PWWP domain found in bromodomain and PHD finger-containing protein 3 (BRPF3); BRPF3 is a homolog of BRPF1 and BRPF2. It is a scaffold protein that forms a novel monocytic leukemic zinc finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with other regulatory subunits. BRPF3 contains a plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, C2HC5HC2H, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The PHD finger binds to lysine 4 of histone H3 (K4H3), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569000412 575 LEPLELVWAKCRGYPSYPALIIDPKMPREGLLHNGVPIPVPPLDVLKLGEQKQAEAGERLFLVLFFDNKRTWQWLPRDKV 654
Cdd:cd20158    1 LEPLELVWAKCRGYPSYPALIIDPKMPREGLLHNGVPIPVPPLDVLKLGEQKQAEAGEKLFLVLFFDNKRTWQWLPRDKV 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 569000412 655 LPLGVEDTVDKLKMLEGRKTSIRKSVQVAYDRAMIHLS 692
Cdd:cd20158   81 LPLGVDDTVDKLKMMEGRKTSIRKSVQVAYDRAMIHLS 118

PWWP domain found in bromodomain and PHD finger-containing protein 3 (BRPF3); BRPF3 is a homolog of BRPF1 and BRPF2. It is a scaffold protein that forms a novel monocytic leukemic zinc finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with other regulatory subunits. BRPF3 contains a plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, C2HC5HC2H, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The PHD finger binds to lysine 4 of histone H3 (K4H3), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569000412 575 LEPLELVWAKCRGYPSYPALIIDPKMPREGLLHNGVPIPVPPLDVLKLGEQKQAEAGERLFLVLFFDNKRTWQWLPRDKV 654
Cdd:cd20158    1 LEPLELVWAKCRGYPSYPALIIDPKMPREGLLHNGVPIPVPPLDVLKLGEQKQAEAGEKLFLVLFFDNKRTWQWLPRDKV 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 569000412 655 LPLGVEDTVDKLKMLEGRKTSIRKSVQVAYDRAMIHLS 692
Cdd:cd20158   81 LPLGVDDTVDKLKMMEGRKTSIRKSVQVAYDRAMIHLS 118

bromo domain;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569000412    88 MELELMPFTVLLRTTLDLLQEKDSAHIFAEPVSLSEVPDYLEFISKPMDFSTMRRKLESHLYHTLEEFEEDFNLIVTNCM 167
Cdd:smart00297   1 DPKLQKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNAR 80

                           90       100
                   ....*....|....*....|....*..
gi 569000412   168 KYNAKDTIFHRAAVRLRDLGGAILRHA 194
Cdd:smart00297  81 TYNGPDSEVYKDAKKLEKFFEKKLREL 107

domain with conserved PWWP motif; conservation of Pro-Trp-Trp-Pro residues

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569000412   575 LEPLELVWAKCRGYPSYPALIIDPKMPREGLLHNgvpipvppldvlklgeqkqaEAGERLFLVLFFDNKRTwQWLPRDKV 654
Cdd:smart00293   1 FKPGDLVWAKMKGFPWWPALVISPKMTPDNIMKR--------------------KSDENLYPVLFFGDKDT-AWIPSSKL 59

                   ....
gi 569000412   655 LPLG 658
Cdd:smart00293  60 FPLT 63

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569000412 114 IFAEPVSLSEVPDYLEFISKPMDFSTMRRKLESHLYHTLEEFEEDFNLIVTNCMKYNAKDTIFHRAAVRLRDLGgaiLRH 193
Cdd:COG5076  168 IFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYF---LKL 244

                         90       100
                 ....*....|....*....|..
gi 569000412 194 ARRQ-AENIGYDPERGTHLPES 214
Cdd:COG5076  245 IEEIpEEMLELSIKPGREEREE 266

PWWP domain found in bromodomain and PHD finger-containing protein 3 (BRPF3); BRPF3 is a homolog of BRPF1 and BRPF2. It is a scaffold protein that forms a novel monocytic leukemic zinc finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with other regulatory subunits. BRPF3 contains a plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, C2HC5HC2H, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The PHD finger binds to lysine 4 of histone H3 (K4H3), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569000412 575 LEPLELVWAKCRGYPSYPALIIDPKMPREGLLHNGVPIPVPPLDVLKLGEQKQAEAGERLFLVLFFDNKRTWQWLPRDKV 654
Cdd:cd20158    1 LEPLELVWAKCRGYPSYPALIIDPKMPREGLLHNGVPIPVPPLDVLKLGEQKQAEAGEKLFLVLFFDNKRTWQWLPRDKV 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 569000412 655 LPLGVEDTVDKLKMLEGRKTSIRKSVQVAYDRAMIHLS 692
Cdd:cd20158   81 LPLGVDDTVDKLKMMEGRKTSIRKSVQVAYDRAMIHLS 118

PWWP domain found in bromodomain and PHD finger-containing protein 1 (BRPF1); BRPF1, also called peregrin, or protein Br140, is a multi-domain protein that binds histones, mediates monocytic leukemic zinc-finger protein (MOZ)-dependent histone acetylation, and is required for Hox gene expression and segmental identity. It is a close partner of the MOZ histone acetyltransferase (HAT) complex and a novel Trithorax group (TrxG) member with a central role during development. BRPF1 is primarily a nuclear protein that has a broad tissue distribution and is abundant in testes and spermatogonia. It may be involved in chromatin remodeling. It contains a plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, C2HC5HC2H, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The PHD finger binds to methylated lysine 4 of histone H3 (K4H3), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569000412 575 LEPLELVWAKCRGYPSYPALIIDPKMPREGLLHNGVPIPVPPLDVLKLGEQKQAEAGERLFLVLFFDNKRTWQWLPRDKV 654
Cdd:cd20156    1 LDALDLVWAKCRGYPSYPALIIDPKMPREGMFHHGVPIPVPPLEVLKLGEQMTQEAREHLYLVLFFDNKRTWQWLPRTKL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 569000412 655 LPLGVEDTVDKLKMLEGRKTSIRKSVQVAYDRAMIHLSRV 694
Cdd:cd20156   81 VPLGVNQDLDKEKMLEGRKSNIRKSVQIAYHRAMQHRNKV 120

PWWP domain found in the bromodomain and PHD finger-containing (BRPF) protein family; The BRPF family of proteins includes BRPF1, BRD1/BRPF2, and BRPF3. They are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, C2HC5HC2H, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The PHD finger binds to lysine 4 of histone H3 (K4H3), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569000412 575 LEPLELVWAKCRGYPSYPALIIDPKMPREGllhNGVPIPVPPLDVLKlgeqkqaEAGERLFLVLFFDNKRTWQWLPRDKV 654
Cdd:cd05839    1 LEPGDLVWAKCRGYPWYPAEIVDPKDPKEG---NGVPIPVPPDRVLK-------KSNEKLYLVLFFDAKRTWGWLPRNKL 70

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 569000412 655 LPLGVEDTVDKLKMLEGRKTSIRKSVQVAYDRAMIH 690
Cdd:cd05839   71 RPLGVDEELDKLKLSEAKKSKRRKEVRKAYERACKH 106

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 569000412  94 PFTVLLRTTLDLLQEKDSAHIFAEPVSLSEVPDYLEFISKPMDFSTMRRKLESHLYHTLEEFEEDFNLIVTNCMKYNAKD 173
Cdd:cd05509    1 PLYTQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPD 80

                         90
                 ....*....|
gi 569000412 174 TIFHRAAVRL 183
Cdd:cd05509   81 TEYYKCANKL 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        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569000412  94 PFTVLLRTTLDLLQEKDSAHIFAEPVSLSEVPDYLEFISKPMDFSTMRRKLESHLYHTLEEFEEDFNLIVTNCMKYNAKD 173
Cdd:cd05513    1 PLQKALEQLIRQLQRKDPHGFFAFPVTDFIAPGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPD 80

                         90
                 ....*....|....*...
gi 569000412 174 TIFHRAAVRLRDLGGAIL 191
Cdd:cd05513   81 TIYYKAAKKLLHSGMKIL 98

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 569000412 112 AHIFAEPV--SLSEVPDYLEFISKPMDFSTMRRKLESHLYHTLEEFEEDFNLIVTNCMKYNAKDTIFHRAAVRLRD 185
Cdd:cd05498   21 AWPFYKPVdpEALGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKLQD 96

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 569000412 115 FAEPVSLSEVPDYLEFISKPMDFSTMRRKLESHLYHTLEEFEEDFNLIVTNCMKYNAKDTIFHRAAVRLRDLGGAILRH 193
Cdd:cd05511   21 FHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSVYTKKAKEMLELAEELLAE 99

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 569000412 114 IFAEPVSLSEVPDYLEFISKPMDFSTMRRKLESHLYHTLEEFEEDFNLIVTNCMKYNAKD-----TIFHRAAvRLRDLGG 188
Cdd:cd05528   23 AFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPDRdpadkLIRSRAC-ELRDEVH 101

                 ....
gi 569000412 189 AILR 192
Cdd:cd05528  102 AMIE 105

PWWP domain; The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain binds to Histone-4 methylated at lysine-20, H4K20me, suggesting that it is methyl-lysine recognition motif. Removal of two conserved aromatic residues in a hydrophobic cavity created by this domain within the full-length protein, Pdp1, abolishes the interaction o f the protein with H4K20me3. In fission yeast, Set9 is the sole enzyme that catalyzes all three states of H4K20me, and Set9-mediated H4K20me is required for efficient recruitment of checkpoint protein Crb2 to sites of DNA damage. The methylation of H4K20 is involved in a diverse array of cellular processes, such as organizing higher-order chromatin, maintaining genome stability, and regulating cell-cycle progression.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569000412  579 ELVWAKCRGYPSYPALIIDPKMPREGLLHNGvpipvppldvlklgeqkqaeAGERLFLVLFFDNKRTwQWLPRDKVLPLG 658
Cdd:pfam00855   2 DLVWAKLKGYPWWPARVVDPEELPENVLKPK--------------------KKDGEYLVRFFGDSEF-AWVKPKDLKPFD 60

                          90       100       110
                  ....*....|....*....|....*....|....
gi 569000412  659 VEDTVDKLKMleGRKTSIRKSVQVAYDRAMIHLS 692
Cdd:pfam00855  61 EGDEFEYLKK--KKKKKKKKAFKKALEEAEEALK 92

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 569000412 104 DLLQEKDSAHiFAEPVSLSEVPDYLEFISKPMDFSTMRRKLESHLYHTLEEFEEDFNLIVTNCMKYNAKDTIFHRAAVRL 183
Cdd:cd05504   23 EIVKHKDSWP-FLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHTSVYKAGTRL 101

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 569000412 101 TTLDLLQEKDSAHIFAEPVSLS--EVPDYLEFISKPMDFSTMRRKLESHLYHTLEEFEEDFNLIVTNCMKYNAKDTIFHR 178
Cdd:cd05506    7 TLLRKLMKHKWGWVFNAPVDVValGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVHT 86

                 ....*
gi 569000412 179 AAVRL 183
Cdd:cd05506   87 MAKEL 91

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 569000412  96 TVLLRTTLD-LLQEKdsAHIFAEPVSLSEVPDYLEFISKPMDFSTMRRKLESHLYHTLEEFEEDFNLIVTNCMKYNAKDT 174
Cdd:cd05508    5 SKLLKFALErMKQPG--AEPFLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYNGGDH 82

                 ....*.
gi 569000412 175 IFHRAA 180
Cdd:cd05508   83 KLTQAA 88

Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 569000412 115 FAEPVSLSEVPDYLEFISKPMDFSTMRRKLESHLYHTLEEFEEDFNLIVTNCMKYNAKDTIFHRAAVRLRDLGGAIL 191
Cdd:cd05505   21 FREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGSYVLSCMRKTEQCCVNLL 97

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 569000412 115 FAEPVSLsEVPDYLEFISKPMDFSTMRRKLESHL---YHTLEEFEEDFNLIVTNCMKYNAKDTIFHRAAVRL 183
Cdd:cd05502   25 FHEPVSP-SVPNYYKIIKTPMDLSLIRKKLQPKSpqhYSSPEEFVADVRLMFKNCYKFNEEDSEVAQAGKEL 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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 569000412  98 LLRTTLDLLQEKDSAHIFAEPVSLS--EVPDYLEFISKPMDFSTMRRKLESHLYHTLEEFEEDFNLIVTNCMKYN 170
Cdd:cd05497    9 LLKVVLKALWKHKFAWPFQQPVDAVklNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYN 83

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        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 569000412 115 FAEPV----SLSEVPDYLEFISKPMDFSTMRRKLESHLYHTLEEFEEDFNLIVTNCMKYNAKDTIFHRAAVRLRDL 186
Cdd:cd05520   23 LAEPFlklpSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPNSRIYKDAEKLQKL 98

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 569000412 104 DLLQEKDSAHiFAEPVSLSEVPDYLEFISKPMDFSTMRRKLESHLYHTLEEFEEDFNLIVTNCMKYN 170
Cdd:cd05496   16 LMWDCEDSEP-FRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYT 81

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

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 569000412 114 IFAEPVSLSEVPDYLEFISKPMDFSTMRRKLESHLYHTLEEFEEDFNLIVTNCMKYN 170
Cdd:cd05518   26 LFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYN 82

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 569000412 114 IFAEPVSLSEVPDYLEFISKPMDFSTMRRKLESHLYHTLEEFEEDFNLIVTNCMKYNAKDTIFHRAAVRLRDL 186
Cdd:cd05519   26 LFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYNQEGSIVYEDAVEMEKA 98

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 569000412 125 PDYLEFISKPMDFSTMRRKLESHLYHTLEEFEEDFNLIVTNCMKYNAKDTIFHRAAVRLRDLggaILRHARRQAEN 200
Cdd:cd05524   39 PEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYKPDSPEHKDACKLWEL---FLSARNEVLSG 111

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 569000412 125 PDYLEFISKPMDFSTMRRKLEShlYHTLEEFEEDFNLIVTNCMKYNAKDTIFHRAAVRL 183
Cdd:cd05521   38 PDYYKIIKNPLSLNTVKKRLPH--YTNAQEFVNDLAQIPWNARLYNTKGSVIYKYALIL 94

PWWP domain found in Saccharomyces cerevisiae ISWI one complex protein 4 (ScIOC4) and similar proteins; ScIOC4 functions as a component of the ISW1B complex, which acts in remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA. The ISW1B complex acts within coding regions to control the amount of RNA polymerase II released into productive elongation and to coordinate elongation with termination and pre-mRNA processing. The family also includes Schizosaccharomyces pombe PWWP domain-containing proteins 1 and 2 (SpPDP1 and SpPDP2). SpPDP1 associates with Set9 to regulate its chromatin localization and methyltransferase activity towards H4K20. Members of this family contain a PWWP domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569000412 580 LVWAKCRGYPSYPALIIdpkmPREGLlhngvpipvpPLDVLKLGEQKQAEAgERLFLVLFFDNKrTWQWLPRDKVLPLGV 659
Cdd:cd05840    3 LVLAKVKGYPPWPAMVL----PEELL----------PKNVLKAKKRKPKSK-KTVYPVQFFPDN-EYYWVSPSSLKPLTK 66

                         90       100
                 ....*....|....*....|....
gi 569000412 660 EDTVDKLKMLEGRKTSIRKSVQVA 683
Cdd:cd05840   67 EEIDKFLSKSKRKNKDLIEAYEVA 90

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
                 ....*....|....*....|....*....|....*....|....*.
gi 569000412 125 PDYLEFISKPMDFSTMRRKLESHLYHTLEEFEEDFNLIVTNCMKYN 170
Cdd:cd05517   37 PDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFN 82

PWWP domain found in Arabidopsis thaliana histone-lysine N-methyltransferase trithorax-like proteins ATX1, ATX2, and similar proteins; This family includes A. thaliana ATX1 and ATX2, which are sister paralogs originating from a segmental chromosomal duplication. They are plant counterparts of the Drosophila melanogaster trithorax (TRX) and mammalian mixed-lineage leukemia (MLL1) proteins. ATX1, also called protein SET domain group 27, or trithorax-homolog protein 1 (TRX-homolog protein 1), is a methyltransferase that trimethylates histone H3 at lysine 4 (H3K4me3). It also acts as a histone modifier and as a positive effector of gene expression. ATX1 regulates transcription from diverse classes of genes implicated in biotic and abiotic stress responses. It is involved in dehydration stress signaling in both abscisic acid (ABA)-dependent and ABA-independent pathways. ATX2, also called protein SET domain group 30, or trithorax-homolog protein 2 (TRX-homolog protein 2), is involved in dimethylating histone H3 at lysine 4 (H3K4me2). Both ATX1 and ATX2 are multi-domain containing proteins that consist of an N-terminal PWWP domain, FYRN- and FYRC (DAST, domain associated with SET in trithorax) domains, a canonical plant homeodomain (PHD) domain, a non-canonical extended PHD (ePHD) domain, and a C-terminal SET domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.

                         10        20
                 ....*....|....*....|..
gi 569000412 576 EPLELVWAKCRGYPSYPALIID 597
Cdd:cd20142    1 SPGDVVWAKVKGYPMWPALVID 22

PWWP domain found in glyoxylate reductase 1 (GLYR1) and similar proteins; GLYR1, also called 3-hydroxyisobutyrate dehydrogenase-like protein, cytokine-like nuclear factor N-PAC, nuclear protein NP60, or nuclear protein of 60 kDa, is a putative oxidoreductase that is recruited on chromatin and promotes KDM1B demethylase activity. It recognizes and binds trimethylated 'Lys-36' of histone H3 (H3K36me3). GLYR1 enhances the activity of MAP2K4 and MAP2K6 kinases to phosphorylate p38-alpha. In addition to the PWWP domain, GLYR1 also contains an AT-hook and a C-terminal NAD-binding domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.

                         10        20
                 ....*....|....*....|.
gi 569000412 579 ELVWAKCRGYPSYPALIIDPK 599
Cdd:cd05836    5 DLVWAKMKGFPPWPGKIVNPP 25