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Conserved domains on  [gi|85861172|ref|NP_084531|]
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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 ...
 21-198 5.28e-82

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: 248.67  E-value: 5.28e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172    21 ISQETFKFHFKNLGYAKGRKDTFLCYEVTRKDCdSPVSLHHGVFKNKDNIHAEICFLYWFHDKVLkvlSPREEFKITWYM 100
Cdd:pfam18772   1 MDPKTFKFQFKNVPYASGRNKTYLCYEVETRSG-SDLSPDRGYLRNQAGCHAELCFLSWILPWQL---DPGQKYQVTWYV 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172   101 SWSPCFECAEQIVRFLATHHNLSLDIFSSRLYNVQDPETQQNLCRLVQEGAQVAAMDLYEFKKCWKKFVDNGGRRFRPWK 180
Cdd:pfam18772  77 SWSPCPDCARKLAEFLARHPNLSLTIFAARLYFFWEPEYQEGLRRLKRAGAQLKIMDYQDFEYCWENFVDNQGRPFEPWE 156

                         170
                  ....*....|....*...
gi 85861172   181 RLLTNFRYQDSKLQEILR 198
Cdd:pfam18772 157 DLDENYEYLSRKLQEILR 174
NAD2 pfam18782
Novel AID APOBEC clade 2; A distnct family of AID/APOBEC deaminases found only in Amphibians.
 201-363 8.79e-70

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: 217.23  E-value: 8.79e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172   201 DPLSEEEFYSQFYNqrvKHLcYYHRMKPYLCYQLEQFNGQAPL---KGCLLSEKgKQHAEILFLDKIRSMELS---QVTI 274
Cdd:pfam18782   1 KRMYPRTFYFNFNN---KPI-LYGRNKTYLCYEVERLDNGTWLpqhRGFFRNQA-KYHAELCFLSWFCGNQLPpyqNYQV 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172   275 TCYLTWSPCPNCAWQLAAFKRDRPDLILHIYTSRLYFHWKRPFQKGLCSLWQSGILVDVMDLPQFTDCWTNFVNPK-RPF 353
Cdd:pfam18782  76 TWYVSWSPCPECAGEVAEFLAEHPNVTLTIFAARLYYFWDPDYQEALRRLRQAGARVKIMDYEEFEYCWENFVYNQgEPF 155

                         170
                  ....*....|
gi 85861172   354 WPWKGLEIIS 363
Cdd:pfam18782 156 QPWDGLEENS 165
 
Name Accession Description Interval E-value
APOBEC2 pfam18772
APOBEC2; APOBEC2 is a highly conserved (slow-evolving) family of AID/APOBECs found in most ...
 21-198 5.28e-82

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: 248.67  E-value: 5.28e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172    21 ISQETFKFHFKNLGYAKGRKDTFLCYEVTRKDCdSPVSLHHGVFKNKDNIHAEICFLYWFHDKVLkvlSPREEFKITWYM 100
Cdd:pfam18772   1 MDPKTFKFQFKNVPYASGRNKTYLCYEVETRSG-SDLSPDRGYLRNQAGCHAELCFLSWILPWQL---DPGQKYQVTWYV 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172   101 SWSPCFECAEQIVRFLATHHNLSLDIFSSRLYNVQDPETQQNLCRLVQEGAQVAAMDLYEFKKCWKKFVDNGGRRFRPWK 180
Cdd:pfam18772  77 SWSPCPDCARKLAEFLARHPNLSLTIFAARLYFFWEPEYQEGLRRLKRAGAQLKIMDYQDFEYCWENFVDNQGRPFEPWE 156

                         170
                  ....*....|....*...
gi 85861172   181 RLLTNFRYQDSKLQEILR 198
Cdd:pfam18772 157 DLDENYEYLSRKLQEILR 174
NAD2 pfam18782
Novel AID APOBEC clade 2; A distnct family of AID/APOBEC deaminases found only in Amphibians.
 201-363 8.79e-70

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: 217.23  E-value: 8.79e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172   201 DPLSEEEFYSQFYNqrvKHLcYYHRMKPYLCYQLEQFNGQAPL---KGCLLSEKgKQHAEILFLDKIRSMELS---QVTI 274
Cdd:pfam18782   1 KRMYPRTFYFNFNN---KPI-LYGRNKTYLCYEVERLDNGTWLpqhRGFFRNQA-KYHAELCFLSWFCGNQLPpyqNYQV 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172   275 TCYLTWSPCPNCAWQLAAFKRDRPDLILHIYTSRLYFHWKRPFQKGLCSLWQSGILVDVMDLPQFTDCWTNFVNPK-RPF 353
Cdd:pfam18782  76 TWYVSWSPCPECAGEVAEFLAEHPNVTLTIFAARLYYFWDPDYQEALRRLRQAGARVKIMDYEEFEYCWENFVYNQgEPF 155

                         170
                  ....*....|
gi 85861172   354 WPWKGLEIIS 363
Cdd:pfam18782 156 QPWDGLEENS 165
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 35-141 3.59e-14

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: 68.14  E-value: 3.59e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172  35 YAKGRKDTFLCYEVTRKdcdspVSLHHGVFKNK----DNIHAEICFLYWFHDKVLKvlspreEFKITWYMS-----WSPC 105
Cdd:cd01283  12 YAPYSNFTVGAALLTKD-----GRIFTGVNVENasygLTLCAERTAIGKAVSEGLR------RYLVTWAVSdeggvWSPC 80

                        90       100       110
                ....*....|....*....|....*....|....*.
gi 85861172 106 FECAEQIVRFLathhnlsldifSSRLYNVQDPETQQ 141
Cdd:cd01283  81 GACRQVLAEFL-----------PSRLYIIIDNPKGE 105
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 221-319 1.94e-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: 66.21  E-value: 1.94e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172 221 CYYHRmKPYLCYQLEqfNGQAPLKGCLL---SEKGKQHAEILFLDKIRSMELSQVTITCYLT-----WSPCPNCAWQLAA 292
Cdd:cd01283  13 APYSN-FTVGAALLT--KDGRIFTGVNVenaSYGLTLCAERTAIGKAVSEGLRRYLVTWAVSdeggvWSPCGACRQVLAE 89

                        90       100
                ....*....|....*....|....*..
gi 85861172 293 FKRdrpdlilhiytSRLYFHWKRPFQK 319
Cdd:cd01283  90 FLP-----------SRLYIIIDNPKGE 105
 
Name Accession Description Interval E-value
APOBEC2 pfam18772
APOBEC2; APOBEC2 is a highly conserved (slow-evolving) family of AID/APOBECs found in most ...
 21-198 5.28e-82

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: 248.67  E-value: 5.28e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172    21 ISQETFKFHFKNLGYAKGRKDTFLCYEVTRKDCdSPVSLHHGVFKNKDNIHAEICFLYWFHDKVLkvlSPREEFKITWYM 100
Cdd:pfam18772   1 MDPKTFKFQFKNVPYASGRNKTYLCYEVETRSG-SDLSPDRGYLRNQAGCHAELCFLSWILPWQL---DPGQKYQVTWYV 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172   101 SWSPCFECAEQIVRFLATHHNLSLDIFSSRLYNVQDPETQQNLCRLVQEGAQVAAMDLYEFKKCWKKFVDNGGRRFRPWK 180
Cdd:pfam18772  77 SWSPCPDCARKLAEFLARHPNLSLTIFAARLYFFWEPEYQEGLRRLKRAGAQLKIMDYQDFEYCWENFVDNQGRPFEPWE 156

                         170
                  ....*....|....*...
gi 85861172   181 RLLTNFRYQDSKLQEILR 198
Cdd:pfam18772 157 DLDENYEYLSRKLQEILR 174
NAD1 pfam18778
Novel AID APOBEC clade 1; A distinct family of AID/APOBEC-like deaminases found in ray-finned ...
 20-197 6.18e-77

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: 235.64  E-value: 6.18e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172    20 LISQETFKFHFKNLGYAKGRKDTFLCYEVTRKdcdSPVSLHHGVFKNKDN-IHAEICFLYWFHDkvLKVLSPREEFKITW 98
Cdd:pfam18778   2 RMSPETFKFQFKNVEYASGRNKTLLCYEVKRG---NSSSLWRGHLRNENSgCHAEICFLRWFSS--WRLFDPSQCYTITW 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172    99 YMSWSPCFECAEQIVRFLATHHNLSLDIFSSRLYNVQDPETQQNLCRLVQEGAQVAAMDLYEFKKCWKKFVDNGGRRFRP 178
Cdd:pfam18778  77 YLSWSPCPSCAAKLAEFLKAHPNVTLTIFAARLYYFEDPWNQEGLRSLASAGVTLSIMDYSDFEYCWENFVDNEGRPFVP 156

                         170
                  ....*....|....*....
gi 85861172   179 WKRLLTNFRYQDSKLQEIL 197
Cdd:pfam18778 157 WEDLEENSRYYHRKLQRIL 175
NAD2 pfam18782
Novel AID APOBEC clade 2; A distnct family of AID/APOBEC deaminases found only in Amphibians.
 20-197 3.34e-73

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: 226.09  E-value: 3.34e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172    20 LISQETFKFHFKNLGYAKGRKDTFLCYEVTRKDCDSPVSLHHGVFKNKDNIHAEICFLYWFhdkVLKVLSPREEFKITWY 99
Cdd:pfam18782   2 RMYPRTFYFNFNNKPILYGRNKTYLCYEVERLDNGTWLPQHRGFFRNQAKYHAELCFLSWF---CGNQLPPYQNYQVTWY 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172   100 MSWSPCFECAEQIVRFLATHHNLSLDIFSSRLYNVQDPETQQNLCRLVQEGAQVAAMDLYEFKKCWKKFVDNGGRRFRPW 179
Cdd:pfam18782  79 VSWSPCPECAGEVAEFLAEHPNVTLTIFAARLYYFWDPDYQEALRRLRQAGARVKIMDYEEFEYCWENFVYNQGEPFQPW 158

                         170
                  ....*....|....*...
gi 85861172   180 KRLLTNFRYQDSKLQEIL 197
Cdd:pfam18782 159 DGLEENSRFLHRRLREIL 176
NAD2 pfam18782
Novel AID APOBEC clade 2; A distnct family of AID/APOBEC deaminases found only in Amphibians.
 201-363 8.79e-70

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: 217.23  E-value: 8.79e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172   201 DPLSEEEFYSQFYNqrvKHLcYYHRMKPYLCYQLEQFNGQAPL---KGCLLSEKgKQHAEILFLDKIRSMELS---QVTI 274
Cdd:pfam18782   1 KRMYPRTFYFNFNN---KPI-LYGRNKTYLCYEVERLDNGTWLpqhRGFFRNQA-KYHAELCFLSWFCGNQLPpyqNYQV 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172   275 TCYLTWSPCPNCAWQLAAFKRDRPDLILHIYTSRLYFHWKRPFQKGLCSLWQSGILVDVMDLPQFTDCWTNFVNPK-RPF 353
Cdd:pfam18782  76 TWYVSWSPCPECAGEVAEFLAEHPNVTLTIFAARLYYFWDPDYQEALRRLRQAGARVKIMDYEEFEYCWENFVYNQgEPF 155

                         170
                  ....*....|
gi 85861172   354 WPWKGLEIIS 363
Cdd:pfam18782 156 QPWDGLEENS 165
NAD1 pfam18778
Novel AID APOBEC clade 1; A distinct family of AID/APOBEC-like deaminases found in ray-finned ...
 201-363 8.80e-64

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: 201.74  E-value: 8.80e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172   201 DPLSEEEFYSQFYNQRVKhlcyYHRMKPYLCYQLEQFNGQAPLKGCLLSEKGKQHAEILFLDKIRSMEL----SQVTITC 276
Cdd:pfam18778   1 ERMSPETFKFQFKNVEYA----SGRNKTLLCYEVKRGNSSSLWRGHLRNENSGCHAEICFLRWFSSWRLfdpsQCYTITW 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172   277 YLTWSPCPNCAWQLAAFKRDRPDLILHIYTSRLYFHWKRPFQKGLCSLWQSGILVDVMDLPQFTDCWTNFVNPK-RPFWP 355
Cdd:pfam18778  77 YLSWSPCPSCAAKLAEFLKAHPNVTLTIFAARLYYFEDPWNQEGLRSLASAGVTLSIMDYSDFEYCWENFVDNEgRPFVP 156


                  ....*...
gi 85861172   356 WKGLEIIS 363
Cdd:pfam18778 157 WEDLEENS 164
APOBEC_N pfam08210
APOBEC-like N-terminal domain; A mechanism of generating protein diversity is mRNA editing. ...
 26-195 1.12e-59

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: 191.04  E-value: 1.12e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172    26 FKFHFKNLGYAKGRKDTFLCYEVTRKDCDSPVsLHHGVFKNK--DNIHAEICFLYWFHDKVLkvlSPREEFKITWYMSWS 103
Cdd:pfam08210   1 FFFHFKNLPYASGRHETYLCYEVKRDSGGLVV-EDKGYLRNQaaSSLHAEERFLRWIHDLAL---DPGSNYEVTWYVSWS 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172   104 PCFECAEQIVRFLATHHNLSLDIFSSRLYNVQDPE--TQQNLCRLVQEGAQVAAMDLYEFKKCWKKFVDNGGRRFRPWKR 181
Cdd:pfam08210  77 PCNECASELAAFLSKHPNVRLRIFVSRLYYWEEPDywNREGLRSLAQAGVQLRPMSYKDFEYCWNNFVDHDGEPFKPWDG 156

                         170
                  ....*....|....
gi 85861172   182 LLTNFRYQDSKLQE 195
Cdd:pfam08210 157 LHENSVYLARKLQE 170
APOBEC2 pfam18772
APOBEC2; APOBEC2 is a highly conserved (slow-evolving) family of AID/APOBECs found in most ...
 203-360 3.75e-54

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: 177.02  E-value: 3.75e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172   203 LSEEEFYSQFYNQRVKhlcyYHRMKPYLCYQLEQFNGQA--PLKGCLLSEKGKqHAEILFLDKIRSMELSQ---VTITCY 277
Cdd:pfam18772   1 MDPKTFKFQFKNVPYA----SGRNKTYLCYEVETRSGSDlsPDRGYLRNQAGC-HAELCFLSWILPWQLDPgqkYQVTWY 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172   278 LTWSPCPNCAWQLAAFKRDRPDLILHIYTSRLYFHWKRPFQKGLCSLWQSGILVDVMDLPQFTDCWTNFV-NPKRPFWPW 356
Cdd:pfam18772  76 VSWSPCPDCARKLAEFLARHPNLSLTIFAARLYFFWEPEYQEGLRRLKRAGAQLKIMDYQDFEYCWENFVdNQGRPFEPW 155


                  ....
gi 85861172   357 KGLE 360
Cdd:pfam18772 156 EDLD 159
SNAD4 pfam18750
Secreted Novel AID/APOBEC-like Deaminase 4; A family of secreted AID/APOBEC like deaminases ...
 46-167 5.62e-46

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: 153.57  E-value: 5.62e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172    46 YEVTRKDcdSPVSLHHGVFKNKDNIHAEICFLYWFHDKVLkvlSPREEFKITWYMSWSPCFECAEQIVRFLATHHNLSLD 125
Cdd:pfam18750   1 YEIKWGN--GSKIWQRGYLSNEHEQHAEICFLENIRSREL---DPSQRYRVTWYLSWSPCPECAQKIAEFLAEHPNVTLT 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 85861172   126 IFSSRLYNvQDPETQQNLCRLVQEGAQVAAMDLYEFKKCWKK 167
Cdd:pfam18750  76 IFAARLYH-WDEDNRQGLRSLAQAGVTLQIMTLEDFEYCWKN 116
APOBEC3 pfam18771
APOBEC3; APOBEC3 deaminases act as restriction factors in the innate response to retroviruses ...
 223-352 3.38e-44

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: 149.95  E-value: 3.38e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172   223 YHRMKPYLCYQLEQFNGQAPLKGCLlSEKGKQHAEILFLDKIRSMELSQV---TITCYLTWSPCPNCAWQLAAFKRDRPD 299
Cdd:pfam18771   1 YYDRKAYLCYQLKGRNGSALDRGYF-SNKKKRHAEIRFIDKIRSLDLDNIqcyRITCYITWSPCPNCAAELVDFISLNPH 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 85861172   300 LILHIYTSRLYFHWKRPFQKGLCSLWQSGILVDVMDLPQFTDCWTNFVNPKRP 352
Cdd:pfam18771  80 LKLRIFASRLYYHWERSYKEGLQKLQRAGVSVAVMTLPEFQDCWEDFVDHQEE 132
SNAD4 pfam18750
Secreted Novel AID/APOBEC-like Deaminase 4; A family of secreted AID/APOBEC like deaminases ...
 232-345 1.22e-41

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: 142.40  E-value: 1.22e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172   232 YQLEQFNGQAPL-KGCLLSEKGkQHAEILFLDKIRSMELSQVT---ITCYLTWSPCPNCAWQLAAFKRDRPDLILHIYTS 307
Cdd:pfam18750   1 YEIKWGNGSKIWqRGYLSNEHE-QHAEICFLENIRSRELDPSQryrVTWYLSWSPCPECAQKIAEFLAEHPNVTLTIFAA 79

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 85861172   308 RLYfHWKRPFQKGLCSLWQSGILVDVMDLPQFTDCWTN 345
Cdd:pfam18750  80 RLY-HWDEDNRQGLRSLAQAGVTLQIMTLEDFEYCWKN 116
APOBEC_C pfam05240
APOBEC-like C-terminal domain; This domain is found at the C-termini of the Apolipoprotein B ...
 120-197 2.00e-32

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: 116.81  E-value: 2.00e-32
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 85861172   120 HNLSLDIFSSRLYNVQDPETQQNLCRLVQEGAQVAAMDLYEFKKCWKKFVDNGGRRFRPWKRLLTNFRYQDSKLQEIL 197
Cdd:pfam05240   1 PNVSLTIFAARLYYHWDPEYQQGLRRLVQAGAQVAIMSYKEFEYCWDNFVDNQGRPFQPWEGLEENSQLLSRRLQEIL 78
APOBEC_N pfam08210
APOBEC-like N-terminal domain; A mechanism of generating protein diversity is mRNA editing. ...
 208-361 1.34e-31

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: 117.85  E-value: 1.34e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172   208 FYSQFYNQRvkhlCYYHRMKPYLCYQLEQFNGQAPL--KGCLLSEKGKQ-HAEILFLDKIRSMELSQV---TITCYLTWS 281
Cdd:pfam08210   1 FFFHFKNLP----YASGRHETYLCYEVKRDSGGLVVedKGYLRNQAASSlHAEERFLRWIHDLALDPGsnyEVTWYVSWS 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172   282 PCPNCAWQLAAFKRDRPDLILHIYTSRLYFHWKR--PFQKGLCSLWQSGILVDVMDLPQFTDCWTNFVNPK-RPFWPWKG 358
Cdd:pfam08210  77 PCNECASELAAFLSKHPNVRLRIFVSRLYYWEEPdyWNREGLRSLAQAGVQLRPMSYKDFEYCWNNFVDHDgEPFKPWDG 156


                  ...
gi 85861172   359 LEI 361
Cdd:pfam08210 157 LHE 159
APOBEC3 pfam18771
APOBEC3; APOBEC3 deaminases act as restriction factors in the innate response to retroviruses ...
 39-177 1.09e-30

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: 114.12  E-value: 1.09e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172    39 RKDTFLCYEVTRKDCDSPVSlhhGVFKNKDNIHAEICFLywfhDKVLKV-LSPREEFKITWYMSWSPCFECAEQIVRFLA 117
Cdd:pfam18771   3 DRKAYLCYQLKGRNGSALDR---GYFSNKKKRHAEIRFI----DKIRSLdLDNIQCYRITCYITWSPCPNCAAELVDFIS 75

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172   118 THHNLSLDIFSSRLYNVQDPETQQNLCRLVQEGAQVAAMDLYEFKKCWKKFVDNGGRRFR 177
Cdd:pfam18771  76 LNPHLKLRIFASRLYYHWERSYKEGLQKLQRAGVSVAVMTLPEFQDCWEDFVDHQEEPFR 135
APOBEC_C pfam05240
APOBEC-like C-terminal domain; This domain is found at the C-termini of the Apolipoprotein B ...
 298-363 2.80e-25

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: 97.94  E-value: 2.80e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 85861172   298 PDLILHIYTSRLYFHWKRPFQKGLCSLWQSGILVDVMDLPQFTDCWTNFVNPK-RPFWPWKGLEIIS 363
Cdd:pfam05240   1 PNVSLTIFAARLYYHWDPEYQQGLRRLVQAGAQVAIMSYKEFEYCWDNFVDNQgRPFQPWEGLEENS 67
APOBEC4 pfam18775
APOBEC4; A member of the AID/APOBEC family of cytosine deaminases. The biological function of ...
 96-169 2.87e-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: 78.53  E-value: 2.87e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 85861172    96 ITWYMSWSPCFECAEQIVRFLATHHNLSLDIFSSRLYNVQDPETQQNLCRLVQEGAQVAAMDLYEFKKCWKKFV 169
Cdd:pfam18775   1 VTLYLSWSPCNECSEKIQEFLKKHPKVNLDIYFAQLYHTEEEDNRQGLRSLVEKGVTLSVMSGEDWIYCLRTFV 74
APOBEC4_like pfam18774
APOBEC4-like -AID/APOBEC-deaminase; Cnidarian and Algal homologs of the APOBEC4-like AID ...
 224-348 6.49e-18

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: 79.53  E-value: 6.49e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172   224 HRMKPYLCYQLEQFNGQAPLKGCllSEKGKQHAEILFLDKIRS-MELSQVTITCYLTWSPCPNCAWQLAAFKRDRPDLIL 302
Cdd:pfam18774   7 HKKEICLLYEIQWGRGTIWRNWT--ENNCTEHAEVNFLENFRSeRPSRSCTITWYLSWSPCWECSGRILEFLSRHPNVTL 84

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 85861172   303 HIYTSRLYFHWKRPFQKGLCSLWQSGILVDVMDLPQFTDCWTNFVN 348
Cdd:pfam18774  85 GIYVARLFMHDDDRNRQGLRILQMNGVTIQVMMNKDYCYCWKAFKN 130
APOBEC4_like pfam18774
APOBEC4-like -AID/APOBEC-deaminase; Cnidarian and Algal homologs of the APOBEC4-like AID ...
 71-170 3.55e-15

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: 71.83  E-value: 3.55e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172    71 HAEICFLYWFHDKvlkvlSPREEFKITWYMSWSPCFECAEQIVRFLATHHNLSLDIFSSRLYNVQDPETQQNLCRLVQEG 150
Cdd:pfam18774  36 HAEVNFLENFRSE-----RPSRSCTITWYLSWSPCWECSGRILEFLSRHPNVTLGIYVARLFMHDDDRNRQGLRILQMNG 110

                          90       100
                  ....*....|....*....|
gi 85861172   151 AQVAAMDLYEFKKCWKKFVD 170
Cdd:pfam18774 111 VTIQVMMNKDYCYCWKAFKN 130
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 35-141 3.59e-14

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: 68.14  E-value: 3.59e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172  35 YAKGRKDTFLCYEVTRKdcdspVSLHHGVFKNK----DNIHAEICFLYWFHDKVLKvlspreEFKITWYMS-----WSPC 105
Cdd:cd01283  12 YAPYSNFTVGAALLTKD-----GRIFTGVNVENasygLTLCAERTAIGKAVSEGLR------RYLVTWAVSdeggvWSPC 80

                        90       100       110
                ....*....|....*....|....*....|....*.
gi 85861172 106 FECAEQIVRFLathhnlsldifSSRLYNVQDPETQQ 141
Cdd:cd01283  81 GACRQVLAEFL-----------PSRLYIIIDNPKGE 105
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 221-319 1.94e-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: 66.21  E-value: 1.94e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172 221 CYYHRmKPYLCYQLEqfNGQAPLKGCLL---SEKGKQHAEILFLDKIRSMELSQVTITCYLT-----WSPCPNCAWQLAA 292
Cdd:cd01283  13 APYSN-FTVGAALLT--KDGRIFTGVNVenaSYGLTLCAERTAIGKAVSEGLRRYLVTWAVSdeggvWSPCGACRQVLAE 89

                        90       100
                ....*....|....*....|....*..
gi 85861172 293 FKRdrpdlilhiytSRLYFHWKRPFQK 319
Cdd:cd01283  90 FLP-----------SRLYIIIDNPKGE 105
APOBEC1 pfam18769
APOBEC1; APOBEC1 deaminates cytosine both in RNA and ssDNA and has roles in both mRNA editing ...
 66-156 6.40e-13

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: 64.45  E-value: 6.40e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85861172    66 NKDNIHAEICFLYWFHDKvlKVLSPREEFKITWYMSWSPCFECAEQIVRFLATHHNLSLDIFSSRLYNVQDPETQQNLCR 145
Cdd:pfam18769  13 NNTTQHAEVNFLEKFFSE--RHFDPSVSCSITWFLSWSPCGECSKAIGEFLSQHPNVTLVIYAARLFKHLDIRNRQGLRD 90

                          90
                  ....*....|.
gi 85861172   146 LVQEGAQVAAM 156
Cdd:pfam18769  91 LAMSGVTIQIM 101
APOBEC4 pfam18775
APOBEC4; A member of the AID/APOBEC family of cytosine deaminases. The biological function of ...
 274-347 3.72e-12

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: 61.20  E-value: 3.72e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 85861172   274 ITCYLTWSPCPNCAWQLAAFKRDRPDLILHIYTSRLYFHWKRPFQKGLCSLWQSGILVDVMDLPQFTDCWTNFV 347
Cdd:pfam18775   1 VTLYLSWSPCNECSEKIQEFLKKHPKVNLDIYFAQLYHTEEEDNRQGLRSLVEKGVTLSVMSGEDWIYCLRTFV 74
 
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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