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Conserved domains on  [gi|669250885|ref|NP_001159474|]
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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 ...
 4-181 6.44e-76

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: 224.79  E-value: 6.44e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 669250885    4 LTAETFRLQFNNKRRLRRPYyprKALLCYQLTPQNGS--TPTRGYFENKKKCHAEICFINEIKSMGLDETQCYQVTCYLT 81
Cdd:pfam18772   1 MDPKTFKFQFKNVPYASGRN---KTYLCYEVETRSGSdlSPDRGYLRNQAGCHAELCFLSWILPWQLDPGQKYQVTWYVS 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 669250885   82 WSPCSSCAWELVDFIKAHDHLNLGIFASRLYYHWCKPQQKGLRLLCGSQVPVEVMGFPEFADCWENFVDHEKPlsfnPYK 161
Cdd:pfam18772  78 WSPCPDCARKLAEFLARHPNLSLTIFAARLYFFWEPEYQEGLRRLKRAGAQLKIMDYQDFEYCWENFVDNQGR----PFE 153

                         170       180
                  ....*....|....*....|
gi 669250885  162 MLEELDKNSRAIKRRLERIK 181
Cdd:pfam18772 154 PWEDLDENYEYLSRKLQEIL 173
 
Name Accession Description Interval E-value
APOBEC2 pfam18772
APOBEC2; APOBEC2 is a highly conserved (slow-evolving) family of AID/APOBECs found in most ...
 4-181 6.44e-76

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: 224.79  E-value: 6.44e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 669250885    4 LTAETFRLQFNNKRRLRRPYyprKALLCYQLTPQNGS--TPTRGYFENKKKCHAEICFINEIKSMGLDETQCYQVTCYLT 81
Cdd:pfam18772   1 MDPKTFKFQFKNVPYASGRN---KTYLCYEVETRSGSdlSPDRGYLRNQAGCHAELCFLSWILPWQLDPGQKYQVTWYVS 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 669250885   82 WSPCSSCAWELVDFIKAHDHLNLGIFASRLYYHWCKPQQKGLRLLCGSQVPVEVMGFPEFADCWENFVDHEKPlsfnPYK 161
Cdd:pfam18772  78 WSPCPDCARKLAEFLARHPNLSLTIFAARLYFFWEPEYQEGLRRLKRAGAQLKIMDYQDFEYCWENFVDNQGR----PFE 153

                         170       180
                  ....*....|....*....|
gi 669250885  162 MLEELDKNSRAIKRRLERIK 181
Cdd:pfam18772 154 PWEDLDENYEYLSRKLQEIL 173
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 30-121 3.49e-13

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: 62.74  E-value: 3.49e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 669250885  30 LCYQLTPQNgsTPTRGYFENKK----KCHAEICFINEIKSMGLdetQCYQVTCYLT-----WSPCSSCAWELVDFikahd 100
Cdd:cd01283   21 GAALLTKDG--RIFTGVNVENAsyglTLCAERTAIGKAVSEGL---RRYLVTWAVSdeggvWSPCGACRQVLAEF----- 90

                         90       100
                 ....*....|....*....|.
gi 669250885 101 hlnlgiFASRLYYHWCKPQQK 121
Cdd:cd01283   91 ------LPSRLYIIIDNPKGE 105
 
Name Accession Description Interval E-value
APOBEC2 pfam18772
APOBEC2; APOBEC2 is a highly conserved (slow-evolving) family of AID/APOBECs found in most ...
 4-181 6.44e-76

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: 224.79  E-value: 6.44e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 669250885    4 LTAETFRLQFNNKRRLRRPYyprKALLCYQLTPQNGS--TPTRGYFENKKKCHAEICFINEIKSMGLDETQCYQVTCYLT 81
Cdd:pfam18772   1 MDPKTFKFQFKNVPYASGRN---KTYLCYEVETRSGSdlSPDRGYLRNQAGCHAELCFLSWILPWQLDPGQKYQVTWYVS 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 669250885   82 WSPCSSCAWELVDFIKAHDHLNLGIFASRLYYHWCKPQQKGLRLLCGSQVPVEVMGFPEFADCWENFVDHEKPlsfnPYK 161
Cdd:pfam18772  78 WSPCPDCARKLAEFLARHPNLSLTIFAARLYFFWEPEYQEGLRRLKRAGAQLKIMDYQDFEYCWENFVDNQGR----PFE 153

                         170       180
                  ....*....|....*....|
gi 669250885  162 MLEELDKNSRAIKRRLERIK 181
Cdd:pfam18772 154 PWEDLDENYEYLSRKLQEIL 173
NAD1 pfam18778
Novel AID APOBEC clade 1; A distinct family of AID/APOBEC-like deaminases found in ray-finned ...
 2-181 3.80e-73

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: 217.92  E-value: 3.80e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 669250885    2 ALLTAETFRLQFNNKRRLRRPYyprKALLCYQLTPQNGSTPTRGYFENKK-KCHAEICFINEIKSMGL-DETQCYQVTCY 79
Cdd:pfam18778   1 ERMSPETFKFQFKNVEYASGRN---KTLLCYEVKRGNSSSLWRGHLRNENsGCHAEICFLRWFSSWRLfDPSQCYTITWY 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 669250885   80 LTWSPCSSCAWELVDFIKAHDHLNLGIFASRLYYHWCKPQQKGLRLLCGSQVPVEVMGFPEFADCWENFVDHEkPLSFNP 159
Cdd:pfam18778  78 LSWSPCPSCAAKLAEFLKAHPNVTLTIFAARLYYFEDPWNQEGLRSLASAGVTLSIMDYSDFEYCWENFVDNE-GRPFVP 156

                         170       180
                  ....*....|....*....|..
gi 669250885  160 YkmlEELDKNSRAIKRRLERIK 181
Cdd:pfam18778 157 W---EDLEENSRYYHRKLQRIL 175
APOBEC3 pfam18771
APOBEC3; APOBEC3 deaminases act as restriction factors in the innate response to retroviruses ...
 27-157 2.89e-72

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: 214.27  E-value: 2.89e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 669250885   27 KALLCYQLTPQNGSTPTRGYFENKKKCHAEICFINEIKSMGLDETQCYQVTCYLTWSPCSSCAWELVDFIKAHDHLNLGI 106
Cdd:pfam18771   5 KAYLCYQLKGRNGSALDRGYFSNKKKRHAEIRFIDKIRSLDLDNIQCYRITCYITWSPCPNCAAELVDFISLNPHLKLRI 84

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 669250885  107 FASRLYYHWCKPQQKGLRLLCGSQVPVEVMGFPEFADCWENFVDHEKPLSF 157
Cdd:pfam18771  85 FASRLYYHWERSYKEGLQKLQRAGVSVAVMTLPEFQDCWEDFVDHQEEPFR 135
NAD2 pfam18782
Novel AID APOBEC clade 2; A distnct family of AID/APOBEC deaminases found only in Amphibians.
 3-181 5.25e-55

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: 171.78  E-value: 5.25e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 669250885    3 LLTAETFRLQFNNKRRLRRPYyprKALLCYQLTPQNGSTPT---RGYFENKKKCHAEICFINEIKSMGLDETQCYQVTCY 79
Cdd:pfam18782   2 RMYPRTFYFNFNNKPILYGRN---KTYLCYEVERLDNGTWLpqhRGFFRNQAKYHAELCFLSWFCGNQLPPYQNYQVTWY 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 669250885   80 LTWSPCSSCAWELVDFIKAHDHLNLGIFASRLYYHWCKPQQKGLRLLCGSQVPVEVMGFPEFADCWENFVDHEKPlSFNP 159
Cdd:pfam18782  79 VSWSPCPECAGEVAEFLAEHPNVTLTIFAARLYYFWDPDYQEALRRLRQAGARVKIMDYEEFEYCWENFVYNQGE-PFQP 157

                         170       180
                  ....*....|....*....|..
gi 669250885  160 YKmleELDKNSRAIKRRLERIK 181
Cdd:pfam18782 158 WD---GLEENSRFLHRRLREIL 176
SNAD4 pfam18750
Secreted Novel AID/APOBEC-like Deaminase 4; A family of secreted AID/APOBEC like deaminases ...
 32-147 6.25e-50

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: 157.04  E-value: 6.25e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 669250885   32 YQLTPQNGSTPT-RGYFENKKKCHAEICFINEIKSMGLDETQCYQVTCYLTWSPCSSCAWELVDFIKAHDHLNLGIFASR 110
Cdd:pfam18750   1 YEIKWGNGSKIWqRGYLSNEHEQHAEICFLENIRSRELDPSQRYRVTWYLSWSPCPECAQKIAEFLAEHPNVTLTIFAAR 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 669250885  111 LyYHWCKPQQKGLRLLCGSQVPVEVMGFPEFADCWEN 147
Cdd:pfam18750  81 L-YHWDEDNRQGLRSLAQAGVTLQIMTLEDFEYCWKN 116
APOBEC_N pfam08210
APOBEC-like N-terminal domain; A mechanism of generating protein diversity is mRNA editing. ...
 9-179 1.94e-39

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: 132.10  E-value: 1.94e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 669250885    9 FRLQFNNkrrLRRPYYPRKALLCYQLTPQNGSTP--TRGYFENKK--KCHAEICFINEIKSMGLDETQCYQVTCYLTWSP 84
Cdd:pfam08210   1 FFFHFKN---LPYASGRHETYLCYEVKRDSGGLVveDKGYLRNQAasSLHAEERFLRWIHDLALDPGSNYEVTWYVSWSP 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 669250885   85 CSSCAWELVDFIKAHDHLNLGIFASRLYYHWCK--PQQKGLRLLCGSQVPVEVMGFPEFADCWENFVDHEkplsFNPYKM 162
Cdd:pfam08210  78 CNECASELAAFLSKHPNVRLRIFVSRLYYWEEPdyWNREGLRSLAQAGVQLRPMSYKDFEYCWNNFVDHD----GEPFKP 153

                         170
                  ....*....|....*..
gi 669250885  163 LEELDKNSRAIKRRLER 179
Cdd:pfam08210 154 WDGLHENSVYLARKLQE 170
APOBEC_C pfam05240
APOBEC-like C-terminal domain; This domain is found at the C-termini of the Apolipoprotein B ...
 101-180 1.42e-30

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: 106.41  E-value: 1.42e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 669250885  101 HLNLGIFASRLYYHWCKPQQKGLRLLCGSQVPVEVMGFPEFADCWENFVDHEKPlSFNPYkmlEELDKNSRAIKRRLERI 180
Cdd:pfam05240   2 NVSLTIFAARLYYHWDPEYQQGLRRLVQAGAQVAIMSYKEFEYCWDNFVDNQGR-PFQPW---EGLEENSQLLSRRLQEI 77
APOBEC4_like pfam18774
APOBEC4-like -AID/APOBEC-deaminase; Cnidarian and Algal homologs of the APOBEC4-like AID ...
 27-150 1.03e-16

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: 72.60  E-value: 1.03e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 669250885   27 KALLCYQLTPQNGS-TPTRGYFENKKKCHAEICFINEIKSMGlDETQCyQVTCYLTWSPCSSCAWELVDFIKAHDHLNLG 105
Cdd:pfam18774   8 KKEICLLYEIQWGRgTIWRNWTENNCTEHAEVNFLENFRSER-PSRSC-TITWYLSWSPCWECSGRILEFLSRHPNVTLG 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 669250885  106 IFASRLYYHWCKPQQKGLRLLCGSQVPVEVMGFPEFADCWENFVD 150
Cdd:pfam18774  86 IYVARLFMHDDDRNRQGLRILQMNGVTIQVMMNKDYCYCWKAFKN 130
APOBEC4 pfam18775
APOBEC4; A member of the AID/APOBEC family of cytosine deaminases. The biological function of ...
 76-149 1.20e-15

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: 68.13  E-value: 1.20e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 669250885   76 VTCYLTWSPCSSCAWELVDFIKAHDHLNLGIFASRLYYHWCKPQQKGLRLLCGSQVPVEVMGFPEFADCWENFV 149
Cdd:pfam18775   1 VTLYLSWSPCNECSEKIQEFLKKHPKVNLDIYFAQLYHTEEEDNRQGLRSLVEKGVTLSVMSGEDWIYCLRTFV 74
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 30-121 3.49e-13

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: 62.74  E-value: 3.49e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 669250885  30 LCYQLTPQNgsTPTRGYFENKK----KCHAEICFINEIKSMGLdetQCYQVTCYLT-----WSPCSSCAWELVDFikahd 100
Cdd:cd01283   21 GAALLTKDG--RIFTGVNVENAsyglTLCAERTAIGKAVSEGL---RRYLVTWAVSdeggvWSPCGACRQVLAEF----- 90

                         90       100
                 ....*....|....*....|.
gi 669250885 101 hlnlgiFASRLYYHWCKPQQK 121
Cdd:cd01283   91 ------LPSRLYIIIDNPKGE 105
 
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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