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Conserved domains on  [gi|393715108|ref|NP_001257335|]
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DNA dC-

Protein Classification

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List of domain hits

 Name Accession Description Interval E-value
NAD2 pfam18782
Novel AID APOBEC clade 2; A distnct family of AID/APOBEC deaminases found only in Amphibians.
 10-176 1.50e-87

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: 254.21  E-value: 1.50e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393715108   10 RHKTYLCYEVERLDNGTSVKmdQHRGFLHNQAKnllcgfygRHAELRFLDLVPSLQLDPAQIYRVTWFISWSPCFSwgCA 89
Cdd:pfam18782  21 RNKTYLCYEVERLDNGTWLP--QHRGFFRNQAK--------YHAELCFLSWFCGNQLPPYQNYQVTWYVSWSPCPE--CA 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393715108   90 GEVRAFLQENTHVRLRIFAARIY-DYDPLYKEALQMLRDAGAQVSIMTYDEFKHCWDTFVDHQGCPFQPWDGLDEHSQAL 168
Cdd:pfam18782  89 GEVAEFLAEHPNVTLTIFAARLYyFWDPDYQEALRRLRQAGARVKIMDYEEFEYCWENFVYNQGEPFQPWDGLEENSRFL 168


                  ....*...
gi 393715108  169 SGRLRAIL 176
Cdd:pfam18782 169 HRRLREIL 176
 
Name Accession Description Interval E-value
NAD2 pfam18782
Novel AID APOBEC clade 2; A distnct family of AID/APOBEC deaminases found only in Amphibians.
 10-176 1.50e-87

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: 254.21  E-value: 1.50e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393715108   10 RHKTYLCYEVERLDNGTSVKmdQHRGFLHNQAKnllcgfygRHAELRFLDLVPSLQLDPAQIYRVTWFISWSPCFSwgCA 89
Cdd:pfam18782  21 RNKTYLCYEVERLDNGTWLP--QHRGFFRNQAK--------YHAELCFLSWFCGNQLPPYQNYQVTWYVSWSPCPE--CA 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393715108   90 GEVRAFLQENTHVRLRIFAARIY-DYDPLYKEALQMLRDAGAQVSIMTYDEFKHCWDTFVDHQGCPFQPWDGLDEHSQAL 168
Cdd:pfam18782  89 GEVAEFLAEHPNVTLTIFAARLYyFWDPDYQEALRRLRQAGARVKIMDYEEFEYCWENFVYNQGEPFQPWDGLEENSRFL 168


                  ....*...
gi 393715108  169 SGRLRAIL 176
Cdd:pfam18782 169 HRRLREIL 176
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 10-102 8.11e-10

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: 53.88  E-value: 8.11e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393715108  10 RHKTYLCYEVERldngtsvKMDQHRGFLHNQAknllCGFYGRHAELRFLDLVPSLQLdpaQIYRVTWFIS-----WSPCF 84
Cdd:cd01283   16 SNFTVGAALLTK-------DGRIFTGVNVENA----SYGLTLCAERTAIGKAVSEGL---RRYLVTWAVSdeggvWSPCG 81

                         90
                 ....*....|....*...
gi 393715108  85 SwgCAGEVRAFLQENTHV 102
Cdd:cd01283   82 A--CRQVLAEFLPSRLYI 97
 
Name Accession Description Interval E-value
NAD2 pfam18782
Novel AID APOBEC clade 2; A distnct family of AID/APOBEC deaminases found only in Amphibians.
 10-176 1.50e-87

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: 254.21  E-value: 1.50e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393715108   10 RHKTYLCYEVERLDNGTSVKmdQHRGFLHNQAKnllcgfygRHAELRFLDLVPSLQLDPAQIYRVTWFISWSPCFSwgCA 89
Cdd:pfam18782  21 RNKTYLCYEVERLDNGTWLP--QHRGFFRNQAK--------YHAELCFLSWFCGNQLPPYQNYQVTWYVSWSPCPE--CA 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393715108   90 GEVRAFLQENTHVRLRIFAARIY-DYDPLYKEALQMLRDAGAQVSIMTYDEFKHCWDTFVDHQGCPFQPWDGLDEHSQAL 168
Cdd:pfam18782  89 GEVAEFLAEHPNVTLTIFAARLYyFWDPDYQEALRRLRQAGARVKIMDYEEFEYCWENFVYNQGEPFQPWDGLEENSRFL 168


                  ....*...
gi 393715108  169 SGRLRAIL 176
Cdd:pfam18782 169 HRRLREIL 176
APOBEC2 pfam18772
APOBEC2; APOBEC2 is a highly conserved (slow-evolving) family of AID/APOBECs found in most ...
 6-177 2.76e-76

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: 225.56  E-value: 2.76e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393715108    6 ASGpRHKTYLCYEVERLDNGTSvkmDQHRGFLHNQAknllcgfyGRHAELRFLDLVPSLQLDPAQIYRVTWFISWSPCFS 85
Cdd:pfam18772  16 ASG-RNKTYLCYEVETRSGSDL---SPDRGYLRNQA--------GCHAELCFLSWILPWQLDPGQKYQVTWYVSWSPCPD 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393715108   86 wgCAGEVRAFLQENTHVRLRIFAARIYDY-DPLYKEALQMLRDAGAQVSIMTYDEFKHCWDTFVDHQGCPFQPWDGLDEH 164
Cdd:pfam18772  84 --CARKLAEFLARHPNLSLTIFAARLYFFwEPEYQEGLRRLKRAGAQLKIMDYQDFEYCWENFVDNQGRPFEPWEDLDEN 161

                         170
                  ....*....|...
gi 393715108  165 SQALSGRLRAILQ 177
Cdd:pfam18772 162 YEYLSRKLQEILR 174
NAD1 pfam18778
Novel AID APOBEC clade 1; A distinct family of AID/APOBEC-like deaminases found in ray-finned ...
 5-176 1.79e-72

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: 215.99  E-value: 1.79e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393715108    5 PASGPRHKTYLCYEVERlDNGTSvkmdQHRGFLHNQAKnllcgfyGRHAELRFLDLVPSLQL-DPAQIYRVTWFISWSPC 83
Cdd:pfam18778  16 EYASGRNKTLLCYEVKR-GNSSS----LWRGHLRNENS-------GCHAEICFLRWFSSWRLfDPSQCYTITWYLSWSPC 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393715108   84 FSwgCAGEVRAFLQENTHVRLRIFAARIYDY-DPLYKEALQMLRDAGAQVSIMTYDEFKHCWDTFVDHQGCPFQPWDGLD 162
Cdd:pfam18778  84 PS--CAAKLAEFLKAHPNVTLTIFAARLYYFeDPWNQEGLRSLASAGVTLSIMDYSDFEYCWENFVDNEGRPFVPWEDLE 161

                         170
                  ....*....|....
gi 393715108  163 EHSQALSGRLRAIL 176
Cdd:pfam18778 162 ENSRYYHRKLQRIL 175
APOBEC_N pfam08210
APOBEC-like N-terminal domain; A mechanism of generating protein diversity is mRNA editing. ...
 10-173 2.96e-64

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: 195.28  E-value: 2.96e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393715108   10 RHKTYLCYEVERLDNGTSVkmdQHRGFLHNQAKNllcgfyGRHAELRFLDLVPSLQLDPAQIYRVTWFISWSPCFSwgCA 89
Cdd:pfam08210  14 RHETYLCYEVKRDSGGLVV---EDKGYLRNQAAS------SLHAEERFLRWIHDLALDPGSNYEVTWYVSWSPCNE--CA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393715108   90 GEVRAFLQENTHVRLRIFAARIY-DYDPLY--KEALQMLRDAGAQVSIMTYDEFKHCWDTFVDHQGCPFQPWDGLDEHSQ 166
Cdd:pfam08210  83 SELAAFLSKHPNVRLRIFVSRLYyWEEPDYwnREGLRSLAQAGVQLRPMSYKDFEYCWNNFVDHDGEPFKPWDGLHENSV 162


                  ....*..
gi 393715108  167 ALSGRLR 173
Cdd:pfam08210 163 YLARKLQ 169
SNAD4 pfam18750
Secreted Novel AID/APOBEC-like Deaminase 4; A family of secreted AID/APOBEC like deaminases ...
 17-146 5.33e-51

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: 159.73  E-value: 5.33e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393715108   17 YEVERLDNGTSVkmdqHRGFLHNQAknllcgfyGRHAELRFLDLVPSLQLDPAQIYRVTWFISWSPCFSwgCAGEVRAFL 96
Cdd:pfam18750   1 YEIKWGNGSKIW----QRGYLSNEH--------EQHAEICFLENIRSRELDPSQRYRVTWYLSWSPCPE--CAQKIAEFL 66

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 393715108   97 QENTHVRLRIFAARIYDYDPLYKEALQMLRDAGAQVSIMTYDEFKHCWDT 146
Cdd:pfam18750  67 AEHPNVTLTIFAARLYHWDEDNRQGLRSLAQAGVTLQIMTLEDFEYCWKN 116
APOBEC3 pfam18771
APOBEC3; APOBEC3 deaminases act as restriction factors in the innate response to retroviruses ...
 10-156 9.59e-44

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: 141.86  E-value: 9.59e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393715108   10 RHKTYLCYEVERLDNGTSVkmdqhRGFLHNQAKnllcgfygRHAELRFLDLVPSLQLDPAQIYRVTWFISWSPCFSwgCA 89
Cdd:pfam18771   3 DRKAYLCYQLKGRNGSALD-----RGYFSNKKK--------RHAEIRFIDKIRSLDLDNIQCYRITCYITWSPCPN--CA 67

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 393715108   90 GEVRAFLQENTHVRLRIFAARIYDYD-PLYKEALQMLRDAGAQVSIMTYDEFKHCWDTFVDHQGCPFQ 156
Cdd:pfam18771  68 AELVDFISLNPHLKLRIFASRLYYHWeRSYKEGLQKLQRAGVSVAVMTLPEFQDCWEDFVDHQEEPFR 135
APOBEC_C pfam05240
APOBEC-like C-terminal domain; This domain is found at the C-termini of the Apolipoprotein B ...
 101-176 2.15e-42

APOBEC-like C-terminal domain; This domain is found at the C-termini of the Apolipoprotein B mRNA editing enzyme.


Pssm-ID: 461599  Cd Length: 78  Bit Score: 136.46  E-value: 2.15e-42
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 393715108  101 HVRLRIFAARIYD-YDPLYKEALQMLRDAGAQVSIMTYDEFKHCWDTFVDHQGCPFQPWDGLDEHSQALSGRLRAIL 176
Cdd:pfam05240   2 NVSLTIFAARLYYhWDPEYQQGLRRLVQAGAQVAIMSYKEFEYCWDNFVDNQGRPFQPWEGLEENSQLLSRRLQEIL 78
APOBEC4_like pfam18774
APOBEC4-like -AID/APOBEC-deaminase; Cnidarian and Algal homologs of the APOBEC4-like AID ...
 46-149 4.86e-16

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: 70.67  E-value: 4.86e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393715108   46 CGFY-GRHAELRFLDLVPSLQldPAQIYRVTWFISWSPCfsWGCAGEVRAFLQENTHVRLRIFAARIYDY-DPLYKEALQ 123
Cdd:pfam18774  29 TENNcTEHAEVNFLENFRSER--PSRSCTITWYLSWSPC--WECSGRILEFLSRHPNVTLGIYVARLFMHdDDRNRQGLR 104

                          90       100
                  ....*....|....*....|....*.
gi 393715108  124 MLRDAGAQVSIMTYDEFKHCWDTFVD 149
Cdd:pfam18774 105 ILQMNGVTIQVMMNKDYCYCWKAFKN 130
APOBEC4 pfam18775
APOBEC4; A member of the AID/APOBEC family of cytosine deaminases. The biological function of ...
 74-148 2.18e-12

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: 59.66  E-value: 2.18e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 393715108   74 VTWFISWSPCfsWGCAGEVRAFLQENTHVRLRIFAARIYDYDPLY-KEALQMLRDAGAQVSIMTYDEFKHCWDTFV 148
Cdd:pfam18775   1 VTLYLSWSPC--NECSEKIQEFLKKHPKVNLDIYFAQLYHTEEEDnRQGLRSLVEKGVTLSVMSGEDWIYCLRTFV 74
APOBEC1 pfam18769
APOBEC1; APOBEC1 deaminates cytosine both in RNA and ssDNA and has roles in both mRNA editing ...
 51-135 2.22e-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: 60.21  E-value: 2.22e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393715108   51 RHAELRFLD-LVPSLQLDPAQIYRVTWFISWSPCfsWGCAGEVRAFLQENTHVRLRIFAARIYDY-DPLYKEALQMLRDA 128
Cdd:pfam18769  17 QHAEVNFLEkFFSERHFDPSVSCSITWFLSWSPC--GECSKAIGEFLSQHPNVTLVIYAARLFKHlDIRNRQGLRDLAMS 94


                  ....*..
gi 393715108  129 GAQVSIM 135
Cdd:pfam18769  95 GVTIQIM 101
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 10-102 8.11e-10

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: 53.88  E-value: 8.11e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 393715108  10 RHKTYLCYEVERldngtsvKMDQHRGFLHNQAknllCGFYGRHAELRFLDLVPSLQLdpaQIYRVTWFIS-----WSPCF 84
Cdd:cd01283   16 SNFTVGAALLTK-------DGRIFTGVNVENA----SYGLTLCAERTAIGKAVSEGL---RRYLVTWAVSdeggvWSPCG 81

                         90
                 ....*....|....*...
gi 393715108  85 SwgCAGEVRAFLQENTHV 102
Cdd:cd01283   82 A--CRQVLAEFLPSRLYI 97
 
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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