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 568972608 2980 KDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPRD 3059
Cdd:cd05509     1 PLYTQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPD 80

                          90       100
                  ....*....|....*....|.
gi 568972608 3060 TPFYQCAEVLESFFVQKLKGF 3080
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 568972608  404 HCRVCHKLGDLLCCETCSAVYHLECVKPPLEEVPEDEWQCEVC 446
Cdd:cd15559     1 HCRVCHKLGDLLCCETCSAVYHLECVDPPLEEVPEEDWQCEVC 43

domain in different transcription and chromosome remodeling factors;

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568972608    252 NEHIMNVIAIYEVVRNFGNVLRLSPF--CFEDFCAALVSQEQCTLMAEMHVALLKAVLREED 311
Cdd:smart00571    1 NEAFGDLLMVYEFLRSFGKVLGLSPFraTLEDFIAALKCRDQNGLLTEVHVVLLRAILKDEG 62

N-terminal domain of transcription factor Specificity Proteins (SP) 1-4; 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. There are many SPs in vertebrates (9 SPs in humans and mice, 7 SPs in chicken, and 11 SPs in teleost fish), but arthropods only have 3 SPs. SPs belong 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 SP1-4.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972608 2119 AVNVPATQGGMVQVQQKVLGII---PSTTGPSQQTFTSFQPRTATVTIRPNtsasagttttsQVITGPQIRPGMTVIRTP 2195
Cdd:cd22540    41 AVEAAVTPPAPPQPTPRKLVPIkpaPLPLGPGKNSIGFLSAKGNIIQLQGS-----------QLSSSAPGGQQVFAIQNP 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972608 2196 LqqpalgkAIIRTPVVVQPGTPQ-QVVTQI-IRGQPVST----AISAPSTASSAPVQKGLTPGAAAGPlQPSAPHSPRPQ 2269
Cdd:cd22540   110 T-------MIIKGSQTRSSTNQQyQISPQIqAAGQINNSgqiqIIPGTNQAIITPVQVLQQPQQAHKP-VPIKPAPLQTS 181

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972608 2270 QGQVKLTMAQLTQLTQGHGGNQGLTV---VIQGQGQTTGQLQLIPQGMTVLPGPGQQLMQAAMPNGTVQrflftplstsa 2346
Cdd:cd22540   182 NTNSASLQVPGNVIKLQSGGNVALTLpvnNLVGTQDGATQLQLAAAPSKPSKKIRKKSAQAAQPAVTVA----------- 250

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972608 2347 taassssnssstttnataagsgEQKQSKILPQTQ---VQPATTLAPTQSSSVSpaeaqpqpaqpaaqpqpqpqppaqpev 2423
Cdd:cd22540   251 ----------------------EQVETVLIETTAdniIQAGNNLLIVQSPGTG--------------------------- 281

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972608 2424 qtQPAVsshvPSETQPSQAQTSKPLVATQCQPQSSVQGQS------PVRVQSPPLTRIRPSTPSQV---TPgqQPQVQTT 2494
Cdd:cd22540   282 --QPAV----LQQVQVLQPKQEQQVVQIPQQALRVVQAASatlptvPQKPLQNIQIQNSEPTPTQVyikTP--SGEVQTV 353

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 568972608 2495 ASQPIPIPPPTslqapsQGQPQSQPQVQSSTQTLSSGQTLNQVTVLSPSCPQPQP 2549
Cdd:cd22540   354 LLQEAPAATAT------PSSSTSTVQQQVTANNGTGTSKPNYNVRKERTLPKIAP 402

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 568972608 2980 KDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPRD 3059
Cdd:cd05509     1 PLYTQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPD 80

                          90       100
                  ....*....|....*....|.
gi 568972608 3060 TPFYQCAEVLESFFVQKLKGF 3080
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 568972608 2918 YCICRTPYDESQFYIGCDRCQNWYHGRCVGILQSEADLIDEYVCPQC 2964
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 568972608 2860 YCICKTPYDESKFYIGCDLCTNWYHGECVGITEKEAKKMDVYICNDC 2906
Cdd:cd15560     1 YCICRTPYDESQFYIGCDRCQDWFHGRCVGILQSEAEKIDEYVCPQC 47

domain in different transcription and chromosome remodeling factors;

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568972608    252 NEHIMNVIAIYEVVRNFGNVLRLSPF--CFEDFCAALVSQEQCTLMAEMHVALLKAVLREED 311
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 568972608   253 EHIMNVIAIYEVVRNFGNVLRLSPFCFEDFCAALVSQEQ-CTLMAEMHVALLKAVLRE 309
Cdd:pfam02791    1 EAFGDLLMVWEFLNSFGEVLGLSPFTLDDFEEALLCTEEpSELLDEIHCALLKALVRD 58

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 568972608   405 CRVCHKL---GDLLCCETCSAVYHLECVKPPLE--EVPEDEWQCEVCVAH 449
Cdd:pfam00628    2 CAVCGKSddgGELVQCDGCDDWFHLACLGPPLDpaEIPSGEWLCPECKPK 51

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 568972608   2918 YC-ICRTPYDESQFyIGCDRCQNWYHGRCVGILQSEADLIDEYVCPQC 2964
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 568972608  2860 YC-ICKTPyDESKFYIGCDLCTNWYHGECVGIT-EKEAKKMDVYICNDCKRA 2909
Cdd:pfam00628    1 YCaVCGKS-DDGGELVQCDGCDDWFHLACLGPPlDPAEIPSGEWLCPECKPK 51

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 568972608 2119 AVNVPATQGGMVQVQQKVLGII---PSTTGPSQQTFTSFQPRTATVTIRPNtsasagttttsQVITGPQIRPGMTVIRTP 2195
Cdd:cd22540    41 AVEAAVTPPAPPQPTPRKLVPIkpaPLPLGPGKNSIGFLSAKGNIIQLQGS-----------QLSSSAPGGQQVFAIQNP 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972608 2196 LqqpalgkAIIRTPVVVQPGTPQ-QVVTQI-IRGQPVST----AISAPSTASSAPVQKGLTPGAAAGPlQPSAPHSPRPQ 2269
Cdd:cd22540   110 T-------MIIKGSQTRSSTNQQyQISPQIqAAGQINNSgqiqIIPGTNQAIITPVQVLQQPQQAHKP-VPIKPAPLQTS 181

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972608 2270 QGQVKLTMAQLTQLTQGHGGNQGLTV---VIQGQGQTTGQLQLIPQGMTVLPGPGQQLMQAAMPNGTVQrflftplstsa 2346
Cdd:cd22540   182 NTNSASLQVPGNVIKLQSGGNVALTLpvnNLVGTQDGATQLQLAAAPSKPSKKIRKKSAQAAQPAVTVA----------- 250

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972608 2347 taassssnssstttnataagsgEQKQSKILPQTQ---VQPATTLAPTQSSSVSpaeaqpqpaqpaaqpqpqpqppaqpev 2423
Cdd:cd22540   251 ----------------------EQVETVLIETTAdniIQAGNNLLIVQSPGTG--------------------------- 281

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972608 2424 qtQPAVsshvPSETQPSQAQTSKPLVATQCQPQSSVQGQS------PVRVQSPPLTRIRPSTPSQV---TPgqQPQVQTT 2494
Cdd:cd22540   282 --QPAV----LQQVQVLQPKQEQQVVQIPQQALRVVQAASatlptvPQKPLQNIQIQNSEPTPTQVyikTP--SGEVQTV 353

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 568972608 2495 ASQPIPIPPPTslqapsQGQPQSQPQVQSSTQTLSSGQTLNQVTVLSPSCPQPQP 2549
Cdd:cd22540   354 LLQEAPAATAT------PSSSTSTVQQQVTANNGTGTSKPNYNVRKERTLPKIAP 402

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 568972608  2655 VMKHNAVIEHLKQKKTMtpAEREENQRMivcnqvMKYILDKIDKEEKQAAKKRKREESVEQKRskqnaSKLSALLFK--- 2731
Cdd:pfam13868  132 IDEFNEEQAEWKELEKE--EEREEDERI------LEYLKEKAEREEEREAEREEIEEEKEREI-----ARLRAQQEKaqd 198

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 568972608  2732 ---HKEQLKAEIL--------RKRALLDKELQIQVQEELKRDLK-MKREREMAQAVQA 2777
Cdd:pfam13868  199 ekaERDELRAKLYqeeqerkeRQKEREEAEKKARQRQELQQAREeQIELKERRLAEEA 256

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 568972608 2856 DTRLYCICKTP-YDEskfYIGCD--LCT-NWYHGECVGIteKEAKKMDVYiCNDCKRA 2909
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 568972608 2980 KDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPRD 3059
Cdd:cd05509     1 PLYTQLKKVLDSLKNHKSAWPFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPD 80

                          90       100
                  ....*....|....*....|.
gi 568972608 3060 TPFYQCAEVLESFFVQKLKGF 3080
Cdd:cd05509    81 TEYYKCANKLEKFFWKKLKEL 101

bromo domain;

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972608   2977 LTEKDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYN 3056
Cdd:smart00297    4 LQKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYN 83

                            90       100
                    ....*....|....*....|..
gi 568972608   3057 PRDTPFYQCAEVLESFFVQKLK 3078
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 568972608  404 HCRVCHKLGDLLCCETCSAVYHLECVKPPLEEVPEDEWQCEVC 446
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 568972608 2985 LKRVLRSlQAHKMAWPFLEPVDPN--DAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPRDTPF 3062
Cdd:cd05498     9 LKELFSK-KHKAYAWPFYKPVDPEalGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPV 87

                          90
                  ....*....|....
gi 568972608 3063 YQCAEVLESFFVQK 3076
Cdd:cd05498    88 HAMARKLQDVFEDR 101

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 568972608 2985 LKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPRDTPFYQ 3064
Cdd:cd05504    17 LEQLLVEIVKHKDSWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHTSVYK 96

                          90
                  ....*....|....
gi 568972608 3065 CAEVLESFFVQKLK 3078
Cdd:cd05504    97 AGTRLQRFFIKRCR 110

Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). 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 568972608 2979 EKDYEGLKRVLRSLQAH-KMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNP 3057
Cdd:cd05510     6 EEFYESLDKVLNELKTYtEHSTPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYNS 85

                          90
                  ....*....|....
gi 568972608 3058 R-DTPFYQCAEVLE 3070
Cdd:cd05510    86 DpSHPLRRHANFMK 99

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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972608 2989 LRSLQAHKMAWPFLEPVDPN--DAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPRDTPFYQCA 3066
Cdd:cd05506     9 LRKLMKHKWGWVFNAPVDVValGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVHTMA 88

                  ....*..
gi 568972608 3067 EVLESFF 3073
Cdd:cd05506    89 KELLKIF 95

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 568972608 2918 YCICRTPYDESQFYIGCDRCQNWYHGRCVGILQSEADLIDEYVCPQC 2964
Cdd:cd15554     1 YCICRQPYDVTRFMIECDVCKDWFHGSCVGVEEHQANDIERYHCPNC 47

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972608 2977 LTEKDYEGLKRVLRSLQAHKMAWPFLEPVdPNDAPDYYGVIKEPMDLATMEERIQKR---YYEKLTEFVADMTKIFDNCR 3053
Cdd:cd05502     1 LSPIDQRKCERLLLELYCHELSLPFHEPV-SPSVPNYYKIIKTPMDLSLIRKKLQPKspqHYSSPEEFVADVRLMFKNCY 79

                          90       100
                  ....*....|....*....|....*
gi 568972608 3054 YYNPRDTPFYQCAEVLESFFVQKLK 3078
Cdd:cd05502    80 KFNEEDSEVAQAGKELELFFEEQLK 104

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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972608 2985 LKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPRDTPFYQ 3064
Cdd:cd05512     6 LRKTLDQLQEKDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKDTIFYR 85

                  ..
gi 568972608 3065 CA 3066
Cdd:cd05512    86 AA 87

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 568972608  405 CRVCHKLGDLLCCETCSAVYHLECVKPPLEEVPEDEWQCEVC 446
Cdd:cd15532     2 CRVCKDGGELLCCDGCPSSYHLHCLNPPLAEIPDGDWFCPRC 43

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972608 2974 LTPLTEKDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCR 3053
Cdd:COG5076   142 LLYADNKAIAKFKKQLFLRDGRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCK 221

                          90       100
                  ....*....|....*....|....*
gi 568972608 3054 YYNPRDTPFYQCAEVLESFFVQKLK 3078
Cdd:COG5076   222 LYNGPDSSVYVDAKELEKYFLKLIE 246

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 568972608 2918 YCICRTPYDESqFYIGCDRCQNWYHGRCVGILQSEADLIDEYVCPQC 2964
Cdd:cd16039     1 YCICQKPDDGR-WMIACDGCDEWYHFTCVNIPEADVELVDSFFCPPC 46

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 568972608 2918 YCICRTPyDESQFYIGCDRCQNWYHGRCVGILQSEADLIDEYVCPQC 2964
Cdd:cd15553     1 YCICRSS-DISRFMIGCDNCEEWYHGDCINITEKEAKAIKEWYCQQC 46

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        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 568972608 2918 YCICRTPYDESQFYIGCDRCQNWYHGRCVGILQSEADLIDEYVCPQCQST 2967
Cdd:cd15641     1 YCICRLPYDVTRFMIECDACKDWFHGSCVGVEEEEAPDIDIYHCPNCEKT 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 568972608 2860 YCICKTPYDEsKFYIGCDLCTNWYHGECVGITEKEAKKMDV----YICNDC 2906
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 568972608 2918 YCICRTPYDEsQFYIGCDRCQNWYHGRCVGILQSEADL----IDEYVCPQC 2964
Cdd:cd15552     1 YCICRKPHNN-RFMICCDRCEEWFHGDCVGITEAQGKEmeenIEEYVCPKC 50

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 568972608 2917 LYCICRTPYDESQFYIGCDRCQNWYHGRCVGILQSEADLIDEYVCPQCQST 2967
Cdd:cd15642     1 VYCLCRLPYDVTRFMIECDVCQDWFHGSCVGVEEEKAAEIDLYHCPNCQVT 51

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 568972608 2860 YCICKTPYDESKFYIGCDLCTNWYHGECVGITEKEAKKMDVYICNDCKR 2908
Cdd:cd15641     1 YCICRLPYDVTRFMIECDACKDWFHGSCVGVEEEEAPDIDIYHCPNCEK 49