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Conserved domains on  [gi|353731090|ref|NP_001238839|]
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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 ...
 12-190 2.29e-95

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: 274.48  E-value: 2.29e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 353731090   12 MYPGTFYFQFKNLWEANDRNETWLCFTVEGiKRRSVVSWKTGVFRNQvdseTHCHAERCFLSWFCDDILSPNTNYQVTWY 91
Cdd:pfam18772   1 MDPKTFKFQFKNVPYASGRNKTYLCYEVET-RSGSDLSPDRGYLRNQ----AGCHAELCFLSWILPWQLDPGQKYQVTWY 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 353731090   92 TSWSPCPECAGKVAEFLARHSNVKLTIFTARLYYFQYPCYQEGLRSLSQEGVAVEIMDYEDFKYCWENFVYNDNEPFKPW 171
Cdd:pfam18772  76 VSWSPCPDCARKLAEFLARHPNLSLTIFAARLYFFWEPEYQEGLRRLKRAGAQLKIMDYQDFEYCWENFVDNQGRPFEPW 155

                         170
                  ....*....|....*....
gi 353731090  172 KGLKTNFRLLKRRLRESLQ 190
Cdd:pfam18772 156 EDLDENYEYLSRKLQEILR 174
 
Name Accession Description Interval E-value
APOBEC2 pfam18772
APOBEC2; APOBEC2 is a highly conserved (slow-evolving) family of AID/APOBECs found in most ...
 12-190 2.29e-95

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: 274.48  E-value: 2.29e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 353731090   12 MYPGTFYFQFKNLWEANDRNETWLCFTVEGiKRRSVVSWKTGVFRNQvdseTHCHAERCFLSWFCDDILSPNTNYQVTWY 91
Cdd:pfam18772   1 MDPKTFKFQFKNVPYASGRNKTYLCYEVET-RSGSDLSPDRGYLRNQ----AGCHAELCFLSWILPWQLDPGQKYQVTWY 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 353731090   92 TSWSPCPECAGKVAEFLARHSNVKLTIFTARLYYFQYPCYQEGLRSLSQEGVAVEIMDYEDFKYCWENFVYNDNEPFKPW 171
Cdd:pfam18772  76 VSWSPCPDCARKLAEFLARHPNLSLTIFAARLYFFWEPEYQEGLRRLKRAGAQLKIMDYQDFEYCWENFVDNQGRPFEPW 155

                         170
                  ....*....|....*....
gi 353731090  172 KGLKTNFRLLKRRLRESLQ 190
Cdd:pfam18772 156 EDLDENYEYLSRKLQEILR 174
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 8-158 2.76e-14

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: 65.83  E-value: 2.76e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 353731090   8 PMKAMYPGTFYfqfknlwEANDRNETWLCFTVEgikrrSVVSWKTGVFRNQVDSETHCHAERCFLSWFCDDILspnTNYQ 87
Cdd:cd01283    1 IEAALAAAEFA-------YAPYSNFTVGAALLT-----KDGRIFTGVNVENASYGLTLCAERTAIGKAVSEGL---RRYL 65

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 353731090  88 VTWYTS-----WSPCPECAGKVAEFLArhsnvkltiftARLYYFQYPCYQeglrslsqegvaveimdyEDFKYCWE 158
Cdd:cd01283   66 VTWAVSdeggvWSPCGACRQVLAEFLP-----------SRLYIIIDNPKG------------------EEFAYTLS 112
 
Name Accession Description Interval E-value
APOBEC2 pfam18772
APOBEC2; APOBEC2 is a highly conserved (slow-evolving) family of AID/APOBECs found in most ...
 12-190 2.29e-95

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: 274.48  E-value: 2.29e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 353731090   12 MYPGTFYFQFKNLWEANDRNETWLCFTVEGiKRRSVVSWKTGVFRNQvdseTHCHAERCFLSWFCDDILSPNTNYQVTWY 91
Cdd:pfam18772   1 MDPKTFKFQFKNVPYASGRNKTYLCYEVET-RSGSDLSPDRGYLRNQ----AGCHAELCFLSWILPWQLDPGQKYQVTWY 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 353731090   92 TSWSPCPECAGKVAEFLARHSNVKLTIFTARLYYFQYPCYQEGLRSLSQEGVAVEIMDYEDFKYCWENFVYNDNEPFKPW 171
Cdd:pfam18772  76 VSWSPCPDCARKLAEFLARHPNLSLTIFAARLYFFWEPEYQEGLRRLKRAGAQLKIMDYQDFEYCWENFVDNQGRPFEPW 155

                         170
                  ....*....|....*....
gi 353731090  172 KGLKTNFRLLKRRLRESLQ 190
Cdd:pfam18772 156 EDLDENYEYLSRKLQEILR 174
NAD2 pfam18782
Novel AID APOBEC clade 2; A distnct family of AID/APOBEC deaminases found only in Amphibians.
 10-189 6.83e-89

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: 258.07  E-value: 6.83e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 353731090   10 KAMYPGTFYFQFKNLWEANDRNETWLCFTVEGIKRRSVVSWKTGVFRNQvdseTHCHAERCFLSWFCDDILSPNTNYQVT 89
Cdd:pfam18782   1 KRMYPRTFYFNFNNKPILYGRNKTYLCYEVERLDNGTWLPQHRGFFRNQ----AKYHAELCFLSWFCGNQLPPYQNYQVT 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 353731090   90 WYTSWSPCPECAGKVAEFLARHSNVKLTIFTARLYYFQYPCYQEGLRSLSQEGVAVEIMDYEDFKYCWENFVYNDNEPFK 169
Cdd:pfam18782  77 WYVSWSPCPECAGEVAEFLAEHPNVTLTIFAARLYYFWDPDYQEALRRLRQAGARVKIMDYEEFEYCWENFVYNQGEPFQ 156

                         170       180
                  ....*....|....*....|
gi 353731090  170 PWKGLKTNFRLLKRRLRESL 189
Cdd:pfam18782 157 PWDGLEENSRFLHRRLREIL 176
NAD1 pfam18778
Novel AID APOBEC clade 1; A distinct family of AID/APOBEC-like deaminases found in ray-finned ...
 10-189 1.04e-87

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: 254.90  E-value: 1.04e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 353731090   10 KAMYPGTFYFQFKNLWEANDRNETWLCFTVEgiKRRSVVSWKtGVFRNQvdsETHCHAERCFLSWFCD-DILSPNTNYQV 88
Cdd:pfam18778   1 ERMSPETFKFQFKNVEYASGRNKTLLCYEVK--RGNSSSLWR-GHLRNE---NSGCHAEICFLRWFSSwRLFDPSQCYTI 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 353731090   89 TWYTSWSPCPECAGKVAEFLARHSNVKLTIFTARLYYFQYPCYQEGLRSLSQEGVAVEIMDYEDFKYCWENFVYNDNEPF 168
Cdd:pfam18778  75 TWYLSWSPCPSCAAKLAEFLKAHPNVTLTIFAARLYYFEDPWNQEGLRSLASAGVTLSIMDYSDFEYCWENFVDNEGRPF 154

                         170       180
                  ....*....|....*....|.
gi 353731090  169 KPWKGLKTNFRLLKRRLRESL 189
Cdd:pfam18778 155 VPWEDLEENSRYYHRKLQRIL 175
APOBEC_N pfam08210
APOBEC-like N-terminal domain; A mechanism of generating protein diversity is mRNA editing. ...
 17-187 8.69e-79

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: 232.26  E-value: 8.69e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 353731090   17 FYFQFKNLWEANDRNETWLCFTVEgIKRRSVVSWKTGVFRNQVDSetHCHAERCFLSWFCDDILSPNTNYQVTWYTSWSP 96
Cdd:pfam08210   1 FFFHFKNLPYASGRHETYLCYEVK-RDSGGLVVEDKGYLRNQAAS--SLHAEERFLRWIHDLALDPGSNYEVTWYVSWSP 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 353731090   97 CPECAGKVAEFLARHSNVKLTIFTARLYYFQYPCYQ--EGLRSLSQEGVAVEIMDYEDFKYCWENFVYNDNEPFKPWKGL 174
Cdd:pfam08210  78 CNECASELAAFLSKHPNVRLRIFVSRLYYWEEPDYWnrEGLRSLAQAGVQLRPMSYKDFEYCWNNFVDHDGEPFKPWDGL 157

                         170
                  ....*....|...
gi 353731090  175 KTNFRLLKRRLRE 187
Cdd:pfam08210 158 HENSVYLARKLQE 170
SNAD4 pfam18750
Secreted Novel AID/APOBEC-like Deaminase 4; A family of secreted AID/APOBEC like deaminases ...
 43-159 3.31e-55

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: 170.52  E-value: 3.31e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 353731090   43 KRRSVVSWKTGVFRNqvdsETHCHAERCFLSWFCDDILSPNTNYQVTWYTSWSPCPECAGKVAEFLARHSNVKLTIFTAR 122
Cdd:pfam18750   5 WGNGSKIWQRGYLSN----EHEQHAEICFLENIRSRELDPSQRYRVTWYLSWSPCPECAQKIAEFLAEHPNVTLTIFAAR 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 353731090  123 LYYfQYPCYQEGLRSLSQEGVAVEIMDYEDFKYCWEN 159
Cdd:pfam18750  81 LYH-WDEDNRQGLRSLAQAGVTLQIMTLEDFEYCWKN 116
APOBEC_C pfam05240
APOBEC-like C-terminal domain; This domain is found at the C-termini of the Apolipoprotein B ...
 112-189 1.99e-40

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: 131.84  E-value: 1.99e-40
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 353731090  112 SNVKLTIFTARLYYFQYPCYQEGLRSLSQEGVAVEIMDYEDFKYCWENFVYNDNEPFKPWKGLKTNFRLLKRRLRESL 189
Cdd:pfam05240   1 PNVSLTIFAARLYYHWDPEYQQGLRRLVQAGAQVAIMSYKEFEYCWDNFVDNQGRPFQPWEGLEENSQLLSRRLQEIL 78
APOBEC3 pfam18771
APOBEC3; APOBEC3 deaminases act as restriction factors in the innate response to retroviruses ...
 33-169 1.61e-36

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: 123.75  E-value: 1.61e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 353731090   33 TWLCFTVEGikrRSVVSWKTGVFRNqvdsETHCHAERCFLSWFCDDILSPNTNYQVTWYTSWSPCPECAGKVAEFLARHS 112
Cdd:pfam18771   6 AYLCYQLKG---RNGSALDRGYFSN----KKKRHAEIRFIDKIRSLDLDNIQCYRITCYITWSPCPNCAAELVDFISLNP 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 353731090  113 NVKLTIFTARLYYFQYPCYQEGLRSLSQEGVAVEIMDYEDFKYCWENFVYNDNEPFK 169
Cdd:pfam18771  79 HLKLRIFASRLYYHWERSYKEGLQKLQRAGVSVAVMTLPEFQDCWEDFVDHQEEPFR 135
APOBEC4_like pfam18774
APOBEC4-like -AID/APOBEC-deaminase; Cnidarian and Algal homologs of the APOBEC4-like AID ...
 50-161 4.36e-26

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: 96.87  E-value: 4.36e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 353731090   50 WKTGV-FRNQVDSETHCHAERCFLSWFCDDilSPNTNYQVTWYTSWSPCPECAGKVAEFLARHSNVKLTIFTARLYYFQY 128
Cdd:pfam18774  19 WGRGTiWRNWTENNCTEHAEVNFLENFRSE--RPSRSCTITWYLSWSPCWECSGRILEFLSRHPNVTLGIYVARLFMHDD 96

                          90       100       110
                  ....*....|....*....|....*....|...
gi 353731090  129 PCYQEGLRSLSQEGVAVEIMDYEDFKYCWENFV 161
Cdd:pfam18774  97 DRNRQGLRILQMNGVTIQVMMNKDYCYCWKAFK 129
APOBEC4 pfam18775
APOBEC4; A member of the AID/APOBEC family of cytosine deaminases. The biological function of ...
 88-161 1.20e-22

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: 86.24  E-value: 1.20e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 353731090   88 VTWYTSWSPCPECAGKVAEFLARHSNVKLTIFTARLYYFQYPCYQEGLRSLSQEGVAVEIMDYEDFKYCWENFV 161
Cdd:pfam18775   1 VTLYLSWSPCNECSEKIQEFLKKHPKVNLDIYFAQLYHTEEEDNRQGLRSLVEKGVTLSVMSGEDWIYCLRTFV 74
APOBEC1 pfam18769
APOBEC1; APOBEC1 deaminates cytosine both in RNA and ssDNA and has roles in both mRNA editing ...
 66-148 4.54e-18

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: 75.23  E-value: 4.54e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 353731090   66 HAERCFL-SWFCDDILSPNTNYQVTWYTSWSPCPECAGKVAEFLARHSNVKLTIFTARLYYFQYPCYQEGLRSLSQEGVA 144
Cdd:pfam18769  18 HAEVNFLeKFFSERHFDPSVSCSITWFLSWSPCGECSKAIGEFLSQHPNVTLVIYAARLFKHLDIRNRQGLRDLAMSGVT 97


                  ....
gi 353731090  145 VEIM 148
Cdd:pfam18769  98 IQIM 101
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 8-158 2.76e-14

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: 65.83  E-value: 2.76e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 353731090   8 PMKAMYPGTFYfqfknlwEANDRNETWLCFTVEgikrrSVVSWKTGVFRNQVDSETHCHAERCFLSWFCDDILspnTNYQ 87
Cdd:cd01283    1 IEAALAAAEFA-------YAPYSNFTVGAALLT-----KDGRIFTGVNVENASYGLTLCAERTAIGKAVSEGL---RRYL 65

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 353731090  88 VTWYTS-----WSPCPECAGKVAEFLArhsnvkltiftARLYYFQYPCYQeglrslsqegvaveimdyEDFKYCWE 158
Cdd:cd01283   66 VTWAVSdeggvWSPCGACRQVLAEFLP-----------SRLYIIIDNPKG------------------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.
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