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 24654638 2541 DVEELKNLIKQMQLHKSAWPFMEPVDPKEAPDYYKVIKEPMDLKRMEIKLESNTYTKLSEFIGDMTKIFDNCRYYNPKES 2620
Cdd:cd05509    2 LYTQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDT 81

                         90       100
                 ....*....|....*....|
gi 24654638 2621 SFYKCAEALESYFVQKIKNF 2640
Cdd:cd05509   82 EYYKCANKLEKFFWKKLKEL 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 24654638  341 HCRVCHRLGDLLCCETCPAVYHLECVDPPMNDVPTEDWQCGLC 383
Cdd:cd15559    1 HCRVCHKLGDLLCCETCSAVYHLECVDPPLEEVPEEDWQCEVC 43

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 24654638 2421 YCICRTPYDDTKFYVGCDLCSNWFHGDCVSITEEASKKLSEFICIDC 2467
Cdd:cd15554    1 YCICRQPYDVTRFMIECDVCKDWFHGSCVGVEEHQANDIERYHCPNC 47

WSTF, HB1, Itc1p, MBD9 motif 1; A conserved alpha helical motif that along with the WHIM2 and WHIM3 motifs, and the DDT domain comprise an alpha helical module found in diverse eukaryotic chromatin proteins.Based on the Ioc3 structure, 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 conserved basic residue in WHIM1 is involved in packing with the DDT motif. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognising and DNA binding domains, some of which discriminate methylated DNA.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 24654638    286 KTFDRNVFHILSHTEYPYTGIDNRLEVLQFLSDQFLTSNSIRDVM 330
Cdd:pfam15612    1 REDLPGLLETLKKGGYYELSPEEKLKILKALCDLLLSSSAIRDEI 45

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 24654638 2541 DVEELKNLIKQMQLHKSAWPFMEPVDPKEAPDYYKVIKEPMDLKRMEIKLESNTYTKLSEFIGDMTKIFDNCRYYNPKES 2620
Cdd:cd05509    2 LYTQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDT 81

                         90       100
                 ....*....|....*....|
gi 24654638 2621 SFYKCAEALESYFVQKIKNF 2640
Cdd:cd05509   82 EYYKCANKLEKFFWKKLKEL 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 24654638 2477 YCSCRQPYDESQFYICCDKCQDWFHGRCVGILQSEAEFIDEYVCPEC 2523
Cdd:cd15560    1 YCICRTPYDESQFYIGCDRCQDWFHGRCVGILQSEAEKIDEYVCPQC 47

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 24654638   2545 LKNLIKQMQLHKSAWPFMEPVDPKEAPDYYKVIKEPMDLKRMEIKLESNTYTKLSEFIGDMTKIFDNCRYYNPKESSFYK 2624
Cdd:pfam00439    1 CLEILDKLMEHPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYK 80

                   ...
gi 24654638   2625 CAE 2627
Cdd:pfam00439   81 AAE 83

domain in different transcription and chromosome remodeling factors;

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24654638     188 NTHVLRALSIYEVLRRFRHMVRLSPFR--FEDLCAALACEEQSALLTEVHIMLLKAILREEDA 248
Cdd:smart00571    1 NEAFGDLLMVYEFLRSFGKVLGLSPFRatLEDFIAALKCRDQNGLLTEVHVVLLRAILKDEGE 63

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 24654638 2421 YCICRTPYDDTKFYVGCDLCSNWFHGDCVSITEEASKKLSEFICIDC 2467
Cdd:cd15554    1 YCICRQPYDVTRFMIECDVCKDWFHGSCVGVEEHQANDIERYHCPNC 47

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 24654638    2477 YCS-CRQPYDESQFyICCDKCQDWFHGRCVGILQSEAEFIDEYVCPEC 2523
Cdd:smart00249    1 YCSvCGKPDDGGEL-LQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47

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 24654638     342 CRVCHR---LGDLLCCETCPAVYHLECVDPPMND-VPTEDWQCGLC 383
Cdd:smart00249    2 CSVCGKpddGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47

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.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 24654638   2421 YC-ICRTPYDDTKFyVGCDLCSNWFHGDCVSITEEASKKLS-EFICIDCKRA 2470
Cdd:pfam00628    1 YCaVCGKSDDGGEL-VQCDGCDDWFHLACLGPPLDPAEIPSgEWLCPECKPK 51

WSTF, HB1, Itc1p, MBD9 motif 1; A conserved alpha helical motif that along with the WHIM2 and WHIM3 motifs, and the DDT domain comprise an alpha helical module found in diverse eukaryotic chromatin proteins.Based on the Ioc3 structure, 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 conserved basic residue in WHIM1 is involved in packing with the DDT motif. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognising and DNA binding domains, some of which discriminate methylated DNA.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 24654638    286 KTFDRNVFHILSHTEYPYTGIDNRLEVLQFLSDQFLTSNSIRDVM 330
Cdd:pfam15612    1 REDLPGLLETLKKGGYYELSPEEKLKILKALCDLLLSSSAIRDEI 45

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 24654638 2541 DVEELKNLIKQMQLHKSAWPFMEPVDPKEAPDYYKVIKEPMDLKRMEIKLESNTYTKLSEFIGDMTKIFDNCRYYNPKES 2620
Cdd:cd05509    2 LYTQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDT 81

                         90       100
                 ....*....|....*....|
gi 24654638 2621 SFYKCAEALESYFVQKIKNF 2640
Cdd:cd05509   82 EYYKCANKLEKFFWKKLKEL 101

Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24654638 2543 EELKNLIKQM--QLHKSAWPFMEPVDPKEAPDYYKVIKEPMDLKRMEIKLESNTYTKLSEFIGDMTKIFDNCRYYNPKES 2620
Cdd:cd04369    3 KKLRSLLDALkkLKRDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGPGS 82

                         90
                 ....*....|....*..
gi 24654638 2621 SFYKCAEALESYFVQKI 2637
Cdd:cd04369   83 PIYKDAKKLEKLFEKLL 99

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 24654638  341 HCRVCHRLGDLLCCETCPAVYHLECVDPPMNDVPTEDWQCGLC 383
Cdd:cd15559    1 HCRVCHKLGDLLCCETCSAVYHLECVDPPLEEVPEEDWQCEVC 43

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 24654638 2545 LKNLIKQMQLHKSAWPFMEPVDPKEAPDYYKVIKEPMDLKRMEIKLESNTYTKLSEFIGDMTKIFDNCRYYNPKESSFYK 2624
Cdd:cd05504   17 LEQLLVEIVKHKDSWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHTSVYK 96

                         90
                 ....*....|....*
gi 24654638 2625 CAEALESYFVQKIKN 2639
Cdd:cd05504   97 AGTRLQRFFIKRCRK 111

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 24654638 2545 LKNLIKQMQLHKSAWPFMEPVDPK--EAPDYYKVIKEPMDLKRMEIKLESNTYTKLSEFIGDMTKIFDNCRYYNPKESSF 2622
Cdd:cd05497   10 LKVVLKALWKHKFAWPFQQPVDAVklNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKPGDDV 89

                         90
                 ....*....|....*.
gi 24654638 2623 YKCAEALESYFVQKIK 2638
Cdd:cd05497   90 VLMAQTLEKLFLQKLA 105

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 24654638 2477 YCSCRQPYDESQFYICCDKCQDWFHGRCVGILQSEAEFIDEYVCPEC 2523
Cdd:cd15554    1 YCICRQPYDVTRFMIECDVCKDWFHGSCVGVEEHQANDIERYHCPNC 47

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 24654638 2545 LKNLIKQMQLHKSAWPFMEPVDPKEAPDYYKVIKEPMDLKRMEIKLESNTYTKLSEFIGDMTKIFDNCRYYNPKESSFYK 2624
Cdd:cd05511    5 LDEIVNELKNLPDSWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSVYTK 84

                         90
                 ....*....|....*....
gi 24654638 2625 CAEALESYFVQKIKNFREN 2643
Cdd:cd05511   85 KAKEMLELAEELLAEREEK 103

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 24654638 2547 NLIKQMQLHKSAWPFMEPVDPK--EAPDYYKVIKEPMDLKRMEIKLESNTYTKLSEFIGDMTKIFDNCRYYNPKESSFYK 2624
Cdd:cd05506    7 TLLRKLMKHKWGWVFNAPVDVValGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVHT 86

                 ....*....
gi 24654638 2625 CAEALESYF 2633
Cdd:cd05506   87 MAKELLKIF 95

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 24654638 2541 DVEELKNLIKQMQLHKSAWPFMEPVDPKEAPDYYKVIKEPMDLKRMEIKLESNTYTKLSEFIGDMTKIFDNCRYYNPKES 2620
Cdd:cd05505    1 ELQKCEEILSKILKYRFSWPFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGS 80

                         90
                 ....*....|....*..
gi 24654638 2621 SFYKCAEALESYFVQKI 2637
Cdd:cd05505   81 YVLSCMRKTEQCCVNLL 97

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 24654638 2561 FMEPVDPKEAPDYYKVIKEPMDLKRMEIKLESNTYTKLSEFIGDMTKIFDNCRYYNPKESSFYKCAEALESYFVQK 2636
Cdd:cd05518   27 FMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYNEEGSQVYEDANILEKVLKEK 102

Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24654638 2545 LKNLIKQmqlHKSAWPFMEPVDPK--EAPDYYKVIKEPMDLKRMEIKLESNTYTKLSEFIGDMTKIFDNCRYYNPKESSF 2622
Cdd:cd05495   12 LEKLYKQ---DPESLPFRQPVDPKllGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYNRKTSRV 88

                         90
                 ....*....|....*
gi 24654638 2623 YKCAEALESYFVQKI 2637
Cdd:cd05495   89 YKYCTKLAEVFEQEI 103

Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24654638 2545 LKNLIKQMQLHKSAWPFMEPVDPKEAPDYYKVIKEPMDLKRMEIKLESNTYTKLSEFIGDMTKIFDNCRYYNPKESSFYK 2624
Cdd:cd05512    6 LRKTLDQLQEKDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKDTIFYR 85

                 ..
gi 24654638 2625 CA 2626
Cdd:cd05512   86 AA 87

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 24654638 2477 YCSCRQPYDESQFYICCDKCQDWFHGRCVGILQSEAEFIDEYVCPECQ 2524
Cdd:cd15640    1 YCVCRQPYDVNRFMIECDICKDWFHGSCVQVEEHHAADIDLYHCPNCE 48

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 24654638    190 HVLRALSIYEVLRRFRHMVRLSPFRFEDLCAALACEEQ-SALLTEVHIMLLKAILRE 245
Cdd:pfam02791    2 AFGDLLMVWEFLNSFGEVLGLSPFTLDDFEEALLCTEEpSELLDEIHCALLKALVRD 58

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 24654638 2421 YCICRTPYDDTKFYVGCDLCSNWFHGDCVSITEEASKKLSEFICIDC 2467
Cdd:cd15554    1 YCICRQPYDVTRFMIECDVCKDWFHGSCVGVEEHQANDIERYHCPNC 47

PHD finger found in PHD finger protein 3 (PHF3), and death-inducer obliterator variants Dido1, Dido2, and Dido3; PHF3 is a human homolog of yeast protein bypass of Ess1 (Bye1), a nuclear protein with a domain resembling the central domain in the transcription elongation factor TFIIS. It is ubiquitously expressed in normal tissues including brain, but its expression is significantly reduced or lost in glioblastomas. PHF3 contains an N-terminal plant homeodomain (PHD) finger, a central RNA polymerase II (Pol II)-binding TFIIS-like domain (TLD) domain, and a C-terminal Spen paralogue and orthologue C-terminal (SPOC) domain. This family also includes Dido gene encoding three alternative splicing variants (Dido1, 2, and 3), which have been implicated in a number of cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. Dido1 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 PHD finger responsible for the binding of histone H3 with a higher affinity for trimethylated lysine4 (H3K4me3). Gene Dido1 is a Bone morphogenetic protein (BMP) target gene and promotes BMP-induced melanoma progression. It also triggers apoptosis after nuclear translocation and caspase upregulation. Dido3 is the largest isoform and is ubiquitously expressed in all human tissues. It is dispensable for ES cell self-renewal and pluripotency, but is 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, a SPOC module, and a long C-terminal region (CT) of unknown homology.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 24654638 2421 YCICRTPYDDtKFYVGCDLCSNWFHGDCVSITEEASKKLSE----FICIDC 2467
Cdd:cd15552    1 YCICRKPHNN-RFMICCDRCEEWFHGDCVGITEAQGKEMEEnieeYVCPKC 50

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 24654638 2421 YCICRTPyDDTKFYVGCDLCSNWFHGDCVSITEEASKKLSEFICIDC 2467
Cdd:cd15553    1 YCICRSS-DISRFMIGCDNCEEWYHGDCINITEKEAKAIKEWYCQQC 46

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 24654638 2476 LYCSCRQPYDeSQFYICCDKCQDWFHGRCVGILQSEAEFI----DEYVCPEC 2523
Cdd:cd15639    4 LYCICRQPHN-NRFMICCDRCEEWFHGDCVGITEARGRLLerngEDYICPNC 54

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
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 24654638 2560 PFMEPVDPKEAPDYYKVIKEPMDLKRMEIKLESNTYTKLSEFIGDMTKIFDNCRYYNP 2617
Cdd:cd05528   23 AFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNP 80

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 24654638  341 HCRVCHRLGDLLCCETCPAVYHLECVDPPMNDVPTEDWQCGLC 383
Cdd:cd15539    1 ECAVCGDGGELLCCDGCPRAFHLACLVPPLTLIPSGTWRCSSC 43

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 24654638 2543 EELKNLIKQMQLHKSAWPFMEPVDPKEAPDYYKVIKEPMDLKRMEIKLESNTYTKLSEFIGDMTKIFDNCRYYNPKESSF 2622
Cdd:cd05513    4 KALEQLIRQLQRKDPHGFFAFPVTDFIAPGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDTIY 83

                 ....*..
gi 24654638 2623 YKCAEAL 2629
Cdd:cd05513   84 YKAAKKL 90

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 24654638 2421 YCICRTPYDDTKFYVGCDLCSNWFHGDCVSITEEASKKLSEFICIDCK 2468
Cdd:cd15640    1 YCVCRQPYDVNRFMIECDICKDWFHGSCVQVEEHHAADIDLYHCPNCE 48

PHD finger found in lysine-specific demethylase PHF2; PHF2, also termed GRC5, or PHD finger protein 2, is a histone lysine demethylase ubiquitously expressed in various tissues. It contains a plant homeodomain (PHD) finger and a JmjC domain and plays an important role in adipogenesis. The PHD finger domain can recognize trimethylated histone H3 lysine 4 (H3K4me3). PHF2 also has dimethylated histone H3 lysine 9(H3K9me2) demethylase activity and acts as a coactivator of several metabolism-related transcription factors. Moreover, it can demethylate ARID5B and further forms a complex with demethylated ARD5B to bind the promoter regions of target genes. The overexpression of PHF2 is involved in the progression of esophageal squamous cell carcinoma (ESCC).

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 24654638 2421 YCICRTPYDDTKFYVGCDLCSNWFHGDCVSITEEASKKLSEFICIDCKR 2469
Cdd:cd15641    1 YCICRLPYDVTRFMIECDACKDWFHGSCVGVEEEEAPDIDIYHCPNCEK 49

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 24654638 2560 PFMEPVDPKEAPDYYKVIKEPMDLKRMEIKLESNTYTKLSEFIGDMTKIFDNCRYYNPKESSFYKCAEALE 2630
Cdd:cd05520   26 PFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPNSRIYKDAEKLQ 96

Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24654638 2543 EELKNLIKQM-QLHKSAwPFMEPVDPKEAPDYYKVIKEPMDLKRMEIKLESNTYTKLSEFIGDMTKIFDNCRYYNP-KES 2620
Cdd:cd05496    8 KQCKELVNLMwDCEDSE-PFRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYTPnKRS 86

                         90
                 ....*....|....*...
gi 24654638 2621 SFYKCAEALESYFVQKIK 2638
Cdd:cd05496   87 RIYSMTLRLSALFEEHIK 104

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.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 24654638    342 CRVCHRL---GDLLCCETCPAVYHLECVDPP--MNDVPTEDWQCGLCRSH 386
Cdd:pfam00628    2 CAVCGKSddgGELVQCDGCDDWFHLACLGPPldPAEIPSGEWLCPECKPK 51

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 24654638 2418 EKLYCICRTPYDDtKFYVGCDLCSNWFHGDCVSITEEASKKL----SEFICIDC 2467
Cdd:cd15639    2 NALYCICRQPHNN-RFMICCDRCEEWFHGDCVGITEARGRLLerngEDYICPNC 54

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 24654638 2421 YCICRTPYDDtKFYVGCDLCSNWFHGDCVSITEEASKKLSEFICIDC 2467
Cdd:cd16039    1 YCICQKPDDG-RWMIACDGCDEWYHFTCVNIPEADVELVDSFFCPPC 46