Zinc-finger double domain;

                           10        20
                   ....*....|....*....|....*
gi 255683388   739 NLTRHLRTHTGEQPYRCKYCDRSFS 763
Cdd:pfam13465    1 NLKRHMRTHTGEKPYKCPECGKSFK 25

hypothetical protein

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255683388  658 EKYLRPSPGFLFHPQMsaienmaEKLESFSALKPEASELLQSVPSMFNFRapPNALPEN------LLRKGKERYTCRYCG 731
Cdd:PHA00733   10 KKYLSNHKGIFIHVTL-------EELKRYHSLTPEQKRLIRAVVKTLIYN--PQLLDESsylyklLTSKAVSPYVCPLCL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 255683388  732 KIFPRSANLTRHLRThtGEQPYRCKYCDRSFSISSNLQRHVRNIHN 777
Cdd:PHA00733   81 MPFSSSVSLKQHIRY--TEHSKVCPVCGKEFRNTDSTLDHVCKKHN 124

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.

                           10        20
                   ....*....|....*....|...
gi 255683388   189 FICEVCHKSYTQFSNLCRHKRMH 211
Cdd:pfam00096    1 YKCPDCGKSFSRKSNLKRHLRTH 23

SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily; The Su(var)3-9, Enhancer-of-zeste, Trithorax (SET) domain superfamily corresponds to SET domain-containing lysine methyltransferases, which catalyze site and state-specific methylation of lysine residues in histones that are fundamental in epigenetic regulation of gene activation and silencing in eukaryotic organisms. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains has been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as N-SET and C-SET. C-SET forms an unusual and conserved knot-like structure of probable functional importance. In addition to N-SET and C-SET, an insert region (I-SET) and flanking regions of high structural variability form part of the overall structure. Some family members contain a pre-SET domain, which is found in a number of histone methyltransferases (HMTase), and a post-SET domain, which harbors a zinc-binding site.

                          10
                  ....*....|....*.
gi 255683388    1 MKSEDYPHETMAPDIH 16
Cdd:cd19214   143 MKSEDYSHETMAPDIH 158

Zinc-finger double domain;

                           10        20
                   ....*....|....*....|....*
gi 255683388   739 NLTRHLRTHTGEQPYRCKYCDRSFS 763
Cdd:pfam13465    1 NLKRHMRTHTGEKPYKCPECGKSFK 25

hypothetical protein

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255683388  658 EKYLRPSPGFLFHPQMsaienmaEKLESFSALKPEASELLQSVPSMFNFRapPNALPEN------LLRKGKERYTCRYCG 731
Cdd:PHA00733   10 KKYLSNHKGIFIHVTL-------EELKRYHSLTPEQKRLIRAVVKTLIYN--PQLLDESsylyklLTSKAVSPYVCPLCL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 255683388  732 KIFPRSANLTRHLRThtGEQPYRCKYCDRSFSISSNLQRHVRNIHN 777
Cdd:PHA00733   81 MPFSSSVSLKQHIRY--TEHSKVCPVCGKEFRNTDSTLDHVCKKHN 124

Transposase InsA [Mobilome: prophages, transposons];

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 255683388  719 RKGKERYTCRYCGkifprSANLTRHLRTHTGEQPYRCKYCDRSFSI 764
Cdd:COG3677    11 IRWPNGPVCPHCG-----STRIVKNGKTRNGRQRYRCKDCGRTFTV 51

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.

                           10        20
                   ....*....|....*....|...
gi 255683388   782 FKCHLCDRCFGQQTNLDRHLKKH 804
Cdd:pfam00096    1 YKCPDCGKSFSRKSNLKRHLRTH 23

N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins; Oryza sativa SUPPRESSOR OF FRI 4 (OsSUF4) is a C2H2-type zinc finger transcription factor which interacts with the major H3K36 methyltransferase SDG725 to promote H3K36me3 (tri-methylation at H3K9) establishment. The transcription factor OsSUF4 recognizes a specific 7-bp DNA element (5'-CGGAAAT-3'), which is contained in the promoter regions of many genes throughout the rice genome. Through interaction with OsSUF4, SDG725 is recruited to the promoters of key florigen genes, RICE FLOWERING LOCUS T1 (RFT1) and Heading date 3a (Hd3a), for H3K36 deposition to promote gene activation and rice plant flowering. OsSUF4 target genes include a number of genes involved in many biological processes. Flowering plant Arabidopsis SUF4 binds to a 15bp DNA element (5'-CCAAATTTTAAGTTT-3') within the promoter of the floral repressor gene FLOWERING LOCUS C (FLC) and recruits the FRI-C transcription activator complex to the FLC promoter. Although the DNA-binding element and target genes of AtSUF4 are different from those of OsSUF4, AtSUF4 is known to interact with the Arabidopsis H3K36 methyltransferase SDG8 (also known as ASHH2/EFS/SET8), and the methylation deposition mechanism mediated by the SUF4 transcription factor and H3K36 methyltransferase may be conserved in Arabidopsis and rice. Proteins in this family have two conserved C2H2-type zinc finger motifs at the N-terminus (included in this model), and a large proline-rich domain at the C-terminus; for OsSUF4, it has been shown that the N-terminal zinc-finger domain is responsible for DNA binding, and that the C-terminal domain interacts with SDG725.

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 255683388  755 CKYCDRSFSISSNLQrhvrnIHNKEKPFKCHLCDR 789
Cdd:cd20908     4 CYYCDREFDDEKILI-----QHQKAKHFKCHICHK 33

zinc finger;

                            10        20
                    ....*....|....*....|...
gi 255683388    725 YTCRYCGKIFPRSANLTRHLRTH 747
Cdd:smart00355    1 YRCPECGKVFKSKSALREHMRTH 23

Zinc-finger double domain;

                           10        20
                   ....*....|....*....|....*
gi 255683388   739 NLTRHLRTHTGEQPYRCKYCDRSFS 763
Cdd:pfam13465    1 NLKRHMRTHTGEKPYKCPECGKSFK 25

hypothetical protein

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255683388  658 EKYLRPSPGFLFHPQMsaienmaEKLESFSALKPEASELLQSVPSMFNFRapPNALPEN------LLRKGKERYTCRYCG 731
Cdd:PHA00733   10 KKYLSNHKGIFIHVTL-------EELKRYHSLTPEQKRLIRAVVKTLIYN--PQLLDESsylyklLTSKAVSPYVCPLCL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 255683388  732 KIFPRSANLTRHLRThtGEQPYRCKYCDRSFSISSNLQRHVRNIHN 777
Cdd:PHA00733   81 MPFSSSVSLKQHIRY--TEHSKVCPVCGKEFRNTDSTLDHVCKKHN 124

Transposase InsA [Mobilome: prophages, transposons];

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 255683388  719 RKGKERYTCRYCGkifprSANLTRHLRTHTGEQPYRCKYCDRSFSI 764
Cdd:COG3677    11 IRWPNGPVCPHCG-----STRIVKNGKTRNGRQRYRCKDCGRTFTV 51

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.

                           10        20
                   ....*....|....*....|...
gi 255683388   782 FKCHLCDRCFGQQTNLDRHLKKH 804
Cdd:pfam00096    1 YKCPDCGKSFSRKSNLKRHLRTH 23

N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins; Oryza sativa SUPPRESSOR OF FRI 4 (OsSUF4) is a C2H2-type zinc finger transcription factor which interacts with the major H3K36 methyltransferase SDG725 to promote H3K36me3 (tri-methylation at H3K9) establishment. The transcription factor OsSUF4 recognizes a specific 7-bp DNA element (5'-CGGAAAT-3'), which is contained in the promoter regions of many genes throughout the rice genome. Through interaction with OsSUF4, SDG725 is recruited to the promoters of key florigen genes, RICE FLOWERING LOCUS T1 (RFT1) and Heading date 3a (Hd3a), for H3K36 deposition to promote gene activation and rice plant flowering. OsSUF4 target genes include a number of genes involved in many biological processes. Flowering plant Arabidopsis SUF4 binds to a 15bp DNA element (5'-CCAAATTTTAAGTTT-3') within the promoter of the floral repressor gene FLOWERING LOCUS C (FLC) and recruits the FRI-C transcription activator complex to the FLC promoter. Although the DNA-binding element and target genes of AtSUF4 are different from those of OsSUF4, AtSUF4 is known to interact with the Arabidopsis H3K36 methyltransferase SDG8 (also known as ASHH2/EFS/SET8), and the methylation deposition mechanism mediated by the SUF4 transcription factor and H3K36 methyltransferase may be conserved in Arabidopsis and rice. Proteins in this family have two conserved C2H2-type zinc finger motifs at the N-terminus (included in this model), and a large proline-rich domain at the C-terminus; for OsSUF4, it has been shown that the N-terminal zinc-finger domain is responsible for DNA binding, and that the C-terminal domain interacts with SDG725.

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 255683388  755 CKYCDRSFSISSNLQrhvrnIHNKEKPFKCHLCDR 789
Cdd:cd20908     4 CYYCDREFDDEKILI-----QHQKAKHFKCHICHK 33

Domain of unknown function (DUF4045); This presumed domain is functionally uncharacterized. This domain family is found in bacteria and eukaryotes, and is typically between 384 and 430 amino acids in length.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255683388   524 PDRDLRSLPLKMEPQSPGEVKKLQKGSSESPFDLTTKRKDEKPLTPVPSKPPVTPATSQDQPLDLSMGSRSR---ASGTK 600
Cdd:pfam13254  277 PSKSAEASTEKKEPDTESSPETSSEKSAPSLLSPVSKASIDKPLSSPDRDPLSPKPKPQSPPKDFRANLRSRevpKDKSK 356

                           90
                   ....*....|.
gi 255683388   601 LTEPRKNHVFG 611
Cdd:pfam13254  357 KDEPEFKNVFG 367

N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins; Oryza sativa SUPPRESSOR OF FRI 4 (OsSUF4) is a C2H2-type zinc finger transcription factor which interacts with the major H3K36 methyltransferase SDG725 to promote H3K36me3 (tri-methylation at H3K9) establishment. The transcription factor OsSUF4 recognizes a specific 7-bp DNA element (5'-CGGAAAT-3'), which is contained in the promoter regions of many genes throughout the rice genome. Through interaction with OsSUF4, SDG725 is recruited to the promoters of key florigen genes, RICE FLOWERING LOCUS T1 (RFT1) and Heading date 3a (Hd3a), for H3K36 deposition to promote gene activation and rice plant flowering. OsSUF4 target genes include a number of genes involved in many biological processes. Flowering plant Arabidopsis SUF4 binds to a 15bp DNA element (5'-CCAAATTTTAAGTTT-3') within the promoter of the floral repressor gene FLOWERING LOCUS C (FLC) and recruits the FRI-C transcription activator complex to the FLC promoter. Although the DNA-binding element and target genes of AtSUF4 are different from those of OsSUF4, AtSUF4 is known to interact with the Arabidopsis H3K36 methyltransferase SDG8 (also known as ASHH2/EFS/SET8), and the methylation deposition mechanism mediated by the SUF4 transcription factor and H3K36 methyltransferase may be conserved in Arabidopsis and rice. Proteins in this family have two conserved C2H2-type zinc finger motifs at the N-terminus (included in this model), and a large proline-rich domain at the C-terminus; for OsSUF4, it has been shown that the N-terminal zinc-finger domain is responsible for DNA binding, and that the C-terminal domain interacts with SDG725.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 255683388  727 CRYCGKIFPRSANLTRHLRTHTgeqpYRCKYCDRSFSISSNLQRHVRNIHnKEK 780
Cdd:cd20908     4 CYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVHCLQVH-KET 52