NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1538055536|ref|XP_027259830|]
View 

DNA dC-

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 187-360 1.02e-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: 237.11  E-value: 1.02e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1538055536 187 LREDIFSLQFNNRHRVkpvqhrYYQRKTYLCYLLEQHNG--QQPLKGCLQNKKGKHAEILFIDEMRSLELGQ---VQITC 261
Cdd:pfam18772   1 MDPKTFKFQFKNVPYA------SGRNKTYLCYEVETRSGsdLSPDRGYLRNQAGCHAELCFLSWILPWQLDPgqkYQVTW 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1538055536 262 YLTWSPCPNCAQELAAFKSDHPDLVLRIYTSRLYFHWRRKYQEGLCCLWRSGIQVDVMDLPQFADCWTNFVNSQS-PFWP 340
Cdd:pfam18772  75 YVSWSPCPDCARKLAEFLARHPNLSLTIFAARLYFFWEPEYQEGLRRLKRAGAQLKIMDYQDFEYCWENFVDNQGrPFEP 154

                         170       180
                  ....*....|....*....|
gi 1538055536 341 WNNLEKNSRCIQRRLQRIKE 360
Cdd:pfam18772 155 WEDLDENYEYLSRKLQEILR 174
NAD2 super family cl40079
Novel AID APOBEC clade 2; A distnct family of AID/APOBEC deaminases found only in Amphibians.
 52-180 4.97e-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: 212.23  E-value: 4.97e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1538055536  52 NLHAEVCFLYWFhtqVLGVLPPDEKYKITWYVSWSPCNECAEKVASFLDTHRNLSLAIFSSRLYYFWDPDYQDKLRRLNQ 131
Cdd:pfam18782  51 KYHAELCFLSWF---CGNQLPPYQNYQVTWYVSWSPCPECAGEVAEFLAEHPNVTLTIFAARLYYFWDPDYQEALRRLRQ 127

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1538055536 132 AGAQIAAMDFPEFEKCWNKFVDNDGKSFRPWKRLKINFRFQDNKLRDIL 180
Cdd:pfam18782 128 AGARVKIMDYEEFEYCWENFVYNQGEPFQPWDGLEENSRFLHRRLREIL 176
 
Name Accession Description Interval E-value
APOBEC2 pfam18772
APOBEC2; APOBEC2 is a highly conserved (slow-evolving) family of AID/APOBECs found in most ...
 187-360 1.02e-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: 237.11  E-value: 1.02e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1538055536 187 LREDIFSLQFNNRHRVkpvqhrYYQRKTYLCYLLEQHNG--QQPLKGCLQNKKGKHAEILFIDEMRSLELGQ---VQITC 261
Cdd:pfam18772   1 MDPKTFKFQFKNVPYA------SGRNKTYLCYEVETRSGsdLSPDRGYLRNQAGCHAELCFLSWILPWQLDPgqkYQVTW 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1538055536 262 YLTWSPCPNCAQELAAFKSDHPDLVLRIYTSRLYFHWRRKYQEGLCCLWRSGIQVDVMDLPQFADCWTNFVNSQS-PFWP 340
Cdd:pfam18772  75 YVSWSPCPDCARKLAEFLARHPNLSLTIFAARLYFFWEPEYQEGLRRLKRAGAQLKIMDYQDFEYCWENFVDNQGrPFEP 154

                         170       180
                  ....*....|....*....|
gi 1538055536 341 WNNLEKNSRCIQRRLQRIKE 360
Cdd:pfam18772 155 WEDLDENYEYLSRKLQEILR 174
NAD2 pfam18782
Novel AID APOBEC clade 2; A distnct family of AID/APOBEC deaminases found only in Amphibians.
 52-180 4.97e-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: 212.23  E-value: 4.97e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1538055536  52 NLHAEVCFLYWFhtqVLGVLPPDEKYKITWYVSWSPCNECAEKVASFLDTHRNLSLAIFSSRLYYFWDPDYQDKLRRLNQ 131
Cdd:pfam18782  51 KYHAELCFLSWF---CGNQLPPYQNYQVTWYVSWSPCPECAGEVAEFLAEHPNVTLTIFAARLYYFWDPDYQEALRRLRQ 127

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1538055536 132 AGAQIAAMDFPEFEKCWNKFVDNDGKSFRPWKRLKINFRFQDNKLRDIL 180
Cdd:pfam18782 128 AGARVKIMDYEEFEYCWENFVYNQGEPFQPWDGLEENSRFLHRRLREIL 176
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 206-311 6.78e-17

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: 75.84  E-value: 6.78e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1538055536 206 QHRYYQRKTYLCYLLEqhNGQQPLKGCLQNKK----GKHAEILFIDEMRSLELGQVQITCYLT-----WSPCPNCAQELA 276
Cdd:cd01283    11 AYAPYSNFTVGAALLT--KDGRIFTGVNVENAsyglTLCAERTAIGKAVSEGLRRYLVTWAVSdeggvWSPCGACRQVLA 88

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1538055536 277 AFKSdhpdlvlriytSRLYFHWRRKYQEGLCCLWR 311
Cdd:cd01283    89 EFLP-----------SRLYIIIDNPKGEEFAYTLS 112
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 50-124 1.34e-10

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: 58.12  E-value: 1.34e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1538055536  50 SINLHAEVCFLYWFHTQVlgvlppDEKYKITWYVS-----WSPCNECAEKVASFLDthrnlslaifsSRLYYFWDPDYQD 124
Cdd:cd01283    43 GLTLCAERTAIGKAVSEG------LRRYLVTWAVSdeggvWSPCGACRQVLAEFLP-----------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 ...
 187-360 1.02e-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: 237.11  E-value: 1.02e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1538055536 187 LREDIFSLQFNNRHRVkpvqhrYYQRKTYLCYLLEQHNG--QQPLKGCLQNKKGKHAEILFIDEMRSLELGQ---VQITC 261
Cdd:pfam18772   1 MDPKTFKFQFKNVPYA------SGRNKTYLCYEVETRSGsdLSPDRGYLRNQAGCHAELCFLSWILPWQLDPgqkYQVTW 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1538055536 262 YLTWSPCPNCAQELAAFKSDHPDLVLRIYTSRLYFHWRRKYQEGLCCLWRSGIQVDVMDLPQFADCWTNFVNSQS-PFWP 340
Cdd:pfam18772  75 YVSWSPCPDCARKLAEFLARHPNLSLTIFAARLYFFWEPEYQEGLRRLKRAGAQLKIMDYQDFEYCWENFVDNQGrPFEP 154

                         170       180
                  ....*....|....*....|
gi 1538055536 341 WNNLEKNSRCIQRRLQRIKE 360
Cdd:pfam18772 155 WEDLDENYEYLSRKLQEILR 174
NAD2 pfam18782
Novel AID APOBEC clade 2; A distnct family of AID/APOBEC deaminases found only in Amphibians.
 52-180 4.97e-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: 212.23  E-value: 4.97e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1538055536  52 NLHAEVCFLYWFhtqVLGVLPPDEKYKITWYVSWSPCNECAEKVASFLDTHRNLSLAIFSSRLYYFWDPDYQDKLRRLNQ 131
Cdd:pfam18782  51 KYHAELCFLSWF---CGNQLPPYQNYQVTWYVSWSPCPECAGEVAEFLAEHPNVTLTIFAARLYYFWDPDYQEALRRLRQ 127

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1538055536 132 AGAQIAAMDFPEFEKCWNKFVDNDGKSFRPWKRLKINFRFQDNKLRDIL 180
Cdd:pfam18782 128 AGARVKIMDYEEFEYCWENFVYNQGEPFQPWDGLEENSRFLHRRLREIL 176
NAD2 pfam18782
Novel AID APOBEC clade 2; A distnct family of AID/APOBEC deaminases found only in Amphibians.
 186-359 7.19e-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: 211.84  E-value: 7.19e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1538055536 186 LLREDIFSLQFNNRHRVkpvqhrYYQRKTYLCYLLEQHNGQQPL---KGCLQNKKGKHAEILFIDEMRS--LELGQ-VQI 259
Cdd:pfam18782   2 RMYPRTFYFNFNNKPIL------YGRNKTYLCYEVERLDNGTWLpqhRGFFRNQAKYHAELCFLSWFCGnqLPPYQnYQV 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1538055536 260 TCYLTWSPCPNCAQELAAFKSDHPDLVLRIYTSRLYFHWRRKYQEGLCCLWRSGIQVDVMDLPQFADCWTNFVNSQS-PF 338
Cdd:pfam18782  76 TWYVSWSPCPECAGEVAEFLAEHPNVTLTIFAARLYYFWDPDYQEALRRLRQAGARVKIMDYEEFEYCWENFVYNQGePF 155

                         170       180
                  ....*....|....*....|.
gi 1538055536 339 WPWNNLEKNSRCIQRRLQRIK 359
Cdd:pfam18782 156 QPWDGLEENSRFLHRRLREIL 176
NAD1 pfam18778
Novel AID APOBEC clade 1; A distinct family of AID/APOBEC-like deaminases found in ray-finned ...
 186-359 8.33e-68

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: 211.75  E-value: 8.33e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1538055536 186 LLREDIFSLQFNNRHRVkpvqhrYYQRKTYLCYLLEQHNGQQPLKGCLQNKK-GKHAEILFIDEMRSLELG----QVQIT 260
Cdd:pfam18778   2 RMSPETFKFQFKNVEYA------SGRNKTLLCYEVKRGNSSSLWRGHLRNENsGCHAEICFLRWFSSWRLFdpsqCYTIT 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1538055536 261 CYLTWSPCPNCAQELAAFKSDHPDLVLRIYTSRLYFHWRRKYQEGLCCLWRSGIQVDVMDLPQFADCWTNFVNSQ-SPFW 339
Cdd:pfam18778  76 WYLSWSPCPSCAAKLAEFLKAHPNVTLTIFAARLYYFEDPWNQEGLRSLASAGVTLSIMDYSDFEYCWENFVDNEgRPFV 155

                         170       180
                  ....*....|....*....|
gi 1538055536 340 PWNNLEKNSRCIQRRLQRIK 359
Cdd:pfam18778 156 PWEDLEENSRYYHRKLQRIL 175
NAD1 pfam18778
Novel AID APOBEC clade 1; A distinct family of AID/APOBEC-like deaminases found in ray-finned ...
 38-180 5.46e-62

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: 196.73  E-value: 5.46e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1538055536  38 GMLPSQTLFTDQSINLHAEVCFLYWFHTqvLGVLPPDEKYKITWYVSWSPCNECAEKVASFLDTHRNLSLAIFSSRLYYF 117
Cdd:pfam18778  35 SSSLWRGHLRNENSGCHAEICFLRWFSS--WRLFDPSQCYTITWYLSWSPCPSCAAKLAEFLKAHPNVTLTIFAARLYYF 112

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1538055536 118 WDPDYQDKLRRLNQAGAQIAAMDFPEFEKCWNKFVDNDGKSFRPWKRLKINFRFQDNKLRDIL 180
Cdd:pfam18778 113 EDPWNQEGLRSLASAGVTLSIMDYSDFEYCWENFVDNEGRPFVPWEDLEENSRYYHRKLQRIL 175
APOBEC2 pfam18772
APOBEC2; APOBEC2 is a highly conserved (slow-evolving) family of AID/APOBECs found in most ...
 54-181 5.71e-62

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: 196.67  E-value: 5.71e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1538055536  54 HAEVCFLYWFHTqvlGVLPPDEKYKITWYVSWSPCNECAEKVASFLDTHRNLSLAIFSSRLYYFWDPDYQDKLRRLNQAG 133
Cdd:pfam18772  50 HAELCFLSWILP---WQLDPGQKYQVTWYVSWSPCPDCARKLAEFLARHPNLSLTIFAARLYFFWEPEYQEGLRRLKRAG 126

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1538055536 134 AQIAAMDFPEFEKCWNKFVDNDGKSFRPWKRLKINFRFQDNKLRDILR 181
Cdd:pfam18772 127 AQLKIMDYQDFEYCWENFVDNQGRPFEPWEDLDENYEYLSRKLQEILR 174
APOBEC_N pfam08210
APOBEC-like N-terminal domain; A mechanism of generating protein diversity is mRNA editing. ...
 51-178 7.20e-57

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: 183.34  E-value: 7.20e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1538055536  51 INLHAEVCFLYWFHTQVLgvlPPDEKYKITWYVSWSPCNECAEKVASFLDTHRNLSLAIFSSRLYYFWDPDYQDK--LRR 128
Cdd:pfam08210  44 SSLHAEERFLRWIHDLAL---DPGSNYEVTWYVSWSPCNECASELAAFLSKHPNVRLRIFVSRLYYWEEPDYWNRegLRS 120

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1538055536 129 LNQAGAQIAAMDFPEFEKCWNKFVDNDGKSFRPWKRLKINFRFQDNKLRD 178
Cdd:pfam08210 121 LAQAGVQLRPMSYKDFEYCWNNFVDHDGEPFKPWDGLHENSVYLARKLQE 170
APOBEC3 pfam18771
APOBEC3; APOBEC3 deaminases act as restriction factors in the innate response to retroviruses ...
 209-337 3.50e-56

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: 180.38  E-value: 3.50e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1538055536 209 YYQRKTYLCYLLEQHNGQQPLKGCLQNKKGKHAEILFIDEMRSLEL---GQVQITCYLTWSPCPNCAQELAAFKSDHPDL 285
Cdd:pfam18771   1 YYDRKAYLCYQLKGRNGSALDRGYFSNKKKRHAEIRFIDKIRSLDLdniQCYRITCYITWSPCPNCAAELVDFISLNPHL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1538055536 286 VLRIYTSRLYFHWRRKYQEGLCCLWRSGIQVDVMDLPQFADCWTNFVNSQSP 337
Cdd:pfam18771  81 KLRIFASRLYYHWERSYKEGLQKLQRAGVSVAVMTLPEFQDCWEDFVDHQEE 132
SNAD4 pfam18750
Secreted Novel AID/APOBEC-like Deaminase 4; A family of secreted AID/APOBEC like deaminases ...
 218-330 7.16e-45

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: 150.49  E-value: 7.16e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1538055536 218 YLLEQHNGQQPL-KGCLQNKKGKHAEILFIDEMRSLEL---GQVQITCYLTWSPCPNCAQELAAFKSDHPDLVLRIYTSR 293
Cdd:pfam18750   1 YEIKWGNGSKIWqRGYLSNEHEQHAEICFLENIRSRELdpsQRYRVTWYLSWSPCPECAQKIAEFLAEHPNVTLTIFAAR 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1538055536 294 LYfHWRRKYQEGLCCLWRSGIQVDVMDLPQFADCWTN 330
Cdd:pfam18750  81 LY-HWDEDNRQGLRSLAQAGVTLQIMTLEDFEYCWKN 116
SNAD4 pfam18750
Secreted Novel AID/APOBEC-like Deaminase 4; A family of secreted AID/APOBEC like deaminases ...
 52-150 4.39e-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: 148.56  E-value: 4.39e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1538055536  52 NLHAEVCFLYWFHtqvLGVLPPDEKYKITWYVSWSPCNECAEKVASFLDTHRNLSLAIFSSRLYYfWDPDYQDKLRRLNQ 131
Cdd:pfam18750  22 EQHAEICFLENIR---SRELDPSQRYRVTWYLSWSPCPECAQKIAEFLAEHPNVTLTIFAARLYH-WDEDNRQGLRSLAQ 97

                          90
                  ....*....|....*....
gi 1538055536 132 AGAQIAAMDFPEFEKCWNK 150
Cdd:pfam18750  98 AGVTLQIMTLEDFEYCWKN 116
APOBEC_N pfam08210
APOBEC-like N-terminal domain; A mechanism of generating protein diversity is mRNA editing. ...
 192-357 3.86e-42

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: 145.20  E-value: 3.86e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1538055536 192 FSLQFNNRHRVKpvqHRyyqRKTYLCYLLEQHNGQQPL--KGCLQNKKGK--HAEILFIDEMRSLELGQV---QITCYLT 264
Cdd:pfam08210   1 FFFHFKNLPYAS---GR---HETYLCYEVKRDSGGLVVedKGYLRNQAASslHAEERFLRWIHDLALDPGsnyEVTWYVS 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1538055536 265 WSPCPNCAQELAAFKSDHPDLVLRIYTSRLYFHWRRKYQ--EGLCCLWRSGIQVDVMDLPQFADCWTNFVNSQS-PFWPW 341
Cdd:pfam08210  75 WSPCNECASELAAFLSKHPNVRLRIFVSRLYYWEEPDYWnrEGLRSLAQAGVQLRPMSYKDFEYCWNNFVDHDGePFKPW 154

                         170
                  ....*....|....*.
gi 1538055536 342 NNLEKNSRCIQRRLQR 357
Cdd:pfam08210 155 DGLHENSVYLARKLQE 170
APOBEC_C pfam05240
APOBEC-like C-terminal domain; This domain is found at the C-termini of the Apolipoprotein B ...
 103-180 8.02e-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: 127.98  E-value: 8.02e-37
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1538055536 103 RNLSLAIFSSRLYYFWDPDYQDKLRRLNQAGAQIAAMDFPEFEKCWNKFVDNDGKSFRPWKRLKINFRFQDNKLRDIL 180
Cdd:pfam05240   1 PNVSLTIFAARLYYHWDPEYQQGLRRLVQAGAQVAIMSYKEFEYCWDNFVDNQGRPFQPWEGLEENSQLLSRRLQEIL 78
APOBEC_C pfam05240
APOBEC-like C-terminal domain; This domain is found at the C-termini of the Apolipoprotein B ...
 283-358 8.01e-33

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: 117.58  E-value: 8.01e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1538055536 283 PDLVLRIYTSRLYFHWRRKYQEGLCCLWRSGIQVDVMDLPQFADCWTNFVNSQ-SPFWPWNNLEKNSRCIQRRLQRI 358
Cdd:pfam05240   1 PNVSLTIFAARLYYHWDPEYQQGLRRLVQAGAQVAIMSYKEFEYCWDNFVDNQgRPFQPWEGLEENSQLLSRRLQEI 77
APOBEC3 pfam18771
APOBEC3; APOBEC3 deaminases act as restriction factors in the innate response to retroviruses ...
 54-160 4.49e-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: 112.20  E-value: 4.49e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1538055536  54 HAEVCFLYwfHTQVLGvLPPDEKYKITWYVSWSPCNECAEKVASFLDTHRNLSLAIFSSRLYYFWDPDYQDKLRRLNQAG 133
Cdd:pfam18771  32 HAEIRFID--KIRSLD-LDNIQCYRITCYITWSPCPNCAAELVDFISLNPHLKLRIFASRLYYHWERSYKEGLQKLQRAG 108

                          90       100
                  ....*....|....*....|....*..
gi 1538055536 134 AQIAAMDFPEFEKCWNKFVDNDGKSFR 160
Cdd:pfam18771 109 VSVAVMTLPEFQDCWEDFVDHQEEPFR 135
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 206-311 6.78e-17

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: 75.84  E-value: 6.78e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1538055536 206 QHRYYQRKTYLCYLLEqhNGQQPLKGCLQNKK----GKHAEILFIDEMRSLELGQVQITCYLT-----WSPCPNCAQELA 276
Cdd:cd01283    11 AYAPYSNFTVGAALLT--KDGRIFTGVNVENAsyglTLCAERTAIGKAVSEGLRRYLVTWAVSdeggvWSPCGACRQVLA 88

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1538055536 277 AFKSdhpdlvlriytSRLYFHWRRKYQEGLCCLWR 311
Cdd:cd01283    89 EFLP-----------SRLYIIIDNPKGEEFAYTLS 112
APOBEC4_like pfam18774
APOBEC4-like -AID/APOBEC-deaminase; Cnidarian and Algal homologs of the APOBEC4-like AID ...
 235-333 2.46e-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: 74.91  E-value: 2.46e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1538055536 235 NKKGKHAEILFIDEMRS-LELGQVQITCYLTWSPCPNCAQELAAFKSDHPDLVLRIYTSRLYFHWRRKYQEGLCCLWRSG 313
Cdd:pfam18774  31 NNCTEHAEVNFLENFRSeRPSRSCTITWYLSWSPCWECSGRILEFLSRHPNVTLGIYVARLFMHDDDRNRQGLRILQMNG 110

                          90       100
                  ....*....|....*....|
gi 1538055536 314 IQVDVMDLPQFADCWTNFVN 333
Cdd:pfam18774 111 VTIQVMMNKDYCYCWKAFKN 130
APOBEC4 pfam18775
APOBEC4; A member of the AID/APOBEC family of cytosine deaminases. The biological function of ...
 79-152 2.84e-16

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: 72.75  E-value: 2.84e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1538055536  79 ITWYVSWSPCNECAEKVASFLDTHRNLSLAIFSSRLYYFWDPDYQDKLRRLNQAGAQIAAMDFPEFEKCWNKFV 152
Cdd:pfam18775   1 VTLYLSWSPCNECSEKIQEFLKKHPKVNLDIYFAQLYHTEEEDNRQGLRSLVEKGVTLSVMSGEDWIYCLRTFV 74
APOBEC4_like pfam18774
APOBEC4-like -AID/APOBEC-deaminase; Cnidarian and Algal homologs of the APOBEC4-like AID ...
 54-153 2.91e-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: 74.52  E-value: 2.91e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1538055536  54 HAEVCFLYWFHTQvlgvlPPDEKYKITWYVSWSPCNECAEKVASFLDTHRNLSLAIFSSRLYYFWDPDYQDKLRRLNQAG 133
Cdd:pfam18774  36 HAEVNFLENFRSE-----RPSRSCTITWYLSWSPCWECSGRILEFLSRHPNVTLGIYVARLFMHDDDRNRQGLRILQMNG 110

                          90       100
                  ....*....|....*....|
gi 1538055536 134 AQIAAMDFPEFEKCWNKFVD 153
Cdd:pfam18774 111 VTIQVMMNKDYCYCWKAFKN 130
APOBEC4 pfam18775
APOBEC4; A member of the AID/APOBEC family of cytosine deaminases. The biological function of ...
 259-332 8.47e-14

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: 65.82  E-value: 8.47e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1538055536 259 ITCYLTWSPCPNCAQELAAFKSDHPDLVLRIYTSRLYFHWRRKYQEGLCCLWRSGIQVDVMDLPQFADCWTNFV 332
Cdd:pfam18775   1 VTLYLSWSPCNECSEKIQEFLKKHPKVNLDIYFAQLYHTEEEDNRQGLRSLVEKGVTLSVMSGEDWIYCLRTFV 74
APOBEC1 pfam18769
APOBEC1; APOBEC1 deaminates cytosine both in RNA and ssDNA and has roles in both mRNA editing ...
 54-139 4.03e-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: 64.83  E-value: 4.03e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1538055536  54 HAEVCFLYWFHTQVLgvLPPDEKYKITWYVSWSPCNECAEKVASFLDTHRNLSLAIFSSRLYYFWDPDYQDKLRRLNQAG 133
Cdd:pfam18769  18 HAEVNFLEKFFSERH--FDPSVSCSITWFLSWSPCGECSKAIGEFLSQHPNVTLVIYAARLFKHLDIRNRQGLRDLAMSG 95


                  ....*.
gi 1538055536 134 AQIAAM 139
Cdd:pfam18769  96 VTIQIM 101
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 50-124 1.34e-10

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: 58.12  E-value: 1.34e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1538055536  50 SINLHAEVCFLYWFHTQVlgvlppDEKYKITWYVS-----WSPCNECAEKVASFLDthrnlslaifsSRLYYFWDPDYQD 124
Cdd:cd01283    43 GLTLCAERTAIGKAVSEG------LRRYLVTWAVSdeggvWSPCGACRQVLAEFLP-----------SRLYIIIDNPKGE 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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH