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 568972604 2923 YCICKTPYDESKFYIGCDRCQNWYHGRCVGILQSEADLIDEYVCPQC 2969
Cdd:cd15560     1 YCICRTPYDESQFYIGCDRCQDWFHGRCVGILQSEAEKIDEYVCPQC 47

domain in different transcription and chromosome remodeling factors;

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568972604    252 NEHIMNVIAIYEVVRNFGNVLRLSPF--CFEDFCAALVSQEQCTLMAEMHVALLKAVLREED 311
Cdd:smart00571    1 NEAFGDLLMVYEFLRSFGKVLGLSPFraTLEDFIAALKCRDQNGLLTEVHVVLLRAILKDEG 62

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972604  2257 TPLQQPALGKAIIRTPVVVQPGTPQQVvTQIIRGQPVSTAISAPSTASSAPVQKGLTPGAAAGPLQPSAPHSP----RPQ 2332
Cdd:pfam03157  285 TSLQQPGQGQSGYYPTSQQQAGQLQQE-QQLGQEQQDQQPGQGRQGQQPGQGQQGQQPAQGQQPGQGQPGYYPtspqQPG 363

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972604  2333 QGQVKLTMAQLTQLTQGHGGNQGLTVVIQGQGQttgQLQLIPQGMTvlPGPGQQLMQAAMPNGTVQ----RFLFTP--LS 2406
Cdd:pfam03157  364 QGQPGYYPTSQQQPQQGQQPEQGQQGQQQGQGQ---QGQQPGQGQQ--PGQGQPGYYPTSPQQSGQgqpgYYPTSPqqSG 438

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972604  2407 TSATAASSSSNSSSTTTNATAAGSGEQKQSKILPQTQVQPATTLAPTQSSSVSPAEAQPQPAQPAAQPQPQPQPPAQPEV 2486
Cdd:pfam03157  439 QGQQPGQGQQPGQEQPGQGQQPGQGQQGQQPGQPEQGQQPGQGQPGYYPTSPQQSGQGQQLGQWQQQGQGQPGYYPTSPL 518

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972604  2487 QTQPAVSSHVP-SETQPSQAQTSKPLVatqcQPQSSVQGQSPVRVQS--PPLTRIRPSTPSQVTPGQQPQVQTTASQPIP 2563
Cdd:pfam03157  519 QPGQGQPGYYPtSPQQPGQGQQLGQLQ----QPTQGQQGQQSGQGQQgqQPGQGQQGQQPGQGQQGQQPGQGQQPGQGQP 594

                   ....*....
gi 568972604  2564 IPPPTSLQA 2572
Cdd:pfam03157  595 GYYPTSPQQ 603

large tegument protein UL36; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972604 1981 PIGVPEAPKETPTPQRKGLRSSALRPKRPETPKQTgpviieswvaeeeLELWEIRAFAERVEKEKAQAAEQQTKKRLEQQ 2060
Cdd:PHA03247 2645 TVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSP-------------PQRPRRRAARPTVGSLTSLADPPPPPPTPEPA 2711

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972604 2061 KPAVIAASTTSPANNTSSTVSPAQKVMVAP---LSGSVTPGTKmvlaTKVGSPATVTfqqnknfhqtfatwvkqgqsnsa 2137
Cdd:PHA03247 2712 PHALVSATPLPPGPAAARQASPALPAAPAPpavPAGPATPGGP----ARPARPPTTA----------------------- 2764

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972604 2138 tSTAATSATTIASTGQTFQITGSPVTMAGKVITKLPLPANSKIVAVNVPAtqggmvqvqqkvlgiiPSTTGPSQQTFTSF 2217
Cdd:PHA03247 2765 -GPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLA----------------PAAALPPAASPAGP 2827

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972604 2218 QPRTATVTirPNTSASAGTTTTSQVITGPQIRPGMTVIRTPLQQPALGK--AIIRTPV--VVQPGTPQQVVTQiirGQPV 2293
Cdd:PHA03247 2828 LPPPTSAQ--PTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKpaAPARPPVrrLARPAVSRSTESF---ALPP 2902

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568972604 2294 STAISAPSTASSAPVQKGLTPGAAAGPlQPSAPHSPRPQqgqvklTMAQLTQLTQGHGGNQG 2355
Cdd:PHA03247 2903 DQPERPPQPQAPPPPQPQPQPPPPPQP-QPPPPPPPRPQ------PPLAPTTDPAGAGEPSG 2957

bromo domain;

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972604   2982 LTEKDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYN 3061
Cdd:smart00297    4 LQKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYN 83

                            90       100
                    ....*....|....*....|..
gi 568972604   3062 PRDTPFYQCAEVLESFFVQKLK 3083
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 568972604  404 HCRVCHKLGDLLCCETCSAVYHLECVKPPLEEVPEDEWQCEVC 446
Cdd:cd15559     1 HCRVCHKLGDLLCCETCSAVYHLECVDPPLEEVPEEDWQCEVC 43

domain in different transcription and chromosome remodeling factors;

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568972604    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 568972604   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 568972604   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 568972604   2923 YC-ICKTPYDESKFyIGCDRCQNWYHGRCVGILQSEADLIDEYVCPQC 2969
Cdd:smart00249    1 YCsVCGKPDDGGEL-LQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972604  2257 TPLQQPALGKAIIRTPVVVQPGTPQQVvTQIIRGQPVSTAISAPSTASSAPVQKGLTPGAAAGPLQPSAPHSP----RPQ 2332
Cdd:pfam03157  285 TSLQQPGQGQSGYYPTSQQQAGQLQQE-QQLGQEQQDQQPGQGRQGQQPGQGQQGQQPAQGQQPGQGQPGYYPtspqQPG 363

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972604  2333 QGQVKLTMAQLTQLTQGHGGNQGLTVVIQGQGQttgQLQLIPQGMTvlPGPGQQLMQAAMPNGTVQ----RFLFTP--LS 2406
Cdd:pfam03157  364 QGQPGYYPTSQQQPQQGQQPEQGQQGQQQGQGQ---QGQQPGQGQQ--PGQGQPGYYPTSPQQSGQgqpgYYPTSPqqSG 438

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972604  2407 TSATAASSSSNSSSTTTNATAAGSGEQKQSKILPQTQVQPATTLAPTQSSSVSPAEAQPQPAQPAAQPQPQPQPPAQPEV 2486
Cdd:pfam03157  439 QGQQPGQGQQPGQEQPGQGQQPGQGQQGQQPGQPEQGQQPGQGQPGYYPTSPQQSGQGQQLGQWQQQGQGQPGYYPTSPL 518

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972604  2487 QTQPAVSSHVP-SETQPSQAQTSKPLVatqcQPQSSVQGQSPVRVQS--PPLTRIRPSTPSQVTPGQQPQVQTTASQPIP 2563
Cdd:pfam03157  519 QPGQGQPGYYPtSPQQPGQGQQLGQLQ----QPTQGQQGQQSGQGQQgqQPGQGQQGQQPGQGQQGQQPGQGQQPGQGQP 594

                   ....*....
gi 568972604  2564 IPPPTSLQA 2572
Cdd:pfam03157  595 GYYPTSPQQ 603

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 568972604  2718 VMKHNAVIEHLKQKKTMtpAEREENQRMivcnqvMKYILDKIDKEEKQAAKKRKREESVEQKRskqnaSKLSALLFK--- 2794
Cdd:pfam13868  132 IDEFNEEQAEWKELEKE--EEREEDERI------LEYLKEKAEREEEREAEREEIEEEKEREI-----ARLRAQQEKaqd 198

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 568972604  2795 ---HKEQLKAEIL--------RKRALLDKELQIQVQEELKRDLK-MKREREMAQAVQA 2840
Cdd:pfam13868  199 ekaERDELRAKLYqeeqerkeRQKEREEAEKKARQRQELQQAREeQIELKERRLAEEA 256

Family of unknown function (DUF5585); This is a family of unknown function found in chordata.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972604  2038 AERVEKEKAQAAEQQTKKRLEQQKPAVIAASTT---------SPANNTSSTVSPAQKVMVAPLSGSVTPGTKMVLATKVG 2108
Cdd:pfam17823  107 ADGAASRALAAAASSSPSSAAQSLPAAIAALPSeafsapraaACRANASAAPRAAIAAASAPHAASPAPRTAASSTTAAS 186

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972604  2109 SPATVTFQQNKNFHQTFATwVKQGQSNSATSTAATSATTIASTGQTFQITGSPVTMAGKVITKLPLPANSKIVAVNVPAT 2188
Cdd:pfam17823  187 STTAASSAPTTAASSAPAT-LTPARGISTAATATGHPAAGTALAAVGNSSPAAGTVTAAVGTVTPAALATLAAAAGTVAS 265

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972604  2189 QGGMVQVQQKVlgiiPSTTGPSQQTFTSFQPRTATVTIRPNTSASAGTTTTSQVITGPQIRPGMTVIRTPLqQPALGKAI 2268
Cdd:pfam17823  266 AAGTINMGDPH----ARRLSPAKHMPSDTMARNPAAPMGAQAQGPIIQVSTDQPVHNTAGEPTPSPSNTTL-EPNTPKSV 340

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972604  2269 IRTPVVVQPGTPQQVVTQIIRGQPV-------STAISAPSTASSA--PVQKGLTPGAAAGPLQ---------PSAPHSPR 2330
Cdd:pfam17823  341 ASTNLAVVTTTKAQAKEPSASPVPVlhtsmipEVEATSPTTQPSPllPTQGAAGPGILLAPEQvateatagtASAGPTPR 420

                          330       340       350
                   ....*....|....*....|....*....|.
gi 568972604  2331 PQQGQVKLTMAQLTQLTQGhggnQGLTVVIQ 2361
Cdd:pfam17823  421 SSGDPKTLAMASCQLSTQG----QYLVVTTD 447

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 568972604 2044 EKAQAAEQQTKKRlEQQKPAVIAASTTSPANNTSSTVSPAQKVMVAPLSGSVTPGtkmVLATKVGSPATVTFQ-QNKNFH 2122
Cdd:cd22553    11 ELAQVATTASNIG-GQQKQAQSDSSETHDPLILSPPLSQPQQIITAQSSGSAAGG---VAYSVSPAVQTVTVDgHEAIFI 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972604 2123 QTFATWVKQGQSnsatstaatsattiastgQTFQITGSPVT--MAGKVITKLP----LPANSKIVAVNVPATQGGMVQVQ 2196
Cdd:cd22553    87 PANSGLLQTNNQ------------------QAIQLAPGGTQaiLANQQTLIRPntvqGQANASNVLQNIAQIASGGNAVQ 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972604 2197 QKVLGI-------IPSTTGPSQQTFTSFQPRTATVTIRPNtsASAGTTTTSQVItgPQIRPGMTVIRTPLQQPALGKAII 2269
Cdd:cd22553   149 LPLNNMtqtipvqVPVSTANGQTVYQTIQVPIQAIQSGNA--GGGNQALQAQVI--PQLAQAAQLQPQQLAQVSSQGYIQ 224

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972604 2270 RTPVVVQPGTPQQV-----VTQIIRGQpVSTAISAPSTASSAPVQKGLTPGAAAGPLQPSAPHSPRPQQGQVKLTMAQLT 2344
Cdd:cd22553   225 QIPANASQQQPQMVqqgpnQSGQIIGQ-VASASSIQAAAIPLTVYTGALAGQNGSNQQQVGQIVTSPIQGMTQGLTAPAS 303

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*
gi 568972604 2345 QltqghggnQGLTVVIQGQGQTTGQlqliPQGMTVLPGpGQQLMQ 2389
Cdd:cd22553   304 S--------SIPTVVQQQAIQGNPL----PPGTQIIAA-GQQLQQ 335

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 568972604 2990 LKRVLRSLQAH--KMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPRDTPF 3067
Cdd:cd04369     5 LRSLLDALKKLkrDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGPGSPI 84

                          90
                  ....*....|....*
gi 568972604 3068 YQCAEVLESFFVQKL 3082
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 568972604 2923 YCICKTPYDESKFYIGCDRCQNWYHGRCVGILQSEADLIDEYVCPQC 2969
Cdd:cd15560     1 YCICRTPYDESQFYIGCDRCQDWFHGRCVGILQSEAEKIDEYVCPQC 47

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 568972604 2990 LKRVLRSlQAHKMAWPFLEPVDPN--DAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPRDTPF 3067
Cdd:cd05498     9 LKELFSK-KHKAYAWPFYKPVDPEalGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPV 87

                          90
                  ....*....|....
gi 568972604 3068 YQCAEVLESFFVQK 3081
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 568972604 2990 LKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPRDTPFYQ 3069
Cdd:cd05504    17 LEQLLVEIVKHKDSWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHTSVYK 96

                          90
                  ....*....|....
gi 568972604 3070 CAEVLESFFVQKLK 3083
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 568972604 2984 EKDYEGLKRVLRSLQAH-KMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNP 3062
Cdd:cd05510     6 EEFYESLDKVLNELKTYtEHSTPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYNS 85

                          90
                  ....*....|....
gi 568972604 3063 R-DTPFYQCAEVLE 3075
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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972604 2994 LRSLQAHKMAWPFLEPVDPN--DAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPRDTPFYQCA 3071
Cdd:cd05506     9 LRKLMKHKWGWVFNAPVDVValGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVHTMA 88

                  ....*..
gi 568972604 3072 EVLESFF 3078
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 568972604 2923 YCICKTPYDESKFYIGCDRCQNWYHGRCVGILQSEADLIDEYVCPQC 2969
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 568972604 2982 LTEKDYEGLKRVLRSLQAHKMAWPFLEPVdPNDAPDYYGVIKEPMDLATMEERIQKR---YYEKLTEFVADMTKIFDNCR 3058
Cdd:cd05502     1 LSPIDQRKCERLLLELYCHELSLPFHEPV-SPSVPNYYKIIKTPMDLSLIRKKLQPKspqHYSSPEEFVADVRLMFKNCY 79

                          90       100
                  ....*....|....*....|....*
gi 568972604 3059 YYNPRDTPFYQCAEVLESFFVQKLK 3083
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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568972604 2990 LKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPRDTPFYQ 3069
Cdd:cd05512     6 LRKTLDQLQEKDTAEIFSEPVDLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKDTIFYR 85

                  ..
gi 568972604 3070 CA 3071
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 568972604  405 CRVCHKLGDLLCCETCSAVYHLECVKPPLEEVPEDEWQCEVC 446
Cdd:cd15532     2 CRVCKDGGELLCCDGCPSSYHLHCLNPPLAEIPDGDWFCPRC 43

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 568972604 2923 YCICKTPYDESkFYIGCDRCQNWYHGRCVGILQSEADLIDEYVCPQC 2969
Cdd:cd16039     1 YCICQKPDDGR-WMIACDGCDEWYHFTCVNIPEADVELVDSFFCPPC 46

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568972604 2990 LKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPRDTP 3066
Cdd:cd05528     8 LRDVLKRLASDKRFNAFTKPVDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPDRDP 84

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 568972604 2986 DYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERIQKRYYEKLTEFVADMTKIFDNCRYYNPRDT 3065
Cdd:cd05505     1 ELQKCEEILSKILKYRFSWPFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGS 80

                          90
                  ....*....|....*..
gi 568972604 3066 PFYQCAEVLESFFVQKL 3082
Cdd:cd05505    81 YVLSCMRKTEQCCVNLL 97

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 568972604 2923 YCICKTPYDESKFYIGCDRCQNWYHGRCVGILQSEADLIDEYVCPQCQ 2970
Cdd:cd15640     1 YCVCRQPYDVNRFMIECDICKDWFHGSCVQVEEHHAADIDLYHCPNCE 48

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