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 568972606 2919 YCICRTPYDESQFYIGCDRCQNWYHGRCVGILQSEADLIDEYVCPQC 2965
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 568972606 2861 YCICKTPYDESKFYIGCDLCTNWYHGECVGITEKEAKKMDVYICNDC 2907
Cdd:cd15560     1 YCICRTPYDESQFYIGCDRCQDWFHGRCVGILQSEAEKIDEYVCPQC 47

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 568972606   468 VRHEPIGYDRSRRKYWFL---NRRLIIEEDTDNEnekkvW-YYSTKVQLAELIDCLD-KGYWEAELCRVLEDIR 536
Cdd:pfam15613    1 IRSLPLGRDRRYNRYWWFdpgTGRLFVESPSDGE-----WgVYSSKEQLDALIASLNpRGVRESALKEALEKIK 69

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 568972606  2656 VMKHNAVIEHLKQKKTMtpAEREENQRMivcnqvMKYILDKIDKEEKQAAKKRKREESVEQKRskqnaSKLSALLFK--- 2732
Cdd:pfam13868  132 IDEFNEEQAEWKELEKE--EEREEDERI------LEYLKEKAEREEEREAEREEIEEEKEREI-----ARLRAQQEKaqd 198

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 568972606  2733 ---HKEQLKAEIL--------RKRALLDKELQIQVQEELKRDLK-MKREREMAQAVQA 2778
Cdd:pfam13868  199 ekaERDELRAKLYqeeqerkeRQKEREEAEKKARQRQELQQAREeQIELKERRLAEEA 256

bromo domain;

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972606   2978 LTEKDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYN 3057
Cdd:smart00297    4 LQKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYN 83

                            90       100
                    ....*....|....*....|..
gi 568972606   3058 PRDTPFYQCAEVLESFFVQKLK 3079
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 568972606  404 HCRVCHKLGDLLCCETCSAVYHLECVKPPLEEVPEDEWQCEVC 446
Cdd:cd15559     1 HCRVCHKLGDLLCCETCSAVYHLECVDPPLEEVPEEDWQCEVC 43

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972606  2986 LKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPRDTPFYQ 3065
Cdd:pfam00439    1 CLEILDKLMEHPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYK 80

                   ...
gi 568972606  3066 CAE 3068
Cdd:pfam00439   81 AAE 83

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972606 2975 LTPLTEKDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCR 3054
Cdd:COG5076   142 LLYADNKAIAKFKKQLFLRDGRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCK 221

                          90       100
                  ....*....|....*....|....*
gi 568972606 3055 YYNPRDTPFYQCAEVLESFFVQKLK 3079
Cdd:COG5076   222 LYNGPDSSVYVDAKELEKYFLKLIE 246

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 568972606   468 VRHEPIGYDRSRRKYWFL---NRRLIIEEDTDNEnekkvW-YYSTKVQLAELIDCLD-KGYWEAELCRVLEDIR 536
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 568972606    405 CRVCHK---LGDLLCCETCSAVYHLECVKPPLEE-VPEDEWQCEVC 446
Cdd:smart00249    2 CSVCGKpddGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 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 568972606   2861 YC-ICKTPYDESKFyIGCDLCTNWYHGECVGITEKEAKKMDVYICNDC 2907
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 568972606  2919 YC-ICRTPYDESQFyIGCDRCQNWYHGRCVGI-LQSEADLIDEYVCPQCQS 2967
Cdd:pfam00628    1 YCaVCGKSDDGGEL-VQCDGCDDWFHLACLGPpLDPAEIPSGEWLCPECKP 50

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 568972606 2120 AVNVPATQGGMVQVQQKVLGII---PSTTGPSQQTFTSFQPRTATVTIRPNtsasagttttsQVITGPQIRPGMTVIRTP 2196
Cdd:cd22540    41 AVEAAVTPPAPPQPTPRKLVPIkpaPLPLGPGKNSIGFLSAKGNIIQLQGS-----------QLSSSAPGGQQVFAIQNP 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972606 2197 LqqpalgkAIIRTPVVVQPGTPQ-QVVTQI-IRGQPVST----AISAPSTASSAPVQKGLTPGAAAGPlQPSAPHSPRPQ 2270
Cdd:cd22540   110 T-------MIIKGSQTRSSTNQQyQISPQIqAAGQINNSgqiqIIPGTNQAIITPVQVLQQPQQAHKP-VPIKPAPLQTS 181

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972606 2271 QGQVKLTMAQLTQLTQGHGGNQGLTV---VIQGQGQTTGQLQLIPQGMTVLPGPGQQLMQAAMPNGTVQrflftplstsa 2347
Cdd:cd22540   182 NTNSASLQVPGNVIKLQSGGNVALTLpvnNLVGTQDGATQLQLAAAPSKPSKKIRKKSAQAAQPAVTVA----------- 250

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972606 2348 taassssnssstttnataagsgEQKQSKILPQTQ---VQPATTLAPTQSSSVSpaeaqpqpaqpaaqpqpqpqppaqpev 2424
Cdd:cd22540   251 ----------------------EQVETVLIETTAdniIQAGNNLLIVQSPGTG--------------------------- 281

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972606 2425 qtQPAVsshvPSETQPSQAQTSKPLVATQCQPQSSVQGQS------PVRVQSPPLTRIRPSTPSQV---TPgqQPQVQTT 2495
Cdd:cd22540   282 --QPAV----LQQVQVLQPKQEQQVVQIPQQALRVVQAASatlptvPQKPLQNIQIQNSEPTPTQVyikTP--SGEVQTV 353

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 568972606 2496 ASQPIPIPPPTslqapsQGQPQSQPQVQSSTQTLSSGQTLNQVTVLSPSCPQPQP 2550
Cdd:cd22540   354 LLQEAPAATAT------PSSSTSTVQQQVTANNGTGTSKPNYNVRKERTLPKIAP 402

large tegument protein UL36; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972606 1919 PIGVPEAPKETPTPQRKGLRSSALRPKRPETPKQTgpviieswvaeeeLELWEIRAFAERVEKEKAQAAEQQTKKRLEQQ 1998
Cdd:PHA03247 2645 TVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSP-------------PQRPRRRAARPTVGSLTSLADPPPPPPTPEPA 2711

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972606 1999 KPAVIAASTTSPANNTSSTVSPAQKVMVAP---LSGSVTPGTKmvlaTKVGSPATVTfqqnknfhqtfatwvkqgqsnsa 2075
Cdd:PHA03247 2712 PHALVSATPLPPGPAAARQASPALPAAPAPpavPAGPATPGGP----ARPARPPTTA----------------------- 2764

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972606 2076 tSTAATSATTIASTGQTFQITGSPVTMAGKVITKLPLPANSKIVAVNVPAtqggmvqvqqkvlgiiPSTTGPSQQTFTSF 2155
Cdd:PHA03247 2765 -GPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLA----------------PAAALPPAASPAGP 2827

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972606 2156 QPRTATVTirPNTSASAGTTTTSQVITGPQIRPGMTVIRTPLQQPALGK--AIIRTPV--VVQPGTPQQVVTQiirGQPV 2231
Cdd:PHA03247 2828 LPPPTSAQ--PTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKpaAPARPPVrrLARPAVSRSTESF---ALPP 2902

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568972606 2232 STAISAPSTASSAPVQKGLTPGAAAGPlQPSAPHSPRPQqgqvklTMAQLTQLTQGHGGNQG 2293
Cdd:PHA03247 2903 DQPERPPQPQAPPPPQPQPQPPPPPQP-QPPPPPPPRPQ------PPLAPTTDPAGAGEPSG 2957

N-terminal domain of transcription factor Specificity Protein (SP) 1-4 from arthropods; 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 the chicken, and 11 SPs in teleost fish), but arthropods only have 3 SPs. One SP is clade SP1-4, which is expressed ubiquitously throughout development. SP1-4 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. This model represents the N-terminal domain of SP1-4 from arthropods.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972606 1982 EKAQAAEQQTKKRlEQQKPAVIAASTTSPANNTSSTVSPAQKVMVAPLSGSVTPGtkmVLATKVGSPATVTFQ-QNKNFH 2060
Cdd:cd22553    11 ELAQVATTASNIG-GQQKQAQSDSSETHDPLILSPPLSQPQQIITAQSSGSAAGG---VAYSVSPAVQTVTVDgHEAIFI 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972606 2061 QTFATWVKQGQSnsatstaatsattiastgQTFQITGSPVT--MAGKVITKLP----LPANSKIVAVNVPATQGGMVQVQ 2134
Cdd:cd22553    87 PANSGLLQTNNQ------------------QAIQLAPGGTQaiLANQQTLIRPntvqGQANASNVLQNIAQIASGGNAVQ 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972606 2135 QKVLGI-------IPSTTGPSQQTFTSFQPRTATVTIRPNtsASAGTTTTSQVItgPQIRPGMTVIRTPLQQPALGKAII 2207
Cdd:cd22553   149 LPLNNMtqtipvqVPVSTANGQTVYQTIQVPIQAIQSGNA--GGGNQALQAQVI--PQLAQAAQLQPQQLAQVSSQGYIQ 224

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972606 2208 RTPVVVQPGTPQQV-----VTQIIRGQpVSTAISAPSTASSAPVQKGLTPGAAAGPLQPSAPHSPRPQQGQVKLTMAQLT 2282
Cdd:cd22553   225 QIPANASQQQPQMVqqgpnQSGQIIGQ-VASASSIQAAAIPLTVYTGALAGQNGSNQQQVGQIVTSPIQGMTQGLTAPAS 303

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*
gi 568972606 2283 QltqghggnQGLTVVIQGQGQTTGQlqliPQGMTVLPGpGQQLMQ 2327
Cdd:cd22553   304 S--------SIPTVVQQQAIQGNPL----PPGTQIIAA-GQQLQQ 335

large tegument protein UL36; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972606 2378 PQTQVQPATTLAPTQSSSVSPAEAQPQPAQPAAQPQPQPQPPAQPEVQTqPAVSSHVPSETQPSQAQTSKPLVATQCQPQ 2457
Cdd:PHA03247 2775 PAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAAS-PAGPLPPPTSAQPTAPPPPPGPPPPSLPLG 2853

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972606 2458 SSVQGQSPVRVQSPP-LTRIRPSTPSQ--VTPGQQPQVQTTaSQPIPIPPPtSLQAPSQGQPQSQPQVQSSTQTLSSGQT 2534
Cdd:PHA03247 2854 GSVAPGGDVRRRPPSrSPAAKPAAPARppVRRLARPAVSRS-TESFALPPD-QPERPPQPQAPPPPQPQPQPPPPPQPQP 2931

                         170       180
                  ....*....|....*....|..
gi 568972606 2535 LNQVTVLSPSCPQPQPQVIAVP 2556
Cdd:PHA03247 2932 PPPPPPRPQPPLAPTTDPAGAG 2953

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 568972606 2986 LKRVLRSLQAH--KMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPRDTPF 3063
Cdd:cd04369     5 LRSLLDALKKLkrDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGPGSPI 84

                          90
                  ....*....|....*
gi 568972606 3064 YQCAEVLESFFVQKL 3078
Cdd:cd04369    85 YKDAKKLEKLFEKLL 99

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 568972606 2919 YCICRTPYDESQFYIGCDRCQNWYHGRCVGILQSEADLIDEYVCPQC 2965
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 568972606 2861 YCICKTPYDESKFYIGCDLCTNWYHGECVGITEKEAKKMDVYICNDC 2907
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 568972606  2986 LKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPRDTPFYQ 3065
Cdd:pfam00439    1 CLEILDKLMEHPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYK 80

                   ...
gi 568972606  3066 CAE 3068
Cdd:pfam00439   81 AAE 83

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 568972606 2989 VLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPRDTPFYQCAE 3068
Cdd:cd05503     8 ILDEMEAHEDAWPFLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSEVGRAGH 87

                  ....*.
gi 568972606 3069 VLESFF 3074
Cdd:cd05503    88 NMRKFF 93

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 568972606 2988 RVLRSLQAHK---MAWPFLEPVDPN--DAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPRDTP 3062
Cdd:cd05499     7 EVLKELMKPKhsaYNWPFLDPVDPValNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTD 86

                          90
                  ....*....|..
gi 568972606 3063 FYQCAEVLESFF 3074
Cdd:cd05499    87 VYMMGHQLEEVF 98

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972606 2988 RVLRSLQAHKMAWPFLEPVDP--NDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPRDTPFYQ 3065
Cdd:cd05500    11 SSIRSLKRLKDARPFLVPVDPvkLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNGPEHPVSQ 90

                          90
                  ....*....|...
gi 568972606 3066 CAEVLESFFVQKL 3078
Cdd:cd05500    91 MGKRLQAAFEKHL 103

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 568972606 2986 LKRVLRSLQAHKMAWPFLEPVDPN--DAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPRDTPF 3063
Cdd:cd05497    10 LKVVLKALWKHKFAWPFQQPVDAVklNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKPGDDV 89

                          90
                  ....*....|....*.
gi 568972606 3064 YQCAEVLESFFVQKLK 3079
Cdd:cd05497    90 VLMAQTLEKLFLQKLA 105

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 568972606 2999 AWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPRDTPFYQCA-EVLE 3071
Cdd:cd05511    18 SWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSVYTKKAkEMLE 91

domain in different transcription and chromosome remodeling factors;

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568972606    252 NEHIMNVIAIYEVVRNFGNVLRLSPF--CFEDFCAALVSQEQCTLMAEMHVALLKAVLREED 311
Cdd:smart00571    1 NEAFGDLLMVYEFLRSFGKVLGLSPFraTLEDFIAALKCRDQNGLLTEVHVVLLRAILKDEG 62

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 568972606 2861 YCICKTPYDESKFYIGCDLCTNWYHGECVGITEKEAKKMDVYICNDC 2907
Cdd:cd15554     1 YCICRQPYDVTRFMIECDVCKDWFHGSCVGVEEHQANDIERYHCPNC 47

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 568972606   253 EHIMNVIAIYEVVRNFGNVLRLSPFCFEDFCAALVSQEQ-CTLMAEMHVALLKAVLRE 309
Cdd:pfam02791    1 EAFGDLLMVWEFLNSFGEVLGLSPFTLDDFEEALLCTEEpSELLDEIHCALLKALVRD 58

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