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Conserved domains on  [gi|44888831|ref|NP_982279|]
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putative C-

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. ...
 47-202 6.65e-43

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: 146.74  E-value: 6.65e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 44888831    47 EFCQIFGFPYGTTFPQTKhlTFYELKTSSGSLV--QKGHASSCTGNYIHPESMLFEmngYLDSAIYNNDSIRHIILYSNN 124
Cdd:pfam08210   1 FFFHFKNLPYASGRHETY--LCYEVKRDSGGLVveDKGYLRNQAASSLHAEERFLR---WIHDLALDPGSNYEVTWYVSW 75

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 44888831   125 SPCNEanhcCISKMYNFLITYPGITLSIYFSQLYHTEMDfpaSAWNREALRSLASLwpRVVLSPISGGIWHSVLHSFI 202
Cdd:pfam08210  76 SPCNE----CASELAAFLSKHPNVRLRIFVSRLYYWEEP---DYWNREGLRSLAQA--GVQLRPMSYKDFEYCWNNFV 144
 
Name Accession Description Interval E-value
APOBEC_N pfam08210
APOBEC-like N-terminal domain; A mechanism of generating protein diversity is mRNA editing. ...
 47-202 6.65e-43

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: 146.74  E-value: 6.65e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 44888831    47 EFCQIFGFPYGTTFPQTKhlTFYELKTSSGSLV--QKGHASSCTGNYIHPESMLFEmngYLDSAIYNNDSIRHIILYSNN 124
Cdd:pfam08210   1 FFFHFKNLPYASGRHETY--LCYEVKRDSGGLVveDKGYLRNQAASSLHAEERFLR---WIHDLALDPGSNYEVTWYVSW 75

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 44888831   125 SPCNEanhcCISKMYNFLITYPGITLSIYFSQLYHTEMDfpaSAWNREALRSLASLwpRVVLSPISGGIWHSVLHSFI 202
Cdd:pfam08210  76 SPCNE----CASELAAFLSKHPNVRLRIFVSRLYYWEEP---DYWNREGLRSLAQA--GVQLRPMSYKDFEYCWNNFV 144
 
Name Accession Description Interval E-value
APOBEC_N pfam08210
APOBEC-like N-terminal domain; A mechanism of generating protein diversity is mRNA editing. ...
 47-202 6.65e-43

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: 146.74  E-value: 6.65e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 44888831    47 EFCQIFGFPYGTTFPQTKhlTFYELKTSSGSLV--QKGHASSCTGNYIHPESMLFEmngYLDSAIYNNDSIRHIILYSNN 124
Cdd:pfam08210   1 FFFHFKNLPYASGRHETY--LCYEVKRDSGGLVveDKGYLRNQAASSLHAEERFLR---WIHDLALDPGSNYEVTWYVSW 75

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 44888831   125 SPCNEanhcCISKMYNFLITYPGITLSIYFSQLYHTEMDfpaSAWNREALRSLASLwpRVVLSPISGGIWHSVLHSFI 202
Cdd:pfam08210  76 SPCNE----CASELAAFLSKHPNVRLRIFVSRLYYWEEP---DYWNREGLRSLAQA--GVQLRPMSYKDFEYCWNNFV 144
NAD1 pfam18778
Novel AID APOBEC clade 1; A distinct family of AID/APOBEC-like deaminases found in ray-finned ...
 50-196 7.83e-35

Novel AID APOBEC clade 1; A distinct family of AID/APOBEC-like deaminases found in ray-finned fishes, the coelacanth, amphibians, lizards, and marsupials.


Pssm-ID: 465865 [Multi-domain]  Cd Length: 175  Bit Score: 125.85  E-value: 7.83e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 44888831    50 QIFGFPYG---TTFPQTKHLTFYELKTSSGSLVQKGHASSCTgNYIHPESMLFemNGYLDSAIYNNDSIRHIILYSNNSP 126
Cdd:pfam18778   6 ETFKFQFKnveYASGRNKTLLCYEVKRGNSSSLWRGHLRNEN-SGCHAEICFL--RWFSSWRLFDPSQCYTITWYLSWSP 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 44888831   127 CNEanhcCISKMYNFLITYPGITLSIYFSQLYHTEMDfpasaWNREALRSLASlWPrVVLSPISGG----IWHS 196
Cdd:pfam18778  83 CPS----CAAKLAEFLKAHPNVTLTIFAARLYYFEDP-----WNQEGLRSLAS-AG-VTLSIMDYSdfeyCWEN 145
SNAD4 pfam18750
Secreted Novel AID/APOBEC-like Deaminase 4; A family of secreted AID/APOBEC like deaminases ...
 69-184 2.34e-21

Secreted Novel AID/APOBEC-like Deaminase 4; A family of secreted AID/APOBEC like deaminases found only in sponges that often shows lineage-specific expansions.


Pssm-ID: 465854 [Multi-domain]  Cd Length: 116  Bit Score: 88.09  E-value: 2.34e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 44888831    69 YELKTSSGSLV-QKGHASSCTgnYIHPESMLFEM--NGYLDSAIYnndsiRHIILYSNNSPCNEanhcCISKMYNFLITY 145
Cdd:pfam18750   1 YEIKWGNGSKIwQRGYLSNEH--EQHAEICFLENirSRELDPSQR-----YRVTWYLSWSPCPE----CAQKIAEFLAEH 69

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 44888831   146 PGITLSIYFSQLYHTEmdfpasAWNREALRSLASLWPRV 184
Cdd:pfam18750  70 PNVTLTIFAARLYHWD------EDNRQGLRSLAQAGVTL 102
APOBEC4 pfam18775
APOBEC4; A member of the AID/APOBEC family of cytosine deaminases. The biological function of ...
 118-202 2.83e-21

APOBEC4; A member of the AID/APOBEC family of cytosine deaminases. The biological function of APOBEC4 is poorly understood. However, it is widely conserved across vertebrates.


Pssm-ID: 436728  Cd Length: 74  Bit Score: 86.62  E-value: 2.83e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 44888831   118 IILYSNNSPCNEanhcCISKMYNFLITYPGITLSIYFSQLYHTEmdfpaSAWNREALRSLASLWprVVLSPISGGIWHSV 197
Cdd:pfam18775   1 VTLYLSWSPCNE----CSEKIQEFLKKHPKVNLDIYFAQLYHTE-----EEDNRQGLRSLVEKG--VTLSVMSGEDWIYC 69


                  ....*
gi 44888831   198 LHSFI 202
Cdd:pfam18775  70 LRTFV 74
 
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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