NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|752507739|ref|NP_005880|]
View 

C-

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
APOBEC1 pfam18769
APOBEC1; APOBEC1 deaminates cytosine both in RNA and ssDNA and has roles in both mRNA editing ...
 2-99 5.83e-61

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: 184.63  E-value: 5.83e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752507739    2 SRKIWRSSGKNTTNHVEVNFIKKFTSERDFHPSMSCSITWFLSWSPCWECSQAIREFLSRHPGVTLVIYVARLFWHMDQQ 81
Cdd:pfam18769   4 RGTIWRNCGNNTTQHAEVNFLEKFFSERHFDPSVSCSITWFLSWSPCGECSKAIGEFLSQHPNVTLVIYAARLFKHLDIR 83

                          90
                  ....*....|....*...
gi 752507739   82 NRQGLRDLVNSGVTIQIM 99
Cdd:pfam18769  84 NRQGLRDLAMSGVTIQIM 101
APOBEC_C pfam05240
APOBEC-like C-terminal domain; This domain is found at the C-termini of the Apolipoprotein B ...
 63-141 9.51e-28

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: 99.48  E-value: 9.51e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752507739   63 PGVTLVIYVARLFWHMDQQNRQGLRDLVNSGVTIQIMRASEYYHCWRNFVNYppgdeAHWPqYPPlWMML------YALE 136
Cdd:pfam05240   1 PNVSLTIFAARLYYHWDPEYQQGLRRLVQAGAQVAIMSYKEFEYCWDNFVDN-----QGRP-FQP-WEGLeensqlLSRR 73


                  ....*
gi 752507739  137 LHCII 141
Cdd:pfam05240  74 LQEIL 78
 
Name Accession Description Interval E-value
APOBEC1 pfam18769
APOBEC1; APOBEC1 deaminates cytosine both in RNA and ssDNA and has roles in both mRNA editing ...
 2-99 5.83e-61

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: 184.63  E-value: 5.83e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752507739    2 SRKIWRSSGKNTTNHVEVNFIKKFTSERDFHPSMSCSITWFLSWSPCWECSQAIREFLSRHPGVTLVIYVARLFWHMDQQ 81
Cdd:pfam18769   4 RGTIWRNCGNNTTQHAEVNFLEKFFSERHFDPSVSCSITWFLSWSPCGECSKAIGEFLSQHPNVTLVIYAARLFKHLDIR 83

                          90
                  ....*....|....*...
gi 752507739   82 NRQGLRDLVNSGVTIQIM 99
Cdd:pfam18769  84 NRQGLRDLAMSGVTIQIM 101
APOBEC_C pfam05240
APOBEC-like C-terminal domain; This domain is found at the C-termini of the Apolipoprotein B ...
 63-141 9.51e-28

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: 99.48  E-value: 9.51e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752507739   63 PGVTLVIYVARLFWHMDQQNRQGLRDLVNSGVTIQIMRASEYYHCWRNFVNYppgdeAHWPqYPPlWMML------YALE 136
Cdd:pfam05240   1 PNVSLTIFAARLYYHWDPEYQQGLRRLVQAGAQVAIMSYKEFEYCWDNFVDN-----QGRP-FQP-WEGLeensqlLSRR 73


                  ....*
gi 752507739  137 LHCII 141
Cdd:pfam05240  74 LQEIL 78
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 12-60 8.25e-06

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: 43.10  E-value: 8.25e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 752507739  12 NTTNHVEVNFIKKFTSERDfhpsMSCSITWFLS-----WSPCWECSQAIREFLS 60
Cdd:cd01283   43 GLTLCAERTAIGKAVSEGL----RRYLVTWAVSdeggvWSPCGACRQVLAEFLP 92
 
Name Accession Description Interval E-value
APOBEC1 pfam18769
APOBEC1; APOBEC1 deaminates cytosine both in RNA and ssDNA and has roles in both mRNA editing ...
 2-99 5.83e-61

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: 184.63  E-value: 5.83e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752507739    2 SRKIWRSSGKNTTNHVEVNFIKKFTSERDFHPSMSCSITWFLSWSPCWECSQAIREFLSRHPGVTLVIYVARLFWHMDQQ 81
Cdd:pfam18769   4 RGTIWRNCGNNTTQHAEVNFLEKFFSERHFDPSVSCSITWFLSWSPCGECSKAIGEFLSQHPNVTLVIYAARLFKHLDIR 83

                          90
                  ....*....|....*...
gi 752507739   82 NRQGLRDLVNSGVTIQIM 99
Cdd:pfam18769  84 NRQGLRDLAMSGVTIQIM 101
NAD1 pfam18778
Novel AID APOBEC clade 1; A distinct family of AID/APOBEC-like deaminases found in ray-finned ...
 1-141 8.38e-61

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: 187.10  E-value: 8.38e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752507739    1 MSRKIWRS--SGKNTTNHVEVNFIKKFTSERDFHPSMSCSITWFLSWSPCWECSQAIREFLSRHPGVTLVIYVARLFWHM 78
Cdd:pfam18778  34 NSSSLWRGhlRNENSGCHAEICFLRWFSSWRLFDPSQCYTITWYLSWSPCPSCAAKLAEFLKAHPNVTLTIFAARLYYFE 113

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 752507739   79 DQQNRQGLRDLVNSGVTIQIMRASEYYHCWRNFVNYPPGDEAHWPQyPPLWMMLYALELHCII 141
Cdd:pfam18778 114 DPWNQEGLRSLASAGVTLSIMDYSDFEYCWENFVDNEGRPFVPWED-LEENSRYYHRKLQRIL 175
APOBEC4_like pfam18774
APOBEC4-like -AID/APOBEC-deaminase; Cnidarian and Algal homologs of the APOBEC4-like AID ...
 4-114 7.50e-52

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: 162.74  E-value: 7.50e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752507739    4 KIWR-SSGKNTTNHVEVNFIKKFTSERdfhPSMSCSITWFLSWSPCWECSQAIREFLSRHPGVTLVIYVARLFWHMDQQN 82
Cdd:pfam18774  23 TIWRnWTENNCTEHAEVNFLENFRSER---PSRSCTITWYLSWSPCWECSGRILEFLSRHPNVTLGIYVARLFMHDDDRN 99

                          90       100       110
                  ....*....|....*....|....*....|..
gi 752507739   83 RQGLRDLVNSGVTIQIMRASEYYHCWRNFVNY 114
Cdd:pfam18774 100 RQGLRILQMNGVTIQVMMNKDYCYCWKAFKNY 131
SNAD4 pfam18750
Secreted Novel AID/APOBEC-like Deaminase 4; A family of secreted AID/APOBEC like deaminases ...
 2-110 1.73e-49

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: 156.27  E-value: 1.73e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752507739    2 SRKIW-RSSGKNTTN-HVEVNFIKKFTSeRDFHPSMSCSITWFLSWSPCWECSQAIREFLSRHPGVTLVIYVARLFwHMD 79
Cdd:pfam18750   8 GSKIWqRGYLSNEHEqHAEICFLENIRS-RELDPSQRYRVTWYLSWSPCPECAQKIAEFLAEHPNVTLTIFAARLY-HWD 85

                          90       100       110
                  ....*....|....*....|....*....|.
gi 752507739   80 QQNRQGLRDLVNSGVTIQIMRASEYYHCWRN 110
Cdd:pfam18750  86 EDNRQGLRSLAQAGVTLQIMTLEDFEYCWKN 116
APOBEC4 pfam18775
APOBEC4; A member of the AID/APOBEC family of cytosine deaminases. The biological function of ...
 39-112 4.37e-30

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: 105.50  E-value: 4.37e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 752507739   39 ITWFLSWSPCWECSQAIREFLSRHPGVTLVIYVARLFWHMDQQNRQGLRDLVNSGVTIQIMRASEYYHCWRNFV 112
Cdd:pfam18775   1 VTLYLSWSPCNECSEKIQEFLKKHPKVNLDIYFAQLYHTEEEDNRQGLRSLVEKGVTLSVMSGEDWIYCLRTFV 74
APOBEC2 pfam18772
APOBEC2; APOBEC2 is a highly conserved (slow-evolving) family of AID/APOBECs found in most ...
 13-112 1.47e-29

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: 107.30  E-value: 1.47e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752507739   13 TTNHVEVNFIKKFTSErDFHPSMSCSITWFLSWSPCWECSQAIREFLSRHPGVTLVIYVARLFWHMDQQNRQGLRDLVNS 92
Cdd:pfam18772  47 AGCHAELCFLSWILPW-QLDPGQKYQVTWYVSWSPCPDCARKLAEFLARHPNLSLTIFAARLYFFWEPEYQEGLRRLKRA 125

                          90       100
                  ....*....|....*....|
gi 752507739   93 GVTIQIMRASEYYHCWRNFV 112
Cdd:pfam18772 126 GAQLKIMDYQDFEYCWENFV 145
APOBEC_N pfam08210
APOBEC-like N-terminal domain; A mechanism of generating protein diversity is mRNA editing. ...
 16-113 4.76e-29

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: 105.91  E-value: 4.76e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752507739   16 HVEVNFIKKFtSERDFHPSMSCSITWFLSWSPCWECSQAIREFLSRHPGVTLVIYVARLFWHMDQ--QNRQGLRDLVNSG 93
Cdd:pfam08210  47 HAEERFLRWI-HDLALDPGSNYEVTWYVSWSPCNECASELAAFLSKHPNVRLRIFVSRLYYWEEPdyWNREGLRSLAQAG 125

                          90       100
                  ....*....|....*....|
gi 752507739   94 VTIQIMRASEYYHCWRNFVN 113
Cdd:pfam08210 126 VQLRPMSYKDFEYCWNNFVD 145
APOBEC_C pfam05240
APOBEC-like C-terminal domain; This domain is found at the C-termini of the Apolipoprotein B ...
 63-141 9.51e-28

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: 99.48  E-value: 9.51e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752507739   63 PGVTLVIYVARLFWHMDQQNRQGLRDLVNSGVTIQIMRASEYYHCWRNFVNYppgdeAHWPqYPPlWMML------YALE 136
Cdd:pfam05240   1 PNVSLTIFAARLYYHWDPEYQQGLRRLVQAGAQVAIMSYKEFEYCWDNFVDN-----QGRP-FQP-WEGLeensqlLSRR 73


                  ....*
gi 752507739  137 LHCII 141
Cdd:pfam05240  74 LQEIL 78
NAD2 pfam18782
Novel AID APOBEC clade 2; A distnct family of AID/APOBEC deaminases found only in Amphibians.
 16-123 1.61e-27

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: 102.06  E-value: 1.61e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752507739   16 HVEVNFIKKFTSeRDFHPSMSCSITWFLSWSPCWECSQAIREFLSRHPGVTLVIYVARLFWHMDQQNRQGLRDLVNSGVT 95
Cdd:pfam18782  53 HAELCFLSWFCG-NQLPPYQNYQVTWYVSWSPCPECAGEVAEFLAEHPNVTLTIFAARLYYFWDPDYQEALRRLRQAGAR 131

                          90       100
                  ....*....|....*....|....*...
gi 752507739   96 IQIMRASEYYHCWRNFVNypPGDEAHWP 123
Cdd:pfam18782 132 VKIMDYEEFEYCWENFVY--NQGEPFQP 157
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 12-60 8.25e-06

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: 43.10  E-value: 8.25e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 752507739  12 NTTNHVEVNFIKKFTSERDfhpsMSCSITWFLS-----WSPCWECSQAIREFLS 60
Cdd:cd01283   43 GLTLCAERTAIGKAVSEGL----RRYLVTWAVSdeggvWSPCGACRQVLAEFLP 92
 
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