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Conserved domains on  [gi|342366802|ref|NP_001230151|]
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single-stranded DNA cytosine deaminase [Gallus gallus]

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 ...
 5-180 3.29e-91

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: 264.14  E-value: 3.29e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 342366802    5 LMKRKLFLYNFKNLRWAKGRRETYLCYVVKRRDSatsCSLDFGYLRN-KMGCHVEVLFLRYISAWDL-DPGRCYRITWFT 82
Cdd:pfam18778   2 RMSPETFKFQFKNVEYASGRNKTLLCYEVKRGNS---SSLWRGHLRNeNSGCHAEICFLRWFSSWRLfDPSQCYTITWYL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 342366802   83 SWSPCYDCARHVADFLRAYPNLTLRIFTARLYFCEDRkAEPEGLRRLHRAGAQIAIMTFKDFFYCWNTFVENREKTFKAW 162
Cdd:pfam18778  79 SWSPCPSCAAKLAEFLKAHPNVTLTIFAARLYYFEDP-WNQEGLRSLASAGVTLSIMDYSDFEYCWENFVDNEGRPFVPW 157

                         170
                  ....*....|....*...
gi 342366802  163 EGLHENSVHLSRKLRRIL 180
Cdd:pfam18778 158 EDLEENSRYYHRKLQRIL 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 ...
 5-180 3.29e-91

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: 264.14  E-value: 3.29e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 342366802    5 LMKRKLFLYNFKNLRWAKGRRETYLCYVVKRRDSatsCSLDFGYLRN-KMGCHVEVLFLRYISAWDL-DPGRCYRITWFT 82
Cdd:pfam18778   2 RMSPETFKFQFKNVEYASGRNKTLLCYEVKRGNS---SSLWRGHLRNeNSGCHAEICFLRWFSSWRLfDPSQCYTITWYL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 342366802   83 SWSPCYDCARHVADFLRAYPNLTLRIFTARLYFCEDRkAEPEGLRRLHRAGAQIAIMTFKDFFYCWNTFVENREKTFKAW 162
Cdd:pfam18778  79 SWSPCPSCAAKLAEFLKAHPNVTLTIFAARLYYFEDP-WNQEGLRSLASAGVTLSIMDYSDFEYCWENFVDNEGRPFVPW 157

                         170
                  ....*....|....*...
gi 342366802  163 EGLHENSVHLSRKLRRIL 180
Cdd:pfam18778 158 EDLEENSRYYHRKLQRIL 175
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 20-129 6.02e-12

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: 59.66  E-value: 6.02e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 342366802  20 WAKGRRETYLCYVVKRrdsatSCSLDFGYLRNK----MGCHVEVLFLRYISAWDLdpgRCYRITWFTS-----WSPCYDC 90
Cdd:cd01283   12 YAPYSNFTVGAALLTK-----DGRIFTGVNVENasygLTLCAERTAIGKAVSEGL---RRYLVTWAVSdeggvWSPCGAC 83

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 342366802  91 ARHVADFLRaypnltlriftARLYFCEDRKAEPEGLRRL 129
Cdd:cd01283   84 RQVLAEFLP-----------SRLYIIIDNPKGEEFAYTL 111
 
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 ...
 5-180 3.29e-91

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: 264.14  E-value: 3.29e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 342366802    5 LMKRKLFLYNFKNLRWAKGRRETYLCYVVKRRDSatsCSLDFGYLRN-KMGCHVEVLFLRYISAWDL-DPGRCYRITWFT 82
Cdd:pfam18778   2 RMSPETFKFQFKNVEYASGRNKTLLCYEVKRGNS---SSLWRGHLRNeNSGCHAEICFLRWFSSWRLfDPSQCYTITWYL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 342366802   83 SWSPCYDCARHVADFLRAYPNLTLRIFTARLYFCEDRkAEPEGLRRLHRAGAQIAIMTFKDFFYCWNTFVENREKTFKAW 162
Cdd:pfam18778  79 SWSPCPSCAAKLAEFLKAHPNVTLTIFAARLYYFEDP-WNQEGLRSLASAGVTLSIMDYSDFEYCWENFVDNEGRPFVPW 157

                         170
                  ....*....|....*...
gi 342366802  163 EGLHENSVHLSRKLRRIL 180
Cdd:pfam18778 158 EDLEENSRYYHRKLQRIL 175
APOBEC2 pfam18772
APOBEC2; APOBEC2 is a highly conserved (slow-evolving) family of AID/APOBECs found in most ...
 6-180 3.02e-87

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: 254.06  E-value: 3.02e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 342366802    6 MKRKLFLYNFKNLRWAKGRRETYLCYVVKRRDSATScSLDFGYLRNKMGCHVEVLFLRYISAWDLDPGRCYRITWFTSWS 85
Cdd:pfam18772   1 MDPKTFKFQFKNVPYASGRNKTYLCYEVETRSGSDL-SPDRGYLRNQAGCHAELCFLSWILPWQLDPGQKYQVTWYVSWS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 342366802   86 PCYDCARHVADFLRAYPNLTLRIFTARLYFCEDRKAEpEGLRRLHRAGAQIAIMTFKDFFYCWNTFVENREKTFKAWEGL 165
Cdd:pfam18772  80 PCPDCARKLAEFLARHPNLSLTIFAARLYFFWEPEYQ-EGLRRLKRAGAQLKIMDYQDFEYCWENFVDNQGRPFEPWEDL 158

                         170
                  ....*....|....*
gi 342366802  166 HENSVHLSRKLRRIL 180
Cdd:pfam18772 159 DENYEYLSRKLQEIL 173
APOBEC_N pfam08210
APOBEC-like N-terminal domain; A mechanism of generating protein diversity is mRNA editing. ...
 11-178 1.33e-80

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: 237.26  E-value: 1.33e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 342366802   11 FLYNFKNLRWAKGRRETYLCYVVKRRDSATSCsLDFGYLRNKMG--CHVEVLFLRYISAWDLDPGRCYRITWFTSWSPCY 88
Cdd:pfam08210   1 FFFHFKNLPYASGRHETYLCYEVKRDSGGLVV-EDKGYLRNQAAssLHAEERFLRWIHDLALDPGSNYEVTWYVSWSPCN 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 342366802   89 DCARHVADFLRAYPNLTLRIFTARLYFCEDRK-AEPEGLRRLHRAGAQIAIMTFKDFFYCWNTFVENREKTFKAWEGLHE 167
Cdd:pfam08210  80 ECASELAAFLSKHPNVRLRIFVSRLYYWEEPDyWNREGLRSLAQAGVQLRPMSYKDFEYCWNNFVDHDGEPFKPWDGLHE 159

                         170
                  ....*....|.
gi 342366802  168 NSVHLSRKLRR 178
Cdd:pfam08210 160 NSVYLARKLQE 170
NAD2 pfam18782
Novel AID APOBEC clade 2; A distnct family of AID/APOBEC deaminases found only in Amphibians.
 5-180 2.72e-69

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: 208.76  E-value: 2.72e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 342366802    5 LMKRKLFLYNFKNLRWAKGRRETYLCYVVKRRDSATSCSLDFGYLRNKMGCHVEVLFLRYISAWDLDPGRCYRITWFTSW 84
Cdd:pfam18782   2 RMYPRTFYFNFNNKPILYGRNKTYLCYEVERLDNGTWLPQHRGFFRNQAKYHAELCFLSWFCGNQLPPYQNYQVTWYVSW 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 342366802   85 SPCYDCARHVADFLRAYPNLTLRIFTARLYFCEDRKAEpEGLRRLHRAGAQIAIMTFKDFFYCWNTFVENREKTFKAWEG 164
Cdd:pfam18782  82 SPCPECAGEVAEFLAEHPNVTLTIFAARLYYFWDPDYQ-EALRRLRQAGARVKIMDYEEFEYCWENFVYNQGEPFQPWDG 160

                         170
                  ....*....|....*.
gi 342366802  165 LHENSVHLSRKLRRIL 180
Cdd:pfam18782 161 LEENSRFLHRRLREIL 176
SNAD4 pfam18750
Secreted Novel AID/APOBEC-like Deaminase 4; A family of secreted AID/APOBEC like deaminases ...
 31-150 2.49e-51

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: 160.89  E-value: 2.49e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 342366802   31 YVVKRRDSatSCSLDFGYLRNKMGCHVEVLFLRYISAWDLDPGRCYRITWFTSWSPCYDCARHVADFLRAYPNLTLRIFT 110
Cdd:pfam18750   1 YEIKWGNG--SKIWQRGYLSNEHEQHAEICFLENIRSRELDPSQRYRVTWYLSWSPCPECAQKIAEFLAEHPNVTLTIFA 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 342366802  111 ARLYFCEDRkaEPEGLRRLHRAGAQIAIMTFKDFFYCWNT 150
Cdd:pfam18750  79 ARLYHWDED--NRQGLRSLAQAGVTLQIMTLEDFEYCWKN 116
APOBEC3 pfam18771
APOBEC3; APOBEC3 deaminases act as restriction factors in the innate response to retroviruses ...
 24-160 3.60e-40

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: 133.38  E-value: 3.60e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 342366802   24 RRETYLCYVVKRRDSATscsLDFGYLRNKMGCHVEVLFLRYISAWDLDPGRCYRITWFTSWSPCYDCARHVADFLRAYPN 103
Cdd:pfam18771   3 DRKAYLCYQLKGRNGSA---LDRGYFSNKKKRHAEIRFIDKIRSLDLDNIQCYRITCYITWSPCPNCAAELVDFISLNPH 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 342366802  104 LTLRIFTARLYFcEDRKAEPEGLRRLHRAGAQIAIMTFKDFFYCWNTFVENREKTFK 160
Cdd:pfam18771  80 LKLRIFASRLYY-HWERSYKEGLQKLQRAGVSVAVMTLPEFQDCWEDFVDHQEEPFR 135
APOBEC_C pfam05240
APOBEC-like C-terminal domain; This domain is found at the C-termini of the Apolipoprotein B ...
 102-180 1.13e-37

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: 124.90  E-value: 1.13e-37
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 342366802  102 PNLTLRIFTARLYFCEDRKaEPEGLRRLHRAGAQIAIMTFKDFFYCWNTFVENREKTFKAWEGLHENSVHLSRKLRRIL 180
Cdd:pfam05240   1 PNVSLTIFAARLYYHWDPE-YQQGLRRLVQAGAQVAIMSYKEFEYCWDNFVDNQGRPFQPWEGLEENSQLLSRRLQEIL 78
APOBEC4_like pfam18774
APOBEC4-like -AID/APOBEC-deaminase; Cnidarian and Algal homologs of the APOBEC4-like AID ...
 50-153 1.69e-22

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: 88.01  E-value: 1.69e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 342366802   50 RNKMGCHVEVLFLRYISawDLDPGRCYRITWFTSWSPCYDCARHVADFLRAYPNLTLRIFTARLYFCEDRKAEpEGLRRL 129
Cdd:pfam18774  30 ENNCTEHAEVNFLENFR--SERPSRSCTITWYLSWSPCWECSGRILEFLSRHPNVTLGIYVARLFMHDDDRNR-QGLRIL 106

                          90       100
                  ....*....|....*....|....
gi 342366802  130 HRAGAQIAIMTFKDFFYCWNTFVE 153
Cdd:pfam18774 107 QMNGVTIQVMMNKDYCYCWKAFKN 130
APOBEC1 pfam18769
APOBEC1; APOBEC1 deaminates cytosine both in RNA and ssDNA and has roles in both mRNA editing ...
 56-139 1.20e-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: 77.16  E-value: 1.20e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 342366802   56 HVEVLFL-RYISAWDLDPGRCYRITWFTSWSPCYDCARHVADFLRAYPNLTLRIFTARLYFCEDRKAEpEGLRRLHRAGA 134
Cdd:pfam18769  18 HAEVNFLeKFFSERHFDPSVSCSITWFLSWSPCGECSKAIGEFLSQHPNVTLVIYAARLFKHLDIRNR-QGLRDLAMSGV 96


                  ....*
gi 342366802  135 QIAIM 139
Cdd:pfam18769  97 TIQIM 101
APOBEC4 pfam18775
APOBEC4; A member of the AID/APOBEC family of cytosine deaminases. The biological function of ...
 78-152 4.66e-18

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: 74.68  E-value: 4.66e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 342366802   78 ITWFTSWSPCYDCARHVADFLRAYPNLTLRIFTARLYFCEDrKAEPEGLRRLHRAGAQIAIMTFKDFFYCWNTFV 152
Cdd:pfam18775   1 VTLYLSWSPCNECSEKIQEFLKKHPKVNLDIYFAQLYHTEE-EDNRQGLRSLVEKGVTLSVMSGEDWIYCLRTFV 74
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 20-129 6.02e-12

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: 59.66  E-value: 6.02e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 342366802  20 WAKGRRETYLCYVVKRrdsatSCSLDFGYLRNK----MGCHVEVLFLRYISAWDLdpgRCYRITWFTS-----WSPCYDC 90
Cdd:cd01283   12 YAPYSNFTVGAALLTK-----DGRIFTGVNVENasygLTLCAERTAIGKAVSEGL---RRYLVTWAVSdeggvWSPCGAC 83

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 342366802  91 ARHVADFLRaypnltlriftARLYFCEDRKAEPEGLRRL 129
Cdd:cd01283   84 RQVLAEFLP-----------SRLYIIIDNPKGEEFAYTL 111
 
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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