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Conserved domains on  [gi|2462491741|ref|XP_054185589|]
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probable DNA dC-

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NAD2 super family cl40079
Novel AID APOBEC clade 2; A distnct family of AID/APOBEC deaminases found only in Amphibians.
 11-157 1.48e-68

Novel AID APOBEC clade 2; A distnct family of AID/APOBEC deaminases found only in Amphibians.


The actual alignment was detected with superfamily member pfam18782:

Pssm-ID: 436733 [Multi-domain]  Cd Length: 176  Bit Score: 207.22  E-value: 1.48e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462491741  11 HLMDPHIFTSNFNN---GIGRHKTYLCYEVERLDNGTSVKmdQHRGFLHNQAKnllcgfygRHAELRFLDLVPSLQLDPA 87
Cdd:pfam18782   1 KRMYPRTFYFNFNNkpiLYGRNKTYLCYEVERLDNGTWLP--QHRGFFRNQAK--------YHAELCFLSWFCGNQLPPY 70

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462491741  88 QIYRVTWFISWSPCFSwgCAGEVRAFLQENTHVRLRIFAARIY-DYDPLYKEALQMLRDAGAQVSIMTYDE 157
Cdd:pfam18782  71 QNYQVTWYVSWSPCPE--CAGEVAEFLAEHPNVTLTIFAARLYyFWDPDYQEALRRLRQAGARVKIMDYEE 139
 
Name Accession Description Interval E-value
NAD2 pfam18782
Novel AID APOBEC clade 2; A distnct family of AID/APOBEC deaminases found only in Amphibians.
 11-157 1.48e-68

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: 207.22  E-value: 1.48e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462491741  11 HLMDPHIFTSNFNN---GIGRHKTYLCYEVERLDNGTSVKmdQHRGFLHNQAKnllcgfygRHAELRFLDLVPSLQLDPA 87
Cdd:pfam18782   1 KRMYPRTFYFNFNNkpiLYGRNKTYLCYEVERLDNGTWLP--QHRGFFRNQAK--------YHAELCFLSWFCGNQLPPY 70

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462491741  88 QIYRVTWFISWSPCFSwgCAGEVRAFLQENTHVRLRIFAARIY-DYDPLYKEALQMLRDAGAQVSIMTYDE 157
Cdd:pfam18782  71 QNYQVTWYVSWSPCPE--CAGEVAEFLAEHPNVTLTIFAARLYyFWDPDYQEALRRLRQAGARVKIMDYEE 139
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 9-120 5.47e-11

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: 57.35  E-value: 5.47e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462491741   9 PRHLMDPHiftsNFNNGIGRHKTYLCYEVERldngtsvKMDQHRGFLHNQAknllCGFYGRHAELRFLDLVPSLQLdpaQ 88
Cdd:cd01283     1 IEAALAAA----EFAYAPYSNFTVGAALLTK-------DGRIFTGVNVENA----SYGLTLCAERTAIGKAVSEGL---R 62

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2462491741  89 IYRVTWFIS-----WSPCFSwgCAGEVRAFLQENTHV 120
Cdd:cd01283    63 RYLVTWAVSdeggvWSPCGA--CRQVLAEFLPSRLYI 97
 
Name Accession Description Interval E-value
NAD2 pfam18782
Novel AID APOBEC clade 2; A distnct family of AID/APOBEC deaminases found only in Amphibians.
 11-157 1.48e-68

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: 207.22  E-value: 1.48e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462491741  11 HLMDPHIFTSNFNN---GIGRHKTYLCYEVERLDNGTSVKmdQHRGFLHNQAKnllcgfygRHAELRFLDLVPSLQLDPA 87
Cdd:pfam18782   1 KRMYPRTFYFNFNNkpiLYGRNKTYLCYEVERLDNGTWLP--QHRGFFRNQAK--------YHAELCFLSWFCGNQLPPY 70

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462491741  88 QIYRVTWFISWSPCFSwgCAGEVRAFLQENTHVRLRIFAARIY-DYDPLYKEALQMLRDAGAQVSIMTYDE 157
Cdd:pfam18782  71 QNYQVTWYVSWSPCPE--CAGEVAEFLAEHPNVTLTIFAARLYyFWDPDYQEALRRLRQAGARVKIMDYEE 139
APOBEC2 pfam18772
APOBEC2; APOBEC2 is a highly conserved (slow-evolving) family of AID/APOBECs found in most ...
 13-157 2.04e-55

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: 173.94  E-value: 2.04e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462491741  13 MDPHIFTSNFNNGI---GRHKTYLCYEVERLDNGTSvkmDQHRGFLHNQAknllcgfyGRHAELRFLDLVPSLQLDPAQI 89
Cdd:pfam18772   1 MDPKTFKFQFKNVPyasGRNKTYLCYEVETRSGSDL---SPDRGYLRNQA--------GCHAELCFLSWILPWQLDPGQK 69

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462491741  90 YRVTWFISWSPCFSwgCAGEVRAFLQENTHVRLRIFAARIYDY-DPLYKEALQMLRDAGAQVSIMTYDE 157
Cdd:pfam18772  70 YQVTWYVSWSPCPD--CARKLAEFLARHPNLSLTIFAARLYFFwEPEYQEGLRRLKRAGAQLKIMDYQD 136
NAD1 pfam18778
Novel AID APOBEC clade 1; A distinct family of AID/APOBEC-like deaminases found in ray-finned ...
 11-157 2.39e-54

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: 171.31  E-value: 2.39e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462491741  11 HLMDPHIFTSNFNN---GIGRHKTYLCYEVERlDNGTSvkmdQHRGFLHNQAKnllcgfyGRHAELRFLDLVPSLQL-DP 86
Cdd:pfam18778   1 ERMSPETFKFQFKNveyASGRNKTLLCYEVKR-GNSSS----LWRGHLRNENS-------GCHAEICFLRWFSSWRLfDP 68

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462491741  87 AQIYRVTWFISWSPCFSwgCAGEVRAFLQENTHVRLRIFAARIYDY-DPLYKEALQMLRDAGAQVSIMTYDE 157
Cdd:pfam18778  69 SQCYTITWYLSWSPCPS--CAAKLAEFLKAHPNVTLTIFAARLYYFeDPWNQEGLRSLASAGVTLSIMDYSD 138
APOBEC_N pfam08210
APOBEC-like N-terminal domain; A mechanism of generating protein diversity is mRNA editing. ...
 20-157 1.08e-46

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: 151.36  E-value: 1.08e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462491741  20 SNFNNGIGRHKTYLCYEVERLDNGTSVkmdQHRGFLHNQAKNllcgfyGRHAELRFLDLVPSLQLDPAQIYRVTWFISWS 99
Cdd:pfam08210   6 KNLPYASGRHETYLCYEVKRDSGGLVV---EDKGYLRNQAAS------SLHAEERFLRWIHDLALDPGSNYEVTWYVSWS 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462491741 100 PCFSwgCAGEVRAFLQENTHVRLRIFAARIY-DYDPLY--KEALQMLRDAGAQVSIMTYDE 157
Cdd:pfam08210  77 PCNE--CASELAAFLSKHPNVRLRIFVSRLYyWEEPDYwnREGLRSLAQAGVQLRPMSYKD 135
SNAD4 pfam18750
Secreted Novel AID/APOBEC-like Deaminase 4; A family of secreted AID/APOBEC like deaminases ...
 35-157 1.50e-44

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: 144.33  E-value: 1.50e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462491741  35 YEVERLDNGTSVkmdqHRGFLHNQAknllcgfyGRHAELRFLDLVPSLQLDPAQIYRVTWFISWSPCFSwgCAGEVRAFL 114
Cdd:pfam18750   1 YEIKWGNGSKIW----QRGYLSNEH--------EQHAEICFLENIRSRELDPSQRYRVTWYLSWSPCPE--CAQKIAEFL 66

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2462491741 115 QENTHVRLRIFAARIYDYDPLYKEALQMLRDAGAQVSIMTYDE 157
Cdd:pfam18750  67 AEHPNVTLTIFAARLYHWDEDNRQGLRSLAQAGVTLQIMTLED 109
APOBEC3 pfam18771
APOBEC3; APOBEC3 deaminases act as restriction factors in the innate response to retroviruses ...
 28-157 1.55e-31

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: 111.81  E-value: 1.55e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462491741  28 RHKTYLCYEVERLDNGTSVkmdqhRGFLHNQAKnllcgfygRHAELRFLDLVPSLQLDPAQIYRVTWFISWSPCFSwgCA 107
Cdd:pfam18771   3 DRKAYLCYQLKGRNGSALD-----RGYFSNKKK--------RHAEIRFIDKIRSLDLDNIQCYRITCYITWSPCPN--CA 67

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2462491741 108 GEVRAFLQENTHVRLRIFAARIYDYD-PLYKEALQMLRDAGAQVSIMTYDE 157
Cdd:pfam18771  68 AELVDFISLNPHLKLRIFASRLYYHWeRSYKEGLQKLQRAGVSVAVMTLPE 118
APOBEC_C pfam05240
APOBEC-like C-terminal domain; This domain is found at the C-termini of the Apolipoprotein B ...
 119-157 2.70e-14

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: 65.20  E-value: 2.70e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2462491741 119 HVRLRIFAARIYD-YDPLYKEALQMLRDAGAQVSIMTYDE 157
Cdd:pfam05240   2 NVSLTIFAARLYYhWDPEYQQGLRRLVQAGAQVAIMSYKE 41
APOBEC1 pfam18769
APOBEC1; APOBEC1 deaminates cytosine both in RNA and ssDNA and has roles in both mRNA editing ...
 69-153 3.96e-12

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: 60.21  E-value: 3.96e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462491741  69 RHAELRFLD-LVPSLQLDPAQIYRVTWFISWSPCfsWGCAGEVRAFLQENTHVRLRIFAARIYDY-DPLYKEALQMLRDA 146
Cdd:pfam18769  17 QHAEVNFLEkFFSERHFDPSVSCSITWFLSWSPC--GECSKAIGEFLSQHPNVTLVIYAARLFKHlDIRNRQGLRDLAMS 94


                  ....*..
gi 2462491741 147 GAQVSIM 153
Cdd:pfam18769  95 GVTIQIM 101
APOBEC4_like pfam18774
APOBEC4-like -AID/APOBEC-deaminase; Cnidarian and Algal homologs of the APOBEC4-like AID ...
 21-157 2.83e-11

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: 58.73  E-value: 2.83e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462491741  21 NFNNGIGRHKTYLCYEVerldngtsvKMDQHRGFLHNQAKNLLCgfygrHAELRFLDLVPSLQldPAQIYRVTWFISWSP 100
Cdd:pfam18774   1 NFDPNNHKKEICLLYEI---------QWGRGTIWRNWTENNCTE-----HAEVNFLENFRSER--PSRSCTITWYLSWSP 64

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462491741 101 CfsWGCAGEVRAFLQENTHVRLRIFAARIYDY-DPLYKEALQMLRDAGAQVSIMTYDE 157
Cdd:pfam18774  65 C--WECSGRILEFLSRHPNVTLGIYVARLFMHdDDRNRQGLRILQMNGVTIQVMMNKD 120
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 9-120 5.47e-11

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: 57.35  E-value: 5.47e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462491741   9 PRHLMDPHiftsNFNNGIGRHKTYLCYEVERldngtsvKMDQHRGFLHNQAknllCGFYGRHAELRFLDLVPSLQLdpaQ 88
Cdd:cd01283     1 IEAALAAA----EFAYAPYSNFTVGAALLTK-------DGRIFTGVNVENA----SYGLTLCAERTAIGKAVSEGL---R 62

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2462491741  89 IYRVTWFIS-----WSPCFSwgCAGEVRAFLQENTHV 120
Cdd:cd01283    63 RYLVTWAVSdeggvWSPCGA--CRQVLAEFLPSRLYI 97
APOBEC4 pfam18775
APOBEC4; A member of the AID/APOBEC family of cytosine deaminases. The biological function of ...
 92-153 1.26e-08

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: 50.03  E-value: 1.26e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462491741  92 VTWFISWSPCfsWGCAGEVRAFLQENTHVRLRIFAARIYDYDPLY-KEALQMLRDAGAQVSIM 153
Cdd:pfam18775   1 VTLYLSWSPC--NECSEKIQEFLKKHPKVNLDIYFAQLYHTEEEDnRQGLRSLVEKGVTLSVM 61
 
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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