leucine rich region;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56118254     37 PETARQLFRQFRYQVMSGPHETLKQLRKLCFQWLQPEVHTKEQILEILMLEQFLTILPGEIQMWVRKQCPGSGEEAVTLV 116
Cdd:smart00431   1 PEIFRQRFRQFRYQETSGPREALSRLRELCRQWLRPELHTKEQILELLVLEQFLTILPGELQAWVREHHPESGEEAVTLL 80

                           90       100       110
                   ....*....|....*....|....*....|..
gi 56118254    117 ESLKGDPQRLWQWISIQVLGQDILSEKMESPS 148
Cdd:smart00431  81 EDLERELDEPGQQVSAHVHGQEVLLEKMVPLG 112

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....*
gi 56118254   506 NFNRHQRVHTGEKPYKCSHCGKSFS 530
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFK 25

FOG: Zn-finger [General function prediction only];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56118254 436 FQCTICKKAFLRSSDFVKHQRT--HTGE--KPCKCDY--CGKGFSDFSGLRHHEKIHTGEKPYKCPI--CEKSFIQRSNF 507
Cdd:COG5048 290 IKSKQCNISFSRSSPLTRHLRSvnHSGEslKPFSCPYslCGKLFSRNDALKRHILLHTSISPAKEKLlnSSSKFSPLLNN 369

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56118254 508 NRHQRVHT-------------------------------------GEKPYKCSHCGKSFSWSSSLDKHQRSHLGKKPFQ 549
Cdd:COG5048 370 EPPQSLQQykdlkndkksetlsnscirnfkrdsnlslhiithlsfRPYNCKNPPCSKSFNRHYNLIPHKKIHTNHAPLL 448

leucine rich region;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56118254     37 PETARQLFRQFRYQVMSGPHETLKQLRKLCFQWLQPEVHTKEQILEILMLEQFLTILPGEIQMWVRKQCPGSGEEAVTLV 116
Cdd:smart00431   1 PEIFRQRFRQFRYQETSGPREALSRLRELCRQWLRPELHTKEQILELLVLEQFLTILPGELQAWVREHHPESGEEAVTLL 80

                           90       100       110
                   ....*....|....*....|....*....|..
gi 56118254    117 ESLKGDPQRLWQWISIQVLGQDILSEKMESPS 148
Cdd:smart00431  81 EDLERELDEPGQQVSAHVHGQEVLLEKMVPLG 112

SCAN oligomerization domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several vertebrate proteins that contain C2H2 zinc finger motifs, many of which may be transcription factors playing roles in cell survival and differentiation. This protein-interaction domain is able to mediate homo- and hetero-oligomerization of SCAN-containing proteins. Some SCAN-containing proteins, including those of lower vertebrates, do not contain zinc finger motifs. It has been noted that the SCAN domain resembles a domain-swapped version of the C-terminal domain of the HIV capsid protein. This domain model features elements common to the three general groups of SCAN domains (SCAN-A1, SCAN-A2, and SCAN-B). The SCAND1 protein is truncated at the C-terminus with respect to this model, the SCAND2 protein appears to have a truncated central helix.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56118254  37 PETARQLFRQFRYQVMSGPHETLKQLRKLCFQWLQPEVHTKEQILEILMLEQFLTILPGEIQMWVRKQCPGSGEEAVTLV 116
Cdd:cd07936   1 PETYRQRFRAFQYQEASGPREALQRLRELCRQWLRPEIHTKEQILELLVLEQFLIILPPEVQAWVRERKPESGEEAATLA 80

                ....
gi 56118254 117 ESLK 120
Cdd:cd07936  81 EDLL 84

KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression module, found in a subgroup of the zinc finger proteins (ZFPs) of the C2H2 family, KRAB-ZFPs. KRAB-ZFPs comprise the largest group of transcriptional regulators in mammals, and are only found in tetrapods. These proteins have been shown to play important roles in cell differentiation and organ development, and in regulating viral replication and transcription. A KRAB domain may consist of an A-box, or of an A-box plus either a B-box, a divergent B-box (b), or a C-box. Only the A-box is included in this model. The A-box is needed for repression, the B- and C- boxes are not. KRAB-ZFPs have one or two KRAB domains at their amino-terminal end, and multiple C2H2 zinc finger motifs at their C-termini. Some KRAB-ZFPs also contain a SCAN domain which mediates homo- and hetero-oligomerization. The KRAB domain is a protein-protein interaction module which represses transcription through recruiting corepressors. A key mechanism appears to be the following: KRAB-AFPs tethered to DNA recruit, via their KRAB domain, the repressor KAP1 (KRAB-associated protein-1, also known as transcription intermediary factor 1 beta , KRAB-A interacting protein , and tripartite motif protein 28). The KAP1/ KRAB-AFP complex in turn recruits the heterochromatin protein 1 (HP1) family, and other chromatin modulating proteins, leading to transcriptional repression through heterochromatin formation.

                        10        20
                ....*....|....*....|....*....
gi 56118254 221 PQEQWRQLDSTQKEQYWDLMLETYGKMVS 249
Cdd:cd07765  11 SQEEWELLDPAQRDLYRDVMLENYENLVS 39

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....*
gi 56118254   506 NFNRHQRVHTGEKPYKCSHCGKSFS 530
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFK 25

FOG: Zn-finger [General function prediction only];

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 56118254 490 KPYKCPICEKSFIQRSNFNRHQRVHTGEKPYKCSH--CGKSFSWSSSLDKHQRSHLGKKPF 548
Cdd:COG5048  32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYsgCDKSFSRPLELSRHLRTHHNNPSD 92

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 56118254 462 KPcKCDYCGKGFSDFSGLRHHEKIHTgekpYKCPICEKSFIQRSNFNRH-QRVH 514
Cdd:cd20908   1 KP-WCYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVHcLQVH 49

zinc finger;

                           10        20
                   ....*....|....*....|...
gi 56118254    492 YKCPICEKSFIQRSNFNRHQRVH 514
Cdd:smart00355   1 YRCPECGKVFKSKSALREHMRTH 23

Transposase InsA [Mobilome: prophages, transposons];

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 56118254 483 EKIHTGEKPyKCPICeksfiQRSNFNRHQRVHTGEKPYKCSHCGKSFS 530
Cdd:COG3677   9 EQIRWPNGP-VCPHC-----GSTRIVKNGKTRNGRQRYRCKDCGRTFT 50

leucine rich region;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56118254     37 PETARQLFRQFRYQVMSGPHETLKQLRKLCFQWLQPEVHTKEQILEILMLEQFLTILPGEIQMWVRKQCPGSGEEAVTLV 116
Cdd:smart00431   1 PEIFRQRFRQFRYQETSGPREALSRLRELCRQWLRPELHTKEQILELLVLEQFLTILPGELQAWVREHHPESGEEAVTLL 80

                           90       100       110
                   ....*....|....*....|....*....|..
gi 56118254    117 ESLKGDPQRLWQWISIQVLGQDILSEKMESPS 148
Cdd:smart00431  81 EDLERELDEPGQQVSAHVHGQEVLLEKMVPLG 112

SCAN oligomerization domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several vertebrate proteins that contain C2H2 zinc finger motifs, many of which may be transcription factors playing roles in cell survival and differentiation. This protein-interaction domain is able to mediate homo- and hetero-oligomerization of SCAN-containing proteins. Some SCAN-containing proteins, including those of lower vertebrates, do not contain zinc finger motifs. It has been noted that the SCAN domain resembles a domain-swapped version of the C-terminal domain of the HIV capsid protein. This domain model features elements common to the three general groups of SCAN domains (SCAN-A1, SCAN-A2, and SCAN-B). The SCAND1 protein is truncated at the C-terminus with respect to this model, the SCAND2 protein appears to have a truncated central helix.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56118254  37 PETARQLFRQFRYQVMSGPHETLKQLRKLCFQWLQPEVHTKEQILEILMLEQFLTILPGEIQMWVRKQCPGSGEEAVTLV 116
Cdd:cd07936   1 PETYRQRFRAFQYQEASGPREALQRLRELCRQWLRPEIHTKEQILELLVLEQFLIILPPEVQAWVRERKPESGEEAATLA 80

                ....
gi 56118254 117 ESLK 120
Cdd:cd07936  81 EDLL 84

KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression module, found in a subgroup of the zinc finger proteins (ZFPs) of the C2H2 family, KRAB-ZFPs. KRAB-ZFPs comprise the largest group of transcriptional regulators in mammals, and are only found in tetrapods. These proteins have been shown to play important roles in cell differentiation and organ development, and in regulating viral replication and transcription. A KRAB domain may consist of an A-box, or of an A-box plus either a B-box, a divergent B-box (b), or a C-box. Only the A-box is included in this model. The A-box is needed for repression, the B- and C- boxes are not. KRAB-ZFPs have one or two KRAB domains at their amino-terminal end, and multiple C2H2 zinc finger motifs at their C-termini. Some KRAB-ZFPs also contain a SCAN domain which mediates homo- and hetero-oligomerization. The KRAB domain is a protein-protein interaction module which represses transcription through recruiting corepressors. A key mechanism appears to be the following: KRAB-AFPs tethered to DNA recruit, via their KRAB domain, the repressor KAP1 (KRAB-associated protein-1, also known as transcription intermediary factor 1 beta , KRAB-A interacting protein , and tripartite motif protein 28). The KAP1/ KRAB-AFP complex in turn recruits the heterochromatin protein 1 (HP1) family, and other chromatin modulating proteins, leading to transcriptional repression through heterochromatin formation.

                        10        20
                ....*....|....*....|....*....
gi 56118254 221 PQEQWRQLDSTQKEQYWDLMLETYGKMVS 249
Cdd:cd07765  11 SQEEWELLDPAQRDLYRDVMLENYENLVS 39

Zinc-finger double domain;

                          10        20
                  ....*....|....*....|....*
gi 56118254   506 NFNRHQRVHTGEKPYKCSHCGKSFS 530
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFK 25

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 56118254   492 YKCPICEKSFIQRSNFNRHQRVH 514
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23

FOG: Zn-finger [General function prediction only];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56118254 436 FQCTICKKAFLRSSDFVKHQRT--HTGE--KPCKCDY--CGKGFSDFSGLRHHEKIHTGEKPYKCPI--CEKSFIQRSNF 507
Cdd:COG5048 290 IKSKQCNISFSRSSPLTRHLRSvnHSGEslKPFSCPYslCGKLFSRNDALKRHILLHTSISPAKEKLlnSSSKFSPLLNN 369

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56118254 508 NRHQRVHT-------------------------------------GEKPYKCSHCGKSFSWSSSLDKHQRSHLGKKPFQ 549
Cdd:COG5048 370 EPPQSLQQykdlkndkksetlsnscirnfkrdsnlslhiithlsfRPYNCKNPPCSKSFNRHYNLIPHKKIHTNHAPLL 448

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 56118254 462 KPcKCDYCGKGFSDFSGLRHHEKIHTgekpYKCPICEKSFIQRSNFNRH-QRVH 514
Cdd:cd20908   1 KP-WCYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVHcLQVH 49

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 56118254   436 FQCTICKKAFLRSSDFVKHQRTH 458
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23

zinc finger;

                           10        20
                   ....*....|....*....|...
gi 56118254    492 YKCPICEKSFIQRSNFNRHQRVH 514
Cdd:smart00355   1 YRCPECGKVFKSKSALREHMRTH 23

zinc finger;

                           10        20
                   ....*....|....*....|...
gi 56118254    520 YKCSHCGKSFSWSSSLDKHQRSH 542
Cdd:smart00355   1 YRCPECGKVFKSKSALREHMRTH 23

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 56118254   409 TCRECGKTFYRNSQLIFHQRTH 430
Cdd:pfam00096   2 KCPDCGKSFSRKSNLKRHLRTH 23