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Conserved domains on  [gi|1159731397|ref|NP_001336367|]
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DNA dC-

Protein Classification

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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 ...
 12-194 5.46e-88

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: 255.99  E-value: 5.46e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159731397  12 MYRDTFSYNFYNRPILSRRNTVWLCYEVKTKGPSrpplDAKIFRGQVYSELKYHPEMRFFHWFSKWrKLHRDQEYEVTWY 91
Cdd:pfam18772   1 MDPKTFKFQFKNVPYASGRNKTYLCYEVETRSGS----DLSPDRGYLRNQAGCHAELCFLSWILPW-QLDPGQKYQVTWY 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159731397  92 ISWSPCTKCTRDMATFLAEDPKVTLTIFVARLYYFWDPDYQEALRSLCQKrdgpRATMKIMNYDEFQHCWSKFVYSQREL 171
Cdd:pfam18772  76 VSWSPCPDCARKLAEFLARHPNLSLTIFAARLYFFWEPEYQEGLRRLKRA----GAQLKIMDYQDFEYCWENFVDNQGRP 151

                         170       180
                  ....*....|....*....|...
gi 1159731397 172 FEPWNNLPKYYILLHIMLGEILR 194
Cdd:pfam18772 152 FEPWEDLDENYEYLSRKLQEILR 174
 
Name Accession Description Interval E-value
APOBEC2 pfam18772
APOBEC2; APOBEC2 is a highly conserved (slow-evolving) family of AID/APOBECs found in most ...
 12-194 5.46e-88

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: 255.99  E-value: 5.46e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159731397  12 MYRDTFSYNFYNRPILSRRNTVWLCYEVKTKGPSrpplDAKIFRGQVYSELKYHPEMRFFHWFSKWrKLHRDQEYEVTWY 91
Cdd:pfam18772   1 MDPKTFKFQFKNVPYASGRNKTYLCYEVETRSGS----DLSPDRGYLRNQAGCHAELCFLSWILPW-QLDPGQKYQVTWY 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159731397  92 ISWSPCTKCTRDMATFLAEDPKVTLTIFVARLYYFWDPDYQEALRSLCQKrdgpRATMKIMNYDEFQHCWSKFVYSQREL 171
Cdd:pfam18772  76 VSWSPCPDCARKLAEFLARHPNLSLTIFAARLYFFWEPEYQEGLRRLKRA----GAQLKIMDYQDFEYCWENFVDNQGRP 151

                         170       180
                  ....*....|....*....|...
gi 1159731397 172 FEPWNNLPKYYILLHIMLGEILR 194
Cdd:pfam18772 152 FEPWEDLDENYEYLSRKLQEILR 174
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 9-133 5.28e-15

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: 67.75  E-value: 5.28e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159731397   9 VERMYRDTFSYNFYnrpilsrRNTVWLCYEVKTKGpsrppldaKIFRGQVYSELKY----HPEMRFFHWFSKWRklhrDQ 84
Cdd:cd01283     2 EAALAAAEFAYAPY-------SNFTVGAALLTKDG--------RIFTGVNVENASYgltlCAERTAIGKAVSEG----LR 62

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1159731397  85 EYEVTWYIS-----WSPCTKCTRDMATFLAedpkvtltifvARLYYFWDPDYQE 133
Cdd:cd01283    63 RYLVTWAVSdeggvWSPCGACRQVLAEFLP-----------SRLYIIIDNPKGE 105
 
Name Accession Description Interval E-value
APOBEC2 pfam18772
APOBEC2; APOBEC2 is a highly conserved (slow-evolving) family of AID/APOBECs found in most ...
 12-194 5.46e-88

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: 255.99  E-value: 5.46e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159731397  12 MYRDTFSYNFYNRPILSRRNTVWLCYEVKTKGPSrpplDAKIFRGQVYSELKYHPEMRFFHWFSKWrKLHRDQEYEVTWY 91
Cdd:pfam18772   1 MDPKTFKFQFKNVPYASGRNKTYLCYEVETRSGS----DLSPDRGYLRNQAGCHAELCFLSWILPW-QLDPGQKYQVTWY 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159731397  92 ISWSPCTKCTRDMATFLAEDPKVTLTIFVARLYYFWDPDYQEALRSLCQKrdgpRATMKIMNYDEFQHCWSKFVYSQREL 171
Cdd:pfam18772  76 VSWSPCPDCARKLAEFLARHPNLSLTIFAARLYFFWEPEYQEGLRRLKRA----GAQLKIMDYQDFEYCWENFVDNQGRP 151

                         170       180
                  ....*....|....*....|...
gi 1159731397 172 FEPWNNLPKYYILLHIMLGEILR 194
Cdd:pfam18772 152 FEPWEDLDENYEYLSRKLQEILR 174
NAD2 pfam18782
Novel AID APOBEC clade 2; A distnct family of AID/APOBEC deaminases found only in Amphibians.
 10-193 3.57e-83

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: 243.81  E-value: 3.57e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159731397  10 ERMYRDTFSYNFYNRPILSRRNTVWLCYEVKTKGPSRPPldaKIFRGQVYSELKYHPEMRFFHWFsKWRKLHRDQEYEVT 89
Cdd:pfam18782   1 KRMYPRTFYFNFNNKPILYGRNKTYLCYEVERLDNGTWL---PQHRGFFRNQAKYHAELCFLSWF-CGNQLPPYQNYQVT 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159731397  90 WYISWSPCTKCTRDMATFLAEDPKVTLTIFVARLYYFWDPDYQEALRSLCQKrdgpRATMKIMNYDEFQHCWSKFVYSQR 169
Cdd:pfam18782  77 WYVSWSPCPECAGEVAEFLAEHPNVTLTIFAARLYYFWDPDYQEALRRLRQA----GARVKIMDYEEFEYCWENFVYNQG 152

                         170       180
                  ....*....|....*....|....
gi 1159731397 170 ELFEPWNNLPKYYILLHIMLGEIL 193
Cdd:pfam18782 153 EPFQPWDGLEENSRFLHRRLREIL 176
NAD1 pfam18778
Novel AID APOBEC clade 1; A distinct family of AID/APOBEC-like deaminases found in ray-finned ...
 10-193 8.00e-78

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: 230.24  E-value: 8.00e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159731397  10 ERMYRDTFSYNFYNRPILSRRNTVWLCYEVKTKGPSRPPLdaKIFRGQvysELKYHPEMRFFHWFSKWRKLHRDQEYEVT 89
Cdd:pfam18778   1 ERMSPETFKFQFKNVEYASGRNKTLLCYEVKRGNSSSLWR--GHLRNE---NSGCHAEICFLRWFSSWRLFDPSQCYTIT 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159731397  90 WYISWSPCTKCTRDMATFLAEDPKVTLTIFVARLYYFWDPDYQEALRSLCQKrdgpRATMKIMNYDEFQHCWSKFVYSQR 169
Cdd:pfam18778  76 WYLSWSPCPSCAAKLAEFLKAHPNVTLTIFAARLYYFEDPWNQEGLRSLASA----GVTLSIMDYSDFEYCWENFVDNEG 151

                         170       180
                  ....*....|....*....|....
gi 1159731397 170 ELFEPWNNLPKYYILLHIMLGEIL 193
Cdd:pfam18778 152 RPFVPWEDLEENSRYYHRKLQRIL 175
SNAD4 pfam18750
Secreted Novel AID/APOBEC-like Deaminase 4; A family of secreted AID/APOBEC like deaminases ...
 37-163 2.44e-47

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: 150.87  E-value: 2.44e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159731397  37 YEVKTKGPSRPpldakIFRGQVYSELKYHPEMRFFHWFSkWRKLHRDQEYEVTWYISWSPCTKCTRDMATFLAEDPKVTL 116
Cdd:pfam18750   1 YEIKWGNGSKI-----WQRGYLSNEHEQHAEICFLENIR-SRELDPSQRYRVTWYLSWSPCPECAQKIAEFLAEHPNVTL 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1159731397 117 TIFVARLYYfWDPDYQEALRSLCQKrdgpRATMKIMNYDEFQHCWSK 163
Cdd:pfam18750  75 TIFAARLYH-WDEDNRQGLRSLAQA----GVTLQIMTLEDFEYCWKN 116
APOBEC_N pfam08210
APOBEC-like N-terminal domain; A mechanism of generating protein diversity is mRNA editing. ...
 17-178 2.82e-47

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: 152.52  E-value: 2.82e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159731397  17 FSYNFYNRPILSRRNTVWLCYEVKTKGPSRPPLDAKIFRGQVYSELkyHPEMRFFHWFSKWrKLHRDQEYEVTWYISWSP 96
Cdd:pfam08210   1 FFFHFKNLPYASGRHETYLCYEVKRDSGGLVVEDKGYLRNQAASSL--HAEERFLRWIHDL-ALDPGSNYEVTWYVSWSP 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159731397  97 CTKCTRDMATFLAEDPKVTLTIFVARLYYFWDPDYQ--EALRSLCQKrdgpRATMKIMNYDEFQHCWSKFVYSQRELFEP 174
Cdd:pfam08210  78 CNECASELAAFLSKHPNVRLRIFVSRLYYWEEPDYWnrEGLRSLAQA----GVQLRPMSYKDFEYCWNNFVDHDGEPFKP 153


                  ....
gi 1159731397 175 WNNL 178
Cdd:pfam08210 154 WDGL 157
APOBEC_C pfam05240
APOBEC-like C-terminal domain; This domain is found at the C-termini of the Apolipoprotein B ...
 112-193 5.17e-36

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: 120.67  E-value: 5.17e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159731397 112 PKVTLTIFVARLYYFWDPDYQEALRSLCQKRdgprATMKIMNYDEFQHCWSKFVYSQRELFEPWNNLPKYYILLHIMLGE 191
Cdd:pfam05240   1 PNVSLTIFAARLYYHWDPEYQQGLRRLVQAG----AQVAIMSYKEFEYCWDNFVDNQGRPFQPWEGLEENSQLLSRRLQE 76


                  ..
gi 1159731397 192 IL 193
Cdd:pfam05240  77 IL 78
APOBEC3 pfam18771
APOBEC3; APOBEC3 deaminases act as restriction factors in the innate response to retroviruses ...
 34-172 1.31e-25

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: 96.02  E-value: 1.31e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159731397  34 WLCYEVKtkgpsrPPLDAKIFRGQVYSELKYHPEMRFFhwfSKWRKLHRD--QEYEVTWYISWSPCTKCTRDMATFLAED 111
Cdd:pfam18771   7 YLCYQLK------GRNGSALDRGYFSNKKKRHAEIRFI---DKIRSLDLDniQCYRITCYITWSPCPNCAAELVDFISLN 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1159731397 112 PKVTLTIFVARLYYFWDPDYQEALRSLCQKrdgpRATMKIMNYDEFQHCWSKFVYSQRELF 172
Cdd:pfam18771  78 PHLKLRIFASRLYYHWERSYKEGLQKLQRA----GVSVAVMTLPEFQDCWEDFVDHQEEPF 134
APOBEC4 pfam18775
APOBEC4; A member of the AID/APOBEC family of cytosine deaminases. The biological function of ...
 88-165 6.26e-17

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: 71.60  E-value: 6.26e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1159731397  88 VTWYISWSPCTKCTRDMATFLAEDPKVTLTIFVARLYYFWDPDYQEALRSLCQKrdgpRATMKIMNYDEFQHCWSKFV 165
Cdd:pfam18775   1 VTLYLSWSPCNECSEKIQEFLKKHPKVNLDIYFAQLYHTEEEDNRQGLRSLVEK----GVTLSVMSGEDWIYCLRTFV 74
APOBEC4_like pfam18774
APOBEC4-like -AID/APOBEC-deaminase; Cnidarian and Algal homologs of the APOBEC4-like AID ...
 72-165 2.01e-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: 72.21  E-value: 2.01e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159731397  72 HWFSKWRKLHRDQEYEVTWYISWSPCTKCTRDMATFLAEDPKVTLTIFVARLYYFWDPDYQEALRSLCQKrdgpRATMKI 151
Cdd:pfam18774  40 NFLENFRSERPSRSCTITWYLSWSPCWECSGRILEFLSRHPNVTLGIYVARLFMHDDDRNRQGLRILQMN----GVTIQV 115

                          90
                  ....*....|....
gi 1159731397 152 MNYDEFQHCWSKFV 165
Cdd:pfam18774 116 MMNKDYCYCWKAFK 129
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 9-133 5.28e-15

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: 67.75  E-value: 5.28e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1159731397   9 VERMYRDTFSYNFYnrpilsrRNTVWLCYEVKTKGpsrppldaKIFRGQVYSELKY----HPEMRFFHWFSKWRklhrDQ 84
Cdd:cd01283     2 EAALAAAEFAYAPY-------SNFTVGAALLTKDG--------RIFTGVNVENASYgltlCAERTAIGKAVSEG----LR 62

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1159731397  85 EYEVTWYIS-----WSPCTKCTRDMATFLAedpkvtltifvARLYYFWDPDYQE 133
Cdd:cd01283    63 RYLVTWAVSdeggvWSPCGACRQVLAEFLP-----------SRLYIIIDNPKGE 105
AID pfam18767
Activation induced deaminase; The activation induced deaminase is a vertebrate-specific member ...
 8-58 6.32e-14

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: 64.50  E-value: 6.32e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1159731397   8 TVERMYRDTFSYNFynRPILSRRNTVWL-------CYEVKTKGPSRPPLDAKIFRGQV 58
Cdd:pfam18767   1 TVDRIHAEIFFIDD--NKDPSRITELWIknspchrCSEVLLKHFSRPPLKPTIHIGRI 56
APOBEC1 pfam18769
APOBEC1; APOBEC1 deaminates cytosine both in RNA and ssDNA and has roles in both mRNA editing ...
 65-138 1.06e-13

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: 64.06  E-value: 1.06e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1159731397  65 HPEMRFFHWFSKWRKLHRDQEYEVTWYISWSPCTKCTRDMATFLAEDPKVTLTIFVARLYYFWDPDYQEALRSL 138
Cdd:pfam18769  18 HAEVNFLEKFFSERHFDPSVSCSITWFLSWSPCGECSKAIGEFLSQHPNVTLVIYAARLFKHLDIRNRQGLRDL 91
 
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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