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Conserved domains on  [gi|742161518|ref|XP_010883228|]
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single-stranded DNA cytosine deaminase [Esox lucius]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NAD1 pfam18778
Novel AID APOBEC clade 1; A distinct family of AID/APOBEC-like deaminases found in ray-finned ...
 9-196 1.50e-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: 232.94  E-value: 1.50e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742161518    9 LLAQKRFIYNYKNVRWAKGRHETYLCFVVKRRNgpnSHSLDFGHLRN-RSGCHVEVLFLRLLGagalcpgLWGYGTPDsg 87
Cdd:pfam18778   2 RMSPETFKFQFKNVEYASGRNKTLLCYEVKRGN---SSSLWRGHLRNeNSGCHAEICFLRWFS-------SWRLFDPS-- 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742161518   88 gLCYSVTWFCSWSPCSDCSYRLAQFLSQTPNLRLRIYVSRLYFCdlEDSLEREGLRLLQRAGVKITIMGYEDYFYCWHTF 167
Cdd:pfam18778  70 -QCYTITWYLSWSPCPSCAAKLAEFLKAHPNVTLTIFAARLYYF--EDPWNQEGLRSLASAGVTLSIMDYSDFEYCWENF 146

                         170       180
                  ....*....|....*....|....*....
gi 742161518  168 VACRNSLFKAWDGLHQNYVRLARKLNHIL 196
Cdd:pfam18778 147 VDNEGRPFVPWEDLEENSRYYHRKLQRIL 175
 
Name Accession Description Interval E-value
NAD1 pfam18778
Novel AID APOBEC clade 1; A distinct family of AID/APOBEC-like deaminases found in ray-finned ...
 9-196 1.50e-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: 232.94  E-value: 1.50e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742161518    9 LLAQKRFIYNYKNVRWAKGRHETYLCFVVKRRNgpnSHSLDFGHLRN-RSGCHVEVLFLRLLGagalcpgLWGYGTPDsg 87
Cdd:pfam18778   2 RMSPETFKFQFKNVEYASGRNKTLLCYEVKRGN---SSSLWRGHLRNeNSGCHAEICFLRWFS-------SWRLFDPS-- 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742161518   88 gLCYSVTWFCSWSPCSDCSYRLAQFLSQTPNLRLRIYVSRLYFCdlEDSLEREGLRLLQRAGVKITIMGYEDYFYCWHTF 167
Cdd:pfam18778  70 -QCYTITWYLSWSPCPSCAAKLAEFLKAHPNVTLTIFAARLYYF--EDPWNQEGLRSLASAGVTLSIMDYSDFEYCWENF 146

                         170       180
                  ....*....|....*....|....*....
gi 742161518  168 VACRNSLFKAWDGLHQNYVRLARKLNHIL 196
Cdd:pfam18778 147 VDNEGRPFVPWEDLEENSRYYHRKLQRIL 175
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 24-129 7.47e-06

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: 43.48  E-value: 7.47e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742161518  24 WAKGRHETYLCFVVKRrngpnSHSLDFGHLRN----RSGCHVEVLFLRLLgagalcpglwgygtPDSGGLCYSVTWFCS- 98
Cdd:cd01283   12 YAPYSNFTVGAALLTK-----DGRIFTGVNVEnasyGLTLCAERTAIGKA--------------VSEGLRRYLVTWAVSd 72

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 742161518  99 ----WSPCSDCSYRLAQFLSQtpnlRLRIYVSRLY 129
Cdd:cd01283   73 eggvWSPCGACRQVLAEFLPS----RLYIIIDNPK 103
 
Name Accession Description Interval E-value
NAD1 pfam18778
Novel AID APOBEC clade 1; A distinct family of AID/APOBEC-like deaminases found in ray-finned ...
 9-196 1.50e-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: 232.94  E-value: 1.50e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742161518    9 LLAQKRFIYNYKNVRWAKGRHETYLCFVVKRRNgpnSHSLDFGHLRN-RSGCHVEVLFLRLLGagalcpgLWGYGTPDsg 87
Cdd:pfam18778   2 RMSPETFKFQFKNVEYASGRNKTLLCYEVKRGN---SSSLWRGHLRNeNSGCHAEICFLRWFS-------SWRLFDPS-- 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742161518   88 gLCYSVTWFCSWSPCSDCSYRLAQFLSQTPNLRLRIYVSRLYFCdlEDSLEREGLRLLQRAGVKITIMGYEDYFYCWHTF 167
Cdd:pfam18778  70 -QCYTITWYLSWSPCPSCAAKLAEFLKAHPNVTLTIFAARLYYF--EDPWNQEGLRSLASAGVTLSIMDYSDFEYCWENF 146

                         170       180
                  ....*....|....*....|....*....
gi 742161518  168 VACRNSLFKAWDGLHQNYVRLARKLNHIL 196
Cdd:pfam18778 147 VDNEGRPFVPWEDLEENSRYYHRKLQRIL 175
APOBEC2 pfam18772
APOBEC2; APOBEC2 is a highly conserved (slow-evolving) family of AID/APOBECs found in most ...
 10-197 1.25e-77

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: 230.56  E-value: 1.25e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742161518   10 LAQKRFIYNYKNVRWAKGRHETYLCFVVKRRNGPNShSLDFGHLRNRSGCHVEVLFLRLLGAGALCPGLwgygtpdsggl 89
Cdd:pfam18772   1 MDPKTFKFQFKNVPYASGRNKTYLCYEVETRSGSDL-SPDRGYLRNQAGCHAELCFLSWILPWQLDPGQ----------- 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742161518   90 CYSVTWFCSWSPCSDCSYRLAQFLSQTPNLRLRIYVSRLYFCDLEDSleREGLRLLQRAGVKITIMGYEDYFYCWHTFVA 169
Cdd:pfam18772  69 KYQVTWYVSWSPCPDCARKLAEFLARHPNLSLTIFAARLYFFWEPEY--QEGLRRLKRAGAQLKIMDYQDFEYCWENFVD 146

                         170       180
                  ....*....|....*....|....*...
gi 742161518  170 CRNSLFKAWDGLHQNYVRLARKLNHILQ 197
Cdd:pfam18772 147 NQGRPFEPWEDLDENYEYLSRKLQEILR 174
APOBEC_N pfam08210
APOBEC-like N-terminal domain; A mechanism of generating protein diversity is mRNA editing. ...
 15-194 3.80e-71

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: 213.77  E-value: 3.80e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742161518   15 FIYNYKNVRWAKGRHETYLCFVVKRRNGpNSHSLDFGHLRNR--SGCHVEVLFLRLLGAGALCPGLwgygtpdsgglCYS 92
Cdd:pfam08210   1 FFFHFKNLPYASGRHETYLCYEVKRDSG-GLVVEDKGYLRNQaaSSLHAEERFLRWIHDLALDPGS-----------NYE 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742161518   93 VTWFCSWSPCSDCSYRLAQFLSQTPNLRLRIYVSRLYFCDLEDSLEREGLRLLQRAGVKITIMGYEDYFYCWHTFVACRN 172
Cdd:pfam08210  69 VTWYVSWSPCNECASELAAFLSKHPNVRLRIFVSRLYYWEEPDYWNREGLRSLAQAGVQLRPMSYKDFEYCWNNFVDHDG 148

                         170       180
                  ....*....|....*....|..
gi 742161518  173 SLFKAWDGLHQNYVRLARKLNH 194
Cdd:pfam08210 149 EPFKPWDGLHENSVYLARKLQE 170
NAD2 pfam18782
Novel AID APOBEC clade 2; A distnct family of AID/APOBEC deaminases found only in Amphibians.
 9-196 5.39e-52

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: 165.62  E-value: 5.39e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742161518    9 LLAQKRFIYNYKNVRWAKGRHETYLCFVVKRRNGPNSHSLDFGHLRNRSGCHVEVLFLRLLGAGALCPGLwgygtpdsgg 88
Cdd:pfam18782   2 RMYPRTFYFNFNNKPILYGRNKTYLCYEVERLDNGTWLPQHRGFFRNQAKYHAELCFLSWFCGNQLPPYQ---------- 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742161518   89 lCYSVTWFCSWSPCSDCSYRLAQFLSQTPNLRLRIYVSRLYFcdLEDSLEREGLRLLQRAGVKITIMGYEDYFYCWHTFV 168
Cdd:pfam18782  72 -NYQVTWYVSWSPCPECAGEVAEFLAEHPNVTLTIFAARLYY--FWDPDYQEALRRLRQAGARVKIMDYEEFEYCWENFV 148

                         170       180
                  ....*....|....*....|....*...
gi 742161518  169 ACRNSLFKAWDGLHQNYVRLARKLNHIL 196
Cdd:pfam18782 149 YNQGEPFQPWDGLEENSRFLHRRLREIL 176
SNAD4 pfam18750
Secreted Novel AID/APOBEC-like Deaminase 4; A family of secreted AID/APOBEC like deaminases ...
 35-166 4.39e-42

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: 138.16  E-value: 4.39e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742161518   35 FVVKRRNGpnSHSLDFGHLRNRSGCHVEVLFLRLLGAGALCPGLwgygtpdsgglCYSVTWFCSWSPCSDCSYRLAQFLS 114
Cdd:pfam18750   1 YEIKWGNG--SKIWQRGYLSNEHEQHAEICFLENIRSRELDPSQ-----------RYRVTWYLSWSPCPECAQKIAEFLA 67

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 742161518  115 QTPNLRLRIYVSRLYFCDLEdslEREGLRLLQRAGVKITIMGYEDYFYCWHT 166
Cdd:pfam18750  68 EHPNVTLTIFAARLYHWDED---NRQGLRSLAQAGVTLQIMTLEDFEYCWKN 116
APOBEC_C pfam05240
APOBEC-like C-terminal domain; This domain is found at the C-termini of the Apolipoprotein B ...
 117-196 1.14e-31

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: 110.27  E-value: 1.14e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742161518  117 PNLRLRIYVSRLYFCDleDSLEREGLRLLQRAGVKITIMGYEDYFYCWHTFVACRNSLFKAWDGLHQNYVRLARKLNHIL 196
Cdd:pfam05240   1 PNVSLTIFAARLYYHW--DPEYQQGLRRLVQAGAQVAIMSYKEFEYCWDNFVDNQGRPFQPWEGLEENSQLLSRRLQEIL 78
APOBEC3 pfam18771
APOBEC3; APOBEC3 deaminases act as restriction factors in the innate response to retroviruses ...
 31-168 3.18e-28

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: 103.34  E-value: 3.18e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742161518   31 TYLCFVVKRRNGpnsHSLDFGHLRNRSGCHVEVLFLRLLGAGALcpglwgygtpdSGGLCYSVTWFCSWSPCSDCSYRLA 110
Cdd:pfam18771   6 AYLCYQLKGRNG---SALDRGYFSNKKKRHAEIRFIDKIRSLDL-----------DNIQCYRITCYITWSPCPNCAAELV 71

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 742161518  111 QFLSQTPNLRLRIYVSRLYFCDLEDSleREGLRLLQRAGVKITIMGYEDYFYCWHTFV 168
Cdd:pfam18771  72 DFISLNPHLKLRIFASRLYYHWERSY--KEGLQKLQRAGVSVAVMTLPEFQDCWEDFV 127
APOBEC4_like pfam18774
APOBEC4-like -AID/APOBEC-deaminase; Cnidarian and Algal homologs of the APOBEC4-like AID ...
 54-170 2.31e-23

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: 90.70  E-value: 2.31e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742161518   54 RNRSGCHVEVLFLRLLgagalcpglwgygTPDSGGLCYSVTWFCSWSPCSDCSYRLAQFLSQTPNLRLRIYVSRLYFCDL 133
Cdd:pfam18774  30 ENNCTEHAEVNFLENF-------------RSERPSRSCTITWYLSWSPCWECSGRILEFLSRHPNVTLGIYVARLFMHDD 96

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 742161518  134 EDSleREGLRLLQRAGVKITIMGYEDYFYCWHTFVAC 170
Cdd:pfam18774  97 DRN--RQGLRILQMNGVTIQVMMNKDYCYCWKAFKNY 131
APOBEC4 pfam18775
APOBEC4; A member of the AID/APOBEC family of cytosine deaminases. The biological function of ...
 93-168 7.22e-21

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: 82.38  E-value: 7.22e-21
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 742161518   93 VTWFCSWSPCSDCSYRLAQFLSQTPNLRLRIYVSRLYFCDLEDSleREGLRLLQRAGVKITIMGYEDYFYCWHTFV 168
Cdd:pfam18775   1 VTLYLSWSPCNECSEKIQEFLKKHPKVNLDIYFAQLYHTEEEDN--RQGLRSLVEKGVTLSVMSGEDWIYCLRTFV 74
APOBEC1 pfam18769
APOBEC1; APOBEC1 deaminates cytosine both in RNA and ssDNA and has roles in both mRNA editing ...
 92-155 5.89e-17

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: 72.92  E-value: 5.89e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 742161518   92 SVTWFCSWSPCSDCSYRLAQFLSQTPNLRLRIYVSRLYfcDLEDSLEREGLRLLQRAGVKITIM 155
Cdd:pfam18769  40 SITWFLSWSPCGECSKAIGEFLSQHPNVTLVIYAARLF--KHLDIRNRQGLRDLAMSGVTIQIM 101
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 24-129 7.47e-06

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: 43.48  E-value: 7.47e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742161518  24 WAKGRHETYLCFVVKRrngpnSHSLDFGHLRN----RSGCHVEVLFLRLLgagalcpglwgygtPDSGGLCYSVTWFCS- 98
Cdd:cd01283   12 YAPYSNFTVGAALLTK-----DGRIFTGVNVEnasyGLTLCAERTAIGKA--------------VSEGLRRYLVTWAVSd 72

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 742161518  99 ----WSPCSDCSYRLAQFLSQtpnlRLRIYVSRLY 129
Cdd:cd01283   73 eggvWSPCGACRQVLAEFLPS----RLYIIIDNPK 103
 
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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