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Conserved domains on  [gi|2064556022|gb|QXI90119|]
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PRDM9, partial [Camelus bactrianus]

Protein Classification

C2H2-type zinc finger protein( domain architecture ID 13826074)

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

CATH:  3.30.160.60
Gene Ontology:  GO:0008270|GO:0003677|GO:0003700
PubMed:  11361095|22803940|30718982|10940247|12665246|11179890
SCOP:  4003583

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
zf-H2C2_2 pfam13465
Zinc-finger double domain;
6-31 1.57e-03

Zinc-finger double domain;


:

Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 34.65  E-value: 1.57e-03
                          10        20
                  ....*....|....*....|....*.
gi 2064556022   6 ALITHKRSHTGEKPFLCTECGQAFNH 31
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
COG5048 super family cl34881
FOG: Zn-finger [General function prediction only];
18-178 1.87e-03

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


The actual alignment was detected with superfamily member COG5048:

Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 38.52  E-value: 1.87e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064556022  18 KPFLCTECGQAFNHKSDLVTHK--MAHSGE--KPFVCqefkprhtpedPLMGEALCFSDKSNLTTHQRTHSGEKPYMCRE 93
Cdd:COG5048   288 LPIKSKQCNISFSRSSPLTRHLrsVNHSGEslKPFSC-----------PYSLCGKLFSRNDALKRHILLHTSISPAKEKL 356

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064556022  94 CGRGF--------RRKSTLTAHQRTHSGETFLC--KECGRDFRQKSHLISHQRTH--SGEKAYVCTECGQGFSQKANLVR 161
Cdd:COG5048   357 LNSSSkfspllnnEPPQSLQQYKDLKNDKKSETlsNSCIRNFKRDSNLSLHIITHlsFRPYNCKNPPCSKSFNRHYNLIP 436

                         170
                  ....*....|....*..
gi 2064556022 162 HKLAHSREKPSVLQPEG 178
Cdd:COG5048   437 HKKIHTNHAPLLCSILK 453
 
Name Accession Description Interval E-value
zf-H2C2_2 pfam13465
Zinc-finger double domain;
6-31 1.57e-03

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 34.65  E-value: 1.57e-03
                          10        20
                  ....*....|....*....|....*.
gi 2064556022   6 ALITHKRSHTGEKPFLCTECGQAFNH 31
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
18-178 1.87e-03

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 38.52  E-value: 1.87e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064556022  18 KPFLCTECGQAFNHKSDLVTHK--MAHSGE--KPFVCqefkprhtpedPLMGEALCFSDKSNLTTHQRTHSGEKPYMCRE 93
Cdd:COG5048   288 LPIKSKQCNISFSRSSPLTRHLrsVNHSGEslKPFSC-----------PYSLCGKLFSRNDALKRHILLHTSISPAKEKL 356

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064556022  94 CGRGF--------RRKSTLTAHQRTHSGETFLC--KECGRDFRQKSHLISHQRTH--SGEKAYVCTECGQGFSQKANLVR 161
Cdd:COG5048   357 LNSSSkfspllnnEPPQSLQQYKDLKNDKKSETlsNSCIRNFKRDSNLSLHIITHlsFRPYNCKNPPCSKSFNRHYNLIP 436

                         170
                  ....*....|....*..
gi 2064556022 162 HKLAHSREKPSVLQPEG 178
Cdd:COG5048   437 HKKIHTNHAPLLCSILK 453
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 89-111 2.34e-03

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


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 34.20  E-value: 2.34e-03
                          10        20
                  ....*....|....*....|...
gi 2064556022  89 YMCRECGRGFRRKSTLTAHQRTH 111
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
 
Name Accession Description Interval E-value
zf-H2C2_2 pfam13465
Zinc-finger double domain;
6-31 1.57e-03

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 34.65  E-value: 1.57e-03
                          10        20
                  ....*....|....*....|....*.
gi 2064556022   6 ALITHKRSHTGEKPFLCTECGQAFNH 31
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
18-178 1.87e-03

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 38.52  E-value: 1.87e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064556022  18 KPFLCTECGQAFNHKSDLVTHK--MAHSGE--KPFVCqefkprhtpedPLMGEALCFSDKSNLTTHQRTHSGEKPYMCRE 93
Cdd:COG5048   288 LPIKSKQCNISFSRSSPLTRHLrsVNHSGEslKPFSC-----------PYSLCGKLFSRNDALKRHILLHTSISPAKEKL 356

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2064556022  94 CGRGF--------RRKSTLTAHQRTHSGETFLC--KECGRDFRQKSHLISHQRTH--SGEKAYVCTECGQGFSQKANLVR 161
Cdd:COG5048   357 LNSSSkfspllnnEPPQSLQQYKDLKNDKKSETlsNSCIRNFKRDSNLSLHIITHlsFRPYNCKNPPCSKSFNRHYNLIP 436

                         170
                  ....*....|....*..
gi 2064556022 162 HKLAHSREKPSVLQPEG 178
Cdd:COG5048   437 HKKIHTNHAPLLCSILK 453
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 89-111 2.34e-03

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


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 34.20  E-value: 2.34e-03
                          10        20
                  ....*....|....*....|...
gi 2064556022  89 YMCRECGRGFRRKSTLTAHQRTH 111
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
zf-H2C2_2 pfam13465
Zinc-finger double domain;
75-100 3.12e-03

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 33.88  E-value: 3.12e-03
                          10        20
                  ....*....|....*....|....*.
gi 2064556022  75 NLTTHQRTHSGEKPYMCRECGRGFRR 100
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 116-138 4.21e-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: 33.43  E-value: 4.21e-03
                          10        20
                  ....*....|....*....|...
gi 2064556022 116 FLCKECGRDFRQKSHLISHQRTH 138
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
114-180 6.59e-03

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 36.60  E-value: 6.59e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2064556022 114 ETFLCKECGRDFRQKSHLISHQRTHSGEKAYVCTECGQGFSQK--ANLVRHKLAHSREKPSVLQPEGGP 180
Cdd:COG5048    32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSrpLELSRHLRTHHNNPSDLNSKSLPL 100
 
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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