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Conserved domains on  [gi|54632755|gb|AAV35723|]
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non-structural protein 5B, partial [Hepacivirus hominis]

Protein Classification

RNA-dependent RNA polymerase family protein( domain architecture ID 1750808)

RNA-dependent RNA polymerase (RdRp) family protein similar to the RdRp catalytic domain of alpha-, beta-, gamma-, delta-coronaviruses, including three highly pathogenic human coronaviruses (CoVs) such as Middle East respiratory syndrome (MERS)-related CoV, Severe acute respiratory syndrome (SARS) CoV, and SARS-CoV-2

EC:  2.7.7.48
Gene Ontology:  GO:0097747
PubMed:  29439438

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ps-ssRNAv_RdRp-like super family cl40470
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
 1-133 2.10e-97

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 cd23202:

Pssm-ID: 477363  Cd Length: 518  Bit Score: 289.06  E-value: 2.10e-97
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54632755   1 GIPYDTRCFDSTVTERDIRVEEEVYQCCDLEPDTRKVISALTERLYVGGPMYNSKGDLCGVRRCRASGVYTTSFGNTLTC 80
Cdd:cd23202 203 GFSYDTRCFDSTVTERDIRTEESIYQCCDLDPEARKAIRSLTERLYVGGPMTNSKGQSCGYRRCRASGVFTTSSGNTLTC 282

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
gi 54632755  81 YLKASAAIRAAGLRDCTMLVCGDDLVVIAESDGVGEDKQALAAFTEAMTRNSA 133
Cdd:cd23202 283 YLKASAACRAAGLKDPTMLVCGDDLVVIAESAGVEEDAAALRAFTEAMTRYSA 335
 
Name Accession Description Interval E-value
Hepacivirus_RdRp cd23202
RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ...
 1-133 2.10e-97

RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the RdRp of RNA viruses belonging to the Hepacivirus genus within the family Flaviviridae, order Amarillovirales. The genus Hepacivirus includes hepatitis C virus, a major human pathogen causing progressive liver disease, and several other viruses of unknown pathogenicity that infect horses, rodents, bats, cows and primates. Infections are typically persistent and target the liver. Virions of Hepacivirus have a single, small, basic capsid (C) protein and two envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. 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: 438052  Cd Length: 518  Bit Score: 289.06  E-value: 2.10e-97
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54632755   1 GIPYDTRCFDSTVTERDIRVEEEVYQCCDLEPDTRKVISALTERLYVGGPMYNSKGDLCGVRRCRASGVYTTSFGNTLTC 80
Cdd:cd23202 203 GFSYDTRCFDSTVTERDIRTEESIYQCCDLDPEARKAIRSLTERLYVGGPMTNSKGQSCGYRRCRASGVFTTSSGNTLTC 282

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
gi 54632755  81 YLKASAAIRAAGLRDCTMLVCGDDLVVIAESDGVGEDKQALAAFTEAMTRNSA 133
Cdd:cd23202 283 YLKASAACRAAGLKDPTMLVCGDDLVVIAESAGVEEDAAALRAFTEAMTRYSA 335
RdRP_3 pfam00998
Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase ...
 1-130 4.43e-54

Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase enzymes from hepatitis C virus and various plant viruses.


Pssm-ID: 395794 [Multi-domain]  Cd Length: 486  Bit Score: 176.27  E-value: 4.43e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54632755     1 GIPYDTRCFDSTVTERDIRVEEEVYQCCDLEPDtrKVISALTERLYVGGPMYNSKGDL-CGVRRCRASGVYTTSFGNTLT 79
Cdd:pfam00998 204 AIGLDASRFDQHVSVEALRFEHSIYLAAFLGPE--ELIRLLTWQLYNGGPMYASDGQIkYGVRGCRMSGDMNTSLGNCLL 281

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 54632755    80 CYLKASAAIRAAGlRDCTMLVCGDDLVVIAESDGVGEDKQALaafTEAMTR 130
Cdd:pfam00998 282 MCLKVHAACKALG-IDARLLNNGDDCVVICESADLDEVKEAL---TEAFAR 328
 
Name Accession Description Interval E-value
Hepacivirus_RdRp cd23202
RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ...
 1-133 2.10e-97

RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the RdRp of RNA viruses belonging to the Hepacivirus genus within the family Flaviviridae, order Amarillovirales. The genus Hepacivirus includes hepatitis C virus, a major human pathogen causing progressive liver disease, and several other viruses of unknown pathogenicity that infect horses, rodents, bats, cows and primates. Infections are typically persistent and target the liver. Virions of Hepacivirus have a single, small, basic capsid (C) protein and two envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. 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: 438052  Cd Length: 518  Bit Score: 289.06  E-value: 2.10e-97
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54632755   1 GIPYDTRCFDSTVTERDIRVEEEVYQCCDLEPDTRKVISALTERLYVGGPMYNSKGDLCGVRRCRASGVYTTSFGNTLTC 80
Cdd:cd23202 203 GFSYDTRCFDSTVTERDIRTEESIYQCCDLDPEARKAIRSLTERLYVGGPMTNSKGQSCGYRRCRASGVFTTSSGNTLTC 282

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
gi 54632755  81 YLKASAAIRAAGLRDCTMLVCGDDLVVIAESDGVGEDKQALAAFTEAMTRNSA 133
Cdd:cd23202 283 YLKASAACRAAGLKDPTMLVCGDDLVVIAESAGVEEDAAALRAFTEAMTRYSA 335
ps-ssRNAv_Flaviviridae_RdRp cd23178
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of ...
 1-133 3.42e-59

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Flaviviridae, order Amarillovirales. Flaviviridae, is a family of small, enveloped viruses with RNA genomes of 9-13 kb. Most infect mammals and birds. Many flaviviruses are host-specific and pathogenic, such as hepatitis C virus in the genus Hepacivirus. The majority of known members in the genus Flavivirus are arthropod borne, and many are important human and veterinary pathogens (e.g., yellow fever virus, dengue virus). Virions are typically spherical in shape with a lipid envelope. Virions have a single, small, basic capsid (C) protein and two (genera Flavivirus, Hepacivirus and Pegivirus) or three (genus Pestivirus) envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. Translational initiation of genomic RNA is cap dependent in the case of members of the genus Flavivirus. 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: 438028  Cd Length: 284  Bit Score: 184.26  E-value: 3.42e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54632755   1 GIPYDTRCFDSTVTERDIRVEEEVYQCCDLEPDtRKVISALTERLYVGGPMYNSKGDLCGVRRCRASGVYTTSFGNTLTC 80
Cdd:cd23178  83 AYSYDTRCFDSTVTEDDIQVEEEIYQACSLKEA-RQAIVSITERLYVEGPMVNSDGQICGRRRCRASGVLTTSAGNT*TC 161

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
gi 54632755  81 YLKASAAIRAAGLRDCTMLVCGDDLVVIAESDGVGEDKQALAAFTEAMTRNSA 133
Cdd:cd23178 162 YLK*LAACREAGIRLPTMLVCGDDCVVICESDGTQEDAALLAAFTEALTRYGK 214
RdRP_3 pfam00998
Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase ...
 1-130 4.43e-54

Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase enzymes from hepatitis C virus and various plant viruses.


Pssm-ID: 395794 [Multi-domain]  Cd Length: 486  Bit Score: 176.27  E-value: 4.43e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54632755     1 GIPYDTRCFDSTVTERDIRVEEEVYQCCDLEPDtrKVISALTERLYVGGPMYNSKGDL-CGVRRCRASGVYTTSFGNTLT 79
Cdd:pfam00998 204 AIGLDASRFDQHVSVEALRFEHSIYLAAFLGPE--ELIRLLTWQLYNGGPMYASDGQIkYGVRGCRMSGDMNTSLGNCLL 281

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 54632755    80 CYLKASAAIRAAGlRDCTMLVCGDDLVVIAESDGVGEDKQALaafTEAMTR 130
Cdd:pfam00998 282 MCLKVHAACKALG-IDARLLNNGDDCVVICESADLDEVKEAL---TEAFAR 328
Pegivirus_RdRp cd23203
RNA-dependent RNA polymerase (RdRp) in the genus Pegivirus, within the family Flaviviridae of ...
 2-124 4.16e-37

RNA-dependent RNA polymerase (RdRp) in the genus Pegivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the RdRp of RNA viruses belonging to the Pegivirus genus within the family Flaviviridae, order Amarillovirales. Members of the Pegivirus genus are widely distributed in a range of mammalian species, in which they cause persistent infections. To date, they have not been clearly associated with disease. Virions of Pegivirus have a single, small, basic capsid (C) protein and two envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. 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: 438053  Cd Length: 476  Bit Score: 131.23  E-value: 4.16e-37
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54632755   2 IPYDTRCFDSTVTERDIRVEEEVYQCCDLEPDtrkVISALTeRLYVGGPMYNSKGDLCGVRRCRASGVYTTSFGNTLTCY 81
Cdd:cd23203 207 ITVDATCFDSSITEEDVARETEIYAAASDDPE---LVRALG-KYYAEGPMVNPEGVPVGERRCRASGVLTTSSSNSITCY 282

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
gi 54632755  82 LKASAAIRAAGLRDCTMLVCGDDLVVIAESDgvGED-----KQALAAF 124
Cdd:cd23203 283 LKVKAACRKAGLKNPSFLIHGDDCLIICERP--EEDpcdalKAALASY 328
RNA_dep_RNAP cd01699
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
 5-128 5.17e-20

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: 82.72  E-value: 5.17e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54632755   5 DTRCFDSTVTERDIRVEEEVYQCCDLEPDTRKVISALTERLYVGGPMYNskGDLCGVRRCRASGVYTTSFGNTLTCYLKA 84
Cdd:cd01699 102 DYSRFDSSLSPQLLEAEHSIYNALYDDDDELERRNLLRSLTNNSLHIGF--NEVYKVRGGRPSGDPLTSIGNSIINCILV 179

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
gi 54632755  85 SAAIRAAG----LRDCTMLVCGDDLVVIAESDgvgEDKQALAAFTEAM 128
Cdd:cd01699 180 RYAFRKLGgksfFKNVRLLNYGDDCLLSVEKA---DDKFNLETLAEWL 224
ps_ssRNAv_Tolivirales_RdRp cd23179
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Toliovirales of ...
 9-112 3.40e-09

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Toliovirales of positive-sense single-stranded RNA (+ssRNA) viruses; This family contains the catalytic core domain of RdRp of Tolivirales, an order of (+)ssRNA viruses which infect insects and plants. The virions are non-enveloped, spherical, and have an icosahedral capsid. The name Tolivirales, is derived from "tombusvirus-like" with the suffix -virales indicating a virus order. This order includes two families: Carmotetraviridae and Tombusviridae. 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: 438029  Cd Length: 227  Bit Score: 52.91  E-value: 3.40e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54632755   9 FDSTVTERDIRVEEEVY-QCCDLEPDTRKVISA-LTERlyvggpMYNSKGDLCGVRRCRASGVYTTSFGNTLTCYLKASA 86
Cdd:cd23179  93 FDAHVSVELLRLEHSVYlACYPGDPELRKLLKWqLVNK------GRTSNGVKYKTRGGRMSGDMNTGLGNCLIMLAMVYA 166

                        90       100
                ....*....|....*....|....*.
gi 54632755  87 AIRAAGLRdCTMLVCGDDLVVIAESD 112
Cdd:cd23179 167 VLRELGIK-YDLLVDGDDALVFVERE 191
ps-ssRNAv_RdRp-like cd23167
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
 64-110 3.33e-07

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.


Pssm-ID: 438017 [Multi-domain]  Cd Length: 73  Bit Score: 44.64  E-value: 3.33e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 54632755  64 CRASGVYTTSFGNTLTCYLKASAAIRAAGLR-----DCTMLVCGDDLVVIAE 110
Cdd:cd23167  22 GQPSGSPNTSADNSLINLLLARLALRKACGRaeflnSVGILVYGDDSLVSVP 73
Tombusvirus-like_RdRp cd23236
RNA-dependent RNA polymerase (RdRp) in the genus Tombusvirus of positive-sense single-stranded ...
 2-111 2.58e-05

RNA-dependent RNA polymerase (RdRp) in the genus Tombusvirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within Procedovirinae subfamily; and related RdRps; This group contains the RdRp of RNA viruses belonging to the Tombusvirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. Tombusvirus is a genus of plant viruses. There are 17 species in the Tombusvirus genus: Artichoke mottled crinkle virus, Carnation Italian ringspot virus, Cucumber Bulgarian virus, Cucumber necrosis virus, Cymbidium ringspot virus, Eggplant mottled crinkle virus, Grapevine Algerian latent virus, Havel River virus, Lato River virus, Limonium flower distortion virus, Moroccan pepper virus, Neckar River virus, Pelargonium leaf curl virus, Pelargonium necrotic spot virus, Petunia asteroid mosaic virus, Sikte waterborne virus, and Tomato bushy stunt virus. Symptoms associated with this genus include mosaic. The name of the genus comes from Tomato bushy stunt virus. 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: 438086 [Multi-domain]  Cd Length: 474  Bit Score: 42.31  E-value: 2.58e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54632755   2 IPYDTRCFDSTVTERDIRVEEEVYQCcdLEPDTRKVISALTERLYVGGPMYNSKGDLCGVRR-CRASGVYTTSFGNTLTC 80
Cdd:cd23236 203 IGLDASRFDQHCSVEALQFEHSFYRA--MYPGNKLLSKLLEWQLHNKGKGYVPDGTITYRKEgCRMSGDINTSLGNYLLM 280

                        90       100       110
                ....*....|....*....|....*....|.
gi 54632755  81 YLKASAAIRAAGLRDCTMLVCGDDLVVIAES 111
Cdd:cd23236 281 CAMVYGYMRHLGINEFSLANCGDDCVLIVER 311
Gammacarmovirus_RdRp cd23242
RNA-dependent RNA polymerase (RdRp) in the genus Gammacarmovirus of positive-sense ...
 2-112 9.28e-04

RNA-dependent RNA polymerase (RdRp) in the genus Gammacarmovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Gammacarmovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. The single genus Carmovirus was split in 2015 into three genera, each retaining -carmovirus as part of their name: Alphacarmovirus, Betacarmovirus, and Gammacarmovirus. Most species have a narrow natural host range. However, different carmoviruses infect a wide range of both monocotyledonous and dicotyledonous plants. Viruses tend to remain localized, forming necrosis in artificially infected hosts. There are 4 species in the genus Gammacarmovirus: Cowpea mottle virus, Melon necrotic spot virus, Pea stem necrosis virus, and Soybean yellow mottle mosaic virus. 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: 438092  Cd Length: 476  Bit Score: 37.80  E-value: 9.28e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54632755   2 IPYDTRCFDSTVTERDIRVEEEVY-QCCDLEPDTRKVISALTERLYVGgpmYNSKGDL-CGVRRCRASGVYTTSFGNTLT 79
Cdd:cd23242 196 IGFDMKRFDQHVSRDALEWEHSVYlDAFCNDPYLAELLSWQLENKGVG---YASDGSIkYKVDGCRMSGDMNTAMGNCLL 272

                        90       100       110
                ....*....|....*....|....*....|...
gi 54632755  80 CYLKASAAIRAAGLRdCTMLVCGDDLVVIAESD 112
Cdd:cd23242 273 ACAITWDFFKGRGIK-ARLLNNGDDCVVITEKE 304
 
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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