NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2217338941|ref|XP_047297098|]
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
NAD2 pfam18782
Novel AID APOBEC clade 2; A distnct family of AID/APOBEC deaminases found only in Amphibians.
 10-201 1.50e-91

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: 267.70  E-value: 1.50e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217338941  10 ERMYRDTFYDNFENEPILYGRSYTWLCYEVKIKRGRSNLLWDTGVFRGpvlpkrQSNHrqevyfrfenHAEMCFLSWFCG 89
Cdd:pfam18782   1 KRMYPRTFYFNFNNKPILYGRNKTYLCYEVERLDNGTWLPQHRGFFRN------QAKY----------HAELCFLSWFCG 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217338941  90 NRLPANRRFQITWFVSWNPCLPCVVKVTKFLAEHPNVTLTISAARLYYYRDRDWRWVLLRLHKAGARVKIMDYEDFAYCW 169
Cdd:pfam18782  65 NQLPPYQNYQVTWYVSWSPCPECAGEVAEFLAEHPNVTLTIFAARLYYFWDPDYQEALRRLRQAGARVKIMDYEEFEYCW 144

                         170       180       190
                  ....*....|....*....|....*....|..
gi 2217338941 170 ENFVCNEGQPFMPWYKFDDNYASLHRTLKEIL 201
Cdd:pfam18782 145 ENFVYNQGEPFQPWDGLEENSRFLHRRLREIL 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.
 10-201 1.50e-91

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: 267.70  E-value: 1.50e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217338941  10 ERMYRDTFYDNFENEPILYGRSYTWLCYEVKIKRGRSNLLWDTGVFRGpvlpkrQSNHrqevyfrfenHAEMCFLSWFCG 89
Cdd:pfam18782   1 KRMYPRTFYFNFNNKPILYGRNKTYLCYEVERLDNGTWLPQHRGFFRN------QAKY----------HAELCFLSWFCG 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217338941  90 NRLPANRRFQITWFVSWNPCLPCVVKVTKFLAEHPNVTLTISAARLYYYRDRDWRWVLLRLHKAGARVKIMDYEDFAYCW 169
Cdd:pfam18782  65 NQLPPYQNYQVTWYVSWSPCPECAGEVAEFLAEHPNVTLTIFAARLYYFWDPDYQEALRRLRQAGARVKIMDYEEFEYCW 144

                         170       180       190
                  ....*....|....*....|....*....|..
gi 2217338941 170 ENFVCNEGQPFMPWYKFDDNYASLHRTLKEIL 201
Cdd:pfam18782 145 ENFVYNQGEPFQPWDGLEENSRFLHRRLREIL 176
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 8-170 4.68e-07

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: 47.34  E-value: 4.68e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217338941   8 PMERMYRDTFYdnfenepILYGRSYTWLCYEVKikrgrsnllWDTGVFRGpvlpkrqSNHRQEVYfRFENHAEMCFLSWF 87
Cdd:cd01283     1 IEAALAAAEFA-------YAPYSNFTVGAALLT---------KDGRIFTG-------VNVENASY-GLTLCAERTAIGKA 56

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217338941  88 CGNRLpanRRFQITWFVS-----WNPCLPCvvkvTKFLAEHpnvtltiSAARLYYYRDRDwrwvllrlhkagarvkimDY 162
Cdd:cd01283    57 VSEGL---RRYLVTWAVSdeggvWSPCGAC----RQVLAEF-------LPSRLYIIIDNP------------------KG 104


                  ....*...
gi 2217338941 163 EDFAYCWE 170
Cdd:cd01283   105 EEFAYTLS 112
 
Name Accession Description Interval E-value
NAD2 pfam18782
Novel AID APOBEC clade 2; A distnct family of AID/APOBEC deaminases found only in Amphibians.
 10-201 1.50e-91

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: 267.70  E-value: 1.50e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217338941  10 ERMYRDTFYDNFENEPILYGRSYTWLCYEVKIKRGRSNLLWDTGVFRGpvlpkrQSNHrqevyfrfenHAEMCFLSWFCG 89
Cdd:pfam18782   1 KRMYPRTFYFNFNNKPILYGRNKTYLCYEVERLDNGTWLPQHRGFFRN------QAKY----------HAELCFLSWFCG 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217338941  90 NRLPANRRFQITWFVSWNPCLPCVVKVTKFLAEHPNVTLTISAARLYYYRDRDWRWVLLRLHKAGARVKIMDYEDFAYCW 169
Cdd:pfam18782  65 NQLPPYQNYQVTWYVSWSPCPECAGEVAEFLAEHPNVTLTIFAARLYYFWDPDYQEALRRLRQAGARVKIMDYEEFEYCW 144

                         170       180       190
                  ....*....|....*....|....*....|..
gi 2217338941 170 ENFVCNEGQPFMPWYKFDDNYASLHRTLKEIL 201
Cdd:pfam18782 145 ENFVYNQGEPFQPWDGLEENSRFLHRRLREIL 176
APOBEC2 pfam18772
APOBEC2; APOBEC2 is a highly conserved (slow-evolving) family of AID/APOBECs found in most ...
 12-202 2.81e-82

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: 244.05  E-value: 2.81e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217338941  12 MYRDTFYDNFENEPILYGRSYTWLCYEVKiKRGRSNLLWDTGVFRGpvlpkrQSNHrqevyfrfenHAEMCFLSWFCGNR 91
Cdd:pfam18772   1 MDPKTFKFQFKNVPYASGRNKTYLCYEVE-TRSGSDLSPDRGYLRN------QAGC----------HAELCFLSWILPWQ 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217338941  92 LPANRRFQITWFVSWNPCLPCVVKVTKFLAEHPNVTLTISAARLYYYRDRDWRWVLLRLHKAGARVKIMDYEDFAYCWEN 171
Cdd:pfam18772  64 LDPGQKYQVTWYVSWSPCPDCARKLAEFLARHPNLSLTIFAARLYFFWEPEYQEGLRRLKRAGAQLKIMDYQDFEYCWEN 143

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2217338941 172 FVCNEGQPFMPWYKFDDNYASLHRTLKEILR 202
Cdd:pfam18772 144 FVDNQGRPFEPWEDLDENYEYLSRKLQEILR 174
NAD1 pfam18778
Novel AID APOBEC clade 1; A distinct family of AID/APOBEC-like deaminases found in ray-finned ...
 10-201 4.31e-75

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: 226.01  E-value: 4.31e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217338941  10 ERMYRDTFYDNFENEPILYGRSYTWLCYEVKikRGRSNLLWdTGVFRGPvlpkrqsnhrqevyfRFENHAEMCFLSWFCG 89
Cdd:pfam18778   1 ERMSPETFKFQFKNVEYASGRNKTLLCYEVK--RGNSSSLW-RGHLRNE---------------NSGCHAEICFLRWFSS 62

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217338941  90 NRL-PANRRFQITWFVSWNPCLPCVVKVTKFLAEHPNVTLTISAARLYYYRDRDWRWVLLRLHKAGARVKIMDYEDFAYC 168
Cdd:pfam18778  63 WRLfDPSQCYTITWYLSWSPCPSCAAKLAEFLKAHPNVTLTIFAARLYYFEDPWNQEGLRSLASAGVTLSIMDYSDFEYC 142

                         170       180       190
                  ....*....|....*....|....*....|...
gi 2217338941 169 WENFVCNEGQPFMPWYKFDDNYASLHRTLKEIL 201
Cdd:pfam18778 143 WENFVDNEGRPFVPWEDLEENSRYYHRKLQRIL 175
APOBEC_N pfam08210
APOBEC-like N-terminal domain; A mechanism of generating protein diversity is mRNA editing. ...
 17-199 1.82e-51

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: 165.62  E-value: 1.82e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217338941  17 FYDNFENEPILYGRSYTWLCYEVKIKRGrSNLLWDTGVFRGPVLPKRqsnhrqevyfrfenHAEMCFLSWFCGNRLPANR 96
Cdd:pfam08210   1 FFFHFKNLPYASGRHETYLCYEVKRDSG-GLVVEDKGYLRNQAASSL--------------HAEERFLRWIHDLALDPGS 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217338941  97 RFQITWFVSWNPCLPCVVKVTKFLAEHPNVTLTISAARLYYYRDRDW--RWVLLRLHKAGARVKIMDYEDFAYCWENFVC 174
Cdd:pfam08210  66 NYEVTWYVSWSPCNECASELAAFLSKHPNVRLRIFVSRLYYWEEPDYwnREGLRSLAQAGVQLRPMSYKDFEYCWNNFVD 145

                         170       180
                  ....*....|....*....|....*
gi 2217338941 175 NEGQPFMPWYKFDDNYASLHRTLKE 199
Cdd:pfam08210 146 HDGEPFKPWDGLHENSVYLARKLQE 170
SNAD4 pfam18750
Secreted Novel AID/APOBEC-like Deaminase 4; A family of secreted AID/APOBEC like deaminases ...
 39-171 2.62e-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: 153.19  E-value: 2.62e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217338941  39 VKIKRGRSNLLWDTGVFRGpvlpkrqsnhrqevyfRFENHAEMCFLSWFCGNRLPANRRFQITWFVSWNPCLPCVVKVTK 118
Cdd:pfam18750   1 YEIKWGNGSKIWQRGYLSN----------------EHEQHAEICFLENIRSRELDPSQRYRVTWYLSWSPCPECAQKIAE 64

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2217338941 119 FLAEHPNVTLTISAARLYYYrDRDWRWVLLRLHKAGARVKIMDYEDFAYCWEN 171
Cdd:pfam18750  65 FLAEHPNVTLTIFAARLYHW-DEDNRQGLRSLAQAGVTLQIMTLEDFEYCWKN 116
APOBEC_C pfam05240
APOBEC-like C-terminal domain; This domain is found at the C-termini of the Apolipoprotein B ...
 124-201 6.98e-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: 122.59  E-value: 6.98e-36
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2217338941 124 PNVTLTISAARLYYYRDRDWRWVLLRLHKAGARVKIMDYEDFAYCWENFVCNEGQPFMPWYKFDDNYASLHRTLKEIL 201
Cdd:pfam05240   1 PNVSLTIFAARLYYHWDPEYQQGLRRLVQAGAQVAIMSYKEFEYCWDNFVDNQGRPFQPWEGLEENSQLLSRRLQEIL 78
APOBEC3 pfam18771
APOBEC3; APOBEC3 deaminases act as restriction factors in the innate response to retroviruses ...
 33-180 2.16e-24

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: 94.48  E-value: 2.16e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217338941  33 TWLCYEVKikrGRSNLLWDTGVFrgpvlpkrqSNHRQevyfrfeNHAEMCFLSWFCGNRLPANRRFQITWFVSWNPCLPC 112
Cdd:pfam18771   6 AYLCYQLK---GRNGSALDRGYF---------SNKKK-------RHAEIRFIDKIRSLDLDNIQCYRITCYITWSPCPNC 66

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2217338941 113 VVKVTKFLAEHPNVTLTISAARLYYYRDRDWRWVLLRLHKAGARVKIMDYEDFAYCWENFVCNEGQPF 180
Cdd:pfam18771  67 AAELVDFISLNPHLKLRIFASRLYYHWERSYKEGLQKLQRAGVSVAVMTLPEFQDCWEDFVDHQEEPF 134
APOBEC4_like pfam18774
APOBEC4-like -AID/APOBEC-deaminase; Cnidarian and Algal homologs of the APOBEC4-like AID ...
 77-173 6.36e-19

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: 80.30  E-value: 6.36e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217338941  77 NHAEMCFLSWFCGNRlpANRRFQITWFVSWNPCLPCVVKVTKFLAEHPNVTLTISAARLYYYRDRDWRWVLLRLHKAGAR 156
Cdd:pfam18774  35 EHAEVNFLENFRSER--PSRSCTITWYLSWSPCWECSGRILEFLSRHPNVTLGIYVARLFMHDDDRNRQGLRILQMNGVT 112

                          90
                  ....*....|....*..
gi 2217338941 157 VKIMDYEDFAYCWENFV 173
Cdd:pfam18774 113 IQVMMNKDYCYCWKAFK 129
APOBEC4 pfam18775
APOBEC4; A member of the AID/APOBEC family of cytosine deaminases. The biological function of ...
 100-173 7.18e-16

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: 70.44  E-value: 7.18e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2217338941 100 ITWFVSWNPCLPCVVKVTKFLAEHPNVTLTISAARLYYYRDRDWRWVLLRLHKAGARVKIMDYEDFAYCWENFV 173
Cdd:pfam18775   1 VTLYLSWSPCNECSEKIQEFLKKHPKVNLDIYFAQLYHTEEEDNRQGLRSLVEKGVTLSVMSGEDWIYCLRTFV 74
APOBEC1 pfam18769
APOBEC1; APOBEC1 deaminates cytosine both in RNA and ssDNA and has roles in both mRNA editing ...
 76-160 2.61e-15

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: 69.46  E-value: 2.61e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217338941  76 ENHAEMCFLSWFCGNR-LPANRRFQITWFVSWNPCLPCVVKVTKFLAEHPNVTLTISAARLYYYRDRDWRWVLLRLHKAG 154
Cdd:pfam18769  16 TQHAEVNFLEKFFSERhFDPSVSCSITWFLSWSPCGECSKAIGEFLSQHPNVTLVIYAARLFKHLDIRNRQGLRDLAMSG 95


                  ....*.
gi 2217338941 155 ARVKIM 160
Cdd:pfam18769  96 VTIQIM 101
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 8-170 4.68e-07

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: 47.34  E-value: 4.68e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217338941   8 PMERMYRDTFYdnfenepILYGRSYTWLCYEVKikrgrsnllWDTGVFRGpvlpkrqSNHRQEVYfRFENHAEMCFLSWF 87
Cdd:cd01283     1 IEAALAAAEFA-------YAPYSNFTVGAALLT---------KDGRIFTG-------VNVENASY-GLTLCAERTAIGKA 56

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217338941  88 CGNRLpanRRFQITWFVS-----WNPCLPCvvkvTKFLAEHpnvtltiSAARLYYYRDRDwrwvllrlhkagarvkimDY 162
Cdd:cd01283    57 VSEGL---RRYLVTWAVSdeggvWSPCGAC----RQVLAEF-------LPSRLYIIIDNP------------------KG 104


                  ....*...
gi 2217338941 163 EDFAYCWE 170
Cdd:cd01283   105 EEFAYTLS 112
 
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