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Conserved domains on  [gi|1028909627]
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Chain B, DNA dC-

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 ...
 21-199 1.67e-101

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: 290.27  E-value: 1.67e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1028909627  21 MDPHIFYFHFKNLRKAYGRNESWLCFTMEVvKHHSPVSWKRGVFRNQvdpeTGRHAERCFLSWFADDILSPNTNYEVTWY 100
Cdd:pfam18772   1 MDPKTFKFQFKNVPYASGRNKTYLCYEVET-RSGSDLSPDRGYLRNQ----AGCHAELCFLSWILPWQLDPGQKYQVTWY 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1028909627 101 TSWSPCPECAGEVAEFLARHSNVNLTIKTARLYYFDDTDYQEGLRSLSQEGASVEIMGYKDFKYCWENFVYNDDEPFKPW 180
Cdd:pfam18772  76 VSWSPCPDCARKLAEFLARHPNLSLTIFAARLYFFWEPEYQEGLRRLKRAGAQLKIMDYQDFEYCWENFVDNQGRPFEPW 155

                         170
                  ....*....|....*....
gi 1028909627 181 DGLDYNFLDLDSKLQEILE 199
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 ...
 21-199 1.67e-101

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: 290.27  E-value: 1.67e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1028909627  21 MDPHIFYFHFKNLRKAYGRNESWLCFTMEVvKHHSPVSWKRGVFRNQvdpeTGRHAERCFLSWFADDILSPNTNYEVTWY 100
Cdd:pfam18772   1 MDPKTFKFQFKNVPYASGRNKTYLCYEVET-RSGSDLSPDRGYLRNQ----AGCHAELCFLSWILPWQLDPGQKYQVTWY 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1028909627 101 TSWSPCPECAGEVAEFLARHSNVNLTIKTARLYYFDDTDYQEGLRSLSQEGASVEIMGYKDFKYCWENFVYNDDEPFKPW 180
Cdd:pfam18772  76 VSWSPCPDCARKLAEFLARHPNLSLTIFAARLYFFWEPEYQEGLRRLKRAGAQLKIMDYQDFEYCWENFVDNQGRPFEPW 155

                         170
                  ....*....|....*....
gi 1028909627 181 DGLDYNFLDLDSKLQEILE 199
Cdd:pfam18772 156 EDLDENYEYLSRKLQEILR 174
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 17-167 9.57e-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: 67.37  E-value: 9.57e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1028909627  17 PMEAMDPHIFYFhfknlrkAYGRNESWLCftMEVVKHHSPVswkRGVFRNQVDPETGRHAERCFLSWFADDILspnTNYE 96
Cdd:cd01283     1 IEAALAAAEFAY-------APYSNFTVGA--ALLTKDGRIF---TGVNVENASYGLTLCAERTAIGKAVSEGL---RRYL 65

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1028909627  97 VTWYTS-----WSPCPECAGEVAEFLArhsnvnltiktARLYYFDDTDYQEglrslsqegasveimgykDFKYCWE 167
Cdd:cd01283    66 VTWAVSdeggvWSPCGACRQVLAEFLP-----------SRLYIIIDNPKGE------------------EFAYTLS 112
 
Name Accession Description Interval E-value
APOBEC2 pfam18772
APOBEC2; APOBEC2 is a highly conserved (slow-evolving) family of AID/APOBECs found in most ...
 21-199 1.67e-101

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: 290.27  E-value: 1.67e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1028909627  21 MDPHIFYFHFKNLRKAYGRNESWLCFTMEVvKHHSPVSWKRGVFRNQvdpeTGRHAERCFLSWFADDILSPNTNYEVTWY 100
Cdd:pfam18772   1 MDPKTFKFQFKNVPYASGRNKTYLCYEVET-RSGSDLSPDRGYLRNQ----AGCHAELCFLSWILPWQLDPGQKYQVTWY 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1028909627 101 TSWSPCPECAGEVAEFLARHSNVNLTIKTARLYYFDDTDYQEGLRSLSQEGASVEIMGYKDFKYCWENFVYNDDEPFKPW 180
Cdd:pfam18772  76 VSWSPCPDCARKLAEFLARHPNLSLTIFAARLYFFWEPEYQEGLRRLKRAGAQLKIMDYQDFEYCWENFVDNQGRPFEPW 155

                         170
                  ....*....|....*....
gi 1028909627 181 DGLDYNFLDLDSKLQEILE 199
Cdd:pfam18772 156 EDLDENYEYLSRKLQEILR 174
NAD2 pfam18782
Novel AID APOBEC clade 2; A distnct family of AID/APOBEC deaminases found only in Amphibians.
 19-198 2.93e-92

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: 266.92  E-value: 2.93e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1028909627  19 EAMDPHIFYFHFKNLRKAYGRNESWLCFTMEVVKHHSPVSWKRGVFRNQvdpeTGRHAERCFLSWFADDILSPNTNYEVT 98
Cdd:pfam18782   1 KRMYPRTFYFNFNNKPILYGRNKTYLCYEVERLDNGTWLPQHRGFFRNQ----AKYHAELCFLSWFCGNQLPPYQNYQVT 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1028909627  99 WYTSWSPCPECAGEVAEFLARHSNVNLTIKTARLYYFDDTDYQEGLRSLSQEGASVEIMGYKDFKYCWENFVYNDDEPFK 178
Cdd:pfam18782  77 WYVSWSPCPECAGEVAEFLAEHPNVTLTIFAARLYYFWDPDYQEALRRLRQAGARVKIMDYEEFEYCWENFVYNQGEPFQ 156

                         170       180
                  ....*....|....*....|
gi 1028909627 179 PWDGLDYNFLDLDSKLQEIL 198
Cdd:pfam18782 157 PWDGLEENSRFLHRRLREIL 176
NAD1 pfam18778
Novel AID APOBEC clade 1; A distinct family of AID/APOBEC-like deaminases found in ray-finned ...
 19-198 8.50e-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: 252.97  E-value: 8.50e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1028909627  19 EAMDPHIFYFHFKNLRKAYGRNESWLCFtmeVVKHHSPVSWKRGVFRNQvdpETGRHAERCFLSWFAD-DILSPNTNYEV 97
Cdd:pfam18778   1 ERMSPETFKFQFKNVEYASGRNKTLLCY---EVKRGNSSSLWRGHLRNE---NSGCHAEICFLRWFSSwRLFDPSQCYTI 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1028909627  98 TWYTSWSPCPECAGEVAEFLARHSNVNLTIKTARLYYFDDTDYQEGLRSLSQEGASVEIMGYKDFKYCWENFVYNDDEPF 177
Cdd:pfam18778  75 TWYLSWSPCPSCAAKLAEFLKAHPNVTLTIFAARLYYFEDPWNQEGLRSLASAGVTLSIMDYSDFEYCWENFVDNEGRPF 154

                         170       180
                  ....*....|....*....|.
gi 1028909627 178 KPWDGLDYNFLDLDSKLQEIL 198
Cdd:pfam18778 155 VPWEDLEENSRYYHRKLQRIL 175
APOBEC_N pfam08210
APOBEC-like N-terminal domain; A mechanism of generating protein diversity is mRNA editing. ...
 26-196 5.46e-85

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: 248.43  E-value: 5.46e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1028909627  26 FYFHFKNLRKAYGRNESWLCFTMEVVKHHSPVsWKRGVFRNQVDPetGRHAERCFLSWFADDILSPNTNYEVTWYTSWSP 105
Cdd:pfam08210   1 FFFHFKNLPYASGRHETYLCYEVKRDSGGLVV-EDKGYLRNQAAS--SLHAEERFLRWIHDLALDPGSNYEVTWYVSWSP 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1028909627 106 CPECAGEVAEFLARHSNVNLTIKTARLYYFDDTDYQ--EGLRSLSQEGASVEIMGYKDFKYCWENFVYNDDEPFKPWDGL 183
Cdd:pfam08210  78 CNECASELAAFLSKHPNVRLRIFVSRLYYWEEPDYWnrEGLRSLAQAGVQLRPMSYKDFEYCWNNFVDHDGEPFKPWDGL 157

                         170
                  ....*....|...
gi 1028909627 184 DYNFLDLDSKLQE 196
Cdd:pfam08210 158 HENSVYLARKLQE 170
SNAD4 pfam18750
Secreted Novel AID/APOBEC-like Deaminase 4; A family of secreted AID/APOBEC like deaminases ...
 49-168 2.71e-58

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: 178.61  E-value: 2.71e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1028909627  49 EVVKHHSPVSWKRGVFRNqvdpETGRHAERCFLSWFADDILSPNTNYEVTWYTSWSPCPECAGEVAEFLARHSNVNLTIK 128
Cdd:pfam18750   2 EIKWGNGSKIWQRGYLSN----EHEQHAEICFLENIRSRELDPSQRYRVTWYLSWSPCPECAQKIAEFLAEHPNVTLTIF 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1028909627 129 TARLYYfDDTDYQEGLRSLSQEGASVEIMGYKDFKYCWEN 168
Cdd:pfam18750  78 AARLYH-WDEDNRQGLRSLAQAGVTLQIMTLEDFEYCWKN 116
APOBEC_C pfam05240
APOBEC-like C-terminal domain; This domain is found at the C-termini of the Apolipoprotein B ...
 121-198 8.91e-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: 130.30  E-value: 8.91e-40
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1028909627 121 SNVNLTIKTARLYYFDDTDYQEGLRSLSQEGASVEIMGYKDFKYCWENFVYNDDEPFKPWDGLDYNFLDLDSKLQEIL 198
Cdd:pfam05240   1 PNVSLTIFAARLYYHWDPEYQQGLRRLVQAGAQVAIMSYKEFEYCWDNFVDNQGRPFQPWEGLEENSQLLSRRLQEIL 78
APOBEC3 pfam18771
APOBEC3; APOBEC3 deaminases act as restriction factors in the innate response to retroviruses ...
 33-178 2.18e-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: 2.18e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1028909627  33 LRKAYgrneswLCFTMEVVKHHSPVswkRGVFRNqvdpETGRHAERCFLSWFADDILSPNTNYEVTWYTSWSPCPECAGE 112
Cdd:pfam18771   3 DRKAY------LCYQLKGRNGSALD---RGYFSN----KKKRHAEIRFIDKIRSLDLDNIQCYRITCYITWSPCPNCAAE 69

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1028909627 113 VAEFLARHSNVNLTIKTARLYYFDDTDYQEGLRSLSQEGASVEIMGYKDFKYCWENFVYNDDEPFK 178
Cdd:pfam18771  70 LVDFISLNPHLKLRIFASRLYYHWERSYKEGLQKLQRAGVSVAVMTLPEFQDCWEDFVDHQEEPFR 135
APOBEC4_like pfam18774
APOBEC4-like -AID/APOBEC-deaminase; Cnidarian and Algal homologs of the APOBEC4-like AID ...
 59-170 1.26e-27

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: 101.10  E-value: 1.26e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1028909627  59 WKRGV-FRNQVDPETGRHAERCFLSWFADDilSPNTNYEVTWYTSWSPCPECAGEVAEFLARHSNVNLTIKTARLYYFDD 137
Cdd:pfam18774  19 WGRGTiWRNWTENNCTEHAEVNFLENFRSE--RPSRSCTITWYLSWSPCWECSGRILEFLSRHPNVTLGIYVARLFMHDD 96

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1028909627 138 TDYQEGLRSLSQEGASVEIMGYKDFKYCWENFV 170
Cdd:pfam18774  97 DRNRQGLRILQMNGVTIQVMMNKDYCYCWKAFK 129
APOBEC4 pfam18775
APOBEC4; A member of the AID/APOBEC family of cytosine deaminases. The biological function of ...
 97-170 5.17e-23

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: 87.39  E-value: 5.17e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1028909627  97 VTWYTSWSPCPECAGEVAEFLARHSNVNLTIKTARLYYFDDTDYQEGLRSLSQEGASVEIMGYKDFKYCWENFV 170
Cdd:pfam18775   1 VTLYLSWSPCNECSEKIQEFLKKHPKVNLDIYFAQLYHTEEEDNRQGLRSLVEKGVTLSVMSGEDWIYCLRTFV 74
APOBEC1 pfam18769
APOBEC1; APOBEC1 deaminates cytosine both in RNA and ssDNA and has roles in both mRNA editing ...
 72-157 9.18e-20

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: 79.86  E-value: 9.18e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1028909627  72 TGRHAERCFL-SWFADDILSPNTNYEVTWYTSWSPCPECAGEVAEFLARHSNVNLTIKTARLYYFDDTDYQEGLRSLSQE 150
Cdd:pfam18769  15 TTQHAEVNFLeKFFSERHFDPSVSCSITWFLSWSPCGECSKAIGEFLSQHPNVTLVIYAARLFKHLDIRNRQGLRDLAMS 94


                  ....*..
gi 1028909627 151 GASVEIM 157
Cdd:pfam18769  95 GVTIQIM 101
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 17-167 9.57e-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: 67.37  E-value: 9.57e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1028909627  17 PMEAMDPHIFYFhfknlrkAYGRNESWLCftMEVVKHHSPVswkRGVFRNQVDPETGRHAERCFLSWFADDILspnTNYE 96
Cdd:cd01283     1 IEAALAAAEFAY-------APYSNFTVGA--ALLTKDGRIF---TGVNVENASYGLTLCAERTAIGKAVSEGL---RRYL 65

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1028909627  97 VTWYTS-----WSPCPECAGEVAEFLArhsnvnltiktARLYYFDDTDYQEglrslsqegasveimgykDFKYCWE 167
Cdd:cd01283    66 VTWAVSdeggvWSPCGACRQVLAEFLP-----------SRLYIIIDNPKGE------------------EFAYTLS 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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