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Conserved domains on  [gi|73656473|gb|AAZ79369|]
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polyprotein, partial [Ranunculus leaf distortion virus]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Poty_coat super family cl02961
Potyvirus coat protein;
204-435 3.94e-103

Potyvirus coat protein;


The actual alignment was detected with superfamily member pfam00767:

Pssm-ID: 279151  Cd Length: 243  Bit Score: 306.45  E-value: 3.94e-103
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73656473   204 DVNVGSAGTFVVPKVKAMTGKLRLPKI-GSKQLVNLDHLLTYTPTQVDLSNTRATTEQLEAWYNGVMNDYEV-DDAQMQI 281
Cdd:pfam00767   1 DVAAATSITFEVPRRKGFGALWRPPKQkGAATPNRIEKLKKYLPDQNDISNTRATQAQLNDWYEAVRDDYGQtEEEFMDT 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73656473   282 ILNGFMVWCIENGTSPNLT--GDW-----VMMDGESQVVYPIAPMQAHAKPTLRQIMAHFSDLAEA-YIEGRNRKEKYIP 353
Cdd:pfam00767  81 ILPGWIVWCIENGTSPENRkaGSWravimAMMEDEEQVLYPIEPIIINAQPTLRQIMRHFSDLARAqYAESRNQGKPYMP 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73656473   354 RYGIQRNLRDRTLARYAFDFYEITSKTTERAREAVLQMKAAALRNVSSKMFGLDGSVSTKEEDTERHTAGDVNRNMHTLL 433
Cdd:pfam00767 161 KGGLKAGLADASLAAYAFDFYEDTSHDTARAREVHHQMKAAAVSGIKIRLFALAGPGSGQEEDTERHTVEDVAEGIHSLG 240

                  ..
gi 73656473   434 GV 435
Cdd:pfam00767 241 GA 242
ps-ssRNAv_RdRp-like super family cl40470
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
1-49 1.70e-25

conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense single-stranded RNA [(+)ssRNA] viruses and closely related viruses; This family contains the catalytic core domain of RdRp of RNA viruses which belong to Group IV of the Baltimore classification system, and are a group of related viruses that have positive-sense (+), single-stranded (ss) genomes made of ribonucleic acid (RNA). RdRp (also known as RNA replicase) catalyzes the replication of RNA from an RNA template; specifically, it catalyzes the synthesis of the RNA strand complementary to a given RNA template. The Baltimore Classification is divided into 7 classes, 3 of which include RNA viruses: Group IV (+) RNA viruses, Group III double-stranded (ds) RNA viruses, and Group V negative-sense (-) RNA viruses. Baltimore groups of viruses differ with respect to the nature of their genome (i.e., the nucleic acid form that is packaged into virions) and correspond to distinct strategies of genome replication and expression. (+) viral RNA is similar to mRNA and thus can be immediately translated by the host cell. (+)ssRNA viruses can also produce (+) copies of the genome from (-) strands of an intermediate dsRNA genome. This acts as both a transcription and a replication process since the replicated RNA is also mRNA. RdRps belong to the expansive class of polymerases containing so-called palm catalytic domains along with the accessory fingers and thumb domains. All RdRps also have six conserved structural motifs (A-F), located in its majority in the palm subdomain (A-E motifs) and the F motif is located on the finger subdomain. All these motifs have been shown to be implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. In addition to Group IV viruses, this model also includes Picobirnaviruses (PBVs), members of the family Picobirnaviridae of dsRNA viruses (Baltimore classification Group III), which are bi-segmented dsRNA viruses. The phylogenetic tree of the RdRps of RNA viruses (realm Riboviria) showed that picobirnaviruses are embedded in the branch of diverse (+)RNA viruses; sometimes they are collectively referred to as the picornavirus supergroup. RdRps of members of the family Permutatetraviridae, a distinct group of RNA viruses that encompass a circular permutation within the RdRp palm domain, are not included in this model.


The actual alignment was detected with superfamily member cd23175:

Pssm-ID: 477363  Cd Length: 236  Bit Score: 103.68  E-value: 1.70e-25
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 73656473   1 VNGDDLLIAIRPDFEWLLDNMQEIFGELGLNYDFSSRTRKREELWFMSH 49
Cdd:cd23175 188 CNGDDLLIAVSPEHEHILDTFSSSFSELGLNYDFSSRTRDKEELWFMSH 236
 
Name Accession Description Interval E-value
Poty_coat pfam00767
Potyvirus coat protein;
204-435 3.94e-103

Potyvirus coat protein;


Pssm-ID: 279151  Cd Length: 243  Bit Score: 306.45  E-value: 3.94e-103
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73656473   204 DVNVGSAGTFVVPKVKAMTGKLRLPKI-GSKQLVNLDHLLTYTPTQVDLSNTRATTEQLEAWYNGVMNDYEV-DDAQMQI 281
Cdd:pfam00767   1 DVAAATSITFEVPRRKGFGALWRPPKQkGAATPNRIEKLKKYLPDQNDISNTRATQAQLNDWYEAVRDDYGQtEEEFMDT 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73656473   282 ILNGFMVWCIENGTSPNLT--GDW-----VMMDGESQVVYPIAPMQAHAKPTLRQIMAHFSDLAEA-YIEGRNRKEKYIP 353
Cdd:pfam00767  81 ILPGWIVWCIENGTSPENRkaGSWravimAMMEDEEQVLYPIEPIIINAQPTLRQIMRHFSDLARAqYAESRNQGKPYMP 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73656473   354 RYGIQRNLRDRTLARYAFDFYEITSKTTERAREAVLQMKAAALRNVSSKMFGLDGSVSTKEEDTERHTAGDVNRNMHTLL 433
Cdd:pfam00767 161 KGGLKAGLADASLAAYAFDFYEDTSHDTARAREVHHQMKAAAVSGIKIRLFALAGPGSGQEEDTERHTVEDVAEGIHSLG 240

                  ..
gi 73656473   434 GV 435
Cdd:pfam00767 241 GA 242
ps-ssRNAv_Potyviridae_RdRp cd23175
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Potyviridae of ...
1-49 1.70e-25

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Potyviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Potyviridae, order: Patatavirales. Potyviridae, is the largest family of RNA plant viruses, members of which have (+)ssRNA genomes and flexuous filamentous particles. The family is divided into eight genera: Brambyvirus, Bymovirus, Ipomovirus, Macluravirus, Poacevirus, Potyvirus, Rymovirus, and Tritimovirus. Most genomes are monopartite but those of members of the genus Bymovirus are bipartite. Some members cause serious disease epidemics in cultivated plants. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438025  Cd Length: 236  Bit Score: 103.68  E-value: 1.70e-25
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 73656473   1 VNGDDLLIAIRPDFEWLLDNMQEIFGELGLNYDFSSRTRKREELWFMSH 49
Cdd:cd23175 188 CNGDDLLIAVSPEHEHILDTFSSSFSELGLNYDFSSRTRDKEELWFMSH 236
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
2-109 9.67e-16

Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase found in many positive strand RNA eukaryotic viruses. Structural studies indicate that these proteins form the "right hand" structure found in all oligonucleotide polymerases, containing thumb, finger and palm domains, and also the additional bridging finger and thumb domains unique to RNA-directed RNA polymerases.


Pssm-ID: 425815  Cd Length: 450  Bit Score: 78.99  E-value: 9.67e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73656473     2 NGDDLLIAIRPDFEWLLDNMQEIFGELGLNYDFSSRT----RKREELWFMSHRGMEKDGLLIPKLEPERIVSILEWDRA- 76
Cdd:pfam00680 337 YGDDSLVAVSPDFDPVLDRLSPHLKELGLTITPAKKTfpvsRELEEVSFLKRTFRKTPGGYRPPLDRKRILAQLEYIRSk 416
                          90       100       110
                  ....*....|....*....|....*....|...
gi 73656473    77 LQPEHRLEAICAsMIEAWGYDDLLQWIRRFYLW 109
Cdd:pfam00680 417 PVPSGQLENIRA-YASHHGYEFYRDLLYRFVEW 448
 
Name Accession Description Interval E-value
Poty_coat pfam00767
Potyvirus coat protein;
204-435 3.94e-103

Potyvirus coat protein;


Pssm-ID: 279151  Cd Length: 243  Bit Score: 306.45  E-value: 3.94e-103
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73656473   204 DVNVGSAGTFVVPKVKAMTGKLRLPKI-GSKQLVNLDHLLTYTPTQVDLSNTRATTEQLEAWYNGVMNDYEV-DDAQMQI 281
Cdd:pfam00767   1 DVAAATSITFEVPRRKGFGALWRPPKQkGAATPNRIEKLKKYLPDQNDISNTRATQAQLNDWYEAVRDDYGQtEEEFMDT 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73656473   282 ILNGFMVWCIENGTSPNLT--GDW-----VMMDGESQVVYPIAPMQAHAKPTLRQIMAHFSDLAEA-YIEGRNRKEKYIP 353
Cdd:pfam00767  81 ILPGWIVWCIENGTSPENRkaGSWravimAMMEDEEQVLYPIEPIIINAQPTLRQIMRHFSDLARAqYAESRNQGKPYMP 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73656473   354 RYGIQRNLRDRTLARYAFDFYEITSKTTERAREAVLQMKAAALRNVSSKMFGLDGSVSTKEEDTERHTAGDVNRNMHTLL 433
Cdd:pfam00767 161 KGGLKAGLADASLAAYAFDFYEDTSHDTARAREVHHQMKAAAVSGIKIRLFALAGPGSGQEEDTERHTVEDVAEGIHSLG 240

                  ..
gi 73656473   434 GV 435
Cdd:pfam00767 241 GA 242
ps-ssRNAv_Potyviridae_RdRp cd23175
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Potyviridae of ...
1-49 1.70e-25

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Potyviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Potyviridae, order: Patatavirales. Potyviridae, is the largest family of RNA plant viruses, members of which have (+)ssRNA genomes and flexuous filamentous particles. The family is divided into eight genera: Brambyvirus, Bymovirus, Ipomovirus, Macluravirus, Poacevirus, Potyvirus, Rymovirus, and Tritimovirus. Most genomes are monopartite but those of members of the genus Bymovirus are bipartite. Some members cause serious disease epidemics in cultivated plants. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438025  Cd Length: 236  Bit Score: 103.68  E-value: 1.70e-25
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 73656473   1 VNGDDLLIAIRPDFEWLLDNMQEIFGELGLNYDFSSRTRKREELWFMSH 49
Cdd:cd23175 188 CNGDDLLIAVSPEHEHILDTFSSSFSELGLNYDFSSRTRDKEELWFMSH 236
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
2-109 9.67e-16

Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase found in many positive strand RNA eukaryotic viruses. Structural studies indicate that these proteins form the "right hand" structure found in all oligonucleotide polymerases, containing thumb, finger and palm domains, and also the additional bridging finger and thumb domains unique to RNA-directed RNA polymerases.


Pssm-ID: 425815  Cd Length: 450  Bit Score: 78.99  E-value: 9.67e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73656473     2 NGDDLLIAIRPDFEWLLDNMQEIFGELGLNYDFSSRT----RKREELWFMSHRGMEKDGLLIPKLEPERIVSILEWDRA- 76
Cdd:pfam00680 337 YGDDSLVAVSPDFDPVLDRLSPHLKELGLTITPAKKTfpvsRELEEVSFLKRTFRKTPGGYRPPLDRKRILAQLEYIRSk 416
                          90       100       110
                  ....*....|....*....|....*....|...
gi 73656473    77 LQPEHRLEAICAsMIEAWGYDDLLQWIRRFYLW 109
Cdd:pfam00680 417 PVPSGQLENIRA-YASHHGYEFYRDLLYRFVEW 448
RNA_dep_RNAP cd01699
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
1-73 8.83e-05

RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage. RdRp catalyzes synthesis of the RNA strand complementary to a given RNA template. RdRps of many viruses are products of processing of polyproteins. Some RdRps consist of one polypeptide chain, and others are complexes of several subunits. The domain organization and the 3D structure of the catalytic center of a wide range of RdRps, including those with a low overall sequence homology, are conserved. The catalytic center is formed by several motifs containing a number of conserved amino acid residues. This subfamily represents the RNA-dependent RNA polymerases from all positive-strand RNA eukaryotic viruses with no DNA stage.


Pssm-ID: 238843 [Multi-domain]  Cd Length: 278  Bit Score: 44.20  E-value: 8.83e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 73656473   1 VNGDDLLIAIRPDFEWL-LDNMQEIFGELGLNY----DFSSRTRKREELWFMSHRGM-EKDGLLIPKLEPERIVSILEW 73
Cdd:cd01699 199 NYGDDCLLSVEKADDKFnLETLAEWLKEYGLTMtdedKVESPFRPLEEVEFLKRRFVlDEGGGWRAPLDPSSILSKLSW 277
 
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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