NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|578811987|ref|XP_006715281|]
View 

zinc finger protein with KRAB and SCAN domains 3 isoform X4 [Homo sapiens]

Protein Classification

KRAB domain-containing zinc finger protein( domain architecture ID 12204726)

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
KRAB smart00349
krueppel associated box;
66-126 5.08e-15

krueppel associated box;


:

Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 69.16  E-value: 5.08e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 578811987    66 LKVEDVALTLTP-EWTQQDSSQGNLCRDEKQENHGSLVSLGDEKqTKSRDLPPAEELPEKEH 126
Cdd:smart00349   1 VTFEDVAVYFTQeEWEQLDPAQKNLYRDVMLENYSNLVSLGFQV-PKPDLISQLEQGEEPWI 61
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
220-367 2.32e-09

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


:

Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 58.94  E-value: 2.32e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578811987 220 KPYECEECGKAFSHSSDLIKHQRT--HTGE--KPYECD--DCGKTFSQSCSLLEHHRIHTGEKPYQCSM--CGKAFRRSS 291
Cdd:COG5048  288 LPIKSKQCNISFSRSSPLTRHLRSvnHSGEslKPFSCPysLCGKLFSRNDALKRHILLHTSISPAKEKLlnSSSKFSPLL 367

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578811987 292 HLLRHQ------RIHTGDKNVQEPEQGEAWKSRMESQLENVET-----PMSYKCNECERSFTQNTGLIEHQKIHTGEKPY 360
Cdd:COG5048  368 NNEPPQslqqykDLKNDKKSETLSNSCIRNFKRDSNLSLHIIThlsfrPYNCKNPPCSKSFNRHYNLIPHKKIHTNHAPL 447


                 ....*..
gi 578811987 361 QCNACGK 367
Cdd:COG5048  448 LCSILKS 454
zf-H2C2_2 pfam13465
Zinc-finger double domain;
181-203 8.12e-05

Zinc-finger double domain;


:

Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 39.28  E-value: 8.12e-05
                          10        20
                  ....*....|....*....|...
gi 578811987  181 LSKHRRIHTGEKPYECEECGKAF 203
Cdd:pfam13465   2 LKRHMRTHTGEKPYKCPECGKSF 24
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 166-188 2.15e-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: 2.15e-03
                          10        20
                  ....*....|....*....|...
gi 578811987  166 HICHECGKSFAQSSGLSKHRRIH 188
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
 
Name Accession Description Interval E-value
KRAB smart00349
krueppel associated box;
66-126 5.08e-15

krueppel associated box;


Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 69.16  E-value: 5.08e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 578811987    66 LKVEDVALTLTP-EWTQQDSSQGNLCRDEKQENHGSLVSLGDEKqTKSRDLPPAEELPEKEH 126
Cdd:smart00349   1 VTFEDVAVYFTQeEWEQLDPAQKNLYRDVMLENYSNLVSLGFQV-PKPDLISQLEQGEEPWI 61
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
220-367 2.32e-09

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 58.94  E-value: 2.32e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578811987 220 KPYECEECGKAFSHSSDLIKHQRT--HTGE--KPYECD--DCGKTFSQSCSLLEHHRIHTGEKPYQCSM--CGKAFRRSS 291
Cdd:COG5048  288 LPIKSKQCNISFSRSSPLTRHLRSvnHSGEslKPFSCPysLCGKLFSRNDALKRHILLHTSISPAKEKLlnSSSKFSPLL 367

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578811987 292 HLLRHQ------RIHTGDKNVQEPEQGEAWKSRMESQLENVET-----PMSYKCNECERSFTQNTGLIEHQKIHTGEKPY 360
Cdd:COG5048  368 NNEPPQslqqykDLKNDKKSETLSNSCIRNFKRDSNLSLHIIThlsfrPYNCKNPPCSKSFNRHYNLIPHKKIHTNHAPL 447


                 ....*..
gi 578811987 361 QCNACGK 367
Cdd:COG5048  448 LCSILKS 454
KRAB_A-box cd07765
KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression ...
 66-104 1.73e-08

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: 49.86  E-value: 1.73e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 578811987  66 LKVEDVALTLTP-EWTQQDSSQGNLCRDEKQENHGSLVSL 104
Cdd:cd07765    1 VTFEDVAVYFSQeEWELLDPAQRDLYRDVMLENYENLVSL 40
KRAB pfam01352
KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc ...
 69-105 4.98e-08

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: 48.62  E-value: 4.98e-08
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 578811987   69 EDVALTLTP-EWTQQDSSQGNLCRDEKQENHGSLVSLG 105
Cdd:pfam01352   5 EDVAVDFTQeEWALLDPAQRNLYRDVMLENYRNLVSLG 42
zf-H2C2_2 pfam13465
Zinc-finger double domain;
236-261 4.01e-05

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 40.05  E-value: 4.01e-05
                          10        20
                  ....*....|....*....|....*.
gi 578811987  236 DLIKHQRTHTGEKPYECDDCGKTFSQ 261
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
zf-H2C2_2 pfam13465
Zinc-finger double domain;
181-203 8.12e-05

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 39.28  E-value: 8.12e-05
                          10        20
                  ....*....|....*....|...
gi 578811987  181 LSKHRRIHTGEKPYECEECGKAF 203
Cdd:pfam13465   2 LKRHMRTHTGEKPYKCPECGKSF 24
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 166-188 2.15e-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: 2.15e-03
                          10        20
                  ....*....|....*....|...
gi 578811987  166 HICHECGKSFAQSSGLSKHRRIH 188
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
SUF4-like cd20908
N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), ...
 333-378 2.74e-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: 36.38  E-value: 2.74e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 578811987 333 KCNECERSFTQNTGLIEHQKIHTgekpYQCNACGKGFTRISYLVQH 378
Cdd:cd20908    3 WCYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVH 44
PHA00733 PHA00733
hypothetical protein
 249-296 7.27e-03

hypothetical protein


Pssm-ID: 177301  Cd Length: 128  Bit Score: 36.39  E-value: 7.27e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 578811987 249 PYECDDCGKTFSQSCSLLEHHRIHTGEKpyQCSMCGKAFRRSSHLLRH 296
Cdd:PHA00733  73 PYVCPLCLMPFSSSVSLKQHIRYTEHSK--VCPVCGKEFRNTDSTLDH 118
 
Name Accession Description Interval E-value
KRAB smart00349
krueppel associated box;
66-126 5.08e-15

krueppel associated box;


Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 69.16  E-value: 5.08e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 578811987    66 LKVEDVALTLTP-EWTQQDSSQGNLCRDEKQENHGSLVSLGDEKqTKSRDLPPAEELPEKEH 126
Cdd:smart00349   1 VTFEDVAVYFTQeEWEQLDPAQKNLYRDVMLENYSNLVSLGFQV-PKPDLISQLEQGEEPWI 61
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
220-367 2.32e-09

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 58.94  E-value: 2.32e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578811987 220 KPYECEECGKAFSHSSDLIKHQRT--HTGE--KPYECD--DCGKTFSQSCSLLEHHRIHTGEKPYQCSM--CGKAFRRSS 291
Cdd:COG5048  288 LPIKSKQCNISFSRSSPLTRHLRSvnHSGEslKPFSCPysLCGKLFSRNDALKRHILLHTSISPAKEKLlnSSSKFSPLL 367

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578811987 292 HLLRHQ------RIHTGDKNVQEPEQGEAWKSRMESQLENVET-----PMSYKCNECERSFTQNTGLIEHQKIHTGEKPY 360
Cdd:COG5048  368 NNEPPQslqqykDLKNDKKSETLSNSCIRNFKRDSNLSLHIIThlsfrPYNCKNPPCSKSFNRHYNLIPHKKIHTNHAPL 447


                 ....*..
gi 578811987 361 QCNACGK 367
Cdd:COG5048  448 LCSILKS 454
KRAB_A-box cd07765
KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression ...
 66-104 1.73e-08

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: 49.86  E-value: 1.73e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 578811987  66 LKVEDVALTLTP-EWTQQDSSQGNLCRDEKQENHGSLVSL 104
Cdd:cd07765    1 VTFEDVAVYFSQeEWELLDPAQRDLYRDVMLENYENLVSL 40
KRAB pfam01352
KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc ...
 69-105 4.98e-08

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: 48.62  E-value: 4.98e-08
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 578811987   69 EDVALTLTP-EWTQQDSSQGNLCRDEKQENHGSLVSLG 105
Cdd:pfam01352   5 EDVAVDFTQeEWALLDPAQRNLYRDVMLENYRNLVSLG 42
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
248-383 6.68e-07

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 51.24  E-value: 6.68e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578811987 248 KPYECDDCGKTFSQSCSLLEH--HRIHTGE--KPYQC--SMCGKAFRRSSHLLRHQRIHTGDKNVQEP-EQGEAWKSRME 320
Cdd:COG5048  288 LPIKSKQCNISFSRSSPLTRHlrSVNHSGEslKPFSCpySLCGKLFSRNDALKRHILLHTSISPAKEKlLNSSSKFSPLL 367

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 578811987 321 -------SQLENVETPMSYKC---NECERSFTQNTGLIEHQKIHTGEKPYQCN--ACGKGFTRISYLVQHQRSHV 383
Cdd:COG5048  368 nneppqsLQQYKDLKNDKKSEtlsNSCIRNFKRDSNLSLHIITHLSFRPYNCKnpPCSKSFNRHYNLIPHKKIHT 442
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
220-285 1.91e-05

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 46.61  E-value: 1.91e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 578811987 220 KPYECEECGKAFSHSSDLIKHQRTHTGEKPYEC--DDCGKTFSQSCSLLEHHRIHTGEKPYQCSMCGK 285
Cdd:COG5048   32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCsySGCDKSFSRPLELSRHLRTHHNNPSDLNSKSLP 99
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
234-305 2.42e-05

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 46.23  E-value: 2.42e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 578811987 234 SSDLIKHQRTHTGE----KPYECDDCGKTFSQSCSLLEHHRIHTGEKPYQCS--MCGKAFRRSSHLLRHQRIHTGDKN 305
Cdd:COG5048   14 SVLSSTPKSTLKSLsnapRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSysGCDKSFSRPLELSRHLRTHHNNPS 91
zf-H2C2_2 pfam13465
Zinc-finger double domain;
236-261 4.01e-05

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 40.05  E-value: 4.01e-05
                          10        20
                  ....*....|....*....|....*.
gi 578811987  236 DLIKHQRTHTGEKPYECDDCGKTFSQ 261
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
192-264 5.02e-05

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 45.07  E-value: 5.02e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 578811987 192 KPYECEECGKAFIGSSALVIHQRVHTGEKPYEC--EECGKAFSHSSDLIKHQRTHTGEKPYECDDCGKTFSQSCS 264
Cdd:COG5048   32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCsySGCDKSFSRPLELSRHLRTHHNNPSDLNSKSLPLSNSKAS 106
zf-H2C2_2 pfam13465
Zinc-finger double domain;
181-203 8.12e-05

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 39.28  E-value: 8.12e-05
                          10        20
                  ....*....|....*....|...
gi 578811987  181 LSKHRRIHTGEKPYECEECGKAF 203
Cdd:pfam13465   2 LKRHMRTHTGEKPYKCPECGKSF 24
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 278-300 8.12e-05

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: 39.21  E-value: 8.12e-05
                          10        20
                  ....*....|....*....|...
gi 578811987  278 YQCSMCGKAFRRSSHLLRHQRIH 300
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 222-244 1.01e-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: 38.82  E-value: 1.01e-04
                          10        20
                  ....*....|....*....|...
gi 578811987  222 YECEECGKAFSHSSDLIKHQRTH 244
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
zf-H2C2_2 pfam13465
Zinc-finger double domain;
208-233 1.13e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 38.89  E-value: 1.13e-04
                          10        20
                  ....*....|....*....|....*.
gi 578811987  208 ALVIHQRVHTGEKPYECEECGKAFSH 233
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
317-382 1.64e-04

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 43.53  E-value: 1.64e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 578811987 317 SRMESQLENVETPMSYKCNECERSFTQNTGLIEHQKIHTGEKPYQCNA--CGKGFTRISYLVQHQRSH 382
Cdd:COG5048   19 TPKSTLKSLSNAPRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYsgCDKSFSRPLELSRHLRTH 86
zf-H2C2_2 pfam13465
Zinc-finger double domain;
264-289 3.27e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 37.74  E-value: 3.27e-04
                          10        20
                  ....*....|....*....|....*.
gi 578811987  264 SLLEHHRIHTGEKPYQCSMCGKAFRR 289
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
zf-H2C2_2 pfam13465
Zinc-finger double domain;
347-371 4.43e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 37.35  E-value: 4.43e-04
                          10        20
                  ....*....|....*....|....*
gi 578811987  347 LIEHQKIHTGEKPYQCNACGKGFTR 371
Cdd:pfam13465   2 LKRHMRTHTGEKPYKCPECGKSFKS 26
SFP1 COG5189
Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division ...
 185-273 8.08e-04

Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning];


Pssm-ID: 227516 [Multi-domain]  Cd Length: 423  Bit Score: 41.24  E-value: 8.08e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578811987 185 RRIHT-GEKPYECE--ECGKAFIGSSALVIHqRVHTgekpyeceECGKAFSHSSDLIKHQRTHTGEKPYECDDCGKTFsQ 261
Cdd:COG5189  340 RMLKVkDGKPYKCPveGCNKKYKNQNGLKYH-MLHG--------HQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRY-K 409

                         90
                 ....*....|..
gi 578811987 262 SCSLLEHHRIHT 273
Cdd:COG5189  410 NLNGLKYHRKHS 421
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 166-188 2.15e-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: 2.15e-03
                          10        20
                  ....*....|....*....|...
gi 578811987  166 HICHECGKSFAQSSGLSKHRRIH 188
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
SUF4-like cd20908
N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), ...
 333-378 2.74e-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: 36.38  E-value: 2.74e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 578811987 333 KCNECERSFTQNTGLIEHQKIHTgekpYQCNACGKGFTRISYLVQH 378
Cdd:cd20908    3 WCYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVH 44
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 250-272 4.80e-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: 4.80e-03
                          10        20
                  ....*....|....*....|...
gi 578811987  250 YECDDCGKTFSQSCSLLEHHRIH 272
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
PHA00733 PHA00733
hypothetical protein
 249-296 7.27e-03

hypothetical protein


Pssm-ID: 177301  Cd Length: 128  Bit Score: 36.39  E-value: 7.27e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 578811987 249 PYECDDCGKTFSQSCSLLEHHRIHTGEKpyQCSMCGKAFRRSSHLLRH 296
Cdd:PHA00733  73 PYVCPLCLMPFSSSVSLKQHIRYTEHSK--VCPVCGKEFRNTDSTLDH 118
InsA COG3677
Transposase InsA [Mobilome: prophages, transposons];
224-294 9.72e-03

Transposase InsA [Mobilome: prophages, transposons];


Pssm-ID: 442893 [Multi-domain]  Cd Length: 241  Bit Score: 37.54  E-value: 9.72e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 578811987 224 CEECGkafshSSDLIKHQRTHTGEKPYECDDCGKTFS-QSCSLLEHHRIHTGEKPYQCSMCGKAFRRSSHLL 294
Cdd:COG3677   19 CPHCG-----STRIVKNGKTRNGRQRYRCKDCGRTFTvTTGTIFEGSKLPLWLQAIRLLLNGISLRQIARVL 85
 
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