NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1720366181|ref|XP_030101891|]
View 

zinc finger protein 496 isoform X3 [Mus musculus]

Protein Classification

KRAB domain-containing zinc finger protein( domain architecture ID 12029596)

KRAB (Kruppel-associated box) domain-containing zinc finger protein (KRAB-ZFP) plays important roles in cell differentiation and organ development, and in regulating viral replication and transcription

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
SCAN pfam02023
SCAN domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found ...
 30-106 1.80e-39

SCAN domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several pfam00096 proteins. The domain has been shown to be able to mediate homo- and hetero-oligomerization.


:

Pssm-ID: 460417 [Multi-domain]  Cd Length: 89  Bit Score: 138.78  E-value: 1.80e-39
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1720366181  30 YQEAAGPREALQRLWELCRGWLRLERHTKEQILELLVLEQFLAILPWEIQSWVRAQEPESGEQAVAAVEALEREPGR 106
Cdd:pfam02023  13 YQEAEGPREALSQLRELCHQWLRPEKHTKEQILELLVLEQFLTILPEEIQSWVREHHPESGEEAVALAEDLLLERGE 89
KRAB_A-box super family cl02581
KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression ...
 201-229 9.06e-06

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.


The actual alignment was detected with superfamily member cd07765:

Pssm-ID: 470626  Cd Length: 40  Bit Score: 42.54  E-value: 9.06e-06
                          10        20
                  ....*....|....*....|....*....
gi 1720366181 201 PFKDMILCFSEEDWSLLDPAQTGFYGEFI 229
Cdd:cd07765     2 TFEDVAVYFSQEEWELLDPAQRDLYRDVM 30
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
315-552 2.15e-05

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


:

Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 47.00  E-value: 2.15e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720366181 315 PGGDPPALKSSLDQEVTIEIVLSSSGDEDSQHSPYCTEELRSPPEdlHSVPAHQSNASAEGEVQTSQKSYVCPNCGKIFR 394
Cdd:COG5048   194 TSIPSSSENSPLSSSYSIPSSSSDQNLENSSSSLPLTTNSQLSPK--SLLSQSPSSLSSSDSSSSASESPRSSLPTASSQ 271

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720366181 395 WRvNFIRHLRS--RREQKPHKCSVCGELFSDSEDL----DGHLETHEAQKPYRCTA--CGKSFRLNSHLISHRRIHLQ-- 464
Cdd:COG5048   272 SS-SPNESDSSseKGFSLPIKSKQCNISFSRSSPLtrhlRSVNHSGESLKPFSCPYslCGKLFSRNDALKRHILLHTSis 350

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720366181 465 --PASQQPMKKSEEEALETEGTGASDLLEKSKAKLSFQC--GDCEKSFQRhDHLVRHRRHCHLKDETRPFQCRYCVKTFR 540
Cdd:COG5048   351 paKEKLLNSSSKFSPLLNNEPPQSLQQYKDLKNDKKSETlsNSCIRNFKR-DSNLSLHIITHLSFRPYNCKNPPCSKSFN 429

                         250
                  ....*....|..
gi 1720366181 541 QNYDLLRHERLH 552
Cdd:COG5048   430 RHYNLIPHKKIH 441
 
Name Accession Description Interval E-value
SCAN pfam02023
SCAN domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found ...
 30-106 1.80e-39

SCAN domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several pfam00096 proteins. The domain has been shown to be able to mediate homo- and hetero-oligomerization.


Pssm-ID: 460417 [Multi-domain]  Cd Length: 89  Bit Score: 138.78  E-value: 1.80e-39
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1720366181  30 YQEAAGPREALQRLWELCRGWLRLERHTKEQILELLVLEQFLAILPWEIQSWVRAQEPESGEQAVAAVEALEREPGR 106
Cdd:pfam02023  13 YQEAEGPREALSQLRELCHQWLRPEKHTKEQILELLVLEQFLTILPEEIQSWVREHHPESGEEAVALAEDLLLERGE 89
SCAN smart00431
leucine rich region;
30-129 1.03e-38

leucine rich region;


Pssm-ID: 128708 [Multi-domain]  Cd Length: 113  Bit Score: 137.82  E-value: 1.03e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720366181   30 YQEAAGPREALQRLWELCRGWLRLERHTKEQILELLVLEQFLAILPWEIQSWVRAQEPESGEQAVAAVEALEREPGRPWQ 109
Cdd:smart00431  13 YQETSGPREALSRLRELCRQWLRPELHTKEQILELLVLEQFLTILPGELQAWVREHHPESGEEAVTLLEDLERELDEPGQ 92

                           90       100
                   ....*....|....*....|.
gi 1720366181  110 WLK-HCEDPVVIDDGDGPAAP 129
Cdd:smart00431  93 QVSaHVHGQEVLLEKMVPLGA 113
SCAN cd07936
SCAN oligomerization domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 ...
 30-102 2.19e-30

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.


Pssm-ID: 153421  Cd Length: 85  Bit Score: 113.89  E-value: 2.19e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1720366181  30 YQEAAGPREALQRLWELCRGWLRLERHTKEQILELLVLEQFLAILPWEIQSWVRAQEPESGEQAVAAVEALER 102
Cdd:cd07936    13 YQEASGPREALQRLRELCRQWLRPEIHTKEQILELLVLEQFLIILPPEVQAWVRERKPESGEEAATLAEDLLA 85
KRAB_A-box cd07765
KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression ...
 201-229 9.06e-06

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: 42.54  E-value: 9.06e-06
                          10        20
                  ....*....|....*....|....*....
gi 1720366181 201 PFKDMILCFSEEDWSLLDPAQTGFYGEFI 229
Cdd:cd07765     2 TFEDVAVYFSQEEWELLDPAQRDLYRDVM 30
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
315-552 2.15e-05

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 47.00  E-value: 2.15e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720366181 315 PGGDPPALKSSLDQEVTIEIVLSSSGDEDSQHSPYCTEELRSPPEdlHSVPAHQSNASAEGEVQTSQKSYVCPNCGKIFR 394
Cdd:COG5048   194 TSIPSSSENSPLSSSYSIPSSSSDQNLENSSSSLPLTTNSQLSPK--SLLSQSPSSLSSSDSSSSASESPRSSLPTASSQ 271

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720366181 395 WRvNFIRHLRS--RREQKPHKCSVCGELFSDSEDL----DGHLETHEAQKPYRCTA--CGKSFRLNSHLISHRRIHLQ-- 464
Cdd:COG5048   272 SS-SPNESDSSseKGFSLPIKSKQCNISFSRSSPLtrhlRSVNHSGESLKPFSCPYslCGKLFSRNDALKRHILLHTSis 350

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720366181 465 --PASQQPMKKSEEEALETEGTGASDLLEKSKAKLSFQC--GDCEKSFQRhDHLVRHRRHCHLKDETRPFQCRYCVKTFR 540
Cdd:COG5048   351 paKEKLLNSSSKFSPLLNNEPPQSLQQYKDLKNDKKSETlsNSCIRNFKR-DSNLSLHIITHLSFRPYNCKNPPCSKSFN 429

                         250
                  ....*....|..
gi 1720366181 541 QNYDLLRHERLH 552
Cdd:COG5048   430 RHYNLIPHKKIH 441
KRAB smart00349
krueppel associated box;
202-227 8.60e-05

krueppel associated box;


Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 40.65  E-value: 8.60e-05
                           10        20
                   ....*....|....*....|....*.
gi 1720366181  202 FKDMILCFSEEDWSLLDPAQTGFYGE 227
Cdd:smart00349   3 FEDVAVYFTQEEWEQLDPAQKNLYRD 28
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 440-462 2.37e-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: 38.44  E-value: 2.37e-04
                          10        20
                  ....*....|....*....|...
gi 1720366181 440 YRCTACGKSFRLNSHLISHRRIH 462
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
KRAB pfam01352
KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc ...
 202-227 1.68e-03

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: 36.29  E-value: 1.68e-03
                          10        20
                  ....*....|....*....|....*.
gi 1720366181 202 FKDMILCFSEEDWSLLDPAQTGFYGE 227
Cdd:pfam01352   4 FEDVAVDFTQEEWALLDPAQRNLYRD 29
 
Name Accession Description Interval E-value
SCAN pfam02023
SCAN domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found ...
 30-106 1.80e-39

SCAN domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several pfam00096 proteins. The domain has been shown to be able to mediate homo- and hetero-oligomerization.


Pssm-ID: 460417 [Multi-domain]  Cd Length: 89  Bit Score: 138.78  E-value: 1.80e-39
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1720366181  30 YQEAAGPREALQRLWELCRGWLRLERHTKEQILELLVLEQFLAILPWEIQSWVRAQEPESGEQAVAAVEALEREPGR 106
Cdd:pfam02023  13 YQEAEGPREALSQLRELCHQWLRPEKHTKEQILELLVLEQFLTILPEEIQSWVREHHPESGEEAVALAEDLLLERGE 89
SCAN smart00431
leucine rich region;
30-129 1.03e-38

leucine rich region;


Pssm-ID: 128708 [Multi-domain]  Cd Length: 113  Bit Score: 137.82  E-value: 1.03e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720366181   30 YQEAAGPREALQRLWELCRGWLRLERHTKEQILELLVLEQFLAILPWEIQSWVRAQEPESGEQAVAAVEALEREPGRPWQ 109
Cdd:smart00431  13 YQETSGPREALSRLRELCRQWLRPELHTKEQILELLVLEQFLTILPGELQAWVREHHPESGEEAVTLLEDLERELDEPGQ 92

                           90       100
                   ....*....|....*....|.
gi 1720366181  110 WLK-HCEDPVVIDDGDGPAAP 129
Cdd:smart00431  93 QVSaHVHGQEVLLEKMVPLGA 113
SCAN cd07936
SCAN oligomerization domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 ...
 30-102 2.19e-30

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.


Pssm-ID: 153421  Cd Length: 85  Bit Score: 113.89  E-value: 2.19e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1720366181  30 YQEAAGPREALQRLWELCRGWLRLERHTKEQILELLVLEQFLAILPWEIQSWVRAQEPESGEQAVAAVEALER 102
Cdd:cd07936    13 YQEASGPREALQRLRELCRQWLRPEIHTKEQILELLVLEQFLIILPPEVQAWVRERKPESGEEAATLAEDLLA 85
KRAB_A-box cd07765
KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression ...
 201-229 9.06e-06

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: 42.54  E-value: 9.06e-06
                          10        20
                  ....*....|....*....|....*....
gi 1720366181 201 PFKDMILCFSEEDWSLLDPAQTGFYGEFI 229
Cdd:cd07765     2 TFEDVAVYFSQEEWELLDPAQRDLYRDVM 30
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
315-552 2.15e-05

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 47.00  E-value: 2.15e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720366181 315 PGGDPPALKSSLDQEVTIEIVLSSSGDEDSQHSPYCTEELRSPPEdlHSVPAHQSNASAEGEVQTSQKSYVCPNCGKIFR 394
Cdd:COG5048   194 TSIPSSSENSPLSSSYSIPSSSSDQNLENSSSSLPLTTNSQLSPK--SLLSQSPSSLSSSDSSSSASESPRSSLPTASSQ 271

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720366181 395 WRvNFIRHLRS--RREQKPHKCSVCGELFSDSEDL----DGHLETHEAQKPYRCTA--CGKSFRLNSHLISHRRIHLQ-- 464
Cdd:COG5048   272 SS-SPNESDSSseKGFSLPIKSKQCNISFSRSSPLtrhlRSVNHSGESLKPFSCPYslCGKLFSRNDALKRHILLHTSis 350

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720366181 465 --PASQQPMKKSEEEALETEGTGASDLLEKSKAKLSFQC--GDCEKSFQRhDHLVRHRRHCHLKDETRPFQCRYCVKTFR 540
Cdd:COG5048   351 paKEKLLNSSSKFSPLLNNEPPQSLQQYKDLKNDKKSETlsNSCIRNFKR-DSNLSLHIITHLSFRPYNCKNPPCSKSFN 429

                         250
                  ....*....|..
gi 1720366181 541 QNYDLLRHERLH 552
Cdd:COG5048   430 RHYNLIPHKKIH 441
KRAB smart00349
krueppel associated box;
202-227 8.60e-05

krueppel associated box;


Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 40.65  E-value: 8.60e-05
                           10        20
                   ....*....|....*....|....*.
gi 1720366181  202 FKDMILCFSEEDWSLLDPAQTGFYGE 227
Cdd:smart00349   3 FEDVAVYFTQEEWEQLDPAQKNLYRD 28
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 440-462 2.37e-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: 38.44  E-value: 2.37e-04
                          10        20
                  ....*....|....*....|...
gi 1720366181 440 YRCTACGKSFRLNSHLISHRRIH 462
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
KRAB pfam01352
KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc ...
 202-227 1.68e-03

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: 36.29  E-value: 1.68e-03
                          10        20
                  ....*....|....*....|....*.
gi 1720366181 202 FKDMILCFSEEDWSLLDPAQTGFYGE 227
Cdd:pfam01352   4 FEDVAVDFTQEEWALLDPAQRNLYRD 29
HVO_2753_ZBP pfam07754
Small zinc finger protein HVO_2753-like, Zn-binding pocket; This domain is found in many ...
 383-418 5.71e-03

Small zinc finger protein HVO_2753-like, Zn-binding pocket; This domain is found in many archaeal proteins, including HVO_2753 (also known as Small CPxCG-related zinc finger protein) from Haloferax volcanii. NMR 3D structure analysis revealed the content of four C(P)XCG motifs, suggesting the presence of two zinc-binding pockets (ZBPs). However, only C(P)XCG motifs 2 and 4 (comprising Cys-32 to Cys-35 and Cys-50 to Cys-53) form a ZBP and binds one zinc atom, while C(P)XCG motifs 1 and 3 (comprising Cys-12 to Cys-15 and Cys-39 to Cys-42) form a four-Cys cluster that do not bind zinc. The four C(P)XCG motifs are critical for protein stability, folding and functionality. This domain can also be present in small zinc finger proteins from bacteria and eukaryotes.


Pssm-ID: 429637  Cd Length: 46  Bit Score: 35.10  E-value: 5.71e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1720366181 383 SYVCPNCGKIFRWRVNfirhlRSRREQKPHKCSVCG 418
Cdd:pfam07754  16 VFPCPNCGEAVIIRCE-----KCRKLSNPYVCPKCG 46
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
487-563 6.81e-03

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 39.29  E-value: 6.81e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720366181 487 SDLLEKSKAKLSFQCGDCEKSFQRHDHLVRHRRHCHLKDE-TRPFQCRY--CVKTFRQNYDLLRHERLHMKRRSKQALNS 563
Cdd:COG5048   278 SDSSSEKGFSLPIKSKQCNISFSRSSPLTRHLRSVNHSGEsLKPFSCPYslCGKLFSRNDALKRHILLHTSISPAKEKLL 357
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 499-519 8.03e-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: 34.20  E-value: 8.03e-03
                          10        20
                  ....*....|....*....|.
gi 1720366181 499 FQCGDCEKSFQRHDHLVRHRR 519
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLR 21
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH