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Conserved domains on  [gi|17566846|ref|NP_505492|]
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CRC domain-containing protein [Caenorhabditis elegans]

Protein Classification

APOBEC family cytidine deaminase( domain architecture ID 12087381)

APOBEC (apolipoprotein B editing catalytic subunit) family cytidine deaminase catalyzes the deamination of cytidine to uridine

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
APOBEC_N pfam08210
APOBEC-like N-terminal domain; A mechanism of generating protein diversity is mRNA editing. ...
 157-348 4.76e-37

APOBEC-like N-terminal domain; A mechanism of generating protein diversity is mRNA editing. Members of this family are C-to-U editing enzymes. The N-terminal domain of APOBEC-1 like proteins is the catalytic domain, while the C-terminal domain is a pseudocatalyitc domain. More specifically, the catalytic domain is a zinc dependent deaminases domain and is essential for cytidine deamination.APOBEC-3 like members contain two copies of this domain. RNA editing by APOBEC-1 requires homodimerization and this complex interacts with RNA binding proteins to from the editosome (and references therein). This family also includes the functionally homologous activation induced deaminase (AID), which is essential for the development of antibody diversity in B lymphocytes, and the sea lamprey PmCDA1 and PmCDA2, which are predicted to play an AID-like role in the adaptive immune response of jawless vertebrates. Divergent members of this family are present in various eukaryotes such as Nematostella, C. elegans, Micromonas and Emiliania, and prokaryotes such as Wolbachia and Pseudomonas brassicacearum.


:

Pssm-ID: 462396 [Multi-domain]  Cd Length: 170  Bit Score: 134.03  E-value: 4.76e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17566846   157 VPKHVQNC-FLEHKHESSglIVTLIGEDYVY-----RGDFYHESKGEPHVEEQLVAAIYDLIsKYTVDLHEIQIFVSKSP 230
Cdd:pfam08210   1 FFFHFKNLpYASGRHETY--LCYEVKRDSGGlvvedKGYLRNQAASSLHAEERFLRWIHDLA-LDPGSNYEVTWYVSWSP 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17566846   231 CFHqdcepkcevvdecksnkaCAKLLGLLLSKVRKeikkVDVKMTVKFLYPHLNRgDLYTKQGILCMLQAGIKVEPLLMK 310
Cdd:pfam08210  78 CNE------------------CASELAAFLSKHPN----VRLRIFVSRLYYWEEP-DYWNREGLRSLAQAGVQLRPMSYK 134

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 17566846   311 DWCSImdWSPHVDHKGDYLQLWNNHHLDKAVAQSQLFI 348
Cdd:pfam08210 135 DFEYC--WNNFVDHDGEPFKPWDGLHENSVYLARKLQE 170
 
Name Accession Description Interval E-value
APOBEC_N pfam08210
APOBEC-like N-terminal domain; A mechanism of generating protein diversity is mRNA editing. ...
 157-348 4.76e-37

APOBEC-like N-terminal domain; A mechanism of generating protein diversity is mRNA editing. Members of this family are C-to-U editing enzymes. The N-terminal domain of APOBEC-1 like proteins is the catalytic domain, while the C-terminal domain is a pseudocatalyitc domain. More specifically, the catalytic domain is a zinc dependent deaminases domain and is essential for cytidine deamination.APOBEC-3 like members contain two copies of this domain. RNA editing by APOBEC-1 requires homodimerization and this complex interacts with RNA binding proteins to from the editosome (and references therein). This family also includes the functionally homologous activation induced deaminase (AID), which is essential for the development of antibody diversity in B lymphocytes, and the sea lamprey PmCDA1 and PmCDA2, which are predicted to play an AID-like role in the adaptive immune response of jawless vertebrates. Divergent members of this family are present in various eukaryotes such as Nematostella, C. elegans, Micromonas and Emiliania, and prokaryotes such as Wolbachia and Pseudomonas brassicacearum.


Pssm-ID: 462396 [Multi-domain]  Cd Length: 170  Bit Score: 134.03  E-value: 4.76e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17566846   157 VPKHVQNC-FLEHKHESSglIVTLIGEDYVY-----RGDFYHESKGEPHVEEQLVAAIYDLIsKYTVDLHEIQIFVSKSP 230
Cdd:pfam08210   1 FFFHFKNLpYASGRHETY--LCYEVKRDSGGlvvedKGYLRNQAASSLHAEERFLRWIHDLA-LDPGSNYEVTWYVSWSP 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17566846   231 CFHqdcepkcevvdecksnkaCAKLLGLLLSKVRKeikkVDVKMTVKFLYPHLNRgDLYTKQGILCMLQAGIKVEPLLMK 310
Cdd:pfam08210  78 CNE------------------CASELAAFLSKHPN----VRLRIFVSRLYYWEEP-DYWNREGLRSLAQAGVQLRPMSYK 134

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 17566846   311 DWCSImdWSPHVDHKGDYLQLWNNHHLDKAVAQSQLFI 348
Cdd:pfam08210 135 DFEYC--WNNFVDHDGEPFKPWDGLHENSVYLARKLQE 170
 
Name Accession Description Interval E-value
APOBEC_N pfam08210
APOBEC-like N-terminal domain; A mechanism of generating protein diversity is mRNA editing. ...
 157-348 4.76e-37

APOBEC-like N-terminal domain; A mechanism of generating protein diversity is mRNA editing. Members of this family are C-to-U editing enzymes. The N-terminal domain of APOBEC-1 like proteins is the catalytic domain, while the C-terminal domain is a pseudocatalyitc domain. More specifically, the catalytic domain is a zinc dependent deaminases domain and is essential for cytidine deamination.APOBEC-3 like members contain two copies of this domain. RNA editing by APOBEC-1 requires homodimerization and this complex interacts with RNA binding proteins to from the editosome (and references therein). This family also includes the functionally homologous activation induced deaminase (AID), which is essential for the development of antibody diversity in B lymphocytes, and the sea lamprey PmCDA1 and PmCDA2, which are predicted to play an AID-like role in the adaptive immune response of jawless vertebrates. Divergent members of this family are present in various eukaryotes such as Nematostella, C. elegans, Micromonas and Emiliania, and prokaryotes such as Wolbachia and Pseudomonas brassicacearum.


Pssm-ID: 462396 [Multi-domain]  Cd Length: 170  Bit Score: 134.03  E-value: 4.76e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17566846   157 VPKHVQNC-FLEHKHESSglIVTLIGEDYVY-----RGDFYHESKGEPHVEEQLVAAIYDLIsKYTVDLHEIQIFVSKSP 230
Cdd:pfam08210   1 FFFHFKNLpYASGRHETY--LCYEVKRDSGGlvvedKGYLRNQAASSLHAEERFLRWIHDLA-LDPGSNYEVTWYVSWSP 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17566846   231 CFHqdcepkcevvdecksnkaCAKLLGLLLSKVRKeikkVDVKMTVKFLYPHLNRgDLYTKQGILCMLQAGIKVEPLLMK 310
Cdd:pfam08210  78 CNE------------------CASELAAFLSKHPN----VRLRIFVSRLYYWEEP-DYWNREGLRSLAQAGVQLRPMSYK 134

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 17566846   311 DWCSImdWSPHVDHKGDYLQLWNNHHLDKAVAQSQLFI 348
Cdd:pfam08210 135 DFEYC--WNNFVDHDGEPFKPWDGLHENSVYLARKLQE 170
 
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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