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Conserved domains on  [gi|768000891|ref|XP_011525999|]
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zinc finger protein 560 isoform X1 [Homo sapiens]

Protein Classification

KRAB domain-containing zinc finger protein( domain architecture ID 12204378)

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

CATH:  3.30.160.60|1.10.287.1360
Gene Ontology:  GO:0003700|GO:0005515|GO:0008270|GO:0003677|GO:0006355|GO:0001217
PubMed:  22803940|8183940|2023909|8183939|10748030|27867147|28765213|11361095|30718982|10940247
SCOP:  4003583|4002243

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
KRAB smart00349
krueppel associated box;
13-69 2.37e-29

krueppel associated box;


:

Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 110.76  E-value: 2.37e-29
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 768000891    13 VTFEDTAVDFTQEEWILLDPVQRNLYRDVMLENYENVAKVGFQLFKPSVISWLEEEE 69
Cdd:smart00349   1 VTFEDVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPKPDLISQLEQGE 57
KRAB smart00349
krueppel associated box;
110-161 6.64e-26

krueppel associated box;


:

Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 100.74  E-value: 6.64e-26
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 768000891   110 VTFDSVAVEFTQEEWTLLDPAQRNLYSDVMLENYKNLSSVGYQLFKPSLISW 161
Cdd:smart00349   1 VTFEDVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPKPDLISQ 52
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
344-754 2.76e-11

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


:

Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 66.64  E-value: 2.76e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768000891 344 IKNPYECKECGKDFRYPTHLNNHMQTHIGIKPYKCKH--CGKTFTVPSGFLEHVRTHTGEKPY-GCKECGKAFGTSAGLI 420
Cdd:COG5048   30 APRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYsgCDKSFSRPLELSRHLRTHHNNPSDlNSKSLPLSNSKASSSS 109

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768000891 421 EHIRCHAREKTFKCDHCGKAFISYPSL--FGHLRVHNGEKPYEHKeygkafgTSSGVIEDRRSNtgqKRFDCDQ--CGKV 496
Cdd:COG5048  110 LSSSSSNSNDNNLLSSHSLPPSSRDPQlpDLLSISNLRNNPLPGN-------NSSSVNTPQSNS---LHPPLPAnsLSKD 179

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768000891 497 FVSFSSLFAHLRTHTGEKPFKCYKCGKPFTS-SACLRIHMRTHTEERLYQCKK---CGKAFTKCSYLTKHLRTHAGEKPY 572
Cdd:COG5048  180 PSSNLSLLISSNVSTSIPSSSENSPLSSSYSiPSSSSDQNLENSSSSLPLTTNsqlSPKSLLSQSPSSLSSSDSSSSASE 259

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768000891 573 ECMKCGKafTERSYLTKHLRRHSGE-----KPYECKKCGKAFTERSDLTKHLR--RHTG--DKPYE--YKDCGKAFVVSS 641
Cdd:COG5048  260 SPRSSLP--TASSQSSSPNESDSSSekgfsLPIKSKQCNISFSRSSPLTRHLRsvNHSGesLKPFScpYSLCGKLFSRND 337

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768000891 642 SLVDHLRTHTGYKPYKCNAC-------EKAYSRSCVLTQHLKTHAAEKTSEC--NACGNSF--RNSMCFHDRLKTLTKIK 710
Cdd:COG5048  338 ALKRHILLHTSISPAKEKLLnssskfsPLLNNEPPQSLQQYKDLKNDKKSETlsNSCIRNFkrDSNLSLHIITHLSFRPY 417

                        410       420       430       440
                 ....*....|....*....|....*....|....*....|....
gi 768000891 711 PYKCKDCGKAFTCHSDLTNHVRIHTGEKPYKCKECGKAFRTSSG 754
Cdd:COG5048  418 NCKNPPCSKSFNRHYNLIPHKKIHTNHAPLLCSILKSFRRDLDL 461
zf-H2C2_2 pfam13465
Zinc-finger double domain;
757-779 3.76e-04

Zinc-finger double domain;


:

Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 38.12  E-value: 3.76e-04
                          10        20
                  ....*....|....*....|...
gi 768000891  757 QHLRTHMGEKPFECDQCGKAFAS 779
Cdd:pfam13465   4 RHMRTHTGEKPYKCPECGKSFKS 26
 
Name Accession Description Interval E-value
KRAB smart00349
krueppel associated box;
13-69 2.37e-29

krueppel associated box;


Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 110.76  E-value: 2.37e-29
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 768000891    13 VTFEDTAVDFTQEEWILLDPVQRNLYRDVMLENYENVAKVGFQLFKPSVISWLEEEE 69
Cdd:smart00349   1 VTFEDVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPKPDLISQLEQGE 57
KRAB smart00349
krueppel associated box;
110-161 6.64e-26

krueppel associated box;


Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 100.74  E-value: 6.64e-26
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 768000891   110 VTFDSVAVEFTQEEWTLLDPAQRNLYSDVMLENYKNLSSVGYQLFKPSLISW 161
Cdd:smart00349   1 VTFEDVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPKPDLISQ 52
KRAB pfam01352
KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc ...
 12-53 2.97e-23

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: 92.92  E-value: 2.97e-23
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 768000891   12 SVTFEDTAVDFTQEEWILLDPVQRNLYRDVMLENYENVAKVG 53
Cdd:pfam01352   1 SVTFEDVAVDFTQEEWALLDPAQRNLYRDVMLENYRNLVSLG 42
KRAB pfam01352
KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc ...
 109-150 4.93e-23

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: 92.15  E-value: 4.93e-23
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 768000891  109 LVTFDSVAVEFTQEEWTLLDPAQRNLYSDVMLENYKNLSSVG 150
Cdd:pfam01352   1 SVTFEDVAVDFTQEEWALLDPAQRNLYRDVMLENYRNLVSLG 42
KRAB_A-box cd07765
KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression ...
 13-50 7.22e-19

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: 80.29  E-value: 7.22e-19
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 768000891  13 VTFEDTAVDFTQEEWILLDPVQRNLYRDVMLENYENVA 50
Cdd:cd07765    1 VTFEDVAVYFSQEEWELLDPAQRDLYRDVMLENYENLV 38
KRAB_A-box cd07765
KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression ...
 110-148 5.48e-18

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: 77.59  E-value: 5.48e-18
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 768000891 110 VTFDSVAVEFTQEEWTLLDPAQRNLYSDVMLENYKNLSS 148
Cdd:cd07765    1 VTFEDVAVYFSQEEWELLDPAQRDLYRDVMLENYENLVS 39
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
344-754 2.76e-11

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 66.64  E-value: 2.76e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768000891 344 IKNPYECKECGKDFRYPTHLNNHMQTHIGIKPYKCKH--CGKTFTVPSGFLEHVRTHTGEKPY-GCKECGKAFGTSAGLI 420
Cdd:COG5048   30 APRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYsgCDKSFSRPLELSRHLRTHHNNPSDlNSKSLPLSNSKASSSS 109

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768000891 421 EHIRCHAREKTFKCDHCGKAFISYPSL--FGHLRVHNGEKPYEHKeygkafgTSSGVIEDRRSNtgqKRFDCDQ--CGKV 496
Cdd:COG5048  110 LSSSSSNSNDNNLLSSHSLPPSSRDPQlpDLLSISNLRNNPLPGN-------NSSSVNTPQSNS---LHPPLPAnsLSKD 179

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768000891 497 FVSFSSLFAHLRTHTGEKPFKCYKCGKPFTS-SACLRIHMRTHTEERLYQCKK---CGKAFTKCSYLTKHLRTHAGEKPY 572
Cdd:COG5048  180 PSSNLSLLISSNVSTSIPSSSENSPLSSSYSiPSSSSDQNLENSSSSLPLTTNsqlSPKSLLSQSPSSLSSSDSSSSASE 259

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768000891 573 ECMKCGKafTERSYLTKHLRRHSGE-----KPYECKKCGKAFTERSDLTKHLR--RHTG--DKPYE--YKDCGKAFVVSS 641
Cdd:COG5048  260 SPRSSLP--TASSQSSSPNESDSSSekgfsLPIKSKQCNISFSRSSPLTRHLRsvNHSGesLKPFScpYSLCGKLFSRND 337

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768000891 642 SLVDHLRTHTGYKPYKCNAC-------EKAYSRSCVLTQHLKTHAAEKTSEC--NACGNSF--RNSMCFHDRLKTLTKIK 710
Cdd:COG5048  338 ALKRHILLHTSISPAKEKLLnssskfsPLLNNEPPQSLQQYKDLKNDKKSETlsNSCIRNFkrDSNLSLHIITHLSFRPY 417

                        410       420       430       440
                 ....*....|....*....|....*....|....*....|....
gi 768000891 711 PYKCKDCGKAFTCHSDLTNHVRIHTGEKPYKCKECGKAFRTSSG 754
Cdd:COG5048  418 NCKNPPCSKSFNRHYNLIPHKKIHTNHAPLLCSILKSFRRDLDL 461
zf-H2C2_2 pfam13465
Zinc-finger double domain;
726-751 1.01e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 40.05  E-value: 1.01e-04
                          10        20
                  ....*....|....*....|....*.
gi 768000891  726 DLTNHVRIHTGEKPYKCKECGKAFRT 751
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
zf-H2C2_2 pfam13465
Zinc-finger double domain;
757-779 3.76e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 38.12  E-value: 3.76e-04
                          10        20
                  ....*....|....*....|...
gi 768000891  757 QHLRTHMGEKPFECDQCGKAFAS 779
Cdd:pfam13465   4 RHMRTHTGEKPYKCPECGKSFKS 26
SUF4-like cd20908
N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), ...
 402-455 6.58e-04

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: 39.08  E-value: 6.58e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 768000891 402 KPYgCKECGKAFGTSAGLIEHirchAREKTFKCDHCGKAFISYPSLFGH-LRVHN 455
Cdd:cd20908    1 KPW-CYYCDREFDDEKILIQH----QKAKHFKCHICHKKLYTAGGLAVHcLQVHK 50
PHA00733 PHA00733
hypothetical protein
 403-455 1.39e-03

hypothetical protein


Pssm-ID: 177301  Cd Length: 128  Bit Score: 39.47  E-value: 1.39e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 768000891 403 PYGCKECGKAFGTSAGLIEHIRchAREKTFKCDHCGKAFISYPSLFGHL-RVHN 455
Cdd:PHA00733  73 PYVCPLCLMPFSSSVSLKQHIR--YTEHSKVCPVCGKEFRNTDSTLDHVcKKHN 124
 
Name Accession Description Interval E-value
KRAB smart00349
krueppel associated box;
13-69 2.37e-29

krueppel associated box;


Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 110.76  E-value: 2.37e-29
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 768000891    13 VTFEDTAVDFTQEEWILLDPVQRNLYRDVMLENYENVAKVGFQLFKPSVISWLEEEE 69
Cdd:smart00349   1 VTFEDVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPKPDLISQLEQGE 57
KRAB smart00349
krueppel associated box;
110-161 6.64e-26

krueppel associated box;


Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 100.74  E-value: 6.64e-26
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 768000891   110 VTFDSVAVEFTQEEWTLLDPAQRNLYSDVMLENYKNLSSVGYQLFKPSLISW 161
Cdd:smart00349   1 VTFEDVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPKPDLISQ 52
KRAB pfam01352
KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc ...
 12-53 2.97e-23

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: 92.92  E-value: 2.97e-23
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 768000891   12 SVTFEDTAVDFTQEEWILLDPVQRNLYRDVMLENYENVAKVG 53
Cdd:pfam01352   1 SVTFEDVAVDFTQEEWALLDPAQRNLYRDVMLENYRNLVSLG 42
KRAB pfam01352
KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc ...
 109-150 4.93e-23

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: 92.15  E-value: 4.93e-23
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 768000891  109 LVTFDSVAVEFTQEEWTLLDPAQRNLYSDVMLENYKNLSSVG 150
Cdd:pfam01352   1 SVTFEDVAVDFTQEEWALLDPAQRNLYRDVMLENYRNLVSLG 42
KRAB_A-box cd07765
KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression ...
 13-50 7.22e-19

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: 80.29  E-value: 7.22e-19
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 768000891  13 VTFEDTAVDFTQEEWILLDPVQRNLYRDVMLENYENVA 50
Cdd:cd07765    1 VTFEDVAVYFSQEEWELLDPAQRDLYRDVMLENYENLV 38
KRAB_A-box cd07765
KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression ...
 110-148 5.48e-18

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: 77.59  E-value: 5.48e-18
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 768000891 110 VTFDSVAVEFTQEEWTLLDPAQRNLYSDVMLENYKNLSS 148
Cdd:cd07765    1 VTFEDVAVYFSQEEWELLDPAQRDLYRDVMLENYENLVS 39
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
344-754 2.76e-11

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 66.64  E-value: 2.76e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768000891 344 IKNPYECKECGKDFRYPTHLNNHMQTHIGIKPYKCKH--CGKTFTVPSGFLEHVRTHTGEKPY-GCKECGKAFGTSAGLI 420
Cdd:COG5048   30 APRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYsgCDKSFSRPLELSRHLRTHHNNPSDlNSKSLPLSNSKASSSS 109

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768000891 421 EHIRCHAREKTFKCDHCGKAFISYPSL--FGHLRVHNGEKPYEHKeygkafgTSSGVIEDRRSNtgqKRFDCDQ--CGKV 496
Cdd:COG5048  110 LSSSSSNSNDNNLLSSHSLPPSSRDPQlpDLLSISNLRNNPLPGN-------NSSSVNTPQSNS---LHPPLPAnsLSKD 179

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768000891 497 FVSFSSLFAHLRTHTGEKPFKCYKCGKPFTS-SACLRIHMRTHTEERLYQCKK---CGKAFTKCSYLTKHLRTHAGEKPY 572
Cdd:COG5048  180 PSSNLSLLISSNVSTSIPSSSENSPLSSSYSiPSSSSDQNLENSSSSLPLTTNsqlSPKSLLSQSPSSLSSSDSSSSASE 259

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768000891 573 ECMKCGKafTERSYLTKHLRRHSGE-----KPYECKKCGKAFTERSDLTKHLR--RHTG--DKPYE--YKDCGKAFVVSS 641
Cdd:COG5048  260 SPRSSLP--TASSQSSSPNESDSSSekgfsLPIKSKQCNISFSRSSPLTRHLRsvNHSGesLKPFScpYSLCGKLFSRND 337

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768000891 642 SLVDHLRTHTGYKPYKCNAC-------EKAYSRSCVLTQHLKTHAAEKTSEC--NACGNSF--RNSMCFHDRLKTLTKIK 710
Cdd:COG5048  338 ALKRHILLHTSISPAKEKLLnssskfsPLLNNEPPQSLQQYKDLKNDKKSETlsNSCIRNFkrDSNLSLHIITHLSFRPY 417

                        410       420       430       440
                 ....*....|....*....|....*....|....*....|....
gi 768000891 711 PYKCKDCGKAFTCHSDLTNHVRIHTGEKPYKCKECGKAFRTSSG 754
Cdd:COG5048  418 NCKNPPCSKSFNRHYNLIPHKKIHTNHAPLLCSILKSFRRDLDL 461
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
477-770 4.02e-10

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 62.79  E-value: 4.02e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768000891 477 EDRRSNTGQKR-FDCDQCGKVFVSFSSLFAHLRTHTGEKPFKCYKCGKP--FTSSACLRIHMRTHTEERLY-QCKKCGKA 552
Cdd:COG5048   22 STLKSLSNAPRpDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDksFSRPLELSRHLRTHHNNPSDlNSKSLPLS 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768000891 553 FTKCSYLTKHLRTHAGEKPYECMKCGKAFTERSYLTKHLRRHSGEKPYECKKCGKAFTERS------------------- 613
Cdd:COG5048  102 NSKASSSSLSSSSSNSNDNNLLSSHSLPPSSRDPQLPDLLSISNLRNNPLPGNNSSSVNTPqsnslhpplpanslskdps 181

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768000891 614 ---DLTKHLRRHTGDKPYEYKDCGKAFVVSSSLVDHLRTHTGYKPYKCNACEKAYSRScvLTQHLKTHAAEKTSeCNACG 690
Cdd:COG5048  182 snlSLLISSNVSTSIPSSSENSPLSSSYSIPSSSSDQNLENSSSSLPLTTNSQLSPKS--LLSQSPSSLSSSDS-SSSAS 258

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768000891 691 NSFRNSMCF----------HDRLKTLTKIKPYKCKDCGKAFTCHSDLTNHVR--IHTGE--KPYKCKE--CGKAFRTSSG 754
Cdd:COG5048  259 ESPRSSLPTassqssspneSDSSSEKGFSLPIKSKQCNISFSRSSPLTRHLRsvNHSGEslKPFSCPYslCGKLFSRNDA 338

                        330
                 ....*....|....*.
gi 768000891 755 RIQHLRTHMGEKPFEC 770
Cdd:COG5048  339 LKRHILLHTSISPAKE 354
zf-H2C2_2 pfam13465
Zinc-finger double domain;
726-751 1.01e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 40.05  E-value: 1.01e-04
                          10        20
                  ....*....|....*....|....*.
gi 768000891  726 DLTNHVRIHTGEKPYKCKECGKAFRT 751
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
zf-H2C2_2 pfam13465
Zinc-finger double domain;
757-779 3.76e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 38.12  E-value: 3.76e-04
                          10        20
                  ....*....|....*....|...
gi 768000891  757 QHLRTHMGEKPFECDQCGKAFAS 779
Cdd:pfam13465   4 RHMRTHTGEKPYKCPECGKSFKS 26
zf-H2C2_2 pfam13465
Zinc-finger double domain;
586-610 4.90e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 38.12  E-value: 4.90e-04
                          10        20
                  ....*....|....*....|....*
gi 768000891  586 YLTKHLRRHSGEKPYECKKCGKAFT 610
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFK 25
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
710-775 6.01e-04

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 43.15  E-value: 6.01e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 768000891 710 KPYKCKDCGKAFTCHSDLTNHVRIHTGEKPYKC--KECGKAFRTSSGRIQHLRTHMGEKPFECDQCGK 775
Cdd:COG5048   32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCsySGCDKSFSRPLELSRHLRTHHNNPSDLNSKSLP 99
SUF4-like cd20908
N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), ...
 402-455 6.58e-04

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: 39.08  E-value: 6.58e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 768000891 402 KPYgCKECGKAFGTSAGLIEHirchAREKTFKCDHCGKAFISYPSLFGH-LRVHN 455
Cdd:cd20908    1 KPW-CYYCDREFDDEKILIQH----QKAKHFKCHICHKKLYTAGGLAVHcLQVHK 50
zf-H2C2_2 pfam13465
Zinc-finger double domain;
362-386 9.94e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 36.97  E-value: 9.94e-04
                          10        20
                  ....*....|....*....|....*
gi 768000891  362 HLNNHMQTHIGIKPYKCKHCGKTFT 386
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFK 25
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
360-534 1.24e-03

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 41.99  E-value: 1.24e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768000891 360 PTHLNNHMQTHIGI-KPYKCKHCGKTFTVPSGFLEHVRT--HTGE--KPYGCKE--CGKAFGTSAGLIEHIRCHAREKTF 432
Cdd:COG5048  273 SSPNESDSSSEKGFsLPIKSKQCNISFSRSSPLTRHLRSvnHSGEslKPFSCPYslCGKLFSRNDALKRHILLHTSISPA 352

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768000891 433 KC--DHCGKAF--ISYPSLFGHLRVHNGEKPY-----EHKEYGKAFGTSSGVIEDRRSNTGQKR--FDCDQCGKVFVSFS 501
Cdd:COG5048  353 KEklLNSSSKFspLLNNEPPQSLQQYKDLKNDkksetLSNSCIRNFKRDSNLSLHIITHLSFRPynCKNPPCSKSFNRHY 432

                        170       180       190
                 ....*....|....*....|....*....|...
gi 768000891 502 SLFAHLRTHTGEKPFKCYKCGKPFTSSACLRIH 534
Cdd:COG5048  433 NLIPHKKIHTNHAPLLCSILKSFRRDLDLSNHG 465
PHA00733 PHA00733
hypothetical protein
 403-455 1.39e-03

hypothetical protein


Pssm-ID: 177301  Cd Length: 128  Bit Score: 39.47  E-value: 1.39e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 768000891 403 PYGCKECGKAFGTSAGLIEHIRchAREKTFKCDHCGKAFISYPSLFGHL-RVHN 455
Cdd:PHA00733  73 PYVCPLCLMPFSSSVSLKQHIR--YTEHSKVCPVCGKEFRNTDSTLDHVcKKHN 124
zf-H2C2_2 pfam13465
Zinc-finger double domain;
558-582 1.74e-03

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 36.20  E-value: 1.74e-03
                          10        20
                  ....*....|....*....|....*
gi 768000891  558 YLTKHLRTHAGEKPYECMKCGKAFT 582
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFK 25
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 544-566 1.80e-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: 36.12  E-value: 1.80e-03
                          10        20
                  ....*....|....*....|...
gi 768000891  544 YQCKKCGKAFTKCSYLTKHLRTH 566
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 600-622 3.28e-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: 35.74  E-value: 3.28e-03
                          10        20
                  ....*....|....*....|...
gi 768000891  600 YECKKCGKAFTERSDLTKHLRRH 622
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
zf-H2C2_2 pfam13465
Zinc-finger double domain;
531-555 4.88e-03

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 35.04  E-value: 4.88e-03
                          10        20
                  ....*....|....*....|....*
gi 768000891  531 LRIHMRTHTEERLYQCKKCGKAFTK 555
Cdd:pfam13465   2 LKRHMRTHTGEKPYKCPECGKSFKS 26
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 348-370 5.46e-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: 5.46e-03
                          10        20
                  ....*....|....*....|...
gi 768000891  348 YECKECGKDFRYPTHLNNHMQTH 370
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 516-538 7.19e-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: 7.19e-03
                          10        20
                  ....*....|....*....|...
gi 768000891  516 FKCYKCGKPFTSSACLRIHMRTH 538
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
zf-H2C2_2 pfam13465
Zinc-finger double domain;
642-667 9.24e-03

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 34.27  E-value: 9.24e-03
                          10        20
                  ....*....|....*....|....*.
gi 768000891  642 SLVDHLRTHTGYKPYKCNACEKAYSR 667
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
 
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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