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Conserved domains on  [gi|1622922163|ref|XP_014989873|]
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zinc finger protein with KRAB and SCAN domains 5 isoform X1 [Macaca mulatta]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SCAN smart00431
leucine rich region;
46-155 1.08e-59

leucine rich region;


:

Pssm-ID: 128708 [Multi-domain]  Cd Length: 113  Bit Score: 197.91  E-value: 1.08e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622922163   46 FETFYQRFRHFQYHEASGPREALSQLRVLCCEWLRPELHTKEQILELLVLEQFLTILPEEFQPWVREHHPESGEEAVAVI 125
Cdd:smart00431   1 PEIFRQRFRQFRYQETSGPREALSRLRELCRQWLRPELHTKEQILELLVLEQFLTILPGELQAWVREHHPESGEEAVTLL 80

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1622922163  126 ENIQRELEERRQQIVACPDG---LPQKMAPPGA 155
Cdd:smart00431  81 EDLERELDEPGQQVSAHVHGqevLLEKMVPLGA 113
KRAB super family cl42959
krueppel associated box;
222-260 1.12e-13

krueppel associated box;


The actual alignment was detected with superfamily member smart00349:

Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 66.08  E-value: 1.12e-13
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 1622922163  222 DVAVSFILEEWGHLDQSQKSLYRDDRKENYGSITSMGYE 260
Cdd:smart00349   5 DVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQ 43
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
539-837 6.18e-08

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


:

Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 55.86  E-value: 6.18e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622922163 539 HKKSSTGERPHKCNECGKSFIQSAHLIQHQRIHTGEKPFRC--EECGKSYNQRVHLTQHQRVHTGEKPYTC--PLCGKAF 614
Cdd:COG5048    24 LKSLSNAPRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCsySGCDKSFSRPLELSRHLRTHHNNPSDLNskSLPLSNS 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622922163 615 RVRSHLVQHQSVHSgERPFKCNECGKGFGRRSHLAGHLRLHSREKAHQCRECGEIFFQY--VSLIEHQVLHMGQKNEKHG 692
Cdd:COG5048   104 KASSSSLSSSSSNS-NDNNLLSSHSLPPSSRDPQLPDLLSISNLRNNPLPGNNSSSVNTpqSNSLHPPLPANSLSKDPSS 182

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622922163 693 VCEEAYSWNLTVIEDKKIELQEQ--------------------PYQCDICGKAFGYSSDLIQHYRTHTAEKPYQCDTCRE 752
Cdd:COG5048   183 NLSLLISSNVSTSIPSSSENSPLsssysipssssdqnlensssSLPLTTNSQLSPKSLLSQSPSSLSSSDSSSSASESPR 262

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622922163 753 NVGQCSHTKQHQKIYSS-------TKSHQCHECGRGFTLKPHLNQHQR--IHTGE--KPFQCKE--CGMNFSWSCSLFKH 819
Cdd:COG5048   263 SSLPTASSQSSSPNESDsssekgfSLPIKSKQCNISFSRSSPLTRHLRsvNHSGEslKPFSCPYslCGKLFSRNDALKRH 342

                         330
                  ....*....|....*...
gi 1622922163 820 LRSHERTDPINTLSVEGS 837
Cdd:COG5048   343 ILLHTSISPAKEKLLNSS 360
zf-H2C2_2 pfam13465
Zinc-finger double domain;
388-411 8.81e-05

Zinc-finger double domain;


:

Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 40.05  E-value: 8.81e-05
                          10        20
                  ....*....|....*....|....
gi 1622922163 388 HLTQHQRVHTGEKPYKCQVCGKAF 411
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSF 24
zf-H2C2_2 pfam13465
Zinc-finger double domain;
360-385 6.58e-04

Zinc-finger double domain;


:

Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 37.74  E-value: 6.58e-04
                          10        20
                  ....*....|....*....|....*.
gi 1622922163 360 NFIQHRRIHTGEKPFKCGECGKSYNQ 385
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
 
Name Accession Description Interval E-value
SCAN smart00431
leucine rich region;
46-155 1.08e-59

leucine rich region;


Pssm-ID: 128708 [Multi-domain]  Cd Length: 113  Bit Score: 197.91  E-value: 1.08e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622922163   46 FETFYQRFRHFQYHEASGPREALSQLRVLCCEWLRPELHTKEQILELLVLEQFLTILPEEFQPWVREHHPESGEEAVAVI 125
Cdd:smart00431   1 PEIFRQRFRQFRYQETSGPREALSRLRELCRQWLRPELHTKEQILELLVLEQFLTILPGELQAWVREHHPESGEEAVTLL 80

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1622922163  126 ENIQRELEERRQQIVACPDG---LPQKMAPPGA 155
Cdd:smart00431  81 EDLERELDEPGQQVSAHVHGqevLLEKMVPLGA 113
SCAN pfam02023
SCAN domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found ...
 47-134 4.50e-48

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: 164.97  E-value: 4.50e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622922163  47 ETFYQRFRHFQYHEASGPREALSQLRVLCCEWLRPELHTKEQILELLVLEQFLTILPEEFQPWVREHHPESGEEAVAVIE 126
Cdd:pfam02023   2 EASRQRFRQFCYQEAEGPREALSQLRELCHQWLRPEKHTKEQILELLVLEQFLTILPEEIQSWVREHHPESGEEAVALAE 81


                  ....*...
gi 1622922163 127 NIQRELEE 134
Cdd:pfam02023  82 DLLLERGE 89
SCAN cd07936
SCAN oligomerization domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 ...
 46-130 1.02e-39

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: 141.24  E-value: 1.02e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622922163  46 FETFYQRFRHFQYHEASGPREALSQLRVLCCEWLRPELHTKEQILELLVLEQFLTILPEEFQPWVREHHPESGEEAVAVI 125
Cdd:cd07936     1 PETYRQRFRAFQYQEASGPREALQRLRELCRQWLRPEIHTKEQILELLVLEQFLIILPPEVQAWVRERKPESGEEAATLA 80


                  ....*
gi 1622922163 126 ENIQR 130
Cdd:cd07936    81 EDLLA 85
KRAB smart00349
krueppel associated box;
222-260 1.12e-13

krueppel associated box;


Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 66.08  E-value: 1.12e-13
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 1622922163  222 DVAVSFILEEWGHLDQSQKSLYRDDRKENYGSITSMGYE 260
Cdd:smart00349   5 DVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQ 43
KRAB_A-box cd07765
KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression ...
 222-257 2.48e-12

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: 61.80  E-value: 2.48e-12
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1622922163 222 DVAVSFILEEWGHLDQSQKSLYRDDRKENYGSITSM 257
Cdd:cd07765     5 DVAVYFSQEEWELLDPAQRDLYRDVMLENYENLVSL 40
KRAB pfam01352
KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc ...
 222-258 6.10e-12

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: 60.56  E-value: 6.10e-12
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1622922163 222 DVAVSFILEEWGHLDQSQKSLYRDDRKENYGSITSMG 258
Cdd:pfam01352   6 DVAVDFTQEEWALLDPAQRNLYRDVMLENYRNLVSLG 42
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
539-837 6.18e-08

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 55.86  E-value: 6.18e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622922163 539 HKKSSTGERPHKCNECGKSFIQSAHLIQHQRIHTGEKPFRC--EECGKSYNQRVHLTQHQRVHTGEKPYTC--PLCGKAF 614
Cdd:COG5048    24 LKSLSNAPRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCsySGCDKSFSRPLELSRHLRTHHNNPSDLNskSLPLSNS 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622922163 615 RVRSHLVQHQSVHSgERPFKCNECGKGFGRRSHLAGHLRLHSREKAHQCRECGEIFFQY--VSLIEHQVLHMGQKNEKHG 692
Cdd:COG5048   104 KASSSSLSSSSSNS-NDNNLLSSHSLPPSSRDPQLPDLLSISNLRNNPLPGNNSSSVNTpqSNSLHPPLPANSLSKDPSS 182

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622922163 693 VCEEAYSWNLTVIEDKKIELQEQ--------------------PYQCDICGKAFGYSSDLIQHYRTHTAEKPYQCDTCRE 752
Cdd:COG5048   183 NLSLLISSNVSTSIPSSSENSPLsssysipssssdqnlensssSLPLTTNSQLSPKSLLSQSPSSLSSSDSSSSASESPR 262

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622922163 753 NVGQCSHTKQHQKIYSS-------TKSHQCHECGRGFTLKPHLNQHQR--IHTGE--KPFQCKE--CGMNFSWSCSLFKH 819
Cdd:COG5048   263 SSLPTASSQSSSPNESDsssekgfSLPIKSKQCNISFSRSSPLTRHLRsvNHSGEslKPFSCPYslCGKLFSRNDALKRH 342

                         330
                  ....*....|....*...
gi 1622922163 820 LRSHERTDPINTLSVEGS 837
Cdd:COG5048   343 ILLHTSISPAKEKLLNSS 360
zf-H2C2_2 pfam13465
Zinc-finger double domain;
563-588 7.91e-05

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 40.43  E-value: 7.91e-05
                          10        20
                  ....*....|....*....|....*.
gi 1622922163 563 HLIQHQRIHTGEKPFRCEECGKSYNQ 588
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
zf-H2C2_2 pfam13465
Zinc-finger double domain;
388-411 8.81e-05

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 40.05  E-value: 8.81e-05
                          10        20
                  ....*....|....*....|....
gi 1622922163 388 HLTQHQRVHTGEKPYKCQVCGKAF 411
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSF 24
zf-H2C2_2 pfam13465
Zinc-finger double domain;
360-385 6.58e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 37.74  E-value: 6.58e-04
                          10        20
                  ....*....|....*....|....*.
gi 1622922163 360 NFIQHRRIHTGEKPFKCGECGKSYNQ 385
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
SUF4-like cd20908
N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), ...
 549-599 2.43e-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: 37.54  E-value: 2.43e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622922163 549 HKCNECGKSFIQSAHLIQHQRIHTgekpFRCEECGKSYNQ----RVHLTQhqrVH 599
Cdd:cd20908     2 PWCYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTagglAVHCLQ---VH 49
 
Name Accession Description Interval E-value
SCAN smart00431
leucine rich region;
46-155 1.08e-59

leucine rich region;


Pssm-ID: 128708 [Multi-domain]  Cd Length: 113  Bit Score: 197.91  E-value: 1.08e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622922163   46 FETFYQRFRHFQYHEASGPREALSQLRVLCCEWLRPELHTKEQILELLVLEQFLTILPEEFQPWVREHHPESGEEAVAVI 125
Cdd:smart00431   1 PEIFRQRFRQFRYQETSGPREALSRLRELCRQWLRPELHTKEQILELLVLEQFLTILPGELQAWVREHHPESGEEAVTLL 80

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1622922163  126 ENIQRELEERRQQIVACPDG---LPQKMAPPGA 155
Cdd:smart00431  81 EDLERELDEPGQQVSAHVHGqevLLEKMVPLGA 113
SCAN pfam02023
SCAN domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found ...
 47-134 4.50e-48

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: 164.97  E-value: 4.50e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622922163  47 ETFYQRFRHFQYHEASGPREALSQLRVLCCEWLRPELHTKEQILELLVLEQFLTILPEEFQPWVREHHPESGEEAVAVIE 126
Cdd:pfam02023   2 EASRQRFRQFCYQEAEGPREALSQLRELCHQWLRPEKHTKEQILELLVLEQFLTILPEEIQSWVREHHPESGEEAVALAE 81


                  ....*...
gi 1622922163 127 NIQRELEE 134
Cdd:pfam02023  82 DLLLERGE 89
SCAN cd07936
SCAN oligomerization domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 ...
 46-130 1.02e-39

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: 141.24  E-value: 1.02e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622922163  46 FETFYQRFRHFQYHEASGPREALSQLRVLCCEWLRPELHTKEQILELLVLEQFLTILPEEFQPWVREHHPESGEEAVAVI 125
Cdd:cd07936     1 PETYRQRFRAFQYQEASGPREALQRLRELCRQWLRPEIHTKEQILELLVLEQFLIILPPEVQAWVRERKPESGEEAATLA 80


                  ....*
gi 1622922163 126 ENIQR 130
Cdd:cd07936    81 EDLLA 85
KRAB smart00349
krueppel associated box;
222-260 1.12e-13

krueppel associated box;


Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 66.08  E-value: 1.12e-13
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 1622922163  222 DVAVSFILEEWGHLDQSQKSLYRDDRKENYGSITSMGYE 260
Cdd:smart00349   5 DVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQ 43
KRAB_A-box cd07765
KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression ...
 222-257 2.48e-12

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: 61.80  E-value: 2.48e-12
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1622922163 222 DVAVSFILEEWGHLDQSQKSLYRDDRKENYGSITSM 257
Cdd:cd07765     5 DVAVYFSQEEWELLDPAQRDLYRDVMLENYENLVSL 40
KRAB pfam01352
KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc ...
 222-258 6.10e-12

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: 60.56  E-value: 6.10e-12
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1622922163 222 DVAVSFILEEWGHLDQSQKSLYRDDRKENYGSITSMG 258
Cdd:pfam01352   6 DVAVDFTQEEWALLDPAQRNLYRDVMLENYRNLVSLG 42
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
539-837 6.18e-08

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 55.86  E-value: 6.18e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622922163 539 HKKSSTGERPHKCNECGKSFIQSAHLIQHQRIHTGEKPFRC--EECGKSYNQRVHLTQHQRVHTGEKPYTC--PLCGKAF 614
Cdd:COG5048    24 LKSLSNAPRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCsySGCDKSFSRPLELSRHLRTHHNNPSDLNskSLPLSNS 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622922163 615 RVRSHLVQHQSVHSgERPFKCNECGKGFGRRSHLAGHLRLHSREKAHQCRECGEIFFQY--VSLIEHQVLHMGQKNEKHG 692
Cdd:COG5048   104 KASSSSLSSSSSNS-NDNNLLSSHSLPPSSRDPQLPDLLSISNLRNNPLPGNNSSSVNTpqSNSLHPPLPANSLSKDPSS 182

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622922163 693 VCEEAYSWNLTVIEDKKIELQEQ--------------------PYQCDICGKAFGYSSDLIQHYRTHTAEKPYQCDTCRE 752
Cdd:COG5048   183 NLSLLISSNVSTSIPSSSENSPLsssysipssssdqnlensssSLPLTTNSQLSPKSLLSQSPSSLSSSDSSSSASESPR 262

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622922163 753 NVGQCSHTKQHQKIYSS-------TKSHQCHECGRGFTLKPHLNQHQR--IHTGE--KPFQCKE--CGMNFSWSCSLFKH 819
Cdd:COG5048   263 SSLPTASSQSSSPNESDsssekgfSLPIKSKQCNISFSRSSPLTRHLRsvNHSGEslKPFSCPYslCGKLFSRNDALKRH 342

                         330
                  ....*....|....*...
gi 1622922163 820 LRSHERTDPINTLSVEGS 837
Cdd:COG5048   343 ILLHTSISPAKEKLLNSS 360
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
318-762 2.13e-06

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 51.24  E-value: 2.13e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622922163 318 SRQNPSQKRNPDVITDLSPKQSTHgERGHRCSDCGKFFLQASNFIQHRRIHTGEKPFKCGECG----------------K 381
Cdd:COG5048     7 QSSSSNNSVLSSTPKSTLKSLSNA-PRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGcdksfsrplelsrhlrT 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622922163 382 SYNQRVHLTQHQRVHTGEKPYKCQV--CGKAFRVSSHLVQHHSVHSGERP----------YGCNECGKNFGRHSHLIEHL 449
Cdd:COG5048    86 HHNNPSDLNSKSLPLSNSKASSSSLssSSSNSNDNNLLSSHSLPPSSRDPqlpdllsisnLRNNPLPGNNSSSVNTPQSN 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622922163 450 KRHFREKSQRCSDKRSKNTKLSVKKKIS--EYSEADMELSGKTQRNVSQVQDFGEGYELQS-KLDRKQGIPMKEIVGQPS 526
Cdd:COG5048   166 SLHPPLPANSLSKDPSSNLSLLISSNVStsIPSSSENSPLSSSYSIPSSSSDQNLENSSSSlPLTTNSQLSPKSLLSQSP 245

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622922163 527 SKRMNYSEvpyvhkksstgerPHKCNECGKSFIQSAHLIQHQRIHTGE-------KPFRCEECGKSYNQRVHLTQHQR-- 597
Cdd:COG5048   246 SSLSSSDS-------------SSSASESPRSSLPTASSQSSSPNESDSssekgfsLPIKSKQCNISFSRSSPLTRHLRsv 312

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622922163 598 VHTGE--KPYTCP--LCGKAFRVRSHLVQHQSVHSGERPFKC--NECGKGFGRRSHLAGHLRLHSREKAHQCREcgeiff 671
Cdd:COG5048   313 NHSGEslKPFSCPysLCGKLFSRNDALKRHILLHTSISPAKEklLNSSSKFSPLLNNEPPQSLQQYKDLKNDKK------ 386

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622922163 672 qyvsliehqvlHMGQKNEKHGVCEEAYswnlTVIEDKKIELQEQPYQCD--ICGKAFGYSSDLIQHYRTHTAEKPYQCDT 749
Cdd:COG5048   387 -----------SETLSNSCIRNFKRDS----NLSLHIITHLSFRPYNCKnpPCSKSFNRHYNLIPHKKIHTNHAPLLCSI 451

                         490
                  ....*....|....*.
gi 1622922163 750 CRENVGQ---CSHTKQ 762
Cdd:COG5048   452 LKSFRRDldlSNHGKD 467
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
400-811 2.28e-05

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 47.77  E-value: 2.28e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622922163 400 KPYKCQVCGKAFRVSSHLVQHHSVHSGERPYGCN--ECGKNFGRHSHLIEHLKRHFREKSQRCSDKRSKNTKLSVKKKIS 477
Cdd:COG5048    32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSysGCDKSFSRPLELSRHLRTHHNNPSDLNSKSLPLSNSKASSSSLS 111

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622922163 478 EYSEADMELSGktqrnvsqvqdfgegyelqskldrkqgipmkeIVGQPSSKRMNYSEVPYVHKKSSTGERPHK-CNECGK 556
Cdd:COG5048   112 SSSSNSNDNNL--------------------------------LSSHSLPPSSRDPQLPDLLSISNLRNNPLPgNNSSSV 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622922163 557 SFIQSAHLIQhqrihtgEKPFRCEECGKSYNQRVHLtqHQRVHTGEKPYTCPLCGKAFRVRSHLVQHQSVHSGERPFKCN 636
Cdd:COG5048   160 NTPQSNSLHP-------PLPANSLSKDPSSNLSLLI--SSNVSTSIPSSSENSPLSSSYSIPSSSSDQNLENSSSSLPLT 230

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622922163 637 ECGKGFGRRSHLAGHLRLHSREKAHQCRECGEIFFQYVSLIEHQVLHMGQKNEKhgvceeayswnltviedkkieLQEQP 716
Cdd:COG5048   231 TNSQLSPKSLLSQSPSSLSSSDSSSSASESPRSSLPTASSQSSSPNESDSSSEK---------------------GFSLP 289

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622922163 717 YQCDICGKAFGYSSDLIQHYRthtaekpyqcdtcrenvgQCSHTKQHQKIYSSTKShqchECGRGFTLKPHLNQHQRIHT 796
Cdd:COG5048   290 IKSKQCNISFSRSSPLTRHLR------------------SVNHSGESLKPFSCPYS----LCGKLFSRNDALKRHILLHT 347

                         410
                  ....*....|....*
gi 1622922163 797 GEKPFQCKECGMNFS 811
Cdd:COG5048   348 SISPAKEKLLNSSSK 362
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
758-823 3.66e-05

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 47.00  E-value: 3.66e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1622922163 758 SHTKQHQKIYSSTKSHQCHECGRGFTLKPHLNQHQRIHTGEKPFQC--KECGMNFSWSCSLFKHLRSH 823
Cdd:COG5048    19 TPKSTLKSLSNAPRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCsySGCDKSFSRPLELSRHLRTH 86
zf-H2C2_2 pfam13465
Zinc-finger double domain;
563-588 7.91e-05

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 40.43  E-value: 7.91e-05
                          10        20
                  ....*....|....*....|....*.
gi 1622922163 563 HLIQHQRIHTGEKPFRCEECGKSYNQ 588
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
zf-H2C2_2 pfam13465
Zinc-finger double domain;
388-411 8.81e-05

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 40.05  E-value: 8.81e-05
                          10        20
                  ....*....|....*....|....
gi 1622922163 388 HLTQHQRVHTGEKPYKCQVCGKAF 411
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSF 24
zf-H2C2_2 pfam13465
Zinc-finger double domain;
591-614 1.17e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 39.66  E-value: 1.17e-04
                          10        20
                  ....*....|....*....|....
gi 1622922163 591 HLTQHQRVHTGEKPYTCPLCGKAF 614
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSF 24
zf-H2C2_2 pfam13465
Zinc-finger double domain;
787-811 2.59e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 38.89  E-value: 2.59e-04
                          10        20
                  ....*....|....*....|....*
gi 1622922163 787 HLNQHQRIHTGEKPFQCKECGMNFS 811
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFK 25
zf-H2C2_2 pfam13465
Zinc-finger double domain;
360-385 6.58e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 37.74  E-value: 6.58e-04
                          10        20
                  ....*....|....*....|....*.
gi 1622922163 360 NFIQHRRIHTGEKPFKCGECGKSYNQ 385
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 549-571 1.05e-03

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 36.89  E-value: 1.05e-03
                          10        20
                  ....*....|....*....|...
gi 1622922163 549 HKCNECGKSFIQSAHLIQHQRIH 571
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
SUF4-like cd20908
N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), ...
 549-599 2.43e-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: 37.54  E-value: 2.43e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1622922163 549 HKCNECGKSFIQSAHLIQHQRIHTgekpFRCEECGKSYNQ----RVHLTQhqrVH 599
Cdd:cd20908     2 PWCYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTagglAVHCLQ---VH 49
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 577-599 3.25e-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: 3.25e-03
                          10        20
                  ....*....|....*....|...
gi 1622922163 577 FRCEECGKSYNQRVHLTQHQRVH 599
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 717-739 3.99e-03

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 35.35  E-value: 3.99e-03
                          10        20
                  ....*....|....*....|...
gi 1622922163 717 YQCDICGKAFGYSSDLIQHYRTH 739
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 374-396 4.62e-03

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 35.35  E-value: 4.62e-03
                          10        20
                  ....*....|....*....|...
gi 1622922163 374 FKCGECGKSYNQRVHLTQHQRVH 396
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
 
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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