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Conserved domains on  [gi|41053607|ref|NP_956779|]
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zinc finger CCCH-type with G patch domain-containing protein [Danio rerio]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Tudor_ZGPAT cd20384
Tudor domain found in zinc finger CCCH-type with G patch domain-containing protein (ZGPAT) and ...
 204-258 1.28e-18

Tudor domain found in zinc finger CCCH-type with G patch domain-containing protein (ZGPAT) and similar proteins; ZGPAT, also called ZIP, G patch domain-containing protein 6 (GPATC6), GPATCH6, zinc finger CCCH domain-containing protein 9 (ZC3HDC9), ZC3H9, or zinc finger and G patch domain-containing protein, is a transcription repressor that specifically binds the 5'-GGAG[GA]A[GA]A-3' consensus sequence. It represses transcription by recruiting the chromatin multiprotein complex NuRD to target promoters. It contains one Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


:

Pssm-ID: 410455  Cd Length: 55  Bit Score: 79.58  E-value: 1.28e-18
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 41053607 204 DISNMESGSACLAKHEDGIWYPARISEI-EGGFYTVKFDSlLLKEAVLEADGIIPP 258
Cdd:cd20384   1 DFSSLKEGSRCLAKYDDGLWYPATVTDIdEDGKYTVKFDS-YGEVAVVELDDILPL 55
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
 308-351 6.63e-11

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.


:

Pssm-ID: 396249 [Multi-domain]  Cd Length: 45  Bit Score: 57.13  E-value: 6.63e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 41053607   308 TRGIGSKLLMKMGYELGKGLGKTLSGRVEPVQAVVLPKGHSLDI 351
Cdd:pfam01585   1 TSNIGFKLLQKMGWKEGQGLGKNEQGIAEPIEAKIKKDRRGLGA 44
zf-CCCH_4 pfam18044
CCCH-type zinc finger; This short zinc binding domain has the pattern of three cysteines and ...
 168-188 2.45e-05

CCCH-type zinc finger; This short zinc binding domain has the pattern of three cysteines and one histidine to coordinate the zinc ion. This domain is found in a wide variety of proteins such as E3 ligases.


:

Pssm-ID: 465626  Cd Length: 22  Bit Score: 41.03  E-value: 2.45e-05
                          10        20
                  ....*....|....*....|.
gi 41053607   168 KPCGFYLEGKCRFMDNCRYSH 188
Cdd:pfam18044   1 RLCRYFQKGGCRYGDNCRFSH 21
 
Name Accession Description Interval E-value
Tudor_ZGPAT cd20384
Tudor domain found in zinc finger CCCH-type with G patch domain-containing protein (ZGPAT) and ...
 204-258 1.28e-18

Tudor domain found in zinc finger CCCH-type with G patch domain-containing protein (ZGPAT) and similar proteins; ZGPAT, also called ZIP, G patch domain-containing protein 6 (GPATC6), GPATCH6, zinc finger CCCH domain-containing protein 9 (ZC3HDC9), ZC3H9, or zinc finger and G patch domain-containing protein, is a transcription repressor that specifically binds the 5'-GGAG[GA]A[GA]A-3' consensus sequence. It represses transcription by recruiting the chromatin multiprotein complex NuRD to target promoters. It contains one Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410455  Cd Length: 55  Bit Score: 79.58  E-value: 1.28e-18
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 41053607 204 DISNMESGSACLAKHEDGIWYPARISEI-EGGFYTVKFDSlLLKEAVLEADGIIPP 258
Cdd:cd20384   1 DFSSLKEGSRCLAKYDDGLWYPATVTDIdEDGKYTVKFDS-YGEVAVVELDDILPL 55
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
 308-351 6.63e-11

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.


Pssm-ID: 396249 [Multi-domain]  Cd Length: 45  Bit Score: 57.13  E-value: 6.63e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 41053607   308 TRGIGSKLLMKMGYELGKGLGKTLSGRVEPVQAVVLPKGHSLDI 351
Cdd:pfam01585   1 TSNIGFKLLQKMGWKEGQGLGKNEQGIAEPIEAKIKKDRRGLGA 44
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
 307-351 3.88e-09

glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins.


Pssm-ID: 197727 [Multi-domain]  Cd Length: 47  Bit Score: 52.16  E-value: 3.88e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 41053607    307 HTRGIGSKLLMKMGYELGKGLGKTLSGRVEPVQAVVLPKGHSLDI 351
Cdd:smart00443   2 STSNIGAKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDRKGLGA 46
TUDOR smart00333
Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in ...
 211-241 1.76e-05

Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).


Pssm-ID: 197660  Cd Length: 57  Bit Score: 42.26  E-value: 1.76e-05
                           10        20        30
                   ....*....|....*....|....*....|..
gi 41053607    211 GSACLAKHEDGIWYPARISEIEG-GFYTVKFD 241
Cdd:smart00333   6 GDKVAARWEDGEWYRARIVKVDGeQLYEVFFI 37
zf-CCCH_4 pfam18044
CCCH-type zinc finger; This short zinc binding domain has the pattern of three cysteines and ...
 168-188 2.45e-05

CCCH-type zinc finger; This short zinc binding domain has the pattern of three cysteines and one histidine to coordinate the zinc ion. This domain is found in a wide variety of proteins such as E3 ligases.


Pssm-ID: 465626  Cd Length: 22  Bit Score: 41.03  E-value: 2.45e-05
                          10        20
                  ....*....|....*....|.
gi 41053607   168 KPCGFYLEGKCRFMDNCRYSH 188
Cdd:pfam18044   1 RLCRYFQKGGCRYGDNCRFSH 21
ZnF_C3H1 smart00356
zinc finger;
167-190 4.16e-04

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 37.61  E-value: 4.16e-04
                           10        20
                   ....*....|....*....|....
gi 41053607    167 MKPCGFYLEGKCRFMDNCRYSHGE 190
Cdd:smart00356   4 TELCKFFKRGYCPRGDRCKFAHPL 27
 
Name Accession Description Interval E-value
Tudor_ZGPAT cd20384
Tudor domain found in zinc finger CCCH-type with G patch domain-containing protein (ZGPAT) and ...
 204-258 1.28e-18

Tudor domain found in zinc finger CCCH-type with G patch domain-containing protein (ZGPAT) and similar proteins; ZGPAT, also called ZIP, G patch domain-containing protein 6 (GPATC6), GPATCH6, zinc finger CCCH domain-containing protein 9 (ZC3HDC9), ZC3H9, or zinc finger and G patch domain-containing protein, is a transcription repressor that specifically binds the 5'-GGAG[GA]A[GA]A-3' consensus sequence. It represses transcription by recruiting the chromatin multiprotein complex NuRD to target promoters. It contains one Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410455  Cd Length: 55  Bit Score: 79.58  E-value: 1.28e-18
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 41053607 204 DISNMESGSACLAKHEDGIWYPARISEI-EGGFYTVKFDSlLLKEAVLEADGIIPP 258
Cdd:cd20384   1 DFSSLKEGSRCLAKYDDGLWYPATVTDIdEDGKYTVKFDS-YGEVAVVELDDILPL 55
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
 308-351 6.63e-11

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.


Pssm-ID: 396249 [Multi-domain]  Cd Length: 45  Bit Score: 57.13  E-value: 6.63e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 41053607   308 TRGIGSKLLMKMGYELGKGLGKTLSGRVEPVQAVVLPKGHSLDI 351
Cdd:pfam01585   1 TSNIGFKLLQKMGWKEGQGLGKNEQGIAEPIEAKIKKDRRGLGA 44
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
 307-351 3.88e-09

glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins.


Pssm-ID: 197727 [Multi-domain]  Cd Length: 47  Bit Score: 52.16  E-value: 3.88e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 41053607    307 HTRGIGSKLLMKMGYELGKGLGKTLSGRVEPVQAVVLPKGHSLDI 351
Cdd:smart00443   2 STSNIGAKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDRKGLGA 46
Tudor_SF cd04508
Tudor domain superfamily; The Tudor domain is a conserved structural domain, originally ...
 211-241 1.09e-05

Tudor domain superfamily; The Tudor domain is a conserved structural domain, originally identified in the Tudor protein of Drosophila, that adopts a beta-barrel-like core structure containing four short beta-strands followed by an alpha-helical region. It binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. Tudor domain-containing proteins may mediate protein-protein interactions required for various DNA-templated biological processes, such as RNA metabolism, as well as histone modification and the DNA damage response. Members of this superfamily contain one or more copies of the Tudor domain.


Pssm-ID: 410449 [Multi-domain]  Cd Length: 47  Bit Score: 42.57  E-value: 1.09e-05
                        10        20        30
                ....*....|....*....|....*....|...
gi 41053607 211 GSACLAKH-EDGIWYPARISEI-EGGFYTVKFD 241
Cdd:cd04508   1 GDRVEAKWsDDGQWYPATVVAVnDDGKYTVLFD 33
TUDOR smart00333
Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in ...
 211-241 1.76e-05

Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).


Pssm-ID: 197660  Cd Length: 57  Bit Score: 42.26  E-value: 1.76e-05
                           10        20        30
                   ....*....|....*....|....*....|..
gi 41053607    211 GSACLAKHEDGIWYPARISEIEG-GFYTVKFD 241
Cdd:smart00333   6 GDKVAARWEDGEWYRARIVKVDGeQLYEVFFI 37
zf-CCCH_4 pfam18044
CCCH-type zinc finger; This short zinc binding domain has the pattern of three cysteines and ...
 168-188 2.45e-05

CCCH-type zinc finger; This short zinc binding domain has the pattern of three cysteines and one histidine to coordinate the zinc ion. This domain is found in a wide variety of proteins such as E3 ligases.


Pssm-ID: 465626  Cd Length: 22  Bit Score: 41.03  E-value: 2.45e-05
                          10        20
                  ....*....|....*....|.
gi 41053607   168 KPCGFYLEGKCRFMDNCRYSH 188
Cdd:pfam18044   1 RLCRYFQKGGCRYGDNCRFSH 21
Tudor_SMN_SPF30-like cd21182
Tudor domain found in survival motor neuron protein (SMN), motor neuron-related-splicing ...
 211-241 2.20e-04

Tudor domain found in survival motor neuron protein (SMN), motor neuron-related-splicing factor 30 (SPF30), and similar proteins; This group contains SMN, SPF30, Tudor domain-containing protein 3 (TDRD3), DNA excision repair protein ERCC-6-like 2 (ERCC6L2), and similar proteins. SMN, also called component of gems 1, or Gemin-1, is part of a multimeric SMN complex that includes spliceosomal Sm core proteins and plays a catalyst role in the assembly of small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. SPF30, also called 30 kDa splicing factor SMNrp, SMN-related protein, or survival motor neuron domain-containing protein 1 (SMNDC1), is an essential pre-mRNA splicing factor required for assembly of the U4/U5/U6 tri-small nuclear ribonucleoprotein into the spliceosome. TDRD3 is a scaffolding protein that specifically recognizes and binds dimethylarginine-containing proteins. ERCC6L2, also called DNA repair and recombination protein RAD26-like (RAD26L), may be involved in early DNA damage response. It regulates RNA Pol II-mediated transcription via its interaction with DNA-dependent protein kinase (DNA-PK) to resolve R loops and minimize transcription-associated genome instability. Members of this group contain a single Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410549  Cd Length: 50  Bit Score: 38.77  E-value: 2.20e-04
                        10        20        30
                ....*....|....*....|....*....|....
gi 41053607 211 GSACLAKH-EDGIWYPARISEI--EGGFYTVKFD 241
Cdd:cd21182   1 GDKCLAPYsDDGKYYEATIEEIteESDTATVVFD 34
zf_CCCH_4 pfam18345
Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch ...
 170-188 2.42e-04

Zinc finger domain; This is a zinc finger domain found in Zinc finger CCCH-type with G patch domain-containing proteins such as ZIP. Functional studies indicate that ZIP specifically targets EGFR and represses its transcription, and that the zinc finger and the coiled-coil domains are central to that process.


Pssm-ID: 465719 [Multi-domain]  Cd Length: 19  Bit Score: 38.17  E-value: 2.42e-04
                          10
                  ....*....|....*....
gi 41053607   170 CGFYLEGKCRFMDNCRYSH 188
Cdd:pfam18345   1 CKFFLKGRCRYGDKCRFAH 19
ZnF_C3H1 smart00356
zinc finger;
167-190 4.16e-04

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 37.61  E-value: 4.16e-04
                           10        20
                   ....*....|....*....|....
gi 41053607    167 MKPCGFYLEGKCRFMDNCRYSHGE 190
Cdd:smart00356   4 TELCKFFKRGYCPRGDRCKFAHPL 27
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
165-190 2.50e-03

Zinc finger C-x8-C-x5-C-x3-H type (and similar);


Pssm-ID: 459885 [Multi-domain]  Cd Length: 27  Bit Score: 35.25  E-value: 2.50e-03
                          10        20
                  ....*....|....*....|....*..
gi 41053607   165 KSMKPCGFYLE-GKCRFMDNCRYSHGE 190
Cdd:pfam00642   1 YKTELCRFFLRtGYCKYGDRCKFAHGQ 27
 
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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