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Conserved domains on  [gi|29789126|ref|NP_067301|]
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RB-associated KRAB zinc finger protein [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
KRAB smart00349
krueppel associated box;
8-68 3.96e-32

krueppel associated box;


:

Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 118.46  E-value: 3.96e-32
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 29789126      8 LSFKDVAVAFSQEEWQQLDPEERTTYRDVMLETYSNLVSVGYDVTKPNMIIKLEQGEEPWT 68
Cdd:smart00349   1 VTFEDVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPKPDLISQLEQGEEPWI 61
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
340-699 9.77e-17

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


:

Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 83.59  E-value: 9.77e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789126 340 KPYECSECGKSFCQKTHLTLHQRNHSGERPYPCN--ECGKSFSRKSALNDHQRTHTGEKLYKCNECGKS--YYRKSTLIT 415
Cdd:COG5048  32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSysGCDKSFSRPLELSRHLRTHHNNPSDLNSKSLPLsnSKASSSSLS 111

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789126 416 HQRTHTgEKPYQCSECGKFFSRVSYLTIHYRSHLEEKPYECTECGKTFN-----------------------LNSAFIRH 472
Cdd:COG5048 112 SSSSNS-NDNNLLSSHSLPPSSRDPQLPDLLSISNLRNNPLPGNNSSSVntpqsnslhpplpanslskdpssNLSLLISS 190

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789126 473 WKVHAEERVQECGECGKPSPLQ-CAPDHTGDLGEKRYECNECGKTFLDSSAFHRHQSVPEGEKTYECNICGKSF--SDSS 549
Cdd:COG5048 191 NVSTSIPSSSENSPLSSSYSIPsSSSDQNLENSSSSLPLTTNSQLSPKSLLSQSPSSLSSSDSSSSASESPRSSlpTASS 270

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789126 550 CYTVHYRGHSEE-----KPFGCSECGKTFSHNSSLFRHQR--VHTGE--KPYECYE--CGKFFSQKSYLTIHHRIHSGEK 618
Cdd:COG5048 271 QSSSPNESDSSSekgfsLPIKSKQCNISFSRSSPLTRHLRsvNHSGEslKPFSCPYslCGKLFSRNDALKRHILLHTSIS 350

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789126 619 PYEC--SKCGKVFSRMSN-----LTVHYRSHSGEKPYEC--NECGKVFSQKSYLTVHYRTHSGEKPYECN--ECGKKFHH 687
Cdd:COG5048 351 PAKEklLNSSSKFSPLLNneppqSLQQYKDLKNDKKSETlsNSCIRNFKRDSNLSLHIITHLSFRPYNCKnpPCSKSFNR 430

                       410
                ....*....|..
gi 29789126 688 RSAFNSHQRIHK 699
Cdd:COG5048 431 HYNLIPHKKIHT 442
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 314-336 1.62e-03

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.


:

Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 36.12  E-value: 1.62e-03
                          10        20
                  ....*....|....*....|...
gi 29789126   314 YKCNECGKTFCQKLHLTQHQRTH 336
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
SUF4-like super family cl41227
N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), ...
 256-304 8.07e-03

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.


The actual alignment was detected with superfamily member cd20908:

Pssm-ID: 411020 [Multi-domain]  Cd Length: 82  Bit Score: 36.00  E-value: 8.07e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 29789126 256 KPFeCTQCGKSFCKKSKFIIHQRAHTgekpYACSVCGKSFSQKGTLTVH 304
Cdd:cd20908   1 KPW-CYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVH 44
 
Name Accession Description Interval E-value
KRAB smart00349
krueppel associated box;
8-68 3.96e-32

krueppel associated box;


Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 118.46  E-value: 3.96e-32
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 29789126      8 LSFKDVAVAFSQEEWQQLDPEERTTYRDVMLETYSNLVSVGYDVTKPNMIIKLEQGEEPWT 68
Cdd:smart00349   1 VTFEDVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPKPDLISQLEQGEEPWI 61
KRAB pfam01352
KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc ...
 7-48 8.04e-21

KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers. The KRAB domain is found to be involved in protein-protein interactions. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation.


Pssm-ID: 460171  Cd Length: 42  Bit Score: 85.60  E-value: 8.04e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 29789126     7 PLSFKDVAVAFSQEEWQQLDPEERTTYRDVMLETYSNLVSVG 48
Cdd:pfam01352   1 SVTFEDVAVDFTQEEWALLDPAQRNLYRDVMLENYRNLVSLG 42
KRAB_A-box cd07765
KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression ...
 8-46 2.91e-17

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.


Pssm-ID: 143639  Cd Length: 40  Bit Score: 75.66  E-value: 2.91e-17
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 29789126   8 LSFKDVAVAFSQEEWQQLDPEERTTYRDVMLETYSNLVS 46
Cdd:cd07765   1 VTFEDVAVYFSQEEWELLDPAQRDLYRDVMLENYENLVS 39
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
340-699 9.77e-17

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 83.59  E-value: 9.77e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789126 340 KPYECSECGKSFCQKTHLTLHQRNHSGERPYPCN--ECGKSFSRKSALNDHQRTHTGEKLYKCNECGKS--YYRKSTLIT 415
Cdd:COG5048  32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSysGCDKSFSRPLELSRHLRTHHNNPSDLNSKSLPLsnSKASSSSLS 111

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789126 416 HQRTHTgEKPYQCSECGKFFSRVSYLTIHYRSHLEEKPYECTECGKTFN-----------------------LNSAFIRH 472
Cdd:COG5048 112 SSSSNS-NDNNLLSSHSLPPSSRDPQLPDLLSISNLRNNPLPGNNSSSVntpqsnslhpplpanslskdpssNLSLLISS 190

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789126 473 WKVHAEERVQECGECGKPSPLQ-CAPDHTGDLGEKRYECNECGKTFLDSSAFHRHQSVPEGEKTYECNICGKSF--SDSS 549
Cdd:COG5048 191 NVSTSIPSSSENSPLSSSYSIPsSSSDQNLENSSSSLPLTTNSQLSPKSLLSQSPSSLSSSDSSSSASESPRSSlpTASS 270

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789126 550 CYTVHYRGHSEE-----KPFGCSECGKTFSHNSSLFRHQR--VHTGE--KPYECYE--CGKFFSQKSYLTIHHRIHSGEK 618
Cdd:COG5048 271 QSSSPNESDSSSekgfsLPIKSKQCNISFSRSSPLTRHLRsvNHSGEslKPFSCPYslCGKLFSRNDALKRHILLHTSIS 350

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789126 619 PYEC--SKCGKVFSRMSN-----LTVHYRSHSGEKPYEC--NECGKVFSQKSYLTVHYRTHSGEKPYECN--ECGKKFHH 687
Cdd:COG5048 351 PAKEklLNSSSKFSPLLNneppqSLQQYKDLKNDKKSETlsNSCIRNFKRDSNLSLHIITHLSFRPYNCKnpPCSKSFNR 430

                       410
                ....*....|..
gi 29789126 688 RSAFNSHQRIHK 699
Cdd:COG5048 431 HYNLIPHKKIHT 442
zf-H2C2_2 pfam13465
Zinc-finger double domain;
578-603 4.42e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 38.12  E-value: 4.42e-04
                          10        20
                  ....*....|....*....|....*.
gi 29789126   578 SLFRHQRVHTGEKPYECYECGKFFSQ 603
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 314-336 1.62e-03

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.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 36.12  E-value: 1.62e-03
                          10        20
                  ....*....|....*....|...
gi 29789126   314 YKCNECGKTFCQKLHLTQHQRTH 336
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
SUF4-like cd20908
N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), ...
 256-304 8.07e-03

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.


Pssm-ID: 411020 [Multi-domain]  Cd Length: 82  Bit Score: 36.00  E-value: 8.07e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 29789126 256 KPFeCTQCGKSFCKKSKFIIHQRAHTgekpYACSVCGKSFSQKGTLTVH 304
Cdd:cd20908   1 KPW-CYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVH 44
 
Name Accession Description Interval E-value
KRAB smart00349
krueppel associated box;
8-68 3.96e-32

krueppel associated box;


Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 118.46  E-value: 3.96e-32
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 29789126      8 LSFKDVAVAFSQEEWQQLDPEERTTYRDVMLETYSNLVSVGYDVTKPNMIIKLEQGEEPWT 68
Cdd:smart00349   1 VTFEDVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPKPDLISQLEQGEEPWI 61
KRAB pfam01352
KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc ...
 7-48 8.04e-21

KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers. The KRAB domain is found to be involved in protein-protein interactions. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation.


Pssm-ID: 460171  Cd Length: 42  Bit Score: 85.60  E-value: 8.04e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 29789126     7 PLSFKDVAVAFSQEEWQQLDPEERTTYRDVMLETYSNLVSVG 48
Cdd:pfam01352   1 SVTFEDVAVDFTQEEWALLDPAQRNLYRDVMLENYRNLVSLG 42
KRAB_A-box cd07765
KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression ...
 8-46 2.91e-17

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.


Pssm-ID: 143639  Cd Length: 40  Bit Score: 75.66  E-value: 2.91e-17
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 29789126   8 LSFKDVAVAFSQEEWQQLDPEERTTYRDVMLETYSNLVS 46
Cdd:cd07765   1 VTFEDVAVYFSQEEWELLDPAQRDLYRDVMLENYENLVS 39
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
340-699 9.77e-17

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 83.59  E-value: 9.77e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789126 340 KPYECSECGKSFCQKTHLTLHQRNHSGERPYPCN--ECGKSFSRKSALNDHQRTHTGEKLYKCNECGKS--YYRKSTLIT 415
Cdd:COG5048  32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSysGCDKSFSRPLELSRHLRTHHNNPSDLNSKSLPLsnSKASSSSLS 111

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789126 416 HQRTHTgEKPYQCSECGKFFSRVSYLTIHYRSHLEEKPYECTECGKTFN-----------------------LNSAFIRH 472
Cdd:COG5048 112 SSSSNS-NDNNLLSSHSLPPSSRDPQLPDLLSISNLRNNPLPGNNSSSVntpqsnslhpplpanslskdpssNLSLLISS 190

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789126 473 WKVHAEERVQECGECGKPSPLQ-CAPDHTGDLGEKRYECNECGKTFLDSSAFHRHQSVPEGEKTYECNICGKSF--SDSS 549
Cdd:COG5048 191 NVSTSIPSSSENSPLSSSYSIPsSSSDQNLENSSSSLPLTTNSQLSPKSLLSQSPSSLSSSDSSSSASESPRSSlpTASS 270

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789126 550 CYTVHYRGHSEE-----KPFGCSECGKTFSHNSSLFRHQR--VHTGE--KPYECYE--CGKFFSQKSYLTIHHRIHSGEK 618
Cdd:COG5048 271 QSSSPNESDSSSekgfsLPIKSKQCNISFSRSSPLTRHLRsvNHSGEslKPFSCPYslCGKLFSRNDALKRHILLHTSIS 350

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789126 619 PYEC--SKCGKVFSRMSN-----LTVHYRSHSGEKPYEC--NECGKVFSQKSYLTVHYRTHSGEKPYECN--ECGKKFHH 687
Cdd:COG5048 351 PAKEklLNSSSKFSPLLNneppqSLQQYKDLKNDKKSETlsNSCIRNFKRDSNLSLHIITHLSFRPYNCKnpPCSKSFNR 430

                       410
                ....*....|..
gi 29789126 688 RSAFNSHQRIHK 699
Cdd:COG5048 431 HYNLIPHKKIHT 442
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
251-694 5.00e-14

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 75.12  E-value: 5.00e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789126 251 SQMELKPFECTQCGKSFCKKSKFIIHQRAHTGEKPYACSV--CGKSFSQKGTLTVHRRSHLEEKPYKCNecgktfcQKLH 328
Cdd:COG5048  27 LSNAPRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYsgCDKSFSRPLELSRHLRTHHNNPSDLNS-------KSLP 99

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789126 329 LTQHQRTHSGEkpyecSECGKSFCQKTHLTLHQRNHSGERPYPCNECGKSFSRKSALNDHQRTHTGEKLYKC-------N 401
Cdd:COG5048 100 LSNSKASSSSL-----SSSSSNSNDNNLLSSHSLPPSSRDPQLPDLLSISNLRNNPLPGNNSSSVNTPQSNSlhpplpaN 174

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789126 402 ECGKSYYRKSTLITHQRTHTGEKPYQCSECGKFFSRVSYLTIHYRSHLEEKPYECTECGKTFNLNSafirhwkvhaeERV 481
Cdd:COG5048 175 SLSKDPSSNLSLLISSNVSTSIPSSSENSPLSSSYSIPSSSSDQNLENSSSSLPLTTNSQLSPKSL-----------LSQ 243

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789126 482 QECGECGKPSPLQCAPDHTGDLGEKRyecnecgktFLDSSAFHRHQSVPEGEKT-YECNICGKSFSDSSCYTVHYRG--H 558
Cdd:COG5048 244 SPSSLSSSDSSSSASESPRSSLPTAS---------SQSSSPNESDSSSEKGFSLpIKSKQCNISFSRSSPLTRHLRSvnH 314

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789126 559 SEE--KPFGCSE--CGKTFSHNSSLFRHQRVHTGEKPYECY--ECGKFFSQKSY-----LTIHHRIHSGEKPYEC--SKC 625
Cdd:COG5048 315 SGEslKPFSCPYslCGKLFSRNDALKRHILLHTSISPAKEKllNSSSKFSPLLNneppqSLQQYKDLKNDKKSETlsNSC 394

                       410       420       430       440       450       460       470
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 29789126 626 GKVFSRMSNLTVHYRSHSGEKPYECN--ECGKVFSQKSYLTVHYRTHSGEKPYECNECgKKFHHRSAFNSH 694
Cdd:COG5048 395 IRNFKRDSNLSLHIITHLSFRPYNCKnpPCSKSFNRHYNLIPHKKIHTNHAPLLCSIL-KSFRRDLDLSNH 464
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
352-583 2.73e-07

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 53.55  E-value: 2.73e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789126 352 CQKTHLTLHQRNHSGERPYPCNECGKSFSRKSALNDHQRTHTGEKL-YKCNECGKSYYRKSTLITHQRT--HTGE--KPY 426
Cdd:COG5048 243 QSPSSLSSSDSSSSASESPRSSLPTASSQSSSPNESDSSSEKGFSLpIKSKQCNISFSRSSPLTRHLRSvnHSGEslKPF 322

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789126 427 QCSE--CGKFFSRVSYLTIHYRSHLEEKPYECTECGKTFNLNSAFIrhwkvhaeervqecgecgkPSPLQCAPDHTGDLG 504
Cdd:COG5048 323 SCPYslCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLN-------------------NEPPQSLQQYKDLKN 383

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789126 505 EKRYEC--NECGKTFLDSS--AFHRHQSVPEGEKTYECNICGKSFSDSSCYTVHYRGHSEEKPFGCSECGKTFSHNSSLF 580
Cdd:COG5048 384 DKKSETlsNSCIRNFKRDSnlSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHTNHAPLLCSILKSFRRDLDLSN 463


                ...
gi 29789126 581 RHQ 583
Cdd:COG5048 464 HGK 466
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
284-445 1.49e-06

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 51.24  E-value: 1.49e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789126 284 KPYACSVCGKSFSQKGTLTVHRRSHLEE----KPYKCNE--CGKTFCQKLHLTQHQRTHSGEKPYEC--SECGKSFCQKT 355
Cdd:COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSgeslKPFSCPYslCGKLFSRNDALKRHILLHTSISPAKEklLNSSSKFSPLL 367

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789126 356 ----HLTLHQRNHSGERPYPC---NECGKSFSRKSALNDHQRTHT--GEKLYKCNECGKSYYRKSTLITHQRTHTGEKPY 426
Cdd:COG5048 368 nnepPQSLQQYKDLKNDKKSEtlsNSCIRNFKRDSNLSLHIITHLsfRPYNCKNPPCSKSFNRHYNLIPHKKIHTNHAPL 447

                       170
                ....*....|....*....
gi 29789126 427 QCSECGKFFSRVSYLTIHY 445
Cdd:COG5048 448 LCSILKSFRRDLDLSNHGK 466
zf-H2C2_2 pfam13465
Zinc-finger double domain;
328-351 3.97e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 38.12  E-value: 3.97e-04
                          10        20
                  ....*....|....*....|....
gi 29789126   328 HLTQHQRTHSGEKPYECSECGKSF 351
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSF 24
zf-H2C2_2 pfam13465
Zinc-finger double domain;
578-603 4.42e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 38.12  E-value: 4.42e-04
                          10        20
                  ....*....|....*....|....*.
gi 29789126   578 SLFRHQRVHTGEKPYECYECGKFFSQ 603
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 370-392 7.78e-04

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.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 37.28  E-value: 7.78e-04
                          10        20
                  ....*....|....*....|...
gi 29789126   370 YPCNECGKSFSRKSALNDHQRTH 392
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
zf-H2C2_2 pfam13465
Zinc-finger double domain;
413-437 1.10e-03

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 36.97  E-value: 1.10e-03
                          10        20
                  ....*....|....*....|....*
gi 29789126   413 LITHQRTHTGEKPYQCSECGKFFSR 437
Cdd:pfam13465   2 LKRHMRTHTGEKPYKCPECGKSFKS 26
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 648-670 1.13e-03

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.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 36.89  E-value: 1.13e-03
                          10        20
                  ....*....|....*....|...
gi 29789126   648 YECNECGKVFSQKSYLTVHYRTH 670
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 314-336 1.62e-03

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.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 36.12  E-value: 1.62e-03
                          10        20
                  ....*....|....*....|...
gi 29789126   314 YKCNECGKTFCQKLHLTQHQRTH 336
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
zf-H2C2_2 pfam13465
Zinc-finger double domain;
634-659 1.95e-03

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 36.20  E-value: 1.95e-03
                          10        20
                  ....*....|....*....|....*.
gi 29789126   634 NLTVHYRSHSGEKPYECNECGKVFSQ 659
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 398-420 1.98e-03

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.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 36.12  E-value: 1.98e-03
                          10        20
                  ....*....|....*....|...
gi 29789126   398 YKCNECGKSYYRKSTLITHQRTH 420
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
zf-H2C2_2 pfam13465
Zinc-finger double domain;
356-381 2.02e-03

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 36.20  E-value: 2.02e-03
                          10        20
                  ....*....|....*....|....*.
gi 29789126   356 HLTLHQRNHSGERPYPCNECGKSFSR 381
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 620-642 3.81e-03

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.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 35.35  E-value: 3.81e-03
                          10        20
                  ....*....|....*....|...
gi 29789126   620 YECSKCGKVFSRMSNLTVHYRSH 642
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
zf-H2C2_2 pfam13465
Zinc-finger double domain;
662-685 4.07e-03

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 35.04  E-value: 4.07e-03
                          10        20
                  ....*....|....*....|....
gi 29789126   662 YLTVHYRTHSGEKPYECNECGKKF 685
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSF 24
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 342-364 4.69e-03

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.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 34.97  E-value: 4.69e-03
                          10        20
                  ....*....|....*....|...
gi 29789126   342 YECSECGKSFCQKTHLTLHQRNH 364
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 566-586 5.82e-03

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.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 34.58  E-value: 5.82e-03
                          10        20
                  ....*....|....*....|.
gi 29789126   566 CSECGKTFSHNSSLFRHQRVH 586
Cdd:pfam00096   3 CPDCGKSFSRKSNLKRHLRTH 23
SUF4-like cd20908
N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), ...
 256-304 8.07e-03

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.


Pssm-ID: 411020 [Multi-domain]  Cd Length: 82  Bit Score: 36.00  E-value: 8.07e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 29789126 256 KPFeCTQCGKSFCKKSKFIIHQRAHTgekpYACSVCGKSFSQKGTLTVH 304
Cdd:cd20908   1 KPW-CYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVH 44
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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