NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|672075408|ref|XP_008768139|]
View 

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

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

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
255-417 5.97e-07

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


:

Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 51.62  E-value: 5.97e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672075408 255 SYKCIKCSKVFSTPHGLEVHVR-RSHSG--TRPFAC--EMCGKTFGHAVSLEQHKAVHSQERSFDCKI--CGKSFKRSST 327
Cdd:COG5048  289 PIKSKQCNISFSRSSPLTRHLRsVNHSGesLKPFSCpySLCGKLFSRNDALKRHILLHTSISPAKEKLlnSSSKFSPLLN 368

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672075408 328 LSTHLLIH-----SDTRPYPCQYCGKRFHQKSD--MKKHTFIHTGEKPH--KCQVCGKAFSQSSNLITHSRKHTGFKPFG 398
Cdd:COG5048  369 NEPPQSLQqykdlKNDKKSETLSNSCIRNFKRDsnLSLHIITHLSFRPYncKNPPCSKSFNRHYNLIPHKKIHTNHAPLL 448

                        170
                 ....*....|....*....
gi 672075408 399 CDLCGKGFQRKVDLRRHRE 417
Cdd:COG5048  449 CSILKSFRRDLDLSNHGKD 467
 
Name Accession Description Interval E-value
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
255-417 5.97e-07

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 51.62  E-value: 5.97e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672075408 255 SYKCIKCSKVFSTPHGLEVHVR-RSHSG--TRPFAC--EMCGKTFGHAVSLEQHKAVHSQERSFDCKI--CGKSFKRSST 327
Cdd:COG5048  289 PIKSKQCNISFSRSSPLTRHLRsVNHSGesLKPFSCpySLCGKLFSRNDALKRHILLHTSISPAKEKLlnSSSKFSPLLN 368

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672075408 328 LSTHLLIH-----SDTRPYPCQYCGKRFHQKSD--MKKHTFIHTGEKPH--KCQVCGKAFSQSSNLITHSRKHTGFKPFG 398
Cdd:COG5048  369 NEPPQSLQqykdlKNDKKSETLSNSCIRNFKRDsnLSLHIITHLSFRPYncKNPPCSKSFNRHYNLIPHKKIHTNHAPLL 448

                        170
                 ....*....|....*....
gi 672075408 399 CDLCGKGFQRKVDLRRHRE 417
Cdd:COG5048  449 CSILKSFRRDLDLSNHGKD 467
zf-H2C2_2 pfam13465
Zinc-finger double domain;
355-380 1.17e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 38.89  E-value: 1.17e-04
                          10        20
                  ....*....|....*....|....*.
gi 672075408  355 DMKKHTFIHTGEKPHKCQVCGKAFSQ 380
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
SUF4-like cd20908
N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), ...
 283-338 3.23e-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: 36.38  E-value: 3.23e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 672075408 283 RPFaCEMCGKTFGHAVSLEQH-KAVHsqersFDCKICGKSFKRSSTLSTHLL-IHSDT 338
Cdd:cd20908    1 KPW-CYYCDREFDDEKILIQHqKAKH-----FKCHICHKKLYTAGGLAVHCLqVHKET 52
PHA00733 PHA00733
hypothetical protein
 284-332 3.31e-03

hypothetical protein


Pssm-ID: 177301  Cd Length: 128  Bit Score: 37.55  E-value: 3.31e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 672075408 284 PFACEMCGKTFGHAVSLEQHkaVHSQERSFDCKICGKSFKRSSTLSTHL 332
Cdd:PHA00733  73 PYVCPLCLMPFSSSVSLKQH--IRYTEHSKVCPVCGKEFRNTDSTLDHV 119
 
Name Accession Description Interval E-value
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
255-417 5.97e-07

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 51.62  E-value: 5.97e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672075408 255 SYKCIKCSKVFSTPHGLEVHVR-RSHSG--TRPFAC--EMCGKTFGHAVSLEQHKAVHSQERSFDCKI--CGKSFKRSST 327
Cdd:COG5048  289 PIKSKQCNISFSRSSPLTRHLRsVNHSGesLKPFSCpySLCGKLFSRNDALKRHILLHTSISPAKEKLlnSSSKFSPLLN 368

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672075408 328 LSTHLLIH-----SDTRPYPCQYCGKRFHQKSD--MKKHTFIHTGEKPH--KCQVCGKAFSQSSNLITHSRKHTGFKPFG 398
Cdd:COG5048  369 NEPPQSLQqykdlKNDKKSETLSNSCIRNFKRDsnLSLHIITHLSFRPYncKNPPCSKSFNRHYNLIPHKKIHTNHAPLL 448

                        170
                 ....*....|....*....
gi 672075408 399 CDLCGKGFQRKVDLRRHRE 417
Cdd:COG5048  449 CSILKSFRRDLDLSNHGKD 467
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
323-392 1.85e-06

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 50.08  E-value: 1.85e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 672075408 323 KRSSTLSTHLLIHSDTRPYPCQYCGKRFHQKSDMKKHTFIHTGEKPHKCQV--CGKAFSQSSNLITHSRKHT 392
Cdd:COG5048   16 LSSTPKSTLKSLSNAPRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYsgCDKSFSRPLELSRHLRTHH 87
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
268-402 8.91e-05

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 44.69  E-value: 8.91e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672075408 268 PHGLEVHVRRSHSGTRPFACEMCGKTfGHAVSlEQHKAVHSQERSFDCKICGKSFKRSSTLSTHLLIHSD-------TRP 340
Cdd:COG5048  212 PSSSSDQNLENSSSSLPLTTNSQLSP-KSLLS-QSPSSLSSSDSSSSASESPRSSLPTASSQSSSPNESDsssekgfSLP 289

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 672075408 341 YPCQYCGKRFHQKSDMKKH--TFIHTGE--KPHKC--QVCGKAFSQSSNLITHSRKHTGFKPFGCDLC 402
Cdd:COG5048  290 IKSKQCNISFSRSSPLTRHlrSVNHSGEslKPFSCpySLCGKLFSRNDALKRHILLHTSISPAKEKLL 357
zf-H2C2_2 pfam13465
Zinc-finger double domain;
355-380 1.17e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 38.89  E-value: 1.17e-04
                          10        20
                  ....*....|....*....|....*.
gi 672075408  355 DMKKHTFIHTGEKPHKCQVCGKAFSQ 380
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
SFP1 COG5189
Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division ...
 310-392 5.56e-04

Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning];


Pssm-ID: 227516 [Multi-domain]  Cd Length: 423  Bit Score: 42.01  E-value: 5.56e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672075408 310 ERSFDCKI--CGKSFKRSSTLSTHLLiHSdtrpypcqYCGKRFHQKSDMKKHTFIHTGEKPHKCQVCGKAFSQSSNLITH 387
Cdd:COG5189  347 GKPYKCPVegCNKKYKNQNGLKYHML-HG--------HQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYH 417


                 ....*
gi 672075408 388 sRKHT 392
Cdd:COG5189  418 -RKHS 421
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 369-391 9.60e-04

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: 9.60e-04
                          10        20
                  ....*....|....*....|...
gi 672075408  369 HKCQVCGKAFSQSSNLITHSRKH 391
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 313-335 1.18e-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: 1.18e-03
                          10        20
                  ....*....|....*....|...
gi 672075408  313 FDCKICGKSFKRSSTLSTHLLIH 335
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
SUF4-like cd20908
N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), ...
 283-338 3.23e-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: 36.38  E-value: 3.23e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 672075408 283 RPFaCEMCGKTFGHAVSLEQH-KAVHsqersFDCKICGKSFKRSSTLSTHLL-IHSDT 338
Cdd:cd20908    1 KPW-CYYCDREFDDEKILIQHqKAKH-----FKCHICHKKLYTAGGLAVHCLqVHKET 52
PHA00733 PHA00733
hypothetical protein
 284-332 3.31e-03

hypothetical protein


Pssm-ID: 177301  Cd Length: 128  Bit Score: 37.55  E-value: 3.31e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 672075408 284 PFACEMCGKTFGHAVSLEQHkaVHSQERSFDCKICGKSFKRSSTLSTHL 332
Cdd:PHA00733  73 PYVCPLCLMPFSSSVSLKQH--IRYTEHSKVCPVCGKEFRNTDSTLDHV 119
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
367-420 4.15e-03

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 39.29  E-value: 4.15e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 672075408 367 KPHKCQVCGKAFSQSSNLITHSRKHTGFKPFGC--DLCGKGFQRKVDLRRHRETQH 420
Cdd:COG5048   32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCsySGCDKSFSRPLELSRHLRTHH 87
PHA00733 PHA00733
hypothetical protein
 340-391 9.51e-03

hypothetical protein


Pssm-ID: 177301  Cd Length: 128  Bit Score: 36.01  E-value: 9.51e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 672075408 340 PYPCQYCGKRFHQKSDMKKHtfIHTGEKPHKCQVCGKAFSQSSNLITH-SRKH 391
Cdd:PHA00733  73 PYVCPLCLMPFSSSVSLKQH--IRYTEHSKVCPVCGKEFRNTDSTLDHvCKKH 123
 
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