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Conserved domains on  [gi|1930685751|dbj|BCG55388|]
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putative RNA-dependent RNA polymerase, partial [Simulium aureohirtum associated A virus]

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 ...
1-172 5.84e-77

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 cd23174:

Pssm-ID: 477363  Cd Length: 229  Bit Score: 229.28  E-value: 5.84e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930685751   1 EELATQDRPTGRQCRVKNFVKFETTEKYVDPRNISPREDGFLATVGPYIAAIEKAAKAAPFLIKGLTPSAKCKKVNWLLE 80
Cdd:cd23174     1 NRVLSDPEPRRKYALIKNFVKNETTAKFVDPRNISPRSDEFLVVVGPYISAIEHAAVHCPFLIKGLTPKKRCDKLSWLTE 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930685751  81 YALFCEIDYTRFDMSISEEILRIFEDYVLLRPF--RNHTLFILLVQAARRTYGISRYGTRYSVNGTRCSGDAWTSIANGL 158
Cdd:cd23174    81 YERFLEIDFSRFDMTLMKDLLRIVELRFLLDPYtqRAHQLFIAFMLYTLTNVGVSRFGTHYKRDGTRCSGDPHTSIGNGF 160
                         170
                  ....*....|....
gi 1930685751 159 LNYFLTWLCMRKLP 172
Cdd:cd23174   161 LNAFIIWLCLRKLP 174
 
Name Accession Description Interval E-value
ps-ssRNAv_CBPV-like_RdRp cd23174
catalytic core domain of RNA-dependent RNA polymerase (RdRp) chronic bee paralysis virus (CBPV) ...
1-172 5.84e-77

catalytic core domain of RNA-dependent RNA polymerase (RdRp) chronic bee paralysis virus (CBPV) and related positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of the chronic bee paralysis virus (CBPV) and related (+)ssRNA viruses. The CBPV is the causative agent of severe, usually fatal, paralysis in adult honey bees. CBPV has not been assigned to any group or class of viruses because it has a unique genome organization and virion morphology. However, analyses of the nucleic acid sequence showed similarities between the RdRp of CBPV and the RdRps of Tombusviruses, Nodaviruses, Lake Sinai virus 1 and 2 as well as the Anopheline associated C virus (AACV). CBPV was one of the first viruses in honey bees to be described and isolated as it causes characteristic signs of disease in adult honey bees. 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: 438024  Cd Length: 229  Bit Score: 229.28  E-value: 5.84e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930685751   1 EELATQDRPTGRQCRVKNFVKFETTEKYVDPRNISPREDGFLATVGPYIAAIEKAAKAAPFLIKGLTPSAKCKKVNWLLE 80
Cdd:cd23174     1 NRVLSDPEPRRKYALIKNFVKNETTAKFVDPRNISPRSDEFLVVVGPYISAIEHAAVHCPFLIKGLTPKKRCDKLSWLTE 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930685751  81 YALFCEIDYTRFDMSISEEILRIFEDYVLLRPF--RNHTLFILLVQAARRTYGISRYGTRYSVNGTRCSGDAWTSIANGL 158
Cdd:cd23174    81 YERFLEIDFSRFDMTLMKDLLRIVELRFLLDPYtqRAHQLFIAFMLYTLTNVGVSRFGTHYKRDGTRCSGDPHTSIGNGF 160
                         170
                  ....*....|....
gi 1930685751 159 LNYFLTWLCMRKLP 172
Cdd:cd23174   161 LNAFIIWLCLRKLP 174
RdRP_3 pfam00998
Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase ...
88-171 2.12e-05

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: 43.76  E-value: 2.12e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930685751  88 DYTRFDMSISEEILRiFEDYVLLRPFRNHTLFILLV--QAARRTYGISRYGT-RYSVNGTRCSGDAWTSIANGLLNYFLT 164
Cdd:pfam00998 208 DASRFDQHVSVEALR-FEHSIYLAAFLGPEELIRLLtwQLYNGGPMYASDGQiKYGVRGCRMSGDMNTSLGNCLLMCLKV 286

                  ....*..
gi 1930685751 165 WLCMRKL 171
Cdd:pfam00998 287 HAACKAL 293
 
Name Accession Description Interval E-value
ps-ssRNAv_CBPV-like_RdRp cd23174
catalytic core domain of RNA-dependent RNA polymerase (RdRp) chronic bee paralysis virus (CBPV) ...
1-172 5.84e-77

catalytic core domain of RNA-dependent RNA polymerase (RdRp) chronic bee paralysis virus (CBPV) and related positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of the chronic bee paralysis virus (CBPV) and related (+)ssRNA viruses. The CBPV is the causative agent of severe, usually fatal, paralysis in adult honey bees. CBPV has not been assigned to any group or class of viruses because it has a unique genome organization and virion morphology. However, analyses of the nucleic acid sequence showed similarities between the RdRp of CBPV and the RdRps of Tombusviruses, Nodaviruses, Lake Sinai virus 1 and 2 as well as the Anopheline associated C virus (AACV). CBPV was one of the first viruses in honey bees to be described and isolated as it causes characteristic signs of disease in adult honey bees. 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: 438024  Cd Length: 229  Bit Score: 229.28  E-value: 5.84e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930685751   1 EELATQDRPTGRQCRVKNFVKFETTEKYVDPRNISPREDGFLATVGPYIAAIEKAAKAAPFLIKGLTPSAKCKKVNWLLE 80
Cdd:cd23174     1 NRVLSDPEPRRKYALIKNFVKNETTAKFVDPRNISPRSDEFLVVVGPYISAIEHAAVHCPFLIKGLTPKKRCDKLSWLTE 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930685751  81 YALFCEIDYTRFDMSISEEILRIFEDYVLLRPF--RNHTLFILLVQAARRTYGISRYGTRYSVNGTRCSGDAWTSIANGL 158
Cdd:cd23174    81 YERFLEIDFSRFDMTLMKDLLRIVELRFLLDPYtqRAHQLFIAFMLYTLTNVGVSRFGTHYKRDGTRCSGDPHTSIGNGF 160
                         170
                  ....*....|....
gi 1930685751 159 LNYFLTWLCMRKLP 172
Cdd:cd23174   161 LNAFIIWLCLRKLP 174
ps_ssRNAv_Tolivirales_RdRp cd23179
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Toliovirales of ...
15-172 5.37e-20

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: 82.96  E-value: 5.37e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930685751  15 RVKNFVKFE---TTEKYVDPRNISPREDGFLATVGPY--------IAAIEKAAKAAPFLIKGLTPSAKC----KKVNWLL 79
Cdd:cd23179     2 RVKAFLKAEkynPLAKNKKPRMIQPRSPRYNLELARYlkpiehalYGALDAGRGGTRVVAKGLNPRQRAnlirRKWDEFD 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930685751  80 EYALFcEIDYTRFDMSISEEILRIfEDYVLLRPFRNHTLFILLVQAARRTYGISRYGTRYSVNGTRCSGDAWTSIANGLL 159
Cdd:cd23179    82 DPVVF-SLDASRFDAHVSVELLRL-EHSVYLACYPGDPELRKLLKWQLVNKGRTSNGVKYKTRGGRMSGDMNTGLGNCLI 159
                         170
                  ....*....|...
gi 1930685751 160 NYFLTWLCMRKLP 172
Cdd:cd23179   160 MLAMVYAVLRELG 172
Tombusviridae_RdRp cd23206
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tombusviridae of ...
15-171 3.13e-12

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: 62.13  E-value: 3.13e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930685751  15 RVKNFVKFETTEKYV----DPRNISPREDGFLATVGPYIA-------AIEKAAKAAPFLIKGLTP--SAKCKKVNWlLEY 81
Cdd:cd23206     3 RVKTFVKAEKINLTKkpdpAPRVIQPRSPRYNVELGRYLKplehrlyKAIDRVFGSPTVMKGYNAeeRGRILREKW-DSF 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930685751  82 ALFCEI--DYTRFDMSISEEILRiFEDYVLLRPFRNHTLFILLVQAARRTYGISRY--GT-RYSVNGTRCSGDAWTSIAN 156
Cdd:cd23206    82 RDPVAVglDASRFDQHVSVDALK-WEHSVYLRIFPDDKELSRLLRWQLHNKGVARCkdGKvKYKVKGGRMSGDMNTSLGN 160
                         170
                  ....*....|....*
gi 1930685751 157 GLLNYFLTWLCMRKL 171
Cdd:cd23206   161 CLIMCAMVYAYLEEL 175
ps-ssRNAv_Nodaviridae_RdRp cd23173
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Nodaviridae of ...
13-171 1.37e-10

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Nodaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Nodaviridae, order Nodamuvirales. The family name Nodaviridae, derives from the Japanese village of Nodamura where Nodamura virus was first isolated from Culex tritaeniorhynchus mosquitoes. Virions are non-enveloped and spherical in shape with icosahedral symmetry and diameters ranging from 25 to 33 nm. The members of the two genera in this family infect insects (Alphanodavirus) or fish (Betanodavirus). Alphanodavirus infection results in the stunting, paralysis and death of the insect host. The infection of fish by betanodaviruses such as striped jack nervous necrosis virus or red-spotted grouper nervous necrosis virus causes neural necrosis, encephalopathy or retinopathy and is associated with behavioral abnormalities and high mortality, posing significant problems for marine aquaculture. The genome consists of two molecules of (+)ssRNA: RNA1 and RNA2. 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: 438023  Cd Length: 236  Bit Score: 57.91  E-value: 1.37e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930685751  13 QCRVKNFVKFETTEKYVDPRNISPREDGFLATVGPYIAaiekaakaaPF---LIK-------GLTPS--AK-----CKKV 75
Cdd:cd23173    12 RNLVKAFIKREAYAKPKDPRNISTVDPEHTLKLSRYTY---------AFkeeVLKnqpwyapGKTPKeiAErvqeiASSS 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930685751  76 NWLleyalfCEIDYTRFDMSISEEILRIFEDYVLLRPFRN--HTLFILLVQAARRTYGISRYGTRYSVNGTRCSGDAWTS 153
Cdd:cd23173    83 DGV------IETDYSRFDGTISEWLRRNVEFAAYLRWFHPeyRAELLKLLDAEINCPARTKTGVKYDPGVSRLSGSPTTT 156
                         170
                  ....*....|....*...
gi 1930685751 154 IANGLLNYFLTWLCMRKL 171
Cdd:cd23173   157 DGNTIINAFVSYCALRET 174
RNA_dep_RNAP cd01699
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
84-171 2.32e-09

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: 54.60  E-value: 2.32e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930685751  84 FCEIDYTRFDMSISEEILRIFEDyVLLRPFRNHTLFILLVQaaRRTYGISR----YGTRYSVNGTRCSGDAWTSIANGLL 159
Cdd:cd01699    98 AIALDYSRFDSSLSPQLLEAEHS-IYNALYDDDDELERRNL--LRSLTNNSlhigFNEVYKVRGGRPSGDPLTSIGNSII 174
                          90
                  ....*....|..
gi 1930685751 160 NYFLTWLCMRKL 171
Cdd:cd01699   175 NCILVRYAFRKL 186
Betacarmovirus_RdRp cd23240
RNA-dependent RNA polymerase (RdRp) in the genus Betacarmovirus of positive-sense ...
7-169 3.02e-06

RNA-dependent RNA polymerase (RdRp) in the genus Betacarmovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Betacarmovirus 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. 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 Betacarmovirus: Cardamine chlorotic fleck virus, Hibiscus chlorotic ringspot virus, Japanese iris necrotic ring virus, and Turnip crinkle 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: 438090  Cd Length: 451  Bit Score: 45.99  E-value: 3.02e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930685751   7 DRP-TGRQCRVKNFVKFE----TTEKYVDPRNISPREDGFLATVGPYIAAIEKAAKAA-------PFLIKGLTPSAKCKK 74
Cdd:cd23240    93 DRPvTRKDAFLKTFVKAEkinfTAKPDPAPRVIQPRDPRYNIEVGKYLKPYEHHLYRAidvvwggPTVLKGYTVEELGNI 172
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930685751  75 V-NWLLEYALFCEI--DYTRFDMSISEEILRiFEDYVLLRPFRNHTLFILLV-QAARRTYGISRYG-TRYSVNGTRCSGD 149
Cdd:cd23240   173 MhNHWSQFQKPCAVgfDMKRFDQHVSVDALR-FEHSVYNRSFCSPELARLLEwQLLNSGVGHASDGfIRYKVDGCRMSGD 251
                         170       180
                  ....*....|....*....|
gi 1930685751 150 AWTSIANGLLNYFLTWLCMR 169
Cdd:cd23240   252 VNTALGNCLLACLITKYLLK 271
Gammacarmovirus_RdRp cd23242
RNA-dependent RNA polymerase (RdRp) in the genus Gammacarmovirus of positive-sense ...
88-169 7.41e-06

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: 45.12  E-value: 7.41e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930685751  88 DYTRFDMSISEEILRiFEDYVLLRPFRN--HTLFILLVQAARRTYGISRYGT-RYSVNGTRCSGDAWTSIANGLLNYFLT 164
Cdd:cd23242   199 DMKRFDQHVSRDALE-WEHSVYLDAFCNdpYLAELLSWQLENKGVGYASDGSiKYKVDGCRMSGDMNTAMGNCLLACAIT 277

                  ....*
gi 1930685751 165 WLCMR 169
Cdd:cd23242   278 WDFFK 282
Pelarspovirus_RdRp cd23241
RNA-dependent RNA polymerase (RdRp) in the genus Pelarspovirus of positive-sense ...
7-171 1.16e-05

RNA-dependent RNA polymerase (RdRp) in the genus Pelarspovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Pelarspovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. The genus name "Pelarspovirus" is derived from the pelargonium ringspot virus, which was the first virus to be named. There are 8 species in the Pelarspovirus genus: Clematis chlorotic mottle virus, Elderberry latent virus, Jasmine mosaic-associated virus, Jasmine virus H, Pelargonium chlorotic ring pattern virus, Pelargonium line pattern virus, Pelargonium ringspot virus, and Rosa rugosa leaf distortion virus. Members of the Pelarspovirus have monopartite genomes encoding five open reading frames (ORFs) that include two 5'-proximal replication proteins, two centrally located movement proteins (MP1 and MP2) and a 3'-proximal coat protein that, at least for pelargonium line pattern virus (PLPV), has been shown to act also as suppressor of RNA silencing. 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: 438091 [Multi-domain]  Cd Length: 497  Bit Score: 44.35  E-value: 1.16e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930685751   7 DRPTG-RQCRVKNFVKFETT--EKYVDP--RNISPREDGFLATVGPYIAAIEKAAKAA-------PFLIKGLTPS--AKC 72
Cdd:cd23241   111 DRPYNvRDSYLKTFVKCEKLnfSKKPDPapRVIQPRDPRYNVELGRYLKPFEHHCYRAldklwggPTVMKGYTVQemGNI 190
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930685751  73 KKVNWLlEYALFCEI--DYTRFDMSISEEILRiFEDYVLLRPFRNHTLFILLV--QAARRTYGISRYGT-RYSVNGTRCS 147
Cdd:cd23241   191 IRDKWN-KYQKPAAIgfDMSRFDQHVSVDALK-FEHKIYRRCFSNDGNLARLLghQIENRGVAYAKDGWlKYKVEGKRMS 268
                         170       180
                  ....*....|....*....|....
gi 1930685751 148 GDAWTSIANGLLNYFLTWLCMRKL 171
Cdd:cd23241   269 GDVNTALGNCILACCITKELMGGI 292
RdRP_3 pfam00998
Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase ...
88-171 2.12e-05

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: 43.76  E-value: 2.12e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930685751  88 DYTRFDMSISEEILRiFEDYVLLRPFRNHTLFILLV--QAARRTYGISRYGT-RYSVNGTRCSGDAWTSIANGLLNYFLT 164
Cdd:pfam00998 208 DASRFDQHVSVEALR-FEHSIYLAAFLGPEELIRLLtwQLYNGGPMYASDGQiKYGVRGCRMSGDMNTSLGNCLLMCLKV 286

                  ....*..
gi 1930685751 165 WLCMRKL 171
Cdd:pfam00998 287 HAACKAL 293
ps-ssRNAv_Nidovirales_RdRp cd23168
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Nidovirales of ...
62-171 7.14e-04

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Nidovirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This family contains the catalytic core domain of RdRP of Nidovirales, an order of enveloped, (+)ssRNA viruses which infect vertebrates and invertebrates. Host organisms include mammals, birds, reptiles, amphibians, fish, arthropods, mollusks, and helminths. The order Nidovirales currently comprises 88 formally recognized virus species of (+)ssRNA viruses which are classified into nine virus families: Abyssoviridae, Arteriviridae, Coronaviridae, Euroniviridae, Medioniviridae, Mesoniviridae, Mononiviridae, Roniviridae, and Tobaniviridae. Based on the genome size, the members of the order Nidovirales can be divided into two groups, large and small nidoviruses. The genomes of the large nidoviruses are well over 25 kb in length with size differences in the 5 kb range. Planarian secretory cell nidovirus (PSCNV), only member of the Mononiviridae family, has the largest known non-segmented RNA genome of 41.1 kb; its host is the planarian flatworm. 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: 438018 [Multi-domain]  Cd Length: 310  Bit Score: 38.88  E-value: 7.14e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930685751  62 LIKGLTPSAKCKKVnWLleyalfcEIDYTRFDMSISEeILRIFEDYVLLRPFRNHT-------LFILLVQAARRTYGISr 134
Cdd:cd23168    64 MLRYLYPGVIEDPV-LM-------GWDYPKCDRSVPN-MLRYLANLLLASLYDNCCnlseivhLLINECAQVLYDYVVY- 133
                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1930685751 135 YGTRYSVNGTRCSGDAWTSIANGLLNYFLTWLCMRKL 171
Cdd:cd23168   134 GGNLYRKPGGVSSGDSTTAISNSIYNYFQTFIANVRL 170
Aureusvirus_RdRp cd23243
RNA-dependent RNA polymerase (RdRp) in the genus Aureusvirus of positive-sense single-stranded ...
3-159 1.64e-03

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: 37.89  E-value: 1.64e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930685751   3 LATQDRP-TGRQCRVKNFVKFE----TTEKYVDPRNISPREDGFLATVGPYIAAIEKAAKA-------APFLIKGLTpsa 70
Cdd:cd23243   110 LSLDVLPcTRSDAYLKTFVKAEkiniTLKPDPAPRVIQPRDPRYNVEVGRYLKPLEPRLMKaidklwgEKTAIKGYT--- 186
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930685751  71 kCKKVNWLL-------EYALFCEIDYTRFDMSISEEILRiFEDYVLLRPFRNHTLFILLvqaarrTYGISRYGT------ 137
Cdd:cd23243   187 -VEKVGEILhekslrfREPVFVGLDASRFDQHCSRQALE-WEHSVYNAIFRDPYLAELL------TWQIDNVGTaylkdg 258
                         170       180
                  ....*....|....*....|....
gi 1930685751 138 --RYSVNGTRCSGDAWTSIANGLL 159
Cdd:cd23243   259 fvRYRVDGCRMSGDMNTSMGNYLI 282
Calvusvirinae_RdRp cd23234
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Calvusvirinae of ...
10-164 2.23e-03

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Calvusvirinae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the subfamily Calvusvirinae, family Tombusviridae, order Tolivirales. Umbravirus is a genus of plant viruses assigned to this subfamily. The genus includes nine distinct virus species: Carrot mottle mimic virus (CMoMV), Groundnut rosette virus (GRV), Ethiopian tobacco bushy top virus (ETBTV), Lettuce speckles mottle virus (LSMV), Opium poppy mosaic virus (OPMV), Pea enation mosaic virus-2 (PEMV-2), Tobacco mottle virus (TMoV), and Tobacco bushy top virus (TBTV). Umbraviruses differ from other plant viruses in that they do not encode a coat protein (CP), and thus no conventional virus particles are formed in the infected plants. However, they encode RdRp domain typical to that of other members of the family Tombusviridae, allowing to classify the genus Umbravirus within this family. 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: 438084  Cd Length: 471  Bit Score: 37.80  E-value: 2.23e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930685751  10 TGRQCRVKNFVKFE----TTEKYVDPRNISPREDGFLATVGPYIAAIEkaakaaPFLIKGL-----------------TP 68
Cdd:cd23234   111 TRRDARVSTFIKAEkinfTAKPDPAPRVIQPRDPRFNVVFAKYIKPLE------PLLYKALgklykypcvakgfnaveTG 184
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930685751  69 SAKCKKvnWLLEYALFC-EIDYTRFDMSISEEILRiFEDYVLLRPFRNHTLFILLVQA-ARRTYGISRYG-TRYSVNGTR 145
Cdd:cd23234   185 EIIAKK--WKMFRDPVCvGLDASRFDQHVSVEALR-FTHSVYKRFIKSREFNKLLQWMyTNRGLGTAKDGfVKYKVKGCR 261
                         170
                  ....*....|....*....
gi 1930685751 146 CSGDAWTSIANGLLNYFLT 164
Cdd:cd23234   262 MSGDMDTALGNCVLMVLMT 280
Carmotetraviridae_RdRp cd23205
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Carmotetraviridae ...
16-172 3.33e-03

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Carmotetraviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, and related Erinaceus virus H14; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Carmotetraviridae, and related Erinaceus virus H14, order Tolivirales. Carmotetraviridae includes only one genus, Alphacarmotetravirus, which has one species: Providence virus. Lepidopteran insects serve as the natural host. Recent studies indicated that Providence virus, a non-enveloped insect RNA virus, isolated from a lepidopteran midgut cell line can establish a productive infection in plants as well as in animal cells. 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: 438055  Cd Length: 268  Bit Score: 36.92  E-value: 3.33e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930685751  16 VKNFVKFETTE---KYVDPRNISPREDGF---LATVGP----YIAAIEKAAKAAPFLIKGLTPSAKCKKVN--W-LLEYA 82
Cdd:cd23205     3 IKAFVKMEKLQillKHGDPRLIQSRGTVFhllFSTMTKplehALMHVSDPETNLPMVAKGRNLDQRANLLQrmWhLYERP 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930685751  83 LFCEIDYTRFDMSISEEIL-RIFEDYvlLRPFRNHTLFILLvQAARRTYGISRYGTRYSVNGTRCSGDAWTSIANGLLNY 161
Cdd:cd23205    83 VSISFDLSRWDMHVQVPLLkRVLEIY--SQHVTCPLLLDMC-QNLLKNVCYTNKGIRYHVDGGIMSGDMTTGLGNCIAVL 159
                         170       180       190
                  ....*....|....*....|....*....|....
gi 1930685751 162 FL-----------------------TWLCMRKLP 172
Cdd:cd23205   160 VIvmsfrlsilddgddhviicekshTWICERVLP 193
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
86-164 3.81e-03

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: 37.00  E-value: 3.81e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930685751  86 EIDYTRFDMSISEEILRIFEDyvLLRPF----RNHTLFILLVQAARRTYGISRYGTRYSVNGTRCSGDAWTSIANGLLNY 161
Cdd:pfam00680 230 ELDYSGFDSSVPPWLIRFAFE--ILRELlgfpSNVKEWRAILELLIYTPIALPNGTVFKKTGGLPSGSPFTSIINSIVNY 307

                  ...
gi 1930685751 162 FLT 164
Cdd:pfam00680 308 LLI 310
Mayoviridae_RdRp cd23256
RNA-dependent RNA polymerase (RdRp) in the family Mayoviridae of positive-sense ...
84-171 7.47e-03

RNA-dependent RNA polymerase (RdRp) in the family Mayoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Mayoviridae, order Martellivirales. The Mayoviridae family consists of two genera, Idaeovirus and Pteridovirus. The genus Idaeovirus contains Raspberry bushy dwarf virus (RBDV), named after the host with which it was first associated (red raspberry, Rubus idaeu) and the disease which is characterized by bushiness (stunting and proliferation of canes); RBDV has recently been found causing an infection in grapevines. RBDV occurs in all tissues of the plant, including seed and pollen, and is transmitted in association with pollen, both vertically to the seed and horizontally to the pollinated plant; this is the only known method of natural spread of RBDV. 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: 438106  Cd Length: 329  Bit Score: 35.87  E-value: 7.47e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1930685751  84 FCEIDYTRFDMSiSEEILRIFEDYVLLRpFRNHTLFILLVQAARRTYGI--SRYGTRYSVNGTRCSGDAWTSIANGL--- 158
Cdd:cd23256   117 FTEIDFSKFDKS-QGELHQLIQDLILLR-FGCDPEFVSLWSTAHRSSSIkdQNVGISFKTDFQRRTGDAFTFLGNSLvta 194
                          90
                  ....*....|....*
gi 1930685751 159 --LNYFLTWLCMRKL 171
Cdd:cd23256   195 vmLAYVLSFEDEKKI 209
 
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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