW 413
Cdd:cd05506    81 GNDVHTMAKELLKIFETRW 99

Bromodomain extra-terminal - transcription regulation; The BET, or bromodomain extra-terminal domain, is found on bromodomain proteins that play key roles in development, cancer progression and virus-host pathogenesis. It interacts with NSD3, JMJD6, CHD4, GLTSCR1, and ATAD5 all of which are shown to impart a pTEFb-independent transcriptional activation function on the bromodomain proteins.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1002244640 488 MTIDEKRKLSNNLQNLPPEKLDVVVQIIKNKNLSVRQHDDEIEVEIDSMDTETLWELDRFVAN 550
Cdd:pfam17035   2 MTYEEKRELSERINKLPGEKLGRVIEIIKERNPELQSDDDEIELDIDALDDDTLRKLYNFVKK 64

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244640 309 QRLYSHAFK--KSMSLLSRLMKHKFGWVFNKPVDAVALGlhDYFAIIKHPMDLGTIKTRLTHGQYRNPREFADDVRLTFH 386
Cdd:COG5076   141 ELLYADNKAiaKFKKQLFLRDGRFLSSIFLGLPSKREYP--DYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFD 218

                          90
                  ....*....|....*....
gi 1002244640 387 NAMTYNPKGQDVHFMAEQL 405
Cdd:COG5076   219 NCKLYNGPDSSVYVDAKEL 237

Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244640 315 AFKKSMSLLSRLMKHKFGWVFNKPVDAVALGLHDYFAIIKHPMDLGTIKTRLTHGQYRNPREFADDVRLTFHNAMTYNPK 394
Cdd:cd05506     1 VMKQCGTLLRKLMKHKWGWVFNAPVDVVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPP 80

                          90
                  ....*....|....*....
gi 1002244640 395 GQDVHFMAEQLLGIFEAQW 413
Cdd:cd05506    81 GNDVHTMAKELLKIFETRW 99

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 1002244640 316 FKKSMSLLSRLMKHK---FGWVFNKPVDAVALGLHDYFAIIKHPMDLGTIKTRLTHGQYRNPREFADDVRLTFHNAMTYN 392
Cdd:cd05499     2 LKFCEEVLKELMKPKhsaYNWPFLDPVDPVALNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFN 81

                          90       100
                  ....*....|....*....|.
gi 1002244640 393 PKGQDVHFMAEQLLGIFEAQW 413
Cdd:cd05499    82 PEGTDVYMMGHQLEEVFNDKW 102

Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244640 322 LLSRLMKHKFGWVFNKPVDAVALGLHDYFAIIKHPMDLGTIKTRLTHGQYRNPREFADDVRLTFHNAMTYNPKGQDVHFM 401
Cdd:cd05497    13 VLKALWKHKFAWPFQQPVDAVKLNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKPGDDVVLM 92

                  ....*...
gi 1002244640 402 AEQLLGIF 409
Cdd:cd05497    93 AQTLEKLF 100

Bromodomain extra-terminal - transcription regulation; The BET, or bromodomain extra-terminal domain, is found on bromodomain proteins that play key roles in development, cancer progression and virus-host pathogenesis. It interacts with NSD3, JMJD6, CHD4, GLTSCR1, and ATAD5 all of which are shown to impart a pTEFb-independent transcriptional activation function on the bromodomain proteins.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1002244640 488 MTIDEKRKLSNNLQNLPPEKLDVVVQIIKNKNLSVRQHDDEIEVEIDSMDTETLWELDRFVAN 550
Cdd:pfam17035   2 MTYEEKRELSERINKLPGEKLGRVIEIIKERNPELQSDDDEIELDIDALDDDTLRKLYNFVKK 64

Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244640 322 LLSRLMKHKFGWVFNKPVDAVALGlhDYFAIIKHPMDLGTIKTRLTHGQYRNPREFADDVRLTFHNAMTYNPKGQDVHFM 401
Cdd:cd05504    20 LLVEIVKHKDSWPFLRPVSKIEVP--DYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHTSVYKA 97

                          90
                  ....*....|.
gi 1002244640 402 AEQLLGIFEAQ 412
Cdd:cd05504    98 GTRLQRFFIKR 108

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 1002244640 322 LLSRLMKHKFGWVFNKPVDA--VAlglhDYFAIIKHPMDLGTIKTRLTHGQYRNPREFADDVRLTFHNAMTYNPKGQDVH 399
Cdd:cd05509     9 VLDSLKNHKSAWPFLEPVDKeeAP----DYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEYY 84

                  ....*.
gi 1002244640 400 FMAEQL 405
Cdd:cd05509    85 KCANKL 90

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1002244640 335 FNKPVDAVALGlhDYFAIIKHPMDLGTIKTRLTHGQYRNPREFADDVRLTFHNAMTYNP-KGQDVHFMAEQLLGIFEAQ 412
Cdd:cd05496    26 FRQPVDLLKYP--DYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYTPnKRSRIYSMTLRLSALFEEH 102

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 1002244640 322 LLSRLMKHKFGWVFNKPVDAVALGlhDYFAIIKHPMDLGTIKTRLTHGQYRNPREFADDVRLTFHNAMTYN----PKGQD 397
Cdd:cd05503     8 ILDEMEAHEDAWPFLEPVNTKLVP--GYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNeddsEVGRA 85

                          90
                  ....*....|....*.
gi 1002244640 398 VHFMAEqllgIFEAQW 413
Cdd:cd05503    86 GHNMRK----FFEKRW 97

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002244640 347 HDYFAIIKHPMDLGTIKTRLTHGQYRNPREFADDVRLTFHNAMTYN-----PKGQDVHFM---AEQLL 406
Cdd:cd05510    39 PDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYNsdpshPLRRHANFMkkkAEHLL 106

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 1002244640 323 LSRLMKHKFGWVFNKPVDAVALglHDYFAIIKHPMDLGTIKTRLTHGQYRNPREFADDVRLTFHNAMTYNP----KGQDV 398
Cdd:cd05528    12 LKRLASDKRFNAFTKPVDEEEV--PDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPdrdpADKLI 89

                          90       100
                  ....*....|....*....|.
gi 1002244640 399 HFMAEQLL----GIFEAQWPE 415
Cdd:cd05528    90 RSRACELRdevhAMIEAELDP 110

Bromodomain, repeat I 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
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1002244640 348 DYFAIIKHPMDLGTIKTRLTHgqYRNPREFADDVRLTFHNAMTYNPKGQDVH 399
Cdd:cd05521    39 DYYKIIKNPLSLNTVKKRLPH--YTNAQEFVNDLAQIPWNARLYNTKGSVIY 88

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 1002244640 333 WVFNKPVDAVALglHDYFAIIKHPMDLGTIKTRLTHGQYRNPREFADDVRLTFHNAMTYN-------PKGQDVHFMAEQL 405
Cdd:cd05511    19 WPFHTPVNKKKV--PDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNgpdsvytKKAKEMLELAEEL 96

                          90
                  ....*....|..
gi 1002244640 406 LGIFEAQWPEIE 417
Cdd:cd05511    97 LAEREEKLTQLE 108

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244640 309 QRLYSHAFK--KSMSLLSRLMKHKFGWVFNKPVDAVALGlhDYFAIIKHPMDLGTIKTRLTHGQYRNPREFADDVRLTFH 386
Cdd:COG5076   141 ELLYADNKAiaKFKKQLFLRDGRFLSSIFLGLPSKREYP--DYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFD 218

                          90
                  ....*....|....*....
gi 1002244640 387 NAMTYNPKGQDVHFMAEQL 405
Cdd:COG5076   219 NCKLYNGPDSSVYVDAKEL 237

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
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1002244640 348 DYFAIIKHPMDLGTIKTRLTHGQYRNPREFADDVRLTFHNAMTYNPKGQDVH 399
Cdd:cd05519    38 DYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYNQEGSIVY 89

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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1002244640 348 DYFAIIKHPMDLGTIKTRLTHGQYRNPREFADDVRLTFHNAMTYNPKG----QDVHfMAEQLL 406
Cdd:cd05518    38 DYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYNEEGsqvyEDAN-ILEKVL 99

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1002244640 348 DYFAIIKHPMDLGTIKTRLTHGQYRNPREFADDVRLTFHNAMTYNPKGQDVHFMAEQLLGIFEAQWPEI 416
Cdd:cd05524    40 EYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYKPDSPEHKDACKLWELFLSARNEV 108

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1002244640 348 DYFAIIKHPMDLGTIKTRLTHGQYRNPREFADDVRLTFHNAMTYNPKGQDVHFMAEQLLGIFEA 411
Cdd:cd05517    38 DYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFNEPGSQVYKDANAIKKIFTA 101

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
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1002244640 348 DYFAIIKHPMDLGTIKTRLTHGQYRNPREFADDVRLTFHNAMTYNPKGQDVHFMAEQL 405
Cdd:cd05522    39 EYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYKDAVLL 96

Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) was identified as a potential tumor suppressor genes, it shares domain architecture with BS69/ZMYND11; both have been implicated in the regulation of cellular proliferation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002244640 327 MKHKFGWVFNKPVDavaLGLH-DYFAIIKHPMDLGTIKTRLTHGQYRNPREFADDVRLTFHNAMTYNPKGQDVHFMAEQL 405
Cdd:cd05508    15 MKQPGAEPFLKPVD---LEQFpDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYNGGDHKLTQAAKAI 91

                  ....*
gi 1002244640 406 LGIFE 410
Cdd:cd05508    92 VKICE 96

Bromodomain; ZMYND11_like sub-family. ZMYND11 or BS69 is a ubiquitously expressed nuclear protein that has been shown to associate with chromatin. It interacts with chromatin remodeling factors and might play a role in chromatin remodeling and gene expression. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1002244640 353 IKHPMDLGTIKTRLTHGQYRNPREFADDVRLTFHN 387
Cdd:cd05492    43 IHTHLDVADIQEKINSEKYTSLEEFKADALLLLHN 77