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 1958662797 3049 KDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPSD 3128
Cdd:cd05509      1 PLYTQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPD 80

                           90       100
                   ....*....|....*....|.
gi 1958662797 3129 SPFYQCAEVLESFFVQKLKGF 3149
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 1958662797  402 HCRVCHKLGDLLCCETCSAVYHLECVKPPLEEVPEDEWQCEVC 444
Cdd:cd15559      1 HCRVCHKLGDLLCCETCSAVYHLECVDPPLEEVPEEDWQCEVC 43

domain in different transcription and chromosome remodeling factors;

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958662797   250 NEHIMNVIAIYEVVRNFGNVLRLSPF--CFEDFCAALVSQEQCTLMAEMHVALLKAVLREED 309
Cdd:smart00571    1 NEAFGDLLMVYEFLRSFGKVLGLSPFraTLEDFIAALKCRDQNGLLTEVHVVLLRAILKDEG 62

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662797 2384 QQLMQAAMPNGTVQRFLFTPLSTPVTAVSSSSSSSSTNATATGSGE----------QKQSKLSPQTQVQPATTLAPTQSS 2453
Cdd:pfam03154  164 QQILQTQPPVLQAQSGAASPPSPPPPGTTQAATAGPTPSAPSVPPQgspatsqppnQTQSTAAPHTLIQQTPTLHPQRLP 243

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662797 2454 SVSPAEAQPQPAQPAAQPQPQPQPPAQPEVQTQP------AASSHVPSETQPSQAqsSKPLVATQCQ----PQSSVQGQS 2523
Cdd:pfam03154  244 SPHPPLQPMTQPPPPSQVSPQPLPQPSLHGQMPPmphslqTGPSHMQHPVPPQPF--PLTPQSSQSQvppgPSPAAPGQS 321

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|...
gi 1958662797 2524 PVRVQSPPltrIRPSTPSQVTPGQQPQVQTTASQPIPIPPPTS 2566
Cdd:pfam03154  322 QQRIHTPP---SQSQLQSQQPPREQPLPPAPLSMPHIKPPPTT 361

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662797 2702 EMEREHTLQASNQSEIiqkqvvMKHNAVIEHLKQKKTMtpAEREENQRMivcnqvMKYILDKIDKEEKQAAKKRKREESV 2781
Cdd:pfam13868  117 EAEEKLEKQRQLREEI------DEFNEEQAEWKELEKE--EEREEDERI------LEYLKEKAEREEEREAEREEIEEEK 182

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958662797 2782 EQKRSKqnaskLSALLfkhkeqlkAEILKKRALLDKELQMQVQEELKRDLKmKRERE 2838
Cdd:pfam13868  183 EREIAR-----LRAQQ--------EKAQDEKAERDELRAKLYQEEQERKER-QKERE 225

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 1958662797 3049 KDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPSD 3128
Cdd:cd05509      1 PLYTQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPD 80

                           90       100
                   ....*....|....*....|.
gi 1958662797 3129 SPFYQCAEVLESFFVQKLKGF 3149
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 1958662797 2987 YCICRTPYDESQFYIGCDRCQNWFHGRCVGILQSEAELIDEYVCPQC 3033
Cdd:cd15560      1 YCICRTPYDESQFYIGCDRCQDWFHGRCVGILQSEAEKIDEYVCPQC 47

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 1958662797 2929 YCICKTPYDESKFYIGCDLCTNWYHGDCVGITEKEAKKMDVYICNDC 2975
Cdd:cd15560      1 YCICRTPYDESQFYIGCDRCQDWFHGRCVGILQSEAEKIDEYVCPQC 47

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662797 3043 LTPLTEKDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCR 3122
Cdd:COG5076    142 LLYADNKAIAKFKKQLFLRDGRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCK 221

                           90       100
                   ....*....|....*....|....*
gi 1958662797 3123 YYNPSDSPFYQCAEVLESFFVQKLK 3147
Cdd:COG5076    222 LYNGPDSSVYVDAKELEKYFLKLIE 246

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 1958662797  251 EHIMNVIAIYEVVRNFGNVLRLSPFCFEDFCAALVSQEQ-CTLMAEMHVALLKAVLRE 307
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 1958662797  466 VRHEPIGYDRSRRKYWFL---NRRLIIEEDTENEnekkvW-YYSTKVQLAELIDCLDKDYW-EAELCRVLEDIR 534
Cdd:pfam15613    1 IRSLPLGRDRRYNRYWWFdpgTGRLFVESPSDGE-----WgVYSSKEQLDALIASLNPRGVrESALKEALEKIK 69

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 1958662797  2987 YC-ICRTPYDESQFyIGCDRCQNWFHGRCVGILQSEAELIDEYVCPQC 3033
Cdd:smart00249    1 YCsVCGKPDDGGEL-LQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 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 1958662797 2929 YC-ICKTPyDESKFYIGCDLCTNWYHGDCVGIT-EKEAKKMDVYICNDCKRA 2978
Cdd:pfam00628    1 YCaVCGKS-DDGGELVQCDGCDDWFHLACLGPPlDPAEIPSGEWLCPECKPK 51

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662797 2384 QQLMQAAMPNGTVQRFLFTPLSTPVTAVSSSSSSSSTNATATGSGE----------QKQSKLSPQTQVQPATTLAPTQSS 2453
Cdd:pfam03154  164 QQILQTQPPVLQAQSGAASPPSPPPPGTTQAATAGPTPSAPSVPPQgspatsqppnQTQSTAAPHTLIQQTPTLHPQRLP 243

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662797 2454 SVSPAEAQPQPAQPAAQPQPQPQPPAQPEVQTQP------AASSHVPSETQPSQAqsSKPLVATQCQ----PQSSVQGQS 2523
Cdd:pfam03154  244 SPHPPLQPMTQPPPPSQVSPQPLPQPSLHGQMPPmphslqTGPSHMQHPVPPQPF--PLTPQSSQSQvppgPSPAAPGQS 321

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|...
gi 1958662797 2524 PVRVQSPPltrIRPSTPSQVTPGQQPQVQTTASQPIPIPPPTS 2566
Cdd:pfam03154  322 QQRIHTPP---SQSQLQSQQPPREQPLPPAPLSMPHIKPPPTT 361

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 1958662797 2172 PLPANSKIVAVNVPATQGGVVQVQQKVLGiipSTAGPSQQTFTSFQP--RTATVTIRPNTSASAGTTTTSQVITGP---- 2245
Cdd:cd22540     66 PLPLGPGKNSIGFLSAKGNIIQLQGSQLS---SSAPGGQQVFAIQNPtmIIKGSQTRSSTNQQYQISPQIQAAGQInnsg 142

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662797 2246 --QIRPG-----MTVIRAPLQQPALGKAVIRTPVTMQPG----APQQVVTQIIR--GQPVSTAISASSTASSAPVQKGLT 2312
Cdd:cd22540    143 qiQIIPGtnqaiITPVQVLQQPQQAHKPVPIKPAPLQTSntnsASLQVPGNVIKlqSGGNVALTLPVNNLVGTQDGATQL 222

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662797 2313 PGAAAGTLQ--------PSAPHSPRPQQGQVKLTMAQLTQLTQGHGGNQGLTVVIQGQGQ--TTGQLQLIP----QGMTV 2378
Cdd:cd22540    223 QLAAAPSKPskkirkksAQAAQPAVTVAEQVETVLIETTADNIIQAGNNLLIVQSPGTGQpaVLQQVQVLQpkqeQQVVQ 302

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662797 2379 LPGPGQQLMQAA---------MPNGTVQRFLFTPLSTPVTAVsssssssstnataTGSGEQkqsklspQT-QVQPATTLA 2448
Cdd:cd22540    303 IPQQALRVVQAAsatlptvpqKPLQNIQIQNSEPTPTQVYIK-------------TPSGEV-------QTvLLQEAPAAT 362

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662797 2449 PTQSSSVSPAEAQPQPAQPAAQPqpqpqppaqpevqTQPAASSHVPSETQPSQAQSSKPLVATQCQ-PQSSVQ--GQSPV 2525
Cdd:cd22540    363 ATPSSSTSTVQQQVTANNGTGTS-------------KPNYNVRKERTLPKIAPAGGIISLNAAQLAaAAQAIQtiNINGV 429

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|...
gi 1958662797 2526 RVQSPPLTRirpstpSQVTPGQQPQVQTTASQPIPIPPPTSLQ 2568
Cdd:cd22540    430 QVQGVPVTI------TNAGGQQQLTVQTVSSNNLTISGLSPTQ 466

Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958662797 2925 DTRLYCICKTP-YDEskfYIGCD--LCT-NWYHGDCVGIteKEAKKMDVYiCNDCKRA 2978
Cdd:COG5034    219 GEELYCFCQQVsYGQ---MVACDnaNCKrEWFHLECVGL--KEPPKGKWY-CPECKKA 270

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 1958662797 3049 KDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPSD 3128
Cdd:cd05509      1 PLYTQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPD 80

                           90       100
                   ....*....|....*....|.
gi 1958662797 3129 SPFYQCAEVLESFFVQKLKGF 3149
Cdd:cd05509     81 TEYYKCANKLEKFFWKKLKEL 101

bromo domain;

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662797  3046 LTEKDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYN 3125
Cdd:smart00297    4 LQKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYN 83

                            90       100
                    ....*....|....*....|..
gi 1958662797  3126 PSDSPFYQCAEVLESFFVQKLK 3147
Cdd:smart00297   84 GPDSEVYKDAKKLEKFFEKKLR 105

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 1958662797  402 HCRVCHKLGDLLCCETCSAVYHLECVKPPLEEVPEDEWQCEVC 444
Cdd:cd15559      1 HCRVCHKLGDLLCCETCSAVYHLECVDPPLEEVPEEDWQCEVC 43

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        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662797 3054 LKRVLRSlQAHKMAWPFLEPVDPN--DAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPSDSPF 3131
Cdd:cd05498      9 LKELFSK-KHKAYAWPFYKPVDPEalGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPV 87

                           90
                   ....*....|....
gi 1958662797 3132 YQCAEVLESFFVQK 3145
Cdd:cd05498     88 HAMARKLQDVFEDR 101

Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662797 3057 VLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAE 3136
Cdd:cd05503      8 ILDEMEAHEDAWPFLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSEVGRAGH 87

                   ....*.
gi 1958662797 3137 VLESFF 3142
Cdd:cd05503     88 NMRKFF 93

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 1958662797 2987 YCICRTPYDESQFYIGCDRCQNWFHGRCVGILQSEAELIDEYVCPQC 3033
Cdd:cd15554      1 YCICRQPYDVTRFMIECDVCKDWFHGSCVGVEEHQANDIERYHCPNC 47

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662797 3058 LRSLQAHKMAWPFLEPVDPN--DAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCA 3135
Cdd:cd05499     12 LMKPKHSAYNWPFLDPVDPValNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTDVYMMG 91

                   ....*..
gi 1958662797 3136 EVLESFF 3142
Cdd:cd05499     92 HQLEEVF 98

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 1958662797 3067 AWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCA-EVLE 3139
Cdd:cd05511     18 SWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSVYTKKAkEMLE 91

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 1958662797 3054 LKRVLRSLQAHKMAWPFLEPVDPN--DAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPSDSPF 3131
Cdd:cd05497     10 LKVVLKALWKHKFAWPFQQPVDAVklNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKPGDDV 89

                           90
                   ....*....|....*.
gi 1958662797 3132 YQCAEVLESFFVQKLK 3147
Cdd:cd05497     90 VLMAQTLEKLFLQKLA 105

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958662797 3043 LTPLTEKDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCR 3122
Cdd:COG5076    142 LLYADNKAIAKFKKQLFLRDGRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCK 221

                           90       100
                   ....*....|....*....|....*
gi 1958662797 3123 YYNPSDSPFYQCAEVLESFFVQKLK 3147
Cdd:COG5076    222 LYNGPDSSVYVDAKELEKYFLKLIE 246

PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the second PHD finger.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1958662797  403 CRVCHKLGDLLCCETCSAVYHLECVKPPLEEVPEDEWQCEVC 444
Cdd:cd15532      2 CRVCKDGGELLCCDGCPSSYHLHCLNPPLAEIPDGDWFCPRC 43

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 1958662797 2929 YCICKTPYDESKFYIGCDLCTNWYHGDCVGITEKEAKKMDVYICNDC 2975
Cdd:cd15554      1 YCICRQPYDVTRFMIECDVCKDWFHGSCVGVEEHQANDIERYHCPNC 47

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 1958662797 3054 LKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPSDSP 3130
Cdd:cd05528      8 LRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPDRDP 84

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 1958662797 2987 YCICRTPYDESQFYIGCDRCQNWFHGRCVGILQSEAELIDEYVCPQCQ 3034
Cdd:cd15640      1 YCVCRQPYDVNRFMIECDICKDWFHGSCVQVEEHHAADIDLYHCPNCE 48

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 1958662797 2987 YCICRTPYDEsQFYIGCDRCQNWFHGRCVGILQSE----AELIDEYVCPQC 3033
Cdd:cd15552      1 YCICRKPHNN-RFMICCDRCEEWFHGDCVGITEAQgkemEENIEEYVCPKC 50

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 1958662797 2929 YCICKTPYDEsKFYIGCDLCTNWYHGDCVGITEKEAKKMDV----YICNDC 2975
Cdd:cd15552      1 YCICRKPHNN-RFMICCDRCEEWFHGDCVGITEAQGKEMEEnieeYVCPKC 50

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 1958662797 2929 YCICKTPYDESKFYIGCDLCTNWYHGDCVGITEKEAKKMDVYICNDCK 2976
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 1958662797 3050 DYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPSDS 3129
Cdd:cd05505      1 ELQKCEEILSKILKYRFSWPFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGS 80

                           90
                   ....*....|....*..
gi 1958662797 3130 PFYQCAEVLESFFVQKL 3146
Cdd:cd05505     81 YVLSCMRKTEQCCVNLL 97

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 1958662797 3064 HKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFV 3143
Cdd:cd05515     21 RRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYNEPDSQIYKDALTLQKVLL 100