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 1622880856 2836 YCICRTPYDESQFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQC 2882
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 1622880856 2778 YCICKTPYDESKFYIGCDLCTNWYHGECVGITEKEAKKMDVYICNDC 2824
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 1622880856  455 IRHEPIGYDRSRRKYWFL---NRRLIIEEDTENEnekkIWYYSTKVQLAELIDCLDKDYW-EAELCKILEE 521
Cdd:pfam15613    1 IRSLPLGRDRRYNRYWWFdpgTGRLFVESPSDGE----WGVYSSKEQLDALIASLNPRGVrESALKEALEK 67

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 1622880856 2836 YCICRTPYDESQFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQC 2882
Cdd:cd15560      1 YCICRTPYDESQFYIGCDRCQDWFHGRCVGILQSEAEKIDEYVCPQC 47

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 1622880856  391 HCRVCHKLGDLLCCETCSAVYHLECVKPPLEEVPEDEWQCEVC 433
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 1622880856 2903 LKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQ 2982
Cdd:pfam00439    1 CLEILDKLMEHPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYK 80

                   ...
gi 1622880856 2983 CAE 2985
Cdd:pfam00439   81 AAE 83

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 1622880856  240 EHIMNVIAIYEVLRNFGTVLRLSPFRFEDFCAALVSQEQ-CTLMAEMHVVLLKAVLRE 296
Cdd:pfam02791    1 EAFGDLLMVWEFLNSFGEVLGLSPFTLDDFEEALLCTEEpSELLDEIHCALLKALVRD 58

Williams-Beuren syndrome DDT (WSD), D-TOX E motif; This family represents the combined alpha-helical module found in diverse eukaryotic chromatin proteins. Based on the Ioc3 structure, the N-terminus of this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. The acidic residue from the GxD signature at the N-terminus is a major determinant of the interaction between the ISWI and WHIM motifs. The N-terminal portion also contacts the inter-nucleosomal linker DNA. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognizing and DNA binding domains, some of which discriminate methylated DNA. The WSD module constitutes the inter-nucleosomal linker DNA binding site in the major groove of DNA, and was first identified as WSD, the D-TOX E motif of plant homeodomains homologous with the mutant transcription factor causing Williams-Beuren syndrome in association with the DDT-domain.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1622880856  455 IRHEPIGYDRSRRKYWFL---NRRLIIEEDTENEnekkIWYYSTKVQLAELIDCLDKDYW-EAELCKILEE 521
Cdd:pfam15613    1 IRSLPLGRDRRYNRYWWFdpgTGRLFVESPSDGE----WGVYSSKEQLDALIASLNPRGVrESALKEALEK 67

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 1622880856   392 CRVCHK---LGDLLCCETCSAVYHLECVKPPLEE-VPEDEWQCEVC 433
Cdd:smart00249    2 CSVCGKpddGGELLQCDGCDRWYHQTCLGPPLLEeEPDGKWYCPKC 47

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 1622880856 2161 LPANSKIV-----AVNVPATQGG-VVQVQQKVLGIIPSSTG--TSQQTFTSFQPRTATVTIRPNTSGSGGTTsNSQVITG 2232
Cdd:cd22540     79 LSAKGNIIqlqgsQLSSSAPGGQqVFAIQNPTMIIKGSQTRssTNQQYQISPQIQAAGQINNSGQIQIIPGT-NQAIITP 157

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622880856 2233 PQIRPG-------MTVIRTPLQQSTLGKAIIRTP--VMVQPGA-------PQQVMTQIIRGQPVSTAISAPNTVSSTPGQ 2296
Cdd:cd22540    158 VQVLQQpqqahkpVPIKPAPLQTSNTNSASLQVPgnVIKLQSGgnvaltlPVNNLVGTQDGATQLQLAAAPSKPSKKIRK 237

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622880856 2297 KSLTSAtstsniqssasQPPRPQQGQVKLTMAQLTQLTQGHGGNQGLTVVIQGQGQ--TTGQLQLIP----QGVTVLPGP 2370
Cdd:cd22540    238 KSAQAA-----------QPAVTVAEQVETVLIETTADNIIQAGNNLLIVQSPGTGQpaVLQQVQVLQpkqeQQVVQIPQQ 306

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622880856 2371 GQQLMQAA-MPNGTV-QRflftPLATTATTASTTTTTVSTTAAGTGEQrqsklspQTQVHQDKTLPAAQSSSVGPAEAQP 2448
Cdd:cd22540    307 ALRVVQAAsATLPTVpQK----PLQNIQIQNSEPTPTQVYIKTPSGEV-------QTVLLQEAPAATATPSSSTSTVQQQ 375

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622880856 2449 QTAQPSAQPQPQTQPQSPAQPEVQTQPEVQTQTTVSSHVPSEAQPTQaQSSKPQVAAQSQP--QSNVQGQSPVRVQSPSQ 2526
Cdd:cd22540    376 VTANNGTGTSKPNYNVRKERTLPKIAPAGGIISLNAAQLAAAAQAIQ-TININGVQVQGVPvtITNAGGQQQLTVQTVSS 454

                          410       420       430
                   ....*....|....*....|....*....|.
gi 1622880856 2527 ARIrpsTPSQLSPGQQSQVQTTTSQpIPIQP 2557
Cdd:cd22540    455 NNL---TISGLSPTQIQLQMEQALE-IETQP 481

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 1622880856  2778 YC-ICKTPYDESKFyIGCDLCTNWYHGECVGITEKEAKKMDVYICNDC 2824
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 1622880856 2836 YC-ICRTPYDESQFyIGCDRCQNWYHGRCVGILQSEAELID-EYVCPQCQS 2884
Cdd:pfam00628    1 YCaVCGKSDDGGEL-VQCDGCDDWFHLACLGPPLDPAEIPSgEWLCPECKP 50

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 1622880856 2903 LKRVLRSLQAH--KMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPF 2980
Cdd:cd04369      5 LRSLLDALKKLkrDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGPGSPI 84

                           90
                   ....*....|....*
gi 1622880856 2981 YQCAEVLESFFVQKL 2995
Cdd:cd04369     85 YKDAKKLEKLFEKLL 99

bromo domain;

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622880856  2895 LTEKDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYN 2974
Cdd:smart00297    4 LQKKLQELLKAVLDKLDSHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYN 83

                            90       100
                    ....*....|....*....|..
gi 1622880856  2975 PSDSPFYQCAEVLESFFVQKLK 2996
Cdd:smart00297   84 GPDSEVYKDAKKLEKFFEKKLR 105

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 1622880856 2778 YCICKTPYDESKFYIGCDLCTNWYHGECVGITEKEAKKMDVYICNDC 2824
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 1622880856 2903 LKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQ 2982
Cdd:pfam00439    1 CLEILDKLMEHPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYK 80

                   ...
gi 1622880856 2983 CAE 2985
Cdd:pfam00439   81 AAE 83

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 1622880856 2903 LKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQ 2982
Cdd:cd05504     17 LEQLLVEIVKHKDSWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHTSVYK 96

                           90
                   ....*....|....
gi 1622880856 2983 CAEVLESFFVQKLK 2996
Cdd:cd05504     97 AGTRLQRFFIKRCR 110

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 1622880856 2836 YCICRTPYDESQFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQC 2882
Cdd:cd15554      1 YCICRQPYDVTRFMIECDVCKDWFHGSCVGVEEHQANDIERYHCPNC 47

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622880856 2907 LRSLQAHKMAWPFLEPVDPN--DAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCA 2984
Cdd:cd05499     12 LMKPKHSAYNWPFLDPVDPValNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTDVYMMG 91

                   ....*..
gi 1622880856 2985 EVLESFF 2991
Cdd:cd05499     92 HQLEEVF 98

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 1622880856 2907 LRSLQAHKMAWPFLEPVDPN--DAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCA 2984
Cdd:cd05506      9 LRKLMKHKWGWVFNAPVDVValGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVHTMA 88

                   ....*..
gi 1622880856 2985 EVLESFF 2991
Cdd:cd05506     89 KELLKIF 95

domain in different transcription and chromosome remodeling factors;

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1622880856   239 NEHIMNVIAIYEVLRNFGTVLRLSPFR--FEDFCAALVSQEQCTLMAEMHVVLLKAVLREED 298
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 1622880856  240 EHIMNVIAIYEVLRNFGTVLRLSPFRFEDFCAALVSQEQ-CTLMAEMHVVLLKAVLRE 296
Cdd:pfam02791    1 EAFGDLLMVWEFLNSFGEVLGLSPFTLDDFEEALLCTEEpSELLDEIHCALLKALVRD 58

PHD finger found in PHF2, PHF8 and KDM7; This family includes PHF2, PHF8, KDM7, and similar proteins. PHF2, also termed GRC5, or PHD finger protein 2, is a histone lysine demethylase ubiquitously expressed in various tissues. PHF8, also termed PHD finger protein 8, or KDM7B, is a monomethylated histone H4 lysine 20(H4K20me1) demethylase that transcriptionally regulates many cell cycle genes. It also preferentially acts on H3K9me2 and H3K9me1. PHF8 is modulated by CDC20-containing anaphase-promoting complex (APC (cdc20)) and plays an important role in the G2/M transition. It acts as a critical molecular sensor for mediating retinoic acid (RA) treatment response in RAR alpha-fusion-induced leukemia. Moreover, PHF8 is essential for cytoskeleton dynamics and is associated with X-linked mental retardation. KDM7, also termed JmjC domain-containing histone demethylation protein 1D (JHDM1D), or KIAA1718, is a dual histone demethylase that catalyzes demethylation of monomethylated and dimethylated H3K9 (H3K9me2/me1) and H3K27 (H3K27me2/me1), which functions as an eraser of silencing marks on chromatin during brain development. It also plays a tumor-suppressive role by regulating angiogenesis. All family members contain a plant homeodomain (PHD) finger and a JmjC domain.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1622880856 2778 YCICKTPYDESKFYIGCDLCTNWYHGECVGITEKEAKKMDVYICNDC 2824
Cdd:cd15554      1 YCICRQPYDVTRFMIECDVCKDWFHGSCVGVEEHQANDIERYHCPNC 47

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 1622880856 2836 YCICRTPYDESqFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQC 2882
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 1622880856 2836 YCICRTPyDESQFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQC 2882
Cdd:cd15553      1 YCICRSS-DISRFMIGCDNCEEWYHGDCINITEKEAKAIKEWYCQQC 46

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 1622880856 2836 YCICRTPYDEsQFYIGCDRCQNWYHGRCVGILQSE----AELIDEYVCPQC 2882
Cdd:cd15552      1 YCICRKPHNN-RFMICCDRCEEWFHGDCVGITEAQgkemEENIEEYVCPKC 50

PHD finger found in lysine-specific demethylase 7 (KDM7); KDM7, also termed JmjC domain-containing histone demethylation protein 1D (JHDM1D), or KIAA1718, is a dual histone demethylase that catalyzes demethylation of monomethylated and dimethylated H3K9 (H3K9me2/me1) and H3K27 (H3K27me2/me1), which functions as an eraser of silencing marks on chromatin during brain development. It also plays a tumor-suppressive role by regulating angiogenesis. KDM7 contains a plant homeodomain (PHD) that binds Lys4-trimethylated histone 3 (H3K4me3) and a jumonji domain that demethylates either H3K9me2 or H3K27me2.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1622880856 2836 YCICRTPYDESQFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQ 2883
Cdd:cd15640      1 YCVCRQPYDVNRFMIECDICKDWFHGSCVQVEEHHAADIDLYHCPNCE 48

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

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1622880856 2778 YCICKTPYDEsKFYIGCDLCTNWYHGECVGITEKEAKKMDV----YICNDC 2824
Cdd:cd15552      1 YCICRKPHNN-RFMICCDRCEEWFHGDCVGITEAQGKEMEEnieeYVCPKC 50

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 1622880856 2899 DYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDS 2978
Cdd:cd05505      1 ELQKCEEILSKILKYRFSWPFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGS 80

                           90
                   ....*....|....*..
gi 1622880856 2979 PFYQCAEVLESFFVQKL 2995
Cdd:cd05505     81 YVLSCMRKTEQCCVNLL 97

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 1622880856 2778 YCICKTPyDESKFYIGCDLCTNWYHGECVGITEKEAKKMDVYICNDC 2824
Cdd:cd15553      1 YCICRSS-DISRFMIGCDNCEEWYHGDCINITEKEAKAIKEWYCQQC 46

PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar proteins; The TIF1 family of transcriptional cofactors includes TIF1alpha (TRIM24), TIF1beta (TRIM28), TIF1gamma (TRIM33), and TIF1delta (TRIM66), which are characterized by an N-terminal RING-finger B-box coiled-coil (RBCC/TRIM) motif and plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region. TIF1 proteins couple chromatin modifications to transcriptional regulation, signaling, and tumor suppression. They exert a deacetylase-dependent silencing effect when tethered to a promoter region. TIF1alpha, TIF1beta, and TIF1delta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. TIF1alpha and TIF1beta bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. In contrast, TIF1delta appears to lack nuclear receptor- and KRAB-binding activity. Moreover, TIF1delta is specifically involved in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. TIF1gamma is structurally closely related to TIF1alpha and TIF1beta, but has very little functional features in common with them. It does not interact with the KRAB silencing domain of KOX1 or the heterochromatinic proteins HP1alpha, beta, and gamma. It cannot bind to nuclear receptors (NRs). This family also includes Sp100/Sp140 family proteins, the nuclear body SP100 and SP140. Sp110 is a leukocyte-specific component of the nuclear body. It may function as a nuclear hormone receptor transcriptional coactivator that may play a role in inducing differentiation of myeloid cells. It is also involved in resisting intracellular pathogens and functions as an important drug target for preventing intracellular pathogen diseases, such as tuberculosis, hepatic veno-occlusive disease, and intracellular cancers. SP140 is an interferon inducible nuclear leukocyte-specific protein involved in primary biliary cirrhosis and a risk factor in chronic lymphocytic leukemia. It is also implicated in innate immune response to human immunodeficiency virus type 1 (HIV-1) by binding to the virus viral infectivity factor (Vif) protein. Both Sp110 and Sp140 contain a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD).

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1622880856  392 CRVCHKLGDLLCCETCSAVYHLECVKPPLEEVPEDEWQCEVC 433
Cdd:cd15541      2 CAVCQNGGELLCCDKCPRVFHLDCHIPPIPEFPSGEWSCSLC 43

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622880856 2913 HKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFV 2992
Cdd:cd05515     21 RRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYNEPDSQIYKDALTLQKVLL 100

                   ....*
gi 1622880856 2993 QKLKG 2997
Cdd:cd05515    101 ETKRE 105

PHD finger found in death-inducer obliterator variants Dido1, Dido2, and Dido3; This family includes three alternative splicing variants (Dido1, 2, and 3) encoded by the Dido gene, which have been implicated in a number of cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. Dido1, also termed DIO-1, or death-associated transcription factor 1 (DATF-1), is important for maintaining embryonic stem (ES) cells and directly regulates the expression of pluripotency factors. It is the shortest isoform that contains only a highly conserved plant homeodomain (PHD) finger responsible for the binding of histone H3 with a higher affinity for trimethylated lysine 4 (H3K4me3). Gene Dido is a Bonemorphogenetic protein (BMP) target gene, which promotes BMP-induced melanoma progression. It also triggers apoptosis after nuclear translocation and caspase upregulation. Dido3 is the largest isoform ubiquitously expressed in all human tissues. It is dispensable for ES cell self-renewal and pluripotency, but involved in the maintenance of stem cell genomic stability and tumorigenesis. Dido3 contains a PHD finger, a transcription elongation factor S-II subunit M (TFSIIM) domain, aspen paralog and ortholog (SPOC) module, and a long C-terminal region (CT) of unknown homology. Its PHD finger interacts with H3K4me3.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1622880856 2833 EELYCICRTPYDeSQFYIGCDRCQNWYHGRCVGILQSEAELI----DEYVCPQC 2882
Cdd:cd15639      2 NALYCICRQPHN-NRFMICCDRCEEWFHGDCVGITEARGRLLerngEDYICPNC 54