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Conserved domains on  [gi|928013317|ref|XP_013873612|]
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PREDICTED: probable C-

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
APOBEC2 pfam18772
APOBEC2; APOBEC2 is a highly conserved (slow-evolving) family of AID/APOBECs found in most ...
 96-266 2.40e-84

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: 249.44  E-value: 2.40e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928013317   96 MSPFYFKFQFRNVEYSSGRNKTFLCYRVDTAGG-DTEPLKGYMEDEhAMAHVEEAFFQQVLP---NSSKEHDITWFVSSS 171
Cdd:pfam18772   1 MDPKTFKFQFKNVPYASGRNKTYLCYEVETRSGsDLSPDRGYLRNQ-AGCHAELCFLSWILPwqlDPGQKYQVTWYVSWS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928013317  172 PCAACAAKLATILQQRKKLRLTIFCSRLFEWEEPEIREGLKALARAGCKLRMMKPADFQLVWEMYVDKEDEEFAPWEDCK 251
Cdd:pfam18772  80 PCPDCARKLAEFLARHPNLSLTIFAARLYFFWEPEYQEGLRRLKRAGAQLKIMDYQDFEYCWENFVDNQGRPFEPWEDLD 159

                         170
                  ....*....|....*
gi 928013317  252 ENYEYYLEKLGEILN 266
Cdd:pfam18772 160 ENYEYLSRKLQEILR 174
 
Name Accession Description Interval E-value
APOBEC2 pfam18772
APOBEC2; APOBEC2 is a highly conserved (slow-evolving) family of AID/APOBECs found in most ...
 96-266 2.40e-84

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: 249.44  E-value: 2.40e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928013317   96 MSPFYFKFQFRNVEYSSGRNKTFLCYRVDTAGG-DTEPLKGYMEDEhAMAHVEEAFFQQVLP---NSSKEHDITWFVSSS 171
Cdd:pfam18772   1 MDPKTFKFQFKNVPYASGRNKTYLCYEVETRSGsDLSPDRGYLRNQ-AGCHAELCFLSWILPwqlDPGQKYQVTWYVSWS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928013317  172 PCAACAAKLATILQQRKKLRLTIFCSRLFEWEEPEIREGLKALARAGCKLRMMKPADFQLVWEMYVDKEDEEFAPWEDCK 251
Cdd:pfam18772  80 PCPDCARKLAEFLARHPNLSLTIFAARLYFFWEPEYQEGLRRLKRAGAQLKIMDYQDFEYCWENFVDNQGRPFEPWEDLD 159

                         170
                  ....*....|....*
gi 928013317  252 ENYEYYLEKLGEILN 266
Cdd:pfam18772 160 ENYEYLSRKLQEILR 174
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 110-187 7.39e-06

Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. Cytidine deaminases catalyze the deamination of cytidine to uridine and are important in the pyrimadine salvage pathway in many cell types, from bacteria to humans. This family also includes the apoBec proteins, which are a mammal specific expansion of RNA editing enzymes, and the closely related phorbolins, and the AID (activation-induced) enzymes.


Pssm-ID: 238610 [Multi-domain]  Cd Length: 112  Bit Score: 43.87  E-value: 7.39e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928013317 110 YSSGRNKTFLCYRVdtaGGDTEPLKGYMEDEHAM---AHVEEAFFQQVLPNSSKEHDITWFVSS-----SPCAACAAKLA 181
Cdd:cd01283   12 YAPYSNFTVGAALL---TKDGRIFTGVNVENASYgltLCAERTAIGKAVSEGLRRYLVTWAVSDeggvwSPCGACRQVLA 88


                 ....*.
gi 928013317 182 TILQQR 187
Cdd:cd01283   89 EFLPSR 94
 
Name Accession Description Interval E-value
APOBEC2 pfam18772
APOBEC2; APOBEC2 is a highly conserved (slow-evolving) family of AID/APOBECs found in most ...
 96-266 2.40e-84

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: 249.44  E-value: 2.40e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928013317   96 MSPFYFKFQFRNVEYSSGRNKTFLCYRVDTAGG-DTEPLKGYMEDEhAMAHVEEAFFQQVLP---NSSKEHDITWFVSSS 171
Cdd:pfam18772   1 MDPKTFKFQFKNVPYASGRNKTYLCYEVETRSGsDLSPDRGYLRNQ-AGCHAELCFLSWILPwqlDPGQKYQVTWYVSWS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928013317  172 PCAACAAKLATILQQRKKLRLTIFCSRLFEWEEPEIREGLKALARAGCKLRMMKPADFQLVWEMYVDKEDEEFAPWEDCK 251
Cdd:pfam18772  80 PCPDCARKLAEFLARHPNLSLTIFAARLYFFWEPEYQEGLRRLKRAGAQLKIMDYQDFEYCWENFVDNQGRPFEPWEDLD 159

                         170
                  ....*....|....*
gi 928013317  252 ENYEYYLEKLGEILN 266
Cdd:pfam18772 160 ENYEYLSRKLQEILR 174
NAD1 pfam18778
Novel AID APOBEC clade 1; A distinct family of AID/APOBEC-like deaminases found in ray-finned ...
 94-265 2.27e-83

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: 247.19  E-value: 2.27e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928013317   94 ERMSPFYFKFQFRNVEYSSGRNKTFLCYRVDTaGGDTEPLKGYMEDEHAMAHVEEAFFQQV----LPNSSKEHDITWFVS 169
Cdd:pfam18778   1 ERMSPETFKFQFKNVEYASGRNKTLLCYEVKR-GNSSSLWRGHLRNENSGCHAEICFLRWFsswrLFDPSQCYTITWYLS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928013317  170 SSPCAACAAKLATILQQRKKLRLTIFCSRLFEWEEPEIREGLKALARAGCKLRMMKPADFQLVWEMYVDKEDEEFAPWED 249
Cdd:pfam18778  80 WSPCPSCAAKLAEFLKAHPNVTLTIFAARLYYFEDPWNQEGLRSLASAGVTLSIMDYSDFEYCWENFVDNEGRPFVPWED 159

                         170
                  ....*....|....*.
gi 928013317  250 CKENYEYYLEKLGEIL 265
Cdd:pfam18778 160 LEENSRYYHRKLQRIL 175
APOBEC_N pfam08210
APOBEC-like N-terminal domain; A mechanism of generating protein diversity is mRNA editing. ...
 101-261 5.52e-56

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: 177.56  E-value: 5.52e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928013317  101 FKFQFRNVEYSSGRNKTFLCYRVDT-AGGDTEPLKGYMEDEHAM-AHVEEAFF-----QQVLPNSSkeHDITWFVSSSPC 173
Cdd:pfam08210   1 FFFHFKNLPYASGRHETYLCYEVKRdSGGLVVEDKGYLRNQAASsLHAEERFLrwihdLALDPGSN--YEVTWYVSWSPC 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928013317  174 AACAAKLATILQQRKKLRLTIFCSRLFEWEEPEI--REGLKALARAGCKLRMMKPADFQLVWEMYVDKEDEEFAPWEDCK 251
Cdd:pfam08210  79 NECASELAAFLSKHPNVRLRIFVSRLYYWEEPDYwnREGLRSLAQAGVQLRPMSYKDFEYCWNNFVDHDGEPFKPWDGLH 158

                         170
                  ....*....|
gi 928013317  252 ENYEYYLEKL 261
Cdd:pfam08210 159 ENSVYLARKL 168
NAD2 pfam18782
Novel AID APOBEC clade 2; A distnct family of AID/APOBEC deaminases found only in Amphibians.
 94-265 6.34e-42

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: 141.73  E-value: 6.34e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928013317   94 ERMSPFYFKFQFRNVEYSSGRNKTFLCYRVDTAGGDTEPL--KGYMEDEhAMAHVEEAFFQQVLPNS---SKEHDITWFV 168
Cdd:pfam18782   1 KRMYPRTFYFNFNNKPILYGRNKTYLCYEVERLDNGTWLPqhRGFFRNQ-AKYHAELCFLSWFCGNQlppYQNYQVTWYV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928013317  169 SSSPCAACAAKLATILQQRKKLRLTIFCSRLFEWEEPEIREGLKALARAGCKLRMMKPADFQLVWEMYVDKEDEEFAPWE 248
Cdd:pfam18782  80 SWSPCPECAGEVAEFLAEHPNVTLTIFAARLYYFWDPDYQEALRRLRQAGARVKIMDYEEFEYCWENFVYNQGEPFQPWD 159

                         170
                  ....*....|....*..
gi 928013317  249 DCKENYEYYLEKLGEIL 265
Cdd:pfam18782 160 GLEENSRFLHRRLREIL 176
SNAD4 pfam18750
Secreted Novel AID/APOBEC-like Deaminase 4; A family of secreted AID/APOBEC like deaminases ...
 121-234 3.74e-37

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: 127.38  E-value: 3.74e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928013317  121 YRVDTAGGDTEPLKGYMEDEHAmAHVEEAFFQQVLPN---SSKEHDITWFVSSSPCAACAAKLATILQQRKKLRLTIFCS 197
Cdd:pfam18750   1 YEIKWGNGSKIWQRGYLSNEHE-QHAEICFLENIRSReldPSQRYRVTWYLSWSPCPECAQKIAEFLAEHPNVTLTIFAA 79

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 928013317  198 RLFEWEEPEiREGLKALARAGCKLRMMKPADFQLVWE 234
Cdd:pfam18750  80 RLYHWDEDN-RQGLRSLAQAGVTLQIMTLEDFEYCWK 115
APOBEC3 pfam18771
APOBEC3; APOBEC3 deaminases act as restriction factors in the innate response to retroviruses ...
 114-244 3.52e-20

APOBEC3; APOBEC3 deaminases act as restriction factors in the innate response to retroviruses and various retroelements.


Pssm-ID: 465862 [Multi-domain]  Cd Length: 135  Bit Score: 83.69  E-value: 3.52e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928013317  114 RNKTFLCYRVDTAGGDTePLKGYMEDEHAmAHVEEAFFQQVLP---NSSKEHDITWFVSSSPCAACAAKLATILQQRKKL 190
Cdd:pfam18771   3 DRKAYLCYQLKGRNGSA-LDRGYFSNKKK-RHAEIRFIDKIRSldlDNIQCYRITCYITWSPCPNCAAELVDFISLNPHL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 928013317  191 RLTIFCSRLFEWEEPEIREGLKALARAGCKLRMMKPADFQLVWEMYVDKEDEEF 244
Cdd:pfam18771  81 KLRIFASRLYYHWERSYKEGLQKLQRAGVSVAVMTLPEFQDCWEDFVDHQEEPF 134
APOBEC4 pfam18775
APOBEC4; A member of the AID/APOBEC family of cytosine deaminases. The biological function of ...
 164-237 1.90e-15

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: 69.29  E-value: 1.90e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 928013317  164 ITWFVSSSPCAACAAKLATILQQRKKLRLTIFCSRLFEWEEPEIREGLKALARAGCKLRMMKPADFQLVWEMYV 237
Cdd:pfam18775   1 VTLYLSWSPCNECSEKIQEFLKKHPKVNLDIYFAQLYHTEEEDNRQGLRSLVEKGVTLSVMSGEDWIYCLRTFV 74
APOBEC4_like pfam18774
APOBEC4-like -AID/APOBEC-deaminase; Cnidarian and Algal homologs of the APOBEC4-like AID ...
 145-239 3.88e-14

APOBEC4-like -AID/APOBEC-deaminase; Cnidarian and Algal homologs of the APOBEC4-like AID/APOBEC-like deaminases characterized by a distinct Zn chelating site involving residues from the conserved loops 1 and 3.


Pssm-ID: 408545 [Multi-domain]  Cd Length: 131  Bit Score: 67.59  E-value: 3.88e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928013317  145 HVEEAFfqqvLPNSSKEHD-----ITWFVSSSPCAACAAKLATILQQRKKLRLTIFCSRLFEWEEPEIREGLKALARAGC 219
Cdd:pfam18774  36 HAEVNF----LENFRSERPsrsctITWYLSWSPCWECSGRILEFLSRHPNVTLGIYVARLFMHDDDRNRQGLRILQMNGV 111

                          90       100
                  ....*....|....*....|
gi 928013317  220 KLRMMKPADFQLVWEMYVDK 239
Cdd:pfam18774 112 TIQVMMNKDYCYCWKAFKNY 131
APOBEC1 pfam18769
APOBEC1; APOBEC1 deaminates cytosine both in RNA and ssDNA and has roles in both mRNA editing ...
 145-224 4.88e-12

APOBEC1; APOBEC1 deaminates cytosine both in RNA and ssDNA and has roles in both mRNA editing and ssDNA mutagenesis as part of the defense against retroviruses and genomic retrotransposons.


Pssm-ID: 408540  Cd Length: 101  Bit Score: 60.98  E-value: 4.88e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928013317  145 HVE----EAFFQQVLPNSSKEHDITWFVSSSPCAACAAKLATILQQRKKLRLTIFCSRLFEWEEPEIREGLKALARAGCK 220
Cdd:pfam18769  18 HAEvnflEKFFSERHFDPSVSCSITWFLSWSPCGECSKAIGEFLSQHPNVTLVIYAARLFKHLDIRNRQGLRDLAMSGVT 97


                  ....
gi 928013317  221 LRMM 224
Cdd:pfam18769  98 IQIM 101
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 110-187 7.39e-06

Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. Cytidine deaminases catalyze the deamination of cytidine to uridine and are important in the pyrimadine salvage pathway in many cell types, from bacteria to humans. This family also includes the apoBec proteins, which are a mammal specific expansion of RNA editing enzymes, and the closely related phorbolins, and the AID (activation-induced) enzymes.


Pssm-ID: 238610 [Multi-domain]  Cd Length: 112  Bit Score: 43.87  E-value: 7.39e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 928013317 110 YSSGRNKTFLCYRVdtaGGDTEPLKGYMEDEHAM---AHVEEAFFQQVLPNSSKEHDITWFVSS-----SPCAACAAKLA 181
Cdd:cd01283   12 YAPYSNFTVGAALL---TKDGRIFTGVNVENASYgltLCAERTAIGKAVSEGLRRYLVTWAVSDeggvwSPCGACRQVLA 88


                 ....*.
gi 928013317 182 TILQQR 187
Cdd:cd01283   89 EFLPSR 94
 
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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