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 530411796 2842 KDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSD 2921
Cdd:cd05509     1 PLYTQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPD 80

                          90       100
                  ....*....|....*....|.
gi 530411796 2922 SPFYQCAEVLESFFVQKLKGF 2942
Cdd:cd05509    81 TEYYKCANKLEKFFWKKLKEL 101

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

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 530411796  392 HCRVCHKLGDLLCCETCSAVYHLECVKPPLEEVPEDEWQCEVC 434
Cdd:cd15559     1 HCRVCHKLGDLLCCETCSAVYHLECVDPPLEEVPEEDWQCEVC 43

Williams-Beuren syndrome DDT (WSD), D-TOX E motif; This family represents the combined alpha-helical module found in diverse eukaryotic chromatin proteins. Based on the Ioc3 structure, the N-terminus of this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. The acidic residue from the GxD signature at the N-terminus is a major determinant of the interaction between the ISWI and WHIM motifs. The N-terminal portion also contacts the inter-nucleosomal linker DNA. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognizing and DNA binding domains, some of which discriminate methylated DNA. The WSD module constitutes the inter-nucleosomal linker DNA binding site in the major groove of DNA, and was first identified as WSD, the D-TOX E motif of plant homeodomains homologous with the mutant transcription factor causing Williams-Beuren syndrome in association with the DDT-domain.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 530411796   456 IRHEPIGYDRSRRKYWFL---NRRLIIEEDTENEnekkIWYYSTKVQLAELIDCLDKDYW-EAELCKILEE 522
Cdd:pfam15613    1 IRSLPLGRDRRYNRYWWFdpgTGRLFVESPSDGE----WGVYSSKEQLDALIASLNPRGVrESALKEALEK 67

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 530411796 2842 KDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSD 2921
Cdd:cd05509     1 PLYTQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPD 80

                          90       100
                  ....*....|....*....|.
gi 530411796 2922 SPFYQCAEVLESFFVQKLKGF 2942
Cdd:cd05509    81 TEYYKCANKLEKFFWKKLKEL 101

bromo domain;

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530411796   2839 LTEKDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYN 2918
Cdd:smart00297    4 LQKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYN 83

                            90       100
                    ....*....|....*....|..
gi 530411796   2919 PSDSPFYQCAEVLESFFVQKLK 2940
Cdd:smart00297   84 GPDSEVYKDAKKLEKFFEKKLR 105

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 530411796  2847 LKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQ 2926
Cdd:pfam00439    1 CLEILDKLMEHPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYK 80

                   ...
gi 530411796  2927 CAE 2929
Cdd:pfam00439   81 AAE 83

DDT domain; The DDT domain is named after (DNA binding homeobox and Different Transcription factors) and is approximately 60 residues in length. Along with the WHIM motifs, it comprises an entirely alpha helical module found in diverse eukaryotic chromatin proteins. Based on the structure of Ioc3, this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. In particular, the DDT domain, in combination with the WHIM1 and WHIM2 motifs form the SLIDE domain binding pocket.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 530411796   241 EHIMNVIAIYEVLRNFGTVLRLSPFRFEDFCAALVSQEQ-CTLMAEMHVVLLKAVLRE 297
Cdd:pfam02791    1 EAFGDLLMVWEFLNSFGEVLGLSPFTLDDFEEALLCTEEpSELLDEIHCALLKALVRD 58

Williams-Beuren syndrome DDT (WSD), D-TOX E motif; This family represents the combined alpha-helical module found in diverse eukaryotic chromatin proteins. Based on the Ioc3 structure, the N-terminus of this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. The acidic residue from the GxD signature at the N-terminus is a major determinant of the interaction between the ISWI and WHIM motifs. The N-terminal portion also contacts the inter-nucleosomal linker DNA. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognizing and DNA binding domains, some of which discriminate methylated DNA. The WSD module constitutes the inter-nucleosomal linker DNA binding site in the major groove of DNA, and was first identified as WSD, the D-TOX E motif of plant homeodomains homologous with the mutant transcription factor causing Williams-Beuren syndrome in association with the DDT-domain.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 530411796   456 IRHEPIGYDRSRRKYWFL---NRRLIIEEDTENEnekkIWYYSTKVQLAELIDCLDKDYW-EAELCKILEE 522
Cdd:pfam15613    1 IRSLPLGRDRRYNRYWWFdpgTGRLFVESPSDGE----WGVYSSKEQLDALIASLNPRGVrESALKEALEK 67

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.

                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*.
gi 530411796    393 CRVCHK---LGDLLCCETCSAVYHLECVKPPLEE-VPEDEWQCEVC 434
Cdd:smart00249    2 CSVCGKpddGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47

High molecular weight glutenin subunit; Members of this family include high molecular weight subunits of glutenin. This group of gluten proteins is thought to be largely responsible for the elastic properties of gluten, and hence, doughs. Indeed, glutenin high molecular weight subunits are classified as elastomeric proteins, because the glutenin network can withstand significant deformations without breaking, and return to the original conformation when the stress is removed. Elastomeric proteins differ considerably in amino acid sequence, but they are all polymers whose subunits consist of elastomeric domains, composed of repeated motifs, and non-elastic domains that mediate cross-linking between the subunits. The elastomeric domain motifs are all rich in glycine residues in addition to other hydrophobic residues. High molecular weight glutenin subunits have an extensive central elastomeric domain, flanked by two terminal non-elastic domains that form disulphide cross-links. The central elastomeric domain is characterized by the following three repeated motifs: PGQGQQ, GYYPTS[P/L]QQ, GQQ. It possesses overlapping beta-turns within and between the repeated motifs, and assumes a regular helical secondary structure with a diameter of approx. 1.9 nm and a pitch of approx. 1.5 nm.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530411796  2183 QVQQKVLGIIPSSTGTSQQTFTSfQPRTATVTIRPNTSGSGGTTSNSQVITGPQIRPGMTVIRTPLQQSTLGK------- 2255
Cdd:pfam03157  256 QGQQGYYPISPQQPRQWQQSGQG-QQGYYPTSLQQPGQGQSGYYPTSQQQAGQLQQEQQLGQEQQDQQPGQGRqgqqpgq 334

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530411796  2256 -------AIIRTPVMVQPGAPQQVMTQIIRGQPVSTAVSAPN-TVSSTPGQKSLTSATSTSNIQSSASQPPRPQQGQVKL 2327
Cdd:pfam03157  335 gqqgqqpAQGQQPGQGQPGYYPTSPQQPGQGQPGYYPTSQQQpQQGQQPEQGQQGQQQGQGQQGQQPGQGQQPGQGQPGY 414

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530411796  2328 TMAQLTQLTQGHGGNQGLTVVIQGQGQTTGQLQLIPQGVTV---LPGPGQQLMQAAMPNGTVQRFLFTPLATTATTASTT 2404
Cdd:pfam03157  415 YPTSPQQSGQGQPGYYPTSPQQSGQGQQPGQGQQPGQEQPGqgqQPGQGQQGQQPGQPEQGQQPGQGQPGYYPTSPQQSG 494

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530411796  2405 TTTVSTTAAGTGEQRQ-----SKLSP-QMQVHQDKTLP--PAQSSSVGPAE--AQPQTAQPSAQPQPQTQPQSPAQPEVQ 2474
Cdd:pfam03157  495 QGQQLGQWQQQGQGQPgyyptSPLQPgQGQPGYYPTSPqqPGQGQQLGQLQqpTQGQQGQQSGQGQQGQQPGQGQQGQQP 574

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530411796  2475 TQPEvQTQTTVSSHVPSEAQPTHAQSSkpqvaaqsqPQSNVQGQSPVRVQSPSQTR--IRPSTPSQLSPGQQSQVQTTTS 2552
Cdd:pfam03157  575 GQGQ-QGQQPGQGQQPGQGQPGYYPTS---------PQQSGQGQQPGQWQQPGQGQpgYYPTSSLQLGQGQQGYYPTSPQ 644

                   ..
gi 530411796  2553 QP 2554
Cdd:pfam03157  645 QP 646

N-terminal domain of transcription factor Specificity Protein (SP) 2; Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. SP2 contains the least conserved DNA-binding domain within the SP subfamily of proteins, and its DNA sequence specificity differs from the other SP proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate, or in some cases, repress expression from different promoters. The transcription factor SP2 serves as a paradigm for indirect genomic binding. It does not require its DNA-binding domain for genomic DNA binding and occupies target promoters independently of whether they contain a cognate DNA-binding motif. SP2 belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. SP1-4 have similar N-terminal transactivation domains characterized by glutamine-rich regions, which, in most cases, have adjacent serine/threonine-rich regions. This model represents the N-terminal domain of SP2.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530411796 2163 LPANSKIV-----AVNVPATQGG-VVQVQQKVLGIIPSSTG--TSQQTFTSFQPRTATVTIRPNTSGSGGTTsNSQVITG 2234
Cdd:cd22540    79 LSAKGNIIqlqgsQLSSSAPGGQqVFAIQNPTMIIKGSQTRssTNQQYQISPQIQAAGQINNSGQIQIIPGT-NQAIITP 157

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530411796 2235 PQIRPG-------MTVIRTPLQQSTLGKAIIRTP--VMVQPGA-------PQQVMTqiirGQPVSTAVSAPNTVSSTPGQ 2298
Cdd:cd22540   158 VQVLQQpqqahkpVPIKPAPLQTSNTNSASLQVPgnVIKLQSGgnvaltlPVNNLV----GTQDGATQLQLAAAPSKPSK 233

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530411796 2299 KsltsatsTSNIQSSASQPPRPQQGQVKLTMAQLTQLTQGHGGNQGLTVviqgQGQTTGQLQLIPQgvtvlpgpgQQLMQ 2378
Cdd:cd22540   234 K-------IRKKSAQAAQPAVTVAEQVETVLIETTADNIIQAGNNLLIV----QSPGTGQPAVLQQ---------VQVLQ 293

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530411796 2379 AAMPNGTVQrflfTPlattattastttttvstTAAGTGEQRQSKLSPqmqvhqdkTLP--PAQSSSVGPAEAQPqtaqps 2456
Cdd:cd22540   294 PKQEQQVVQ----IP-----------------QQALRVVQAASATLP--------TVPqkPLQNIQIQNSEPTP------ 338

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530411796 2457 aqpqpQTQPQSPAQPEVQTQ-----PEVQTQTTVSSHVPSEAQPTHAQSSKP---------------------------- 2503
Cdd:cd22540   339 -----TQVYIKTPSGEVQTVllqeaPAATATPSSSTSTVQQQVTANNGTGTSkpnynvrkertlpkiapaggiislnaaq 413

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 530411796 2504 -QVAAQSQPQSNVQGqspvrVQSPSQTRIRPSTPSQlspgQQSQVQTTTSQPIPIQPHTSLQI 2565
Cdd:cd22540   414 lAAAAQAIQTINING-----VQVQGVPVTITNAGGQ----QQLTVQTVSSNNLTISGLSPTQI 467

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 530411796 2842 KDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSD 2921
Cdd:cd05509     1 PLYTQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPD 80

                          90       100
                  ....*....|....*....|.
gi 530411796 2922 SPFYQCAEVLESFFVQKLKGF 2942
Cdd:cd05509    81 TEYYKCANKLEKFFWKKLKEL 101

PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, also termed nucleosome-remodeling factor subunit BPTF, or fetal Alz-50 clone 1 protein (FAC1), or fetal Alzheimer antigen, functions as a transcriptional regulator that exhibits altered expression and subcellular localization during neuronal development and neurodegenerative diseases such as Alzheimer's disease. It interacts with the human orthologue of the Kelch-like Ech-associated protein (Keap1). Its function and subcellular localization can be regulated by Keap1. Moreover, BPTF is a novel DNA-binding protein that recognizes the DNA sequence CACAACAC and represses transcription through this site in a phosphorylation-dependent manner. Furthermore, BPTF interacts with the Myc-associated zinc finger protein (ZF87/MAZ) and alters its transcriptional activity, which has been implicated in gene regulation in neurodegeneration. Some family members contain two or three plant homeodomain (PHD) fingers, which may be involved in complex formation with histone H3 trimethylated at K4 (H3K4me3). This family corresponds to the second and third PHD fingers.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 530411796 2780 YCICKTPYDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQC 2826
Cdd:cd15560     1 YCICRTPYDESQFYIGCDRCQDWFHGRCVGILQSEAEKIDEYVCPQC 47

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

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 530411796  392 HCRVCHKLGDLLCCETCSAVYHLECVKPPLEEVPEDEWQCEVC 434
Cdd:cd15559     1 HCRVCHKLGDLLCCETCSAVYHLECVDPPLEEVPEEDWQCEVC 43

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 530411796  2847 LKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQ 2926
Cdd:pfam00439    1 CLEILDKLMEHPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYK 80

                   ...
gi 530411796  2927 CAE 2929
Cdd:pfam00439   81 AAE 83

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 530411796 2847 LKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQ 2926
Cdd:cd05504    17 LEQLLVEIVKHKDSWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHTSVYK 96

                          90
                  ....*....|....
gi 530411796 2927 CAEVLESFFVQKLK 2940
Cdd:cd05504    97 AGTRLQRFFIKRCR 110

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530411796 2849 RVLRSLQAHKMAWPFLEPVDP--NDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQ 2926
Cdd:cd05500    11 SSIRSLKRLKDARPFLVPVDPvkLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNGPEHPVSQ 90

                          90
                  ....*....|...
gi 530411796 2927 CAEVLESFFVQKL 2939
Cdd:cd05500    91 MGKRLQAAFEKHL 103

PHD finger found in PHF2, PHF8 and KDM7; This family includes PHF2, PHF8, KDM7, and similar proteins. PHF2, also termed GRC5, or PHD finger protein 2, is a histone lysine demethylase ubiquitously expressed in various tissues. PHF8, also termed PHD finger protein 8, or KDM7B, is a monomethylated histone H4 lysine 20(H4K20me1) demethylase that transcriptionally regulates many cell cycle genes. It also preferentially acts on H3K9me2 and H3K9me1. PHF8 is modulated by CDC20-containing anaphase-promoting complex (APC (cdc20)) and plays an important role in the G2/M transition. It acts as a critical molecular sensor for mediating retinoic acid (RA) treatment response in RAR alpha-fusion-induced leukemia. Moreover, PHF8 is essential for cytoskeleton dynamics and is associated with X-linked mental retardation. KDM7, also termed JmjC domain-containing histone demethylation protein 1D (JHDM1D), or KIAA1718, is a dual histone demethylase that catalyzes demethylation of monomethylated and dimethylated H3K9 (H3K9me2/me1) and H3K27 (H3K27me2/me1), which functions as an eraser of silencing marks on chromatin during brain development. It also plays a tumor-suppressive role by regulating angiogenesis. All family members contain a plant homeodomain (PHD) finger and a JmjC domain.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 530411796 2780 YCICKTPYDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQC 2826
Cdd:cd15554     1 YCICRQPYDVTRFMIECDVCKDWFHGSCVGVEEHQANDIERYHCPNC 47

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 530411796 2851 LRSLQAHKMAWPFLEPVDPN--DAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCA 2928
Cdd:cd05506     9 LRKLMKHKWGWVFNAPVDVValGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVHTMA 88

                  ....*..
gi 530411796 2929 EVLESFF 2935
Cdd:cd05506    89 KELLKIF 95

domain in different transcription and chromosome remodeling factors;

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 530411796    240 NEHIMNVIAIYEVLRNFGTVLRLSPFR--FEDFCAALVSQEQCTLMAEMHVVLLKAVLREED 299
Cdd:smart00571    1 NEAFGDLLMVYEFLRSFGKVLGLSPFRatLEDFIAALKCRDQNGLLTEVHVVLLRAILKDEG 62

DDT domain; The DDT domain is named after (DNA binding homeobox and Different Transcription factors) and is approximately 60 residues in length. Along with the WHIM motifs, it comprises an entirely alpha helical module found in diverse eukaryotic chromatin proteins. Based on the structure of Ioc3, this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. In particular, the DDT domain, in combination with the WHIM1 and WHIM2 motifs form the SLIDE domain binding pocket.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 530411796   241 EHIMNVIAIYEVLRNFGTVLRLSPFRFEDFCAALVSQEQ-CTLMAEMHVVLLKAVLRE 297
Cdd:pfam02791    1 EAFGDLLMVWEFLNSFGEVLGLSPFTLDDFEEALLCTEEpSELLDEIHCALLKALVRD 58

PHD finger found in Set1 complex component SPP1; Set1C component SPP1, also called COMPASS component Spp1, or Complex proteins associated with set1 protein Spp1, or Suppressor of PRP protein 1, is a component of the COMPASS complex that links histone methylation to initiation of meiotic recombination. It induces double-strand break (DSB) formation by tethering to recombinationally cold regions. SPP1 interacts with H3K4me3 and Mer2, a protein required for DSB formation, to promote recruitment of potential meiotic DSB sites to the chromosomal axis. SPP1 contains a PHD finger, a zinc binding motif.

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                  ....*....|....*....|....*....|....*....|....*..
gi 530411796 2780 YCICKTPYDESkFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQC 2826
Cdd:cd16039     1 YCICQKPDDGR-WMIACDGCDEWYHFTCVNIPEADVELVDSFFCPPC 46

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 530411796 2847 LKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSP 2923
Cdd:cd05528     8 LRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPDRDP 84

PHD finger found in CXXC-type zinc finger protein 1 (Cfp1); Cfp1, also termed CpG-binding protein, or PHD finger and CXXC domain-containing protein 1 (PCCX1), is a specificity factor that binds to unmethylated CpGs and links H3K4me3 with CpG islands (CGIs). It integrates both promoter CpG content and gene activity for accurate trimethylation of histone H3 Lys 4 (H3K4me3) deposition in embryonic stem cells. Moreover, Cfp1 is an essential component of the SETD1 histone H3K4 methyltransferase complex and functions as a critical regulator of histone methylation, cytosine methylation, cellular differentiation, and vertebrate development. Cfp1 contains a plant homeodomain (PHD) finger, a CXXC domain, and a CpG binding protein zinc finger C-terminal domain. Its CXXC domain selectively binds to non-methylated CpG islands, following by a preference for a guanosine nucleotide.

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                  ....*....|....*....|....*....|....*....|....*..
gi 530411796 2780 YCICKTPyDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQC 2826
Cdd:cd15553     1 YCICRSS-DISRFMIGCDNCEEWYHGDCINITEKEAKAIKEWYCQQC 46

PHD finger found in lysine-specific demethylase 7 (KDM7); KDM7, also termed JmjC domain-containing histone demethylation protein 1D (JHDM1D), or KIAA1718, is a dual histone demethylase that catalyzes demethylation of monomethylated and dimethylated H3K9 (H3K9me2/me1) and H3K27 (H3K27me2/me1), which functions as an eraser of silencing marks on chromatin during brain development. It also plays a tumor-suppressive role by regulating angiogenesis. KDM7 contains a plant homeodomain (PHD) that binds Lys4-trimethylated histone 3 (H3K4me3) and a jumonji domain that demethylates either H3K9me2 or H3K27me2.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 530411796 2780 YCICKTPYDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQ 2827
Cdd:cd15640     1 YCVCRQPYDVNRFMIECDICKDWFHGSCVQVEEHHAADIDLYHCPNCE 48

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        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530411796 2843 DYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDS 2922
Cdd:cd05505     1 ELQKCEEILSKILKYRFSWPFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGS 80

                          90
                  ....*....|....*..
gi 530411796 2923 PFYQCAEVLESFFVQKL 2939
Cdd:cd05505    81 YVLSCMRKTEQCCVNLL 97

PHD finger found in histone lysine demethylase PHF8; PHF8, also termed PHD finger protein 8, or KDM7B, is a monomethylated histone H4 lysine 20 (H4K20me1) demethylase that transcriptionally regulates many cell cycle genes. It also preferentially acts on H3K9me2 and H3K9me1. PHF8 is modulated by CDC20-containing anaphase-promoting complex (APC (cdc20)) and plays an important role in the G2/M transition. It acts as a critical molecular sensor for mediating retinoic acid (RA) treatment response in RAR alpha-fusion-induced leukemia. Moreover, PHF8 is essential for cytoskeleton dynamics and is associated with X-linked mental retardation. PHF8 contains an N-terminal plant homeodomain (PHD) finger followed by a JmjC domain. The PHD finger mediates binding to nucleosomes at active gene promoters and the JmjC domain catalyzes the demethylation of mono- or dimethyl-lysines.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 530411796 2779 LYCICKTPYDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQST 2829
Cdd:cd15642     1 VYCLCRLPYDVTRFMIECDVCQDWFHGSCVGVEEEKAAEIDLYHCPNCQVT 51

Bromodomain, polybromo repeat V. 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        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530411796 2857 HKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFV 2936
Cdd:cd05515    21 RRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYNEPDSQIYKDALTLQKVLL 100

                  ....*
gi 530411796 2937 QKLKG 2941
Cdd:cd05515   101 ETKRE 105

PHD finger found in death-inducer obliterator variants Dido1, Dido2, and Dido3; This family includes three alternative splicing variants (Dido1, 2, and 3) encoded by the Dido gene, which have been implicated in a number of cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. Dido1, also termed DIO-1, or death-associated transcription factor 1 (DATF-1), is important for maintaining embryonic stem (ES) cells and directly regulates the expression of pluripotency factors. It is the shortest isoform that contains only a highly conserved plant homeodomain (PHD) finger responsible for the binding of histone H3 with a higher affinity for trimethylated lysine 4 (H3K4me3). Gene Dido is a Bonemorphogenetic protein (BMP) target gene, which promotes BMP-induced melanoma progression. It also triggers apoptosis after nuclear translocation and caspase upregulation. Dido3 is the largest isoform ubiquitously expressed in all human tissues. It is dispensable for ES cell self-renewal and pluripotency, but involved in the maintenance of stem cell genomic stability and tumorigenesis. Dido3 contains a PHD finger, a transcription elongation factor S-II subunit M (TFSIIM) domain, aspen paralog and ortholog (SPOC) module, and a long C-terminal region (CT) of unknown homology. Its PHD finger interacts with H3K4me3.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 530411796 2778 KLYCICKTPYDeSKFYIGCDRCQNWYHGRCVGILQSEAELI----DEYVCPQC 2826
Cdd:cd15639     3 ALYCICRQPHN-NRFMICCDRCEEWFHGDCVGITEARGRLLerngEDYICPNC 54

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.

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                   ....*....|....*....|....*....|....*....|....*....|
gi 530411796   393 CRVCHKL---GDLLCCETCSAVYHLECVKPPLE--EVPEDEWQCEVCVAH 437
Cdd:pfam00628    2 CAVCGKSddgGELVQCDGCDDWFHLACLGPPLDpaEIPSGEWLCPECKPK 51

PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC complex protein BHC80) along with HDAC1/2, CtBP1, CoREST, and BRAF35, is associated with LSD1, a lysine (K)-specific histone demethylase. It inhibits LSD1-mediated histone demethylation in vitro. PHF21A is predominantly present in the central nervous system and spermatogenic cells and is one of the six components of BRAF-HDAC complex (BHC) involved in REST-dependent transcriptional repression of neuron-specific genes in non-neuronal cells. It acts as a scaffold protein in BHC in neuronal as well as non-neuronal cells and also plays a role in spermatogenesis. PHF21A contains a C-terminal plant homeodomain (PHD) finger that is responsible for the binding directly to each of five other components of BHC, and of organizing BHC mediating transcriptional repression.

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                  ....*....|....*....|....*....|....*....|..
gi 530411796  393 CRVCHKLGDLLCCETCSAVYHLECVKPPLEEVPEDEWQCEVC 434
Cdd:cd15523     2 CSVCRKSGELLMCDTCSLVYHLDCLDPPLKTIPKGMWICPKC 43

PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED) protein, functions as a regulator of gene transcription in the thymus. It is essential for prevention of autoimmunity. AIRE plays a critical role in the induction of central tolerance. It promotes self-tolerance through tissue-specific antigen (TSA) expression. It also acts as an active regulator of chondrocyte differentiation. AIRE contains a homogeneously-staining region (HSR) or caspase-recruitment domain (CARD), a nuclear localization signal (NLS), a SAND (for Sp100, AIRE, nuclear phosphoprotein 41/75 or NucP41/75, and deformed epidermal auto regulatory factor 1 or Deaf1) domain, two plant homeodomain (PHD) fingers, and four LXXLL (where L stands for leucine) motifs. This model corresponds to the first PHD finger that recognizes the unmethylated tail of histone H3 and targets AIRE-dependent genes.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 530411796  392 HCRVCHKLGDLLCCETCSAVYHLECVKPPLEEVPEDEWQCEVC 434
Cdd:cd15539     1 ECAVCGDGGELLCCDGCPRAFHLACLVPPLTLIPSGTWRCSSC 43

PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and similar proteins; Rco1 is a component of the Rpd3S histone deacetylase complex that plays an important role at actively transcribed genes. Rco1 contains two plant homeodomain (PHD) fingers, which are required for the methylation of histone H3 lysine 36 (H3K36) nucleosome recognition by Rpd3S. This model corresponds to the first PHD finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 530411796  393 CRVCHKLGDLLCCETCSAVYHLECVKPPLEE--VPEDEWQCEVC 434
Cdd:cd15535     2 CSACGGYGSFLCCDGCPRSFHFSCLDPPLEEdnLPDDEWFCNEC 45

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        40
                  ....*....|....*....|....*....|....*....|....*...
gi 530411796 2780 YC-ICKTPYDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQC 2826
Cdd:cd15489     1 SCiVCGKGGDLGGELLQCDGCGKWFHADCLGPPLSSFVPNGKWICPVC 48

PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the fourth PHD finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 530411796  393 CRVCHKLGDLLCCETCSAVYHLECVKppLEEVPEDEWQCEVC 434
Cdd:cd15567     2 CFICSEGGSLICCESCPASFHPECLG--LEPPPEGKFYCEDC 41