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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1496262832 679 HRLWKKSVMLVYSRLCAHKYASLFLRPISDEEAPGYSLVVKRPMDFNTIRKNIDSGVIRTTAQFQRDVLLMLSNALMYNS 758
Cdd:cd05507     1 YRAWKKAILLVYRTLASHRYASVFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNS 80

                          90       100
                  ....*....|....*....|....
gi 1496262832 759 SEHSVYTMAKEMHAEALGQLGMLL 782
Cdd:cd05507    81 SDHDVYLMAVEMQREVMSQIQQLL 104

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1496262832 679 HRLWKKSVMLVYSRLCAHKYASLFLRPISDEEAPGYSLVVKRPMDFNTIRKNIDSGVIRTTAQFQRDVLLMLSNALMYNS 758
Cdd:cd05507     1 YRAWKKAILLVYRTLASHRYASVFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNS 80

                          90       100
                  ....*....|....*....|....
gi 1496262832 759 SEHSVYTMAKEMHAEALGQLGMLL 782
Cdd:cd05507    81 SDHDVYLMAVEMQREVMSQIQQLL 104

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1496262832 696 HKYASLFLRPISDEEAPGYSLVVKRPMDFNTIRKNIDSGVIRTTAQFQRDVLLMLSNALMYNSSEHSVYTMAKE 769
Cdd:pfam00439  11 HPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYKAAEK 84

ribonuclease E; Reviewed

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1496262832  347 ETSSNVEDQAIKEEPVVPEPVQEELPQEemeTIAEPPTQRPETITKELTPETEVRIAfPEVKFPTTEIKVIQPEVQKIKE 426
Cdd:PRK10811   854 QVEEQREAEEVQVQPVVAEVPVAAAVEP---VVSAPVVEAVAEVVEEPVVVAEPQPE-EVVVVETTHPEVIAAPVTEQPQ 929

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1496262832  427 EIKEPETPTEPETVEEEIIEEQEPVAEVESSVQEEKTEEIPQEQEIVRESETAIEQTSEVELPSEEVA 494
Cdd:PRK10811   930 VITESDVAVAQEVAEHAEPVVEPQDETADIEEAAETAEVVVAEPEVVAQPAAPVVAEVAAEVETVTAV 997

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1496262832 679 HRLWKKSVMLVYSRLCAHKYASLFLRPISDEEAPGYSLVVKRPMDFNTIRKNIDSGVIRTTAQFQRDVLLMLSNALMYNS 758
Cdd:cd05507     1 YRAWKKAILLVYRTLASHRYASVFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNS 80

                          90       100
                  ....*....|....*....|....
gi 1496262832 759 SEHSVYTMAKEMHAEALGQLGMLL 782
Cdd:cd05507    81 SDHDVYLMAVEMQREVMSQIQQLL 104

bromo domain;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1496262832  680 RLWKKSVMLVYSRLCAHKYASLFLRPISDEEAPGYSLVVKRPMDFNTIRKNIDSGVIRTTAQFQRDVLLMLSNALMYNSS 759
Cdd:smart00297   6 KKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYNGP 85

                           90
                   ....*....|..
gi 1496262832  760 EHSVYTMAKEMH 771
Cdd:smart00297  86 DSEVYKDAKKLE 97

Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1496262832 695 AHKYASLFLRPISDEEAPGYSLVVKRPMDFNTIRKNIDSGVIRTTAQFQRDVLLMLSNALMYNSSEHSVYTMAKEM 770
Cdd:cd05509    15 NHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEYYKCANKL 90

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1496262832 702 FLRPISDEEAPGYSLVVKRPMDFNTIRKNIDSGVIRTTAQFQRDVLLMLSNALMYNSSEHSVYTMAKEM 770
Cdd:cd05513    22 FAFPVTDFIAPGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDTIYYKAAKKL 90

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1496262832 696 HKYASLFLRPISDEEAPGYSLVVKRPMDFNTIRKNIDSGVIRTTAQFQRDVLLMLSNALMYNSSEHSVY 764
Cdd:cd05504    27 HKDSWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHTSVY 95

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 1496262832 677 RQHRLWKKSVMlvySRLCAHKYASLFLRPISDEEAPGYSLVVKRPMDFNTIRKNIDSGVIRTTAQFQRDVLLMLSNALMY 756
Cdd:cd05528     2 RELRLFLRDVL---KRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEY 78

                          90       100
                  ....*....|....*....|....*.
gi 1496262832 757 NSSEHS----VYTMAKEMHAEALGQL 778
Cdd:cd05528    79 NPDRDPadklIRSRACELRDEVHAMI 104

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1496262832 698 YASLFLRPISDEEAPGYSLVVKRPMDFNTIRKNIDSGVIRTTAQFQRDVLLMLSNALMYNSSEHSVYTMAKEM 770
Cdd:cd05511    17 DSWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSVYTKKAKEM 89

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1496262832 712 PGYSLVVKRPMDFNTIRKNIDSGVIRTTAQFQRDVLLMLSNALMYNSSEHSVYTMAKEMHA 772
Cdd:cd05500    37 PHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNGPEHPVSQMGKRLQA 97

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1496262832 699 ASLFLRPISDEEAPGYSLVVKRPMDFNTIRKNIDSGVIRTTAQFQRDVLLMLSNALMYNSSEHSVYTMAK 768
Cdd:cd05508    20 AEPFLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYNGGDHKLTQAAK 89

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1496262832 697 KYASLFLRPISDEEAPGYSLVVKRPMDFNTIRKNIDSGVIRTTAQFQRDVLLMLSNALMYNsSEHS-VYTMAKEMH 771
Cdd:cd05519    22 KLSELFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYN-QEGSiVYEDAVEME 96

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 1496262832 692 RLCAHKYASLFLRPISdEEAPGYSLVVKRPMDFNTIRKNIDSGVIR---TTAQFQRDVLLMLSNALMYNSSEHSVYTMAK 768
Cdd:cd05502    15 ELYCHELSLPFHEPVS-PSVPNYYKIIKTPMDLSLIRKKLQPKSPQhysSPEEFVADVRLMFKNCYKFNEEDSEVAQAGK 93

                  ..
gi 1496262832 769 EM 770
Cdd:cd05502    94 EL 95

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 1496262832 689 VYSRLCAHKYASLFLRPIsDEEA---PGYSLVVKRPMDFNTIRKNIDSGVIRTTAQFQRDVLLMLSNALMYNSSEHSVYT 765
Cdd:cd05497    13 VLKALWKHKFAWPFQQPV-DAVKlnlPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKPGDDVVL 91

                          90
                  ....*....|....*.
gi 1496262832 766 MAKEMHAEALGQLGML 781
Cdd:cd05497    92 MAQTLEKLFLQKLAQM 107

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 1496262832 685 SVMLVYSRLCAHKYASLFLRPISDEEAPGYSLVVKRPMDFNTIRKNIDSGVIRTTAQFQRDVLLMLSNALMYN 757
Cdd:cd05516    11 DVVIKYKDSDGRQLAEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTFN 83

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 1496262832 709 EEAPGYSLVVKRPMDFNTIRKNIDSGVIRTTAQFQRDVLLMLSNALMYNSSEHSVYTMAKEMHAEA 774
Cdd:cd05522    35 AREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYKDAVLLEKEA 100

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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1496262832 686 VMLVYSRLCAHKYASLFLRPISDEEAPGYSLVVKRPMDFNTIRKNIDSGVIRTTAQFQRDVLLMLSNALMYNSSEHSVY 764
Cdd:cd05518    11 YVLEYREGSGRRLCDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYNEEGSQVY 89

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
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1496262832 712 PGYSLVVKRPMDFNTIRKNIDSGVIRTTAQFQRDVLLMLSNALMYNsSEHSVYTM 766
Cdd:cd05529    59 PDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFN-EPNSEIAK 112

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        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1496262832 704 RPIsDEEAPGYSLVVKRPMDFNTIRKNIDSGVIRTTAQFQRDVLLMLSNALMYNSSEHSVYTMAKEMHAE 773
Cdd:cd05492    30 RGK-ATKLPKRRRLIHTHLDVADIQEKINSEKYTSLEEFKADALLLLHNTAIFHGADSEQYDAARWLYRD 98

Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. 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
                  ....*....|....*....|....*....|....*....|....*.
gi 1496262832 712 PGYSLVVKRPMDFNTIRKNIDSGVIRTTAQFQRDVLLMLSNALMYN 757
Cdd:cd05525    39 PDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYY 84