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Conserved domains on  [gi|1393630123|gb|AWN85514|]
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PRDM9, partial [Mus musculus domesticus]

Protein Classification

C2H2-type zinc finger protein( domain architecture ID 11472214)

Cys2His2 (C2H2)-type zinc finger protein may be involved in transcriptional regulation

CATH:  3.30.160.60
Gene Ontology:  GO:0008270|GO:0003677
PubMed:  11361095|22803940
SCOP:  4003583

Graphical summary

 Zoom to residue level

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List of domain hits

Name Accession Description Interval E-value
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
32-309 3.04e-10

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


:

Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 60.48  E-value: 3.04e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1393630123  32 KPYVCRECGRGFTQNSHLIQHQRTHTGEKPYVCRECGRG--FTAKSNLIQHQRTHTGEKPYvcRECGRGFTQKSDLIKHQ 109
Cdd:COG5048    32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDksFSRPLELSRHLRTHHNNPSD--LNSKSLPLSNSKASSSS 109
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1393630123 110 RTHTGEKP-YVCRECGRGFTQKSDLIKH----QRTHTGEKPY---------------------VCRECGRGFTAKSVLIQ 163
Cdd:COG5048   110 LSSSSSNSnDNNLLSSHSLPPSSRDPQLpdllSISNLRNNPLpgnnsssvntpqsnslhpplpANSLSKDPSSNLSLLIS 189
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1393630123 164 HQRTHTGEKPYVCRECGRgFTQNSHLIQHQRTHTGEKPYVCRECGRGFTQKSDLIKHQRTHTGEKPYVCRECGRGFTAKS 243
Cdd:COG5048   190 SNVSTSIPSSSENSPLSS-SYSIPSSSSDQNLENSSSSLPLTTNSQLSPKSLLSQSPSSLSSSDSSSSASESPRSSLPTA 268
                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1393630123 244 NLIQHQRTHTGE-------KPYVCRECGRGFTQKSNLIKHQRT--HTGE--KPYVCRE--CGWGFTQKSDLIQHQRTHT 309
Cdd:COG5048   269 SSQSSSPNESDSssekgfsLPIKSKQCNISFSRSSPLTRHLRSvnHSGEslKPFSCPYslCGKLFSRNDALKRHILLHT 347
 
Name Accession Description Interval E-value
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
32-309 3.04e-10

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 60.48  E-value: 3.04e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1393630123  32 KPYVCRECGRGFTQNSHLIQHQRTHTGEKPYVCRECGRG--FTAKSNLIQHQRTHTGEKPYvcRECGRGFTQKSDLIKHQ 109
Cdd:COG5048    32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDksFSRPLELSRHLRTHHNNPSD--LNSKSLPLSNSKASSSS 109
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1393630123 110 RTHTGEKP-YVCRECGRGFTQKSDLIKH----QRTHTGEKPY---------------------VCRECGRGFTAKSVLIQ 163
Cdd:COG5048   110 LSSSSSNSnDNNLLSSHSLPPSSRDPQLpdllSISNLRNNPLpgnnsssvntpqsnslhpplpANSLSKDPSSNLSLLIS 189
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1393630123 164 HQRTHTGEKPYVCRECGRgFTQNSHLIQHQRTHTGEKPYVCRECGRGFTQKSDLIKHQRTHTGEKPYVCRECGRGFTAKS 243
Cdd:COG5048   190 SNVSTSIPSSSENSPLSS-SYSIPSSSSDQNLENSSSSLPLTTNSQLSPKSLLSQSPSSLSSSDSSSSASESPRSSLPTA 268
                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1393630123 244 NLIQHQRTHTGE-------KPYVCRECGRGFTQKSNLIKHQRT--HTGE--KPYVCRE--CGWGFTQKSDLIQHQRTHT 309
Cdd:COG5048   269 SSQSSSPNESDSssekgfsLPIKSKQCNISFSRSSPLTRHLRSvnHSGEslKPFSCPYslCGKLFSRNDALKRHILLHT 347
zf-H2C2_2 pfam13465
Zinc-finger double domain;
76-101 2.88e-03

Zinc-finger double domain;


Pssm-ID: 433230 [Multi-domain]  Cd Length: 26  Bit Score: 34.64  E-value: 2.88e-03
                          10        20
                  ....*....|....*....|....*.
gi 1393630123  76 NLIQHQRTHTGEKPYVCRECGRGFTQ 101
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
 
Name Accession Description Interval E-value
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
32-309 3.04e-10

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 60.48  E-value: 3.04e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1393630123  32 KPYVCRECGRGFTQNSHLIQHQRTHTGEKPYVCRECGRG--FTAKSNLIQHQRTHTGEKPYvcRECGRGFTQKSDLIKHQ 109
Cdd:COG5048    32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDksFSRPLELSRHLRTHHNNPSD--LNSKSLPLSNSKASSSS 109
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1393630123 110 RTHTGEKP-YVCRECGRGFTQKSDLIKH----QRTHTGEKPY---------------------VCRECGRGFTAKSVLIQ 163
Cdd:COG5048   110 LSSSSSNSnDNNLLSSHSLPPSSRDPQLpdllSISNLRNNPLpgnnsssvntpqsnslhpplpANSLSKDPSSNLSLLIS 189
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1393630123 164 HQRTHTGEKPYVCRECGRgFTQNSHLIQHQRTHTGEKPYVCRECGRGFTQKSDLIKHQRTHTGEKPYVCRECGRGFTAKS 243
Cdd:COG5048   190 SNVSTSIPSSSENSPLSS-SYSIPSSSSDQNLENSSSSLPLTTNSQLSPKSLLSQSPSSLSSSDSSSSASESPRSSLPTA 268
                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1393630123 244 NLIQHQRTHTGE-------KPYVCRECGRGFTQKSNLIKHQRT--HTGE--KPYVCRE--CGWGFTQKSDLIQHQRTHT 309
Cdd:COG5048   269 SSQSSSPNESDSssekgfsLPIKSKQCNISFSRSSPLTRHLRSvnHSGEslKPFSCPYslCGKLFSRNDALKRHILLHT 347
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
4-265 3.78e-10

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 60.48  E-value: 3.78e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1393630123   4 ISSIERQCGQYFSDKSNVNEHQKTHTGEKPYVCRECGRgFTQNSHLIQHQRTHTGEKPYVCRECGRGFTAKSNLIQHQRT 83
Cdd:COG5048   170 PLPANSLSKDPSSNLSLLISSNVSTSIPSSSENSPLSS-SYSIPSSSSDQNLENSSSSLPLTTNSQLSPKSLLSQSPSSL 248
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1393630123  84 HTGEKPYVCRECGRGFTQKSDLIKHQRTHTGE-------KPYVCRECGRGFTQKSDLIKHQRT--HTGE--KPYVCRE-- 150
Cdd:COG5048   249 SSSDSSSSASESPRSSLPTASSQSSSPNESDSssekgfsLPIKSKQCNISFSRSSPLTRHLRSvnHSGEslKPFSCPYsl 328
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1393630123 151 CGRGFTAKSVLIQHQRTHTGEKPYVC--RECGRGFTQNSH-----LIQHQRTHTGEKPYVC--RECGRGFTQKSDLIKHQ 221
Cdd:COG5048   329 CGKLFSRNDALKRHILLHTSISPAKEklLNSSSKFSPLLNneppqSLQQYKDLKNDKKSETlsNSCIRNFKRDSNLSLHI 408
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 1393630123 222 RTHTGEKPYVCR--ECGRGFTAKSNLIQHQRTHTGEKPYVCRECGR 265
Cdd:COG5048   409 ITHLSFRPYNCKnpPCSKSFNRHYNLIPHKKIHTNHAPLLCSILKS 454
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
37-304 2.60e-09

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 57.78  E-value: 2.60e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1393630123  37 RECGRGFTQNSHLIQHQRTHTGEKPYVCRECGRgFTAKSNLIQHQRTHTGEKPYVCRECGRGFTQKSDLIKHQRTHTGEK 116
Cdd:COG5048   175 SLSKDPSSNLSLLISSNVSTSIPSSSENSPLSS-SYSIPSSSSDQNLENSSSSLPLTTNSQLSPKSLLSQSPSSLSSSDS 253
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1393630123 117 PYVCRECGRGFTQKSDLIKHQRTHTGE-------KPYVCRECGRGFTAKSVLIQHQRT--HTGE--KPYVCRE--CGRGF 183
Cdd:COG5048   254 SSSASESPRSSLPTASSQSSSPNESDSssekgfsLPIKSKQCNISFSRSSPLTRHLRSvnHSGEslKPFSCPYslCGKLF 333
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1393630123 184 TQNSHLIQHQRTHTGEKPYVCRECGRGFTQKSDLIK-------HQRTHTGEKPYVC--RECGRGFTAKSNLIQHQRTHTG 254
Cdd:COG5048   334 SRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLNNeppqslqQYKDLKNDKKSETlsNSCIRNFKRDSNLSLHIITHLS 413
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1393630123 255 EKPYVCR--ECGRGFTQKSNLIKHQRTHTGEKPYVCreCGWGFTQKSDLIQH 304
Cdd:COG5048   414 FRPYNCKnpPCSKSFNRHYNLIPHKKIHTNHAPLLC--SILKSFRRDLDLSN 463
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
161-229 2.53e-04

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 42.38  E-value: 2.53e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1393630123 161 LIQHQRTHTGE----KPYVCRECGRGFTQNSHLIQHQRTHTGEKPYVCRECGRGFTQK--SDLIKHQRTHTGEKP 229
Cdd:COG5048    17 SSTPKSTLKSLsnapRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSrpLELSRHLRTHHNNPS 91
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
181-257 4.30e-04

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 41.61  E-value: 4.30e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1393630123 181 RGFTQNSHL-IQHQRTHTGE----KPYVCRECGRGFTQKSDLIKHQRTHTGEKPYVCRECGRG--FTAKSNLIQHQRTHT 253
Cdd:COG5048     8 SSSSNNSVLsSTPKSTLKSLsnapRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDksFSRPLELSRHLRTHH 87

                  ....
gi 1393630123 254 GEKP 257
Cdd:COG5048    88 NNPS 91
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
100-173 9.71e-04

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 40.45  E-value: 9.71e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1393630123 100 TQKSDLIKHQRTHTGE----KPYVCRECGRGFTQKSDLIKHQRTHTGEKPYVCRECGRG--FTAKSVLIQHQRTHTGEKP 173
Cdd:COG5048    12 NNSVLSSTPKSTLKSLsnapRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDksFSRPLELSRHLRTHHNNPS 91
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
212-285 1.20e-03

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 40.06  E-value: 1.20e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1393630123 212 TQKSDLIKHQRTHTGE----KPYVCRECGRGFTAKSNLIQHQRTHTGEKPYVCRECGRGFTQK--SNLIKHQRTHTGEKP 285
Cdd:COG5048    12 NNSVLSSTPKSTLKSLsnapRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSrpLELSRHLRTHHNNPS 91
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
242-309 1.68e-03

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 39.68  E-value: 1.68e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1393630123 242 KSNLIQHQRTHTGE----KPYVCRECGRGFTQKSNLIKHQRTHTGEKPYVCRECGWGFTQK--SDLIQHQRTHT 309
Cdd:COG5048    14 SVLSSTPKSTLKSLsnapRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSrpLELSRHLRTHH 87
zf-H2C2_2 pfam13465
Zinc-finger double domain;
76-101 2.88e-03

Zinc-finger double domain;


Pssm-ID: 433230 [Multi-domain]  Cd Length: 26  Bit Score: 34.64  E-value: 2.88e-03
                          10        20
                  ....*....|....*....|....*.
gi 1393630123  76 NLIQHQRTHTGEKPYVCRECGRGFTQ 101
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
zf-H2C2_2 pfam13465
Zinc-finger double domain;
244-269 2.88e-03

Zinc-finger double domain;


Pssm-ID: 433230 [Multi-domain]  Cd Length: 26  Bit Score: 34.64  E-value: 2.88e-03
                          10        20
                  ....*....|....*....|....*.
gi 1393630123 244 NLIQHQRTHTGEKPYVCRECGRGFTQ 269
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
zf-H2C2_2 pfam13465
Zinc-finger double domain;
188-213 3.87e-03

Zinc-finger double domain;


Pssm-ID: 433230 [Multi-domain]  Cd Length: 26  Bit Score: 34.25  E-value: 3.87e-03
                          10        20
                  ....*....|....*....|....*.
gi 1393630123 188 HLIQHQRTHTGEKPYVCRECGRGFTQ 213
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
258-280 5.83e-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: 33.81  E-value: 5.83e-03
                          10        20
                  ....*....|....*....|...
gi 1393630123 258 YVCRECGRGFTQKSNLIKHQRTH 280
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
zf-H2C2_2 pfam13465
Zinc-finger double domain;
48-72 7.40e-03

Zinc-finger double domain;


Pssm-ID: 433230 [Multi-domain]  Cd Length: 26  Bit Score: 33.48  E-value: 7.40e-03
                          10        20
                  ....*....|....*....|....*
gi 1393630123  48 HLIQHQRTHTGEKPYVCRECGRGFT 72
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFK 25
zf-H2C2_2 pfam13465
Zinc-finger double domain;
161-185 7.85e-03

Zinc-finger double domain;


Pssm-ID: 433230 [Multi-domain]  Cd Length: 26  Bit Score: 33.48  E-value: 7.85e-03
                          10        20
                  ....*....|....*....|....*
gi 1393630123 161 LIQHQRTHTGEKPYVCRECGRGFTQ 185
Cdd:pfam13465   2 LKRHMRTHTGEKPYKCPECGKSFKS 26
zf-H2C2_2 pfam13465
Zinc-finger double domain;
104-129 8.17e-03

Zinc-finger double domain;


Pssm-ID: 433230 [Multi-domain]  Cd Length: 26  Bit Score: 33.48  E-value: 8.17e-03
                          10        20
                  ....*....|....*....|....*.
gi 1393630123 104 DLIKHQRTHTGEKPYVCRECGRGFTQ 129
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.20
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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