NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1958762424|ref|XP_038961141|]
View 

zinc finger protein Gfi-1b isoform X1 [Rattus norvegicus]

Protein Classification

C2H2-type zinc finger protein( domain architecture ID 10603440)

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|30718982
SCOP:  4003583

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
zf-H2C2_2 pfam13465
Zinc-finger double domain;
295-320 6.29e-05

Zinc-finger double domain;


:

Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 39.66  E-value: 6.29e-05
                          10        20
                  ....*....|....*....|....*.
gi 1958762424 295 DMKKHTYIHTGEKPHKCQVCGKAFSQ 320
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
COG5048 super family cl34881
FOG: Zn-finger [General function prediction only];
263-340 1.27e-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: 40.45  E-value: 1.27e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958762424 263 KRSSTLSTHLLIHSDTRPYPCQFCGKRFHQKSDMKKHTYIHTGEKPHKCQV--CGKAFSQSSNLITHSRKHTGFKPFSCE 340
Cdd:COG5048    16 LSSTPKSTLKSLSNAPRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYsgCDKSFSRPLELSRHLRTHHNNPSDLNS 95
 
Name Accession Description Interval E-value
zf-H2C2_2 pfam13465
Zinc-finger double domain;
295-320 6.29e-05

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 39.66  E-value: 6.29e-05
                          10        20
                  ....*....|....*....|....*.
gi 1958762424 295 DMKKHTYIHTGEKPHKCQVCGKAFSQ 320
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
263-340 1.27e-03

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 40.45  E-value: 1.27e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958762424 263 KRSSTLSTHLLIHSDTRPYPCQFCGKRFHQKSDMKKHTYIHTGEKPHKCQV--CGKAFSQSSNLITHSRKHTGFKPFSCE 340
Cdd:COG5048    16 LSSTPKSTLKSLSNAPRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYsgCDKSFSRPLELSRHLRTHHNNPSDLNS 95
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 253-275 7.61e-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: 7.61e-03
                          10        20
                  ....*....|....*....|...
gi 1958762424 253 FECRMCGKAFKRSSTLSTHLLIH 275
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
 
Name Accession Description Interval E-value
zf-H2C2_2 pfam13465
Zinc-finger double domain;
295-320 6.29e-05

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 39.66  E-value: 6.29e-05
                          10        20
                  ....*....|....*....|....*.
gi 1958762424 295 DMKKHTYIHTGEKPHKCQVCGKAFSQ 320
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
263-340 1.27e-03

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 40.45  E-value: 1.27e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958762424 263 KRSSTLSTHLLIHSDTRPYPCQFCGKRFHQKSDMKKHTYIHTGEKPHKCQV--CGKAFSQSSNLITHSRKHTGFKPFSCE 340
Cdd:COG5048    16 LSSTPKSTLKSLSNAPRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYsgCDKSFSRPLELSRHLRTHHNNPSDLNS 95
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 309-331 1.55e-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: 1.55e-03
                          10        20
                  ....*....|....*....|...
gi 1958762424 309 HKCQVCGKAFSQSSNLITHSRKH 331
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 253-275 7.61e-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: 7.61e-03
                          10        20
                  ....*....|....*....|...
gi 1958762424 253 FECRMCGKAFKRSSTLSTHLLIH 275
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH