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Conserved domains on  [gi|1895741154|gb|QNI40701|]
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non-structural protein 5B, partial [Hepacivirus hominis]

Protein Classification

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 ...
 1-102 1.51e-71

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: 220.88  E-value: 1.51e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895741154   1 TEESIYLSCSLPEEARTAIHSLTERLYVGGPMTNSKGQSCGYRRCRASGVLTTSMGNTLTCYVKARAACNAAGIVAPTML 80
Cdd:cd23202   222 TEESIYQCCDLDPEARKAIRSLTERLYVGGPMTNSKGQSCGYRRCRASGVFTTSSGNTLTCYLKASAACRAAGLKDPTML 301

                          90       100
                  ....*....|....*....|..
gi 1895741154  81 VCGDDLVVISESQGAEEDERNL 102
Cdd:cd23202   302 VCGDDLVVIAESAGVEEDAAAL 323
 
Name Accession Description Interval E-value
Hepacivirus_RdRp cd23202
RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ...
 1-102 1.51e-71

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: 220.88  E-value: 1.51e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895741154   1 TEESIYLSCSLPEEARTAIHSLTERLYVGGPMTNSKGQSCGYRRCRASGVLTTSMGNTLTCYVKARAACNAAGIVAPTML 80
Cdd:cd23202   222 TEESIYQCCDLDPEARKAIRSLTERLYVGGPMTNSKGQSCGYRRCRASGVFTTSSGNTLTCYLKASAACRAAGLKDPTML 301

                          90       100
                  ....*....|....*....|..
gi 1895741154  81 VCGDDLVVISESQGAEEDERNL 102
Cdd:cd23202   302 VCGDDLVVIAESAGVEEDAAAL 323
RdRP_3 pfam00998
Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase ...
 1-102 4.38e-42

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: 143.14  E-value: 4.38e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895741154   1 TEESIYLSCSLPEEarTAIHSLTERLYVGGPMTNSKGQ-SCGYRRCRASGVLTTSMGNTLTCYVKARAACNAAGIvAPTM 79
Cdd:pfam00998 223 FEHSIYLAAFLGPE--ELIRLLTWQLYNGGPMYASDGQiKYGVRGCRMSGDMNTSLGNCLLMCLKVHAACKALGI-DARL 299

                          90       100
                  ....*....|....*....|...
gi 1895741154  80 LVCGDDLVVISESQGAEEDERNL 102
Cdd:pfam00998 300 LNNGDDCVVICESADLDEVKEAL 322
 
Name Accession Description Interval E-value
Hepacivirus_RdRp cd23202
RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ...
 1-102 1.51e-71

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: 220.88  E-value: 1.51e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895741154   1 TEESIYLSCSLPEEARTAIHSLTERLYVGGPMTNSKGQSCGYRRCRASGVLTTSMGNTLTCYVKARAACNAAGIVAPTML 80
Cdd:cd23202   222 TEESIYQCCDLDPEARKAIRSLTERLYVGGPMTNSKGQSCGYRRCRASGVFTTSSGNTLTCYLKASAACRAAGLKDPTML 301

                          90       100
                  ....*....|....*....|..
gi 1895741154  81 VCGDDLVVISESQGAEEDERNL 102
Cdd:cd23202   302 VCGDDLVVIAESAGVEEDAAAL 323
ps-ssRNAv_Flaviviridae_RdRp cd23178
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of ...
 1-102 4.62e-47

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: 151.90  E-value: 4.62e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895741154   1 TEESIYLSCSlPEEARTAIHSLTERLYVGGPMTNSKGQSCGYRRCRASGVLTTSMGNTLTCYVKARAACNAAGIVAPTML 80
Cdd:cd23178   102 VEEEIYQACS-LKEARQAIVSITERLYVEGPMVNSDGQICGRRRCRASGVLTTSAGNT*TCYLK*LAACREAGIRLPTML 180

                          90       100
                  ....*....|....*....|..
gi 1895741154  81 VCGDDLVVISESQGAEEDERNL 102
Cdd:cd23178   181 VCGDDCVVICESDGTQEDAALL 202
RdRP_3 pfam00998
Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase ...
 1-102 4.38e-42

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: 143.14  E-value: 4.38e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895741154   1 TEESIYLSCSLPEEarTAIHSLTERLYVGGPMTNSKGQ-SCGYRRCRASGVLTTSMGNTLTCYVKARAACNAAGIvAPTM 79
Cdd:pfam00998 223 FEHSIYLAAFLGPE--ELIRLLTWQLYNGGPMYASDGQiKYGVRGCRMSGDMNTSLGNCLLMCLKVHAACKALGI-DARL 299

                          90       100
                  ....*....|....*....|...
gi 1895741154  80 LVCGDDLVVISESQGAEEDERNL 102
Cdd:pfam00998 300 LNNGDDCVVICESADLDEVKEAL 322
Pegivirus_RdRp cd23203
RNA-dependent RNA polymerase (RdRp) in the genus Pegivirus, within the family Flaviviridae of ...
 25-100 2.79e-29

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: 108.51  E-value: 2.79e-29
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1895741154  25 RLYVGGPMTNSKGQSCGYRRCRASGVLTTSMGNTLTCYVKARAACNAAGIVAPTMLVCGDDLVVISESQGAEEDER 100
Cdd:cd23203   245 KYYAEGPMVNPEGVPVGERRCRASGVLTTSSSNSITCYLKVKAACRKAGLKNPSFLIHGDDCLIICERPEEDPCDA 320
RNA_dep_RNAP cd01699
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
 2-92 2.35e-12

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: 60.76  E-value: 2.35e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895741154   2 EESIYLSCSLPEEARTA---IHSLTERLYVGGpmtnsKGQSCGYRRCRASGVLTTSMGNTLTCYVKARAACNAAGIVA-- 76
Cdd:cd01699   118 EHSIYNALYDDDDELERrnlLRSLTNNSLHIG-----FNEVYKVRGGRPSGDPLTSIGNSIINCILVRYAFRKLGGKSff 192

                          90
                  ....*....|....*...
gi 1895741154  77 --PTMLVCGDDLVVISES 92
Cdd:cd01699   193 knVRLLNYGDDCLLSVEK 210
ps-ssRNAv_RdRp-like cd23167
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
 45-91 1.10e-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: 45.02  E-value: 1.10e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1895741154  45 CRASGVLTTSMGNTLTCYVKARAAC-----NAAGIVAPTMLVCGDDLVVISE 91
Cdd:cd23167    22 GQPSGSPNTSADNSLINLLLARLALrkacgRAEFLNSVGILVYGDDSLVSVP 73
ps_ssRNAv_Tolivirales_RdRp cd23179
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Toliovirales of ...
 39-92 2.75e-06

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: 43.66  E-value: 2.75e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1895741154  39 SCG--YRR--CRASGVLTTSMGNTLTCYVKARAACNAAGIVApTMLVCGDDLVVISES 92
Cdd:cd23179   134 SNGvkYKTrgGRMSGDMNTGLGNCLIMLAMVYAVLRELGIKY-DLLVDGDDALVFVER 190
Gammacarmovirus_RdRp cd23242
RNA-dependent RNA polymerase (RdRp) in the genus Gammacarmovirus of positive-sense ...
 42-97 4.54e-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: 4.54e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1895741154  42 YRR--CRASGVLTTSMGNTLTCYVKARAACNAAGIVApTMLVCGDDLVVISESQGAEE 97
Cdd:cd23242   252 YKVdgCRMSGDMNTAMGNCLLACAITWDFFKGRGIKA-RLLNNGDDCVVITEKECAAA 308
Tombusvirus-like_RdRp cd23236
RNA-dependent RNA polymerase (RdRp) in the genus Tombusvirus of positive-sense single-stranded ...
 9-102 6.05e-04

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: 37.30  E-value: 6.05e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1895741154   9 CSLpeEARTAIHSLTERLYVGGPMTN--------SKGQ------SCGYRR--CRASGVLTTSMGNTLTCYVKARAACNAA 72
Cdd:cd23236   214 CSV--EALQFEHSFYRAMYPGNKLLSkllewqlhNKGKgyvpdgTITYRKegCRMSGDINTSLGNYLLMCAMVYGYMRHL 291

                          90       100       110
                  ....*....|....*....|....*....|
gi 1895741154  73 GIVAPTMLVCGDDLVVISESQGAEEDERNL 102
Cdd:cd23236   292 GINEFSLANCGDDCVLIVERRNLKQVQGTL 321
Aureusvirus_RdRp cd23243
RNA-dependent RNA polymerase (RdRp) in the genus Aureusvirus of positive-sense single-stranded ...
 45-91 7.08e-04

RNA-dependent RNA polymerase (RdRp) in the genus Aureusvirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Aureusvirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. In the Aureusvirus genus plants serve as natural hosts. There are six species in this genus: Cucumber leaf spot virus (CLSV), Elderberry aureusvirus 1, Johnsongrass chlorotic stripe mosaic virus (JCSMV), Maize white line mosaic virus (MWLMV), Pothos latent virus (PoLV), and Yam spherical virus (YSV). Aureusviruses infect various natural host plants but their individual range is generally restricted to a few species, pothos and pigeon pea or lisianthus for PoLV, yam for YSV, sesame for SNMV, cucumber, melon or squash for CLSV and various Poaceae species, mainly maize (MWLMV) or johnsongrass (JCSMV). Aureusviruses are transmitted mechanically and by seeds. Transmission through the soil or by the water circulating in hydroponic systems for PoLV, CLSV and MWLMV, or by the fungus Olpidium bornovanus (for CLSV) have also been reported. 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: 438093  Cd Length: 488  Bit Score: 37.12  E-value: 7.08e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1895741154  45 CRASGVLTTSMGNTLTCYVKARAACNAAGIVApTMLVCGDDLVVISE 91
Cdd:cd23243   267 CRMSGDMNTSMGNYLIMSCLVYQFCKEVGLDA-SLANCGDDCVLFLE 312
Tombusviridae_RdRp cd23206
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tombusviridae of ...
 45-92 2.76e-03

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tombusviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Tombusviridae, order Tolivirales. The family Tombusviridae comprises plant viruses, and is classified into 3 subfamilies (Calvusvirinae, Procedovirinae, and Regressovirinae), 17 genera, and 95 species. One genus is unassigned to a subfamily: Luteovirus. The name of the family is derived from Tomato bushy stunt virus (TBSV). Members of Tombusviridae replicate in the cytoplasm, by use of negative strand templates. The replication process leaves a surplus of positive- sense (+)RNA strands, and it is thought that not only does the viral RNA act as a template for replication, but is also able to manipulate and regulate RNA synthesis. 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: 438056  Cd Length: 231  Bit Score: 35.16  E-value: 2.76e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1895741154  45 CRASGVLTTSMGNTLT-C-----YVKARaacnaaGIVApTMLVCGDDLVVISES 92
Cdd:cd23206   148 GRMSGDMNTSLGNCLImCamvyaYLEEL------GIKA-ELANNGDDCVLIMER 194
 
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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