NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|54873619|ref|NP_001006667|]
View 

DNA dC-

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
AID super family cl40070
Activation induced deaminase; The activation induced deaminase is a vertebrate-specific member ...
 8-88 1.94e-30

Activation induced deaminase; The activation induced deaminase is a vertebrate-specific member of the classical AID/APOBEC cytosine deaminases that is involved in antibody diversification.


The actual alignment was detected with superfamily member pfam18767:

Pssm-ID: 408538  Cd Length: 90  Bit Score: 103.41  E-value: 1.94e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54873619     8 TVERMYRDTFSYNFynRPILSRRNTVWL-------CYEVKTKGPSRPRLDAKIFRGQVPRSFIR----APFQVLSSPFGQ 76
Cdd:pfam18767   1 TVDRIHAEIFFIDD--NKDPSRITELWIknspchrCSEVLLKHFSRPPLKPTIHIGRISRSFDSdddkGLIQLLKNGFNI 78

                          90
                  ....*....|..
gi 54873619    77 CAPPHGTAQVQW 88
Cdd:pfam18767  79 KVWPHLTALVCW 90
 
Name Accession Description Interval E-value
AID pfam18767
Activation induced deaminase; The activation induced deaminase is a vertebrate-specific member ...
 8-88 1.94e-30

Activation induced deaminase; The activation induced deaminase is a vertebrate-specific member of the classical AID/APOBEC cytosine deaminases that is involved in antibody diversification.


Pssm-ID: 408538  Cd Length: 90  Bit Score: 103.41  E-value: 1.94e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54873619     8 TVERMYRDTFSYNFynRPILSRRNTVWL-------CYEVKTKGPSRPRLDAKIFRGQVPRSFIR----APFQVLSSPFGQ 76
Cdd:pfam18767   1 TVDRIHAEIFFIDD--NKDPSRITELWIknspchrCSEVLLKHFSRPPLKPTIHIGRISRSFDSdddkGLIQLLKNGFNI 78

                          90
                  ....*....|..
gi 54873619    77 CAPPHGTAQVQW 88
Cdd:pfam18767  79 KVWPHLTALVCW 90
 
Name Accession Description Interval E-value
AID pfam18767
Activation induced deaminase; The activation induced deaminase is a vertebrate-specific member ...
 8-88 1.94e-30

Activation induced deaminase; The activation induced deaminase is a vertebrate-specific member of the classical AID/APOBEC cytosine deaminases that is involved in antibody diversification.


Pssm-ID: 408538  Cd Length: 90  Bit Score: 103.41  E-value: 1.94e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54873619     8 TVERMYRDTFSYNFynRPILSRRNTVWL-------CYEVKTKGPSRPRLDAKIFRGQVPRSFIR----APFQVLSSPFGQ 76
Cdd:pfam18767   1 TVDRIHAEIFFIDD--NKDPSRITELWIknspchrCSEVLLKHFSRPPLKPTIHIGRISRSFDSdddkGLIQLLKNGFNI 78

                          90
                  ....*....|..
gi 54873619    77 CAPPHGTAQVQW 88
Cdd:pfam18767  79 KVWPHLTALVCW 90
NAD2 pfam18782
Novel AID APOBEC clade 2; A distnct family of AID/APOBEC deaminases found only in Amphibians.
 10-57 3.27e-15

Novel AID APOBEC clade 2; A distnct family of AID/APOBEC deaminases found only in Amphibians.


Pssm-ID: 436733 [Multi-domain]  Cd Length: 176  Bit Score: 67.01  E-value: 3.27e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 54873619    10 ERMYRDTFSYNFYNRPILSRRNTVWLCYEVKTK-GPSRPRLDAKIFRGQ 57
Cdd:pfam18782   1 KRMYPRTFYFNFNNKPILYGRNKTYLCYEVERLdNGTWLPQHRGFFRNQ 49
APOBEC2 pfam18772
APOBEC2; APOBEC2 is a highly conserved (slow-evolving) family of AID/APOBECs found in most ...
 12-58 1.64e-14

APOBEC2; APOBEC2 is a highly conserved (slow-evolving) family of AID/APOBECs found in most vertebrates including cartilaginous fishes. APOBEC2 is poorly understood in terms of their molecular functions and substrate specificity.


Pssm-ID: 465863 [Multi-domain]  Cd Length: 174  Bit Score: 64.93  E-value: 1.64e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 54873619    12 MYRDTFSYNFYNRPILSRRNTVWLCYEVKTKGPSrprlDAKIFRGQV 58
Cdd:pfam18772   1 MDPKTFKFQFKNVPYASGRNKTYLCYEVETRSGS----DLSPDRGYL 43
NAD1 pfam18778
Novel AID APOBEC clade 1; A distinct family of AID/APOBEC-like deaminases found in ray-finned ...
 10-47 1.31e-11

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: 57.29  E-value: 1.31e-11
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 54873619    10 ERMYRDTFSYNFYNRPILSRRNTVWLCYEVKTKGPSRP 47
Cdd:pfam18778   1 ERMSPETFKFQFKNVEYASGRNKTLLCYEVKRGNSSSL 38
APOBEC_N pfam08210
APOBEC-like N-terminal domain; A mechanism of generating protein diversity is mRNA editing. ...
 17-88 3.36e-05

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: 40.04  E-value: 3.36e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 54873619    17 FSYNFYNRPILSRRNTVWLCYEVKTKGPSRPRLDAKIFRGQVPRSfIRAPFQVLSSPFGQCAPPHGTAQVQW 88
Cdd:pfam08210   1 FFFHFKNLPYASGRHETYLCYEVKRDSGGLVVEDKGYLRNQAASS-LHAEERFLRWIHDLALDPGSNYEVTW 71
 
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