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Conserved domains on  [gi|371491764|gb|AEX31538|]
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3D protein, partial [Kobuvirus swine/South Korea/2010]

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 ...
 1-151 1.54e-111

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 cd23214:

Pssm-ID: 477363  Cd Length: 459  Bit Score: 324.11  E-value: 1.54e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764   1 TLPSCAFRIVEKHLERLIGDERVTRYIETIRHSRHVFGNETYEMIGGNPSGCVGTSIINTIINNVCVLSALIQHPDFSPE 80
Cdd:cd23214  232 TLPSCAFRIVEDHLERLTGDERVTRYIESIRHSHHVYGNETYEMIGGNPSGCVGTSIINTIINNICVLSALIQHPDFSPE 311

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 371491764  81 SFRILAYGDDVIYGCDPPIHPSFIKEFYDEHTPLVVTPANKTDTFPENSTIYDVTFLKRWFVPDDIRPFYI 151
Cdd:cd23214  312 SFRILAYGDDVIYGCDPPIHPSFIKEFYDKHTPLVVTPANKGSDFPETSTIYDVTFLKRWFVPDDIRPFYI 382
 
Name Accession Description Interval E-value
Kobuvirus_RdRp cd23214
RNA-dependent RNA polymerase (RdRp) in the Kobuvirus genus of positive-sense single-stranded ...
 1-151 1.54e-111

RNA-dependent RNA polymerase (RdRp) in the Kobuvirus genus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Kobuvirus genus within the family Picornaviridae, order Picornavirales. Kobuviruses are small, icosahedral and spherical viruses, with a (+)ssRNA genome. Unlike other picornaviruses, Kobuvirus capsids show a distinctive lumpy morphology when observed by electron microscopy; "kobu" means "knob" in Japanese. There are six species (Aichivirus A-F) in this genus. Initially, the genus Kobuvirus was divided into three species: Aichivirus A (AiVA, formerly Aichi virus), Aichivirus B (AivB, formerly Bovine kobuvirus) and Aichivirus C (AiVC, formerly Porcine kobuvirus) each possessing a single serotype. Canine kobuvirus belong to species Aichivirus A. Aichi virus infects humans, while bovine kobuvirus, porcine kobuvirus and canine kobuvirus infects cattle, swine, dogs and cats, respectively. Kobuviruses have also been detected in black goats, rabbits, European roller, and bats. RdRps are multi-domain proteins that play a pivotal role in enterovirus replication. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of kobuviruses. 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: 438064  Cd Length: 459  Bit Score: 324.11  E-value: 1.54e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764   1 TLPSCAFRIVEKHLERLIGDERVTRYIETIRHSRHVFGNETYEMIGGNPSGCVGTSIINTIINNVCVLSALIQHPDFSPE 80
Cdd:cd23214  232 TLPSCAFRIVEDHLERLTGDERVTRYIESIRHSHHVYGNETYEMIGGNPSGCVGTSIINTIINNICVLSALIQHPDFSPE 311

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 371491764  81 SFRILAYGDDVIYGCDPPIHPSFIKEFYDEHTPLVVTPANKTDTFPENSTIYDVTFLKRWFVPDDIRPFYI 151
Cdd:cd23214  312 SFRILAYGDDVIYGCDPPIHPSFIKEFYDKHTPLVVTPANKGSDFPETSTIYDVTFLKRWFVPDDIRPFYI 382
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
 1-145 4.48e-18

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: 79.38  E-value: 4.48e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764    1 TLPSCAFRIVEKHLERLIG-DERVTR---YIETIRHSRH-VFGNETYEMIGGNPSGCVGTSIINTIINNVCVLSALI--- 72
Cdd:pfam00680 239 SVPPWLIRFAFEILRELLGfPSNVKEwraILELLIYTPIaLPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYALLksl 318

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 371491764   73 --QHPD--FSPESFRILAYGDDVIYGCDPPIHPSF--IKEFYDEHTpLVVTPANKtdTFPENSTIYDVTFLKRWFVPDD 145
Cdd:pfam00680 319 enDGPRvcNLDKYFDFFTYGDDSLVAVSPDFDPVLdrLSPHLKELG-LTITPAKK--TFPVSRELEEVSFLKRTFRKTP 394
 
Name Accession Description Interval E-value
Kobuvirus_RdRp cd23214
RNA-dependent RNA polymerase (RdRp) in the Kobuvirus genus of positive-sense single-stranded ...
 1-151 1.54e-111

RNA-dependent RNA polymerase (RdRp) in the Kobuvirus genus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Kobuvirus genus within the family Picornaviridae, order Picornavirales. Kobuviruses are small, icosahedral and spherical viruses, with a (+)ssRNA genome. Unlike other picornaviruses, Kobuvirus capsids show a distinctive lumpy morphology when observed by electron microscopy; "kobu" means "knob" in Japanese. There are six species (Aichivirus A-F) in this genus. Initially, the genus Kobuvirus was divided into three species: Aichivirus A (AiVA, formerly Aichi virus), Aichivirus B (AivB, formerly Bovine kobuvirus) and Aichivirus C (AiVC, formerly Porcine kobuvirus) each possessing a single serotype. Canine kobuvirus belong to species Aichivirus A. Aichi virus infects humans, while bovine kobuvirus, porcine kobuvirus and canine kobuvirus infects cattle, swine, dogs and cats, respectively. Kobuviruses have also been detected in black goats, rabbits, European roller, and bats. RdRps are multi-domain proteins that play a pivotal role in enterovirus replication. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of kobuviruses. 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: 438064  Cd Length: 459  Bit Score: 324.11  E-value: 1.54e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764   1 TLPSCAFRIVEKHLERLIGDERVTRYIETIRHSRHVFGNETYEMIGGNPSGCVGTSIINTIINNVCVLSALIQHPDFSPE 80
Cdd:cd23214  232 TLPSCAFRIVEDHLERLTGDERVTRYIESIRHSHHVYGNETYEMIGGNPSGCVGTSIINTIINNICVLSALIQHPDFSPE 311

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 371491764  81 SFRILAYGDDVIYGCDPPIHPSFIKEFYDEHTPLVVTPANKTDTFPENSTIYDVTFLKRWFVPDDIRPFYI 151
Cdd:cd23214  312 SFRILAYGDDVIYGCDPPIHPSFIKEFYDKHTPLVVTPANKGSDFPETSTIYDVTFLKRWFVPDDIRPFYI 382
ps-ssRNA_Picornaviridae cd23193
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Picornaviridae of ...
 1-148 1.32e-68

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Picornaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Picornaviridae, order Picornavirales. The Picornaviridae family consists of small, icosahedral viruses with (+)ssRNA genomes. Characteristic features of all members of the family Picornaviridae are three capsid proteins with beta-barrel folding, polyprotein processing by virus-encoded cysteine proteinase(s), and replication by an RdRp with a YGDD sequence motif. The family Picornaviridae comprises 68 genera containing 158 species, but many viruses are presently awaiting classification. The established genera of the family include: Aphthovirus, Avisivirus, Crohivirus, Enterovirus, Teschovirus, Cardiovirus, Erbovirus, Kobuvirus, Hepatovirus, Parechovirus, Aquamavirus, Avihepatovirus, Avisivirus, Cosavirus, Dicipivirus, Fipivirus, Gallivirus, Hunnivirus, Kunsagivirus, Limnipivirus, Megrivirus, Mischivirus, Mosavirus, Oscivirus, Pasivirus, Passerivirus, Rabovirus, Rosavirus, Sakobuvirus, Salivirus, Sapelovirus, Senecavirus, Sicinivirus, and Tremovirus. The Picornaviridae contains many important human and animal pathogens including enteroviruses (such as poliovirus, enterovirus, coxsackievirus, and rhinovirus), cardioviruses (such as encephalomyocarditis virus and Theiler's virus), hepatitis A virus and foot-and-mouth disease virus. Infection with various picornaviruses may cause encephalitis, febrile rash illnesses (hand-foot-and-mouth disease), aseptic meningitis, hepatitis, conjunctivitis, herpangina, myositis and myocarditis, and the common cold. 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: 438043  Cd Length: 345  Bit Score: 210.87  E-value: 1.32e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764   1 TLPSCAFRIVEKHL-ERLIGDERVTRYIETIRHSRHVFGNETYEMIGGNPSGCVGTSIINTIINNVCVLSALIQHPDFSP 79
Cdd:cd23193  147 SLSSQLFEAAVEVLaECHGDPELVLRYLEPIINSKHVVGDERYTVEGGMPSGCPCTSILNSICNNLVVRYALLETGKFDP 226

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 371491764  80 ESFRILAYGDDVIYGCDPPIHPSFIKEFYDEHTPLVVTPANKTDTFPENSTIYDVTFLKRWFVPDD---IRP 148
Cdd:cd23193  227 DEYYILAYGDDVLVSTDEPIDPSDLAEFYKKYFGMTVTPADKSSDFPESSPIEDVFLKRRFFVPDGtflIHP 298
Passerivirus_RdRp cd23224
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Passerivirus of ...
 1-151 3.46e-63

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Passerivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Passerivirus genus within the family Picornaviridae, order Picornavirales. The Passerivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. There are two species in this genus: Passerivirus A and a second, novel passerivirus (Passerivirus B) that was discovered in 2018 in a population of Hungarian home-reared finches, where it achieved an over 50 percent mortality rate. Birds serve as natural hosts. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. 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: 438074  Cd Length: 380  Bit Score: 198.00  E-value: 3.46e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764   1 TLPSCAFRIVEKHLERLI------GDERVTRYIETIRHSRHVFGNETYEMIGGNPSGCVGTSIINTIINNVCVLSALIQH 74
Cdd:cd23224  148 TLPSCCFDLIAQKLAKIItpgegiAPDAIVKYIRSISISKHVFGNEAYLMVGGNPSGCVGTSILNSMINNCVLISAFLTQ 227

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 371491764  75 PDFSPESFRILAYGDDVIYGCDPPIHPSFIKEFYDEHTPLVVTPANKTDTFPENSTIYDVTFLKRWFVPDDIRPFYI 151
Cdd:cd23224  228 KDFNPNQMRILTYGDDVLYATNPPIHPRVVKKFFDENTTLIVTPATKAGDFPDESTIWDVTFLKRYFVPDEIRPWYV 304
Megrivirus_RdRp cd23223
RNA-dependent RNA polymerase (RdRp) in the genus Megrivirus of positive-sense single-stranded ...
 1-151 3.69e-48

RNA-dependent RNA polymerase (RdRp) in the genus Megrivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Megrivirus genus within the family Picornaviridae, order Picornavirales. The Megrivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. The genus Megrivirus contains a five species Megrivirus A, Megrivirus B, Megrivirus C, Megrivirus D and Megrivirus E. The name Megrivirus is derived from the turkey genus name Meleagris. Megrivirus A is comprised of turkey hepatitis virus 1 (THV-1), duck megrivirus and goose megrivirus 1. Megrivirus B contains the mesiviruses. Megrivirus D contains harrier picornavirus 1 (HaPV-1). Megrivirus E was found in an Adelie penguin. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. 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: 438073  Cd Length: 432  Bit Score: 160.39  E-value: 3.69e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764   1 TLPSCAFRIVEKHLERLIGDErVTRYIETIRHSRHVFGNETYEMIGGNPSGCVGTSIINTIINNVCVLSALIQHpDFSPE 80
Cdd:cd23223  226 TEPKIAFRLMAKYLKPYFSVD-VTPFFEALATSKHVYGDKAYEMEGGMPSGCVGTSMFNCINNSAFIVSALIAL-KISPE 303

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 371491764  81 SFRILAYGDDVIYGCDPPIHPSFIKEFYDEHTPLVVTPANKTDTFPENSTIYDVTFLKRWFVPDDIRPFYI 151
Cdd:cd23223  304 DCAWICYGDDVIISTDEKALSKRIADFYHKNTNLVVTPASKSGDFPETSTIYDVTFLKRFFQPDSHYPHLI 374
Mosavirus_RdRp cd23225
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Mosavirus of ...
 1-151 3.37e-39

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Mosavirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Mosavirus genus within the family Picornaviridae, order Picornavirales. The Mosavirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. This genus includes two species: Mosavirus A, which found in the feces of a canyon mouse (Peromyscus crinitus), and Mosavirus B, which contains marmot mosavirus. Mosavirus stands for mouse stool-associated picornavirus. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. 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: 438075  Cd Length: 378  Bit Score: 135.81  E-value: 3.37e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764   1 TLPSCAFRIVEKH--LERLIGDERVTR-YIETIRHSRHVFGNETYEMIGGNPSGCVGTSIINTIINNVCVLSALI---QH 74
Cdd:cd23225  153 THPTAMFNLLAERffTERNGFDQQAVRiFLNGLSDSDHVYEGKHFRIRGGLPSGCPCTSILNTVINNIIVRAAILgayQI 232

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 371491764  75 PDFSPESFRILAYGDDVIYGCDPPIHPSFIKEFYDEHTPLVVTPANKTDTFPENSTIYDVTFLKRWFVPDDIRPFYI 151
Cdd:cd23225  233 DTVDFQKFRMLAYGDDVVYATPQPIKPQDLADWLHANTNYKVTPASKAGTFPEESTIWDVTFLKRSFKPDEDHGHLI 309
Rosavirus_RdRp cd23221
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Rosavirus of ...
 1-151 3.01e-35

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Rosavirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Rosavirus genus within the family Picornaviridae, order Picornavirales. The Rosavirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. This genus contains three species Rosavirus A, Rosavirus B and Rosavirus C found in rats. The name rosavirus is derived from rodent stool-associated picornavirus. Viral RNA was detected in fecal samples of humans and rodents [canyon mouse (Peromyscus crinitus), brown rat (Rattus norvegicus), black rat (R. rattus), Sikkim rat (R. andamanensis), chestnut white-bellied rat (Niviventer fulvescens)]. Eight genetic types are distinguished by means of phylogenetic analysis (Rosavirus A: 2 types; Rosavirus B: 2 types; Rosavirus C: 4 types). RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. 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: 438071  Cd Length: 381  Bit Score: 125.42  E-value: 3.01e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764   1 TLPSCAFRIVEKHLERLI-GDERVTRYIETIRHSRHVFGNETYEMIGGNPSGCVGTSIINTIINNVCVLSALIQ-HPDFS 78
Cdd:cd23221  149 SVPSCCFDALADLLADFVeGEEDVRKYISSLKTSFHHYKGKLWRLDGAMPSGCCGTSVFNSLINAMLLFSAFSQiCPDFR 228

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 371491764  79 PESFRILAYGDDVIYGCDPPIHPSFIKEFYDEHTPLVVTPANKTDTFPENSTIYDVTFLKRWFVPDDIRPFYI 151
Cdd:cd23221  229 ASEPLLVAYGDDVLVGTDQPLFPSKVAEWVNSHTTFRITPADKGSVFNDESDIHSVQFLKRHFTPDPDFPALI 301
Dicipivirus_RdRp cd23222
RNA-dependent RNA polymerase (RdRp) in the genus Dicipivirus of positive-sense single-stranded ...
 1-146 4.98e-34

RNA-dependent RNA polymerase (RdRp) in the genus Dicipivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Dicipivirus genus within the family Picornaviridae, order Picornavirales. The Dicipivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. The genus Dicipivirus contains two species, Cadicivirus A and Cadicivirus B. A new dicipivirus has been found in hedgehogs. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. 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: 438072  Cd Length: 451  Bit Score: 123.54  E-value: 4.98e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764   1 TLPSCAFRIVEKHLERLIGDER-VTRYIETIRHSRHVFGNETYEMIGGNPSGCVGTSIINTIINNVCVLSALIQ-HPDFS 78
Cdd:cd23222  227 SIPSCSFDALADLLCEFVENEDdVRRYISNIKNSYHAYDGNLYLIEGAMPSGCAGTSVFNCLINAMLCFSCFMDlEPEMD 306

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 371491764  79 PESFRILAYGDDVIYGCDPPIHPSFIKEFYDEHTPLVVTPANKTDTFPENSTIYDVTFLKRWFVPDDI 146
Cdd:cd23222  307 PFEPLLIAYGDDILVSSDHDLFPSRVSEWMKANTTFKITPADKGEIFNDDSDVSDVRFLKRLFVEDPV 374
Enterovirus_RdRp cd23213
RNA-dependent RNA polymerase (RdRp) in the Enterovirus genus of positive-sense single-stranded ...
 7-151 6.58e-31

RNA-dependent RNA polymerase (RdRp) in the Enterovirus genus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Enterovirus genus within the family Picornaviridae, order Picornavirales. Enteroviruses have small, non-enveloped (+)ssRNA genomes, and replicate within the gastrointestinal tract or other mucosal surfaces. The genus Enterovirus has been divided into 15 species based on genetic divergence (EV A-L and Rhinovirus A-C), and its major members include poliovirus, coxsackievirus and rhinovirus. More than 100 enterovirus types have been associated with several human diseases, all of which are classified into four species (Enterovirus A, Enterovirus B, Enterovirus C, and Enterovirus D). RdRps are multi-domain proteins that play a pivotal role in enterovirus replication. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of enteroviruses. 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: 438063  Cd Length: 453  Bit Score: 114.93  E-value: 6.58e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764   7 FRIVEKHLErLIGDERVTRYIETIRHSRHVFGNETYEMIGGNPSGCVGTSIINTIINNVCVLSALI---QHPDFspESFR 83
Cdd:cd23213  238 FRALKMVLE-KGYSEEAVSLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLktyKGIDL--DELK 314

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 371491764  84 ILAYGDDVIYGCDPPIHPSFIKEfYDEHTPLVVTPANKTDTFPEnSTIYDVTFLKRWFVPDDIRPFYI 151
Cdd:cd23213  315 MIAYGDDVIASYPHPIDCSLLAR-TGKEYGLTMTPADKSPCFNE-VNWENVTFLKRGFRADEQYPFLI 380
Mischivirus_RdRp cd23227
RNA-dependent RNA polymerase (RdRp) in the genus Mischivirus of positive-sense single-stranded ...
 20-149 1.87e-30

RNA-dependent RNA polymerase (RdRp) in the genus Mischivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Mischivirus genus within the family Picornaviridae, order Picornavirales. The Mischivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. Mischivirus is a picornavirus genus containing five species Mischivirus A, Mischivirus B, Mischivirus C, Mischivirus D and the proposed Mischivirus E. The name is derived from the name originally given to the virus, Miniopterus schreibersii picornavirus, which was found in the common bent-wing bat (aka Schreiber's long-fingered bat or Schreiber's bat) in China and is most closely related to the cardioviruses. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. 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: 438077  Cd Length: 466  Bit Score: 113.89  E-value: 1.87e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764  20 DERVTRYIETIRHSRHVFGNETYEMIGGNPSGCVGTSIINTIINNVCVLSAL-IQHPDFSPESFRILAYGDDVIYGCDPP 98
Cdd:cd23227  266 SPAVAPYLRSLAFSKHAWMDKRYKIEGGLPSGCSATSVLNTVMNNIIIRALLsLTYKNFHPEDVLVLAYGDDLLVASDYQ 345

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 371491764  99 IHPSFIKEFYDEHTPLVVTPANKTDTFPENSTIYDVTFLKRWFVPDDIRPF 149
Cdd:cd23227  346 LDFNRVREKAAEHTLYKLTTANKAPDFPETSTLLDCQFLKRKFVLHSTRNF 396
ps-ssRNAv-Picornavirales cd23169
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of ...
 5-150 2.84e-29

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This family contains the catalytic core domain of RdRp of Picornavirales, an order of (+)ssRNA viruses. The order Picornavirales comprises viruses that historically are referred to as picorna-like viruses and which are classified into eight virus families: Caliciviridae, Dicistroviridae, Iflaviridae, Marnaviridae, Picornaviridae, Polycipiviridae, Secoviridae, and Solinviviridae. All known genomes of Picornavirales members encode proteins with helicase, 3C-like protease, and RdRp domains, as well as capsid proteins with related structures, although the genome organizations can differ among viruses. The picornavirus genome is replicated via a negative-sense (-) RNA intermediate by the viral RdRp, named 3Dpol, which uses VPg (the product of 3B) as a primer to initiate the replication process. 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: 438019  Cd Length: 309  Bit Score: 108.45  E-value: 2.84e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764   5 CAFRIVEKHLERLIGDER---VTRYIETIRHSRHVFGNETYEMIGGNPSGCVGTSIINTIINN---VCVLSALIQHPDFS 78
Cdd:cd23169  100 AAFDIINDWYDEYVDDEDervRKVLFEELINTIHLVGNLVYQVHGGNPSGNPLTTIINSIVNLlyiRYAWLRITGLTSLS 179

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 371491764  79 P--ESFRILAYGDDVIYGCDPPIHPSF----IKEFYDEHTpLVVTPANKTDTFPENSTIYDVTFLKRWFVPDDIRPFY 150
Cdd:cd23169  180 DfkKNVRLVTYGDDVIISVSDEVKDEFnfvtISEFLKELG-ITYTDADKSGDIVPYRPLEEVTFLKRGFRPHPTPGLV 256
Cardiovirus_RdRp cd23211
RNA-dependent RNA polymerase (RdRp) in the Cardiovirus genus of positive-sense single-stranded ...
 20-145 1.15e-28

RNA-dependent RNA polymerase (RdRp) in the Cardiovirus genus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Cardiovirus genus within the family Picornaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. Vertebrates serve as natural hosts for the cardioviruses. There are currently six species in the genus: Cardiovirus A-F. Diseases associated with cardioviruses include: myocarditis, encephalitis, multiple sclerosis, and type 1 diabetes. Cardiovirus A is composed of only one serotype, encephalomycarditis virus (EMCV) which causes encephalomyocarditis and reproductive disease in pigs. Cardiovirus B comprises 15 genetic types, Theiler's murine encephalomyelitis virus (TMEV), Vilyuisk human encephalomyelitis virus (VHEV), thera virus (formerly named Theiler-like virus of rats), Saffold virus (SAFV) types 1 to 11, and genet fecal theilovirus (from Geneta geneta). Of these types, only VHEV and SAFV are thought to cause infection in humans. Thus far, Cardiovirus C has only been observed in the brown rat. 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: 438061  Cd Length: 460  Bit Score: 109.16  E-value: 1.15e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764  20 DERVTRYIETIRHSRHVFGNETYEMIGGNPSGCVGTSIINTIINNVCVLSAL-IQHPDFSPESFRILAYGDDVIYGCDPP 98
Cdd:cd23211  263 DPRIGEYLRSLAVSRHAYEERRVLIRGGLPSGCAATSMLNTIMNNIIIRAGLyLTYKNFEFDDIKVLSYGDDLLVATNYQ 342

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 371491764  99 IHPSFIKEFYDEhTPLVVTPANKTDTFPENSTIYDVTFLKRWFVPDD 145
Cdd:cd23211  343 IDFNLVKARLAK-FGYKITPANKTSTFPLTSTLEDVVFLKRKFVKEN 388
RNA_dep_RNAP cd01699
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
 1-145 2.69e-28

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: 105.06  E-value: 2.69e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764   1 TLPSCAFRIVEKHLERLIGDERVTR---YIETIRHSR-HVFGNETYEMIGGNPSGCVGTSIINTIINNVCVLSALIQH-P 75
Cdd:cd01699  109 SLSPQLLEAEHSIYNALYDDDDELErrnLLRSLTNNSlHIGFNEVYKVRGGRPSGDPLTSIGNSIINCILVRYAFRKLgG 188

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 371491764  76 DFSPESFRILAYGDDVIYGCDP---PIHPSFIKEFYDEhtpLVVTPANKTDTFPENSTIYDVTFLKRWFVPDD 145
Cdd:cd01699  189 KSFFKNVRLLNYGDDCLLSVEKaddKFNLETLAEWLKE---YGLTMTDEDKVESPFRPLEEVEFLKRRFVLDE 258
Sapelovirus_RdRp cd23218
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Sapelovirus of ...
 21-149 3.32e-28

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Sapelovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Sapelovirus genus within the family Picornaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. Viruses in Sapelovirus are non-enveloped, with icosahedral, spherical, and round geometries, and T=pseudo3 symmetry. Sapelovirus, formerly known as porcine enterovirus (PEV)-8, is known to infect pigs asymptomatically but can cause reproductive failure and severe neurologic, enteric, or respiratory signs. Sapelovirus infections have been reported worldwide in pigs. The genus Sapelovirus contains three species, with a unique genome organization: Sapelovirus A, also known as porcine sapelovirus (PSV); Sapelovirus B as simian sapelovirus; and Avian sapelovirus represented by duck picornavirus. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. 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: 438068  Cd Length: 366  Bit Score: 106.52  E-value: 3.32e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764  21 ERVTRYIETIRHSRHVFGNETYEMIGGNPSGCVGTSIINTIINNVCVLSALIQ-HPDFSPESFRILAYGDDVIYGCDPPI 99
Cdd:cd23218  163 ERDIVLIDHLCYSNHIFKNEGYKVAGGMPSGCSGTSIFNSIINNIVVRTLVLLvYKGINLDELRILCYGDDLLVAYPYPL 242

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 371491764 100 HPSFIKEFYDEHTpLVVTPANKTDTFPENSTIYDVTFLKRWFVPDDIRPF 149
Cdd:cd23218  243 DPNVLADLGKSLG-LTMTPADKSDTFQGCTKLTEVTFLKRSFVFDEEFPF 291
Aphthovirus_RdRp cd23210
RNA-dependent RNA polymerase (RdRp) in the Aphthovirus genus of positive-sense single-stranded ...
 20-150 1.47e-25

RNA-dependent RNA polymerase (RdRp) in the Aphthovirus genus of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the Aphthovirus genus within the family Picornaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. This genus includes species such as bovine rhinitis A virus, bovine rhinitis B virus, equine rhinitis A virus, and food-and-mouth disease virus (FMDV). Aphthoviruses primarily infect via the upper respiratory tract. FMDV infects mainly cloven-hoofed animals, but has been isolated from at least 70 species of mammals. Aphthoviruses are non-enveloped and have an icosahedral capsid with a diameter of around 27 to 30 nm. The assembled viral capsid contains a single copy of the RNA genome and 60 copies of the four viral capsid proteins VP1, VP2, VP3, and VP4. 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: 438060  Cd Length: 458  Bit Score: 100.41  E-value: 1.47e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764  20 DERVTRYIETIRHSRHVFGNETYEMIGGNPSGCVGTSIINTIINNVCVLSALIQH-PDFSPESFRILAYGDDVIYGCDPP 98
Cdd:cd23210  261 HPNAEWILKTLVNTEHAYENKRITVEGGMPSGCSATSIINTILNNIYVLYALRRHyEGVELDTYTMISYGDDIVVASDYD 340

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 371491764  99 IHPSFIKEFYDEHTPlVVTPANKTDTFP-ENSTIYDVTFLKRWFVPDDIRPFY 150
Cdd:cd23210  341 LDFEALKPHFKSLGQ-TITPADKSDKGFvLGHSITDVTFLKRHFHMDYGTGFY 392
Rabovirus_RdRp cd23230
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Rabovirus of ...
 25-151 2.18e-23

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Rabovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Rabovirus genus within the family Picornaviridae, order Picornavirales. The Rabovirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. The genus Rabovirus consists of four species Rabovirus A, Rabovirus B, Rabovirus C, and Rabovirus D. Viral RNA of this genus was detected in feces of Norway rats (Rattus norvegicus) and mice (Mus musculus) in USA and Germany, in intestinal contents of Himalayan marmots (Marmota himalayana), and in tissue samples of Gairdner's shrewmice (Mus pahari). RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. 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: 438080  Cd Length: 361  Bit Score: 93.41  E-value: 2.18e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764  25 RYIETIRHSRHVFGNETYEMIGGNPSGCVGTSIINTIINNVCVLSALIQ-HPDFSPESFRILAYGDDVIYGCDPPIHPSF 103
Cdd:cd23230  163 RPIDHIIRSRHIYKGIEYDVEGGMPSGCSGTSIFNSIINNIIIMTLVLDaYKGIDLEQLKIIAYGDDVIVTYPYPLDAAL 242

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 371491764 104 IKEFYDEHTpLVVTPANKTDTFpENSTIYDVTFLKRWFVPDDIRPFYI 151
Cdd:cd23230  243 LADCGKKYG-LKMTPPDKSAEF-KNVTWEDVTFLKRRFKPAKHYPFLI 288
Dicistroviridae_RdRp cd23194
RNA-dependent RNA polymerase (RdRp) in the family Dicistroviridae of positive-sense ...
 28-151 4.59e-22

RNA-dependent RNA polymerase (RdRp) in the family Dicistroviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the RdRp of RNA viruses belonging to the family Dicistroviridae, order Picornavirales. Dicistroviridae is a family of small non-enveloped viruses with a (+)ssRNA genome of approximately 8-10 kilobases. The family contains 3 genera: Aparavirus, Cripavirus, and Triatovirus. All members infect arthropod hosts with some having devastating economic consequences, such as acute bee paralysis virus, Kashmir bee virus, and Israeli acute paralysis virus in domesticated honeybees, and taura syndrome virus and mud crab virus in the seafood industry. On the contrary, host specificity and other desirable traits make several members of this group amenable to development as biopesticides for insect control, such as Solenopsis invicta virus 1 against fire ants, and triatoma virus against triatomine bugs that vector Chagas disease. Members in the family Dicistroviridae have similarity to viruses in the Picornavirales members (Iflaviridae, Picornaviridae, Marnaviridae and Secoviridae). The genomes of viruses of these taxa encode proteins with helicase, 3C-like protease, and RdRp domains, as well as capsid proteins with related structures, although the genome organizations can differ among viruses. 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: 438044 [Multi-domain]  Cd Length: 315  Bit Score: 89.48  E-value: 4.59e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764  28 ETIRHSRHVFGNETYEMIGGNPSGCVGTSIINTIINN-VCVLSALIQHPDFSP-------ESFRILAYGDDVIYGCDPPI 99
Cdd:cd23194  129 EDIVNSVHICGGYVYQWTHSQPSGNPLTAIINSIYNSiIMRYVYLLLTKEAGLmtmsdfnKHVSMVSYGDDNVINVSDEV 208

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 371491764 100 HPSF----IKEFYDEhTPLVVTPANKTDTFPENSTIYDVTFLKRWFVPDDIRPFYI 151
Cdd:cd23194  209 SEWFnqltITEAMAE-IGMTYTDETKTGEIVPYRSLEEVSFLKRGFRYDDDLGRWV 263
Teschovirus_RdRp cd23212
RNA-dependent RNA polymerase (RdRp) in the Teschovirus genus of positive-sense single-stranded ...
 24-148 2.81e-18

RNA-dependent RNA polymerase (RdRp) in the Teschovirus genus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Teschovirus genus within the family Picornaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. Teschoviruses are emerging pathogens and infect the porcine population only. There are two species in this genus, including Teschovirus A (previously Porcine teschovirus), which is responsible for the porcine enteroviral encephalomyelitis disease caused in pigs, and Teschovirus B. Teschovirus is also known by several other names including Teschen disease, Talfan disease, poliomyelitis suum, benign enzootic paresis, Klobauk disease and contagious porcine paralysis. Teschovirus has a single-stranded, linear, non-segmented RNA genome. The RNA genome is positively sensed meaning that it has the same polarity as the mRNA and no reverse transcription is necessary. 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: 438062  Cd Length: 354  Bit Score: 79.66  E-value: 2.81e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764  24 TRYIETIRHSRHVFGNETYEMIGGNPSGCVGTSIINTIINNVCVLSALIQHPDfspESFRILAYGDDVIYGCDPPIHPSF 103
Cdd:cd23212  184 LSYIDSLCYSKHHWDDETYRLDGGLPSGCSGTTIFNTIMNNIVARAAASYAAE---GPVGILCYGDDILVSSPEKFPVSD 260

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 371491764 104 IKEFYDEhTPLVVTPANKTDTFpENSTIYDVTFLKRWFVPDD--IRP 148
Cdd:cd23212  261 WLEFYSK-TPYKVTAADKSEQI-DWRDITQCTFLKRGFVLDGslVRP 305
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
 1-145 4.48e-18

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: 79.38  E-value: 4.48e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764    1 TLPSCAFRIVEKHLERLIG-DERVTR---YIETIRHSRH-VFGNETYEMIGGNPSGCVGTSIINTIINNVCVLSALI--- 72
Cdd:pfam00680 239 SVPPWLIRFAFEILRELLGfPSNVKEwraILELLIYTPIaLPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYALLksl 318

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 371491764   73 --QHPD--FSPESFRILAYGDDVIYGCDPPIHPSF--IKEFYDEHTpLVVTPANKtdTFPENSTIYDVTFLKRWFVPDD 145
Cdd:pfam00680 319 enDGPRvcNLDKYFDFFTYGDDSLVAVSPDFDPVLdrLSPHLKELG-LTITPAKK--TFPVSRELEEVSFLKRTFRKTP 394
Cosavirus_RdRp cd23226
RNA-dependent RNA polymerase (RdRp) in the genus Cosavirus of positive-sense single-stranded ...
 20-142 2.30e-17

RNA-dependent RNA polymerase (RdRp) in the genus Cosavirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Cosavirus genus within the family Picornaviridae, order Picornavirales. The Cosavirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. This genus consists of five species Cosavirus A, Cosavirus B, Cosavirus D, Cosavirus E and Cosavirus F. The candidate species, Cosavirus C, remains unclassified due to a lack of full genome sequence data. Cosaviruses (formerly called Dekaviruses) have been identified in the stools of south Asian children. Cosaviruses are most closely related to members of the Cardiovirus and Senecavirus genera, but they lack a leader polypeptide. The name Cosavirus stands for common stool-associated picornavirus. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. 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: 438076  Cd Length: 461  Bit Score: 77.37  E-value: 2.30e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764  20 DERVTRYIETIRHSRHVFGNETYEMIGGNPSGCVGTSIINTIINNVCVLSALIQ-HPDFSPESFRILAYGDDVIYGCDPP 98
Cdd:cd23226  265 DHRCSLMIDSLVTSTHCYEDQRMTIRGGLPSGTSGTSVINTIINNIIFKAALYHtYSNFEWDDVQMLAYGDDIVAASDCL 344

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 371491764  99 IHPSFIKEFYdEHTPLVVTPANKTDTF-PENstIYDVTFLKRWFV 142
Cdd:cd23226  345 LDLDRVKYFM-ALIGYKITPADKGEKFiPKD--MQNIQFLKRSFR 386
Caliciviridae_RdRp cd23192
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Caliciviridae of ...
 32-147 6.30e-15

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Caliciviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Caliciviridae, order Picornavirales. Member viruses have a viral (+)ssRNA genome, which is not segmented. The family Caliciviridae, includes eleven genera: seven genera of which infect mammals (Lagovirus, Norovirus, Nebovirus, Recovirus, Sapovirus, Valovirus, and Vesivirus), two genera of which infect birds (Bavovirus, Nacovirus), and two genera of which infect fish (Minovirus and Salovirus). Each genus includes 1-2 species. Human noroviruses are a leading cause of acute gastroenteritis in humans. Furthermore, unclassified caliciviruses have been detected in geese, yellowfin seabream, greater green snake, arctic lamprey, frogs and various Australian birds, highlighting the wide host range of viruses in the family Caliciviridae. 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: 438042  Cd Length: 310  Bit Score: 69.98  E-value: 6.30e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764  32 HSRHVFGNETYEMIGGNPSGCVGTSIINTIINNVCVLSALIQH-------PDFSPESFRILAYGDDVIYGCDPPIHpSFI 104
Cdd:cd23192  124 PPMGIFDDVIFVTKRGLPSGMPFTSVINSLNHWLLFSAAVLKAyelvgiyTGNVFDEADFFTYGDDGVYAMPPATA-SVM 202

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 371491764 105 KEFYD--EHTPLVVTPANKTDtFPENSTIYDVTFLKRWFVPDDIR 147
Cdd:cd23192  203 DEIIEnlKSYGLKPTAADKTE-NPDIPPLQGPVFLKRTFVRTPGG 246
Hepatovirus_RdRp cd23215
RNA-dependent RNA polymerase (RdRp) in the genus Hepatovirus of positive-sense single-stranded ...
 18-148 1.79e-14

RNA-dependent RNA polymerase (RdRp) in the genus Hepatovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Hepatovirus genus within the family Picornaviridae, order Picornavirales. Hepatoviruses are 27- to 32-nm, nonenveloped, icosahedral viruses with a (+)ssRNA linear genome of approximately 7.5-kb. The Hepatovirus genus has nine species, Hepatovirus A-I, of which Hepatovirus A is responsible for a self-limiting viral hepatitis in human beings and may be transmitted by the fecal-oral route during acute infection or by the ingestion of uncooked contaminated shellfish. RdRps are multi-domain proteins that play a pivotal role in enterovirus replication. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of hepatoviruses. 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: 438065  Cd Length: 464  Bit Score: 69.11  E-value: 1.79e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764  18 IGDERVTRYIETIRHSRHVFGNETYEMIGGNPSGCVGTSIINTIINNV---CVLSALI-QHPDFSPESFRILAYGDDV-- 91
Cdd:cd23215  245 VPDHQGQALINTIIYSKHLLYNLCYHVCGSMPSGSPCTSLLNSIVNNVnlyYVFSKIFkKSPVFFYDAVKFLCYGDDVli 324

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 371491764  92 IYGCDPPIH--PSFIKEFYDEHTPLVVTPANKTDTFPENSTIYDVTFLKRWF--VPDDIRP 148
Cdd:cd23215  325 VFSRDLEIKnlDKLGQRIQDEFKLLGMTATSADKGEPQVVPVSELTFLKRSFnlIEDRFRP 385
Fipivirus_RdRp cd23229
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Fipivirus of ...
 20-150 1.84e-14

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Fipivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Fipivirus genus within the family Picornaviridae, order Picornavirales. The Fipivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. This genus contains five species: Fipivirus A (Wuhan sharpbelly picornavirus 2), Fipivirus B (Wuhan sharpbelly picornavirus 3), Fipivirus C (Wenling crossorhombus picornavirus), Fipivirus D (Wenling jack mackerels picornavirus) and Fipivirus E (Wenling banjofish picornavirus 1). All contain viruses from fish. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. 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: 438079  Cd Length: 394  Bit Score: 69.07  E-value: 1.84e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764  20 DERVTRYIETIRHSRHVFGNETYEMIGGNPSGCVGTSIINTIIN------NVCVLSALIQHPDFspESFRILAYGDDVIY 93
Cdd:cd23229  180 DGQSYRLAEFVYDVKQIVGKYLYTTVGPLPSGCPSTSIIGSLCNvlmllyTLSHATGQRYSAFR--DWMHVVTYGDDVLV 257

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 371491764  94 GcdppIHPSFIK-------EFYdEHTPLVVTPANKTDTFPENSTIYDVTFLKRWFVPDDIRPFY 150
Cdd:cd23229  258 F----VHPEVVVvldtlahEMY-LVFGVTATDATDKRAPPQLRELSNVTFLKRGFRQCSSVPFL 316
Marnaviridae_RdRp cd23195
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Marnaviridae of ...
 5-145 1.12e-12

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Marnaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Marnaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. They are mono- or dicistronic, have a polyadenylate tail and have conserved motifs for RNA helicase, RdRp, and structural protein domains. The first RNA virus isolated and characterized that infects a marine protist was Heterosigma akashiwo RNA virus (HaRNAV) in the genus Marnavirus, that infects the toxic bloom-forming Raphidophyte alga, Heterosigma akashiwo. Recently, it has undergone a major taxonomic revision and now includes 20 species within 7 genera, which include Bacillarnavirus, Kusarnavirus, Labyrnavirus, Locarnavirus, Marnavirus, Salisharnavirus, and Sogarnavirus. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. 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: 438045  Cd Length: 310  Bit Score: 63.62  E-value: 1.12e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764   5 CAFRIVEKHLERLIG-DERVTRYIETIRHS-----RHVFGnETYEMIGGNPSGCVGTSIINTIINNVCVLSA-LIQHPDF 77
Cdd:cd23195   98 AAFKILIDIAAKSGGySEEDLKIMRGIATDiayplVDFNG-DLIQFFGSNPSGHPLTVIINSIVNSLYMRYAyYSLYPEK 176

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 371491764  78 SPESFR----ILAYGDDVIYGCDPPI----HPSfIKEFYDEHTpLVVTPANKTDTFPENSTIYDVTFLKRWFVPDD 145
Cdd:cd23195  177 EVPPFRdvvaLMTYGDDNIMSVSPGYpwfnHTS-IAEFLAKIG-IKYTMADKEAESVPFIHISEADFLKRKFVFDP 250
Kunsagivirus_RdRp cd23219
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Kunsagivirus of ...
 2-139 6.29e-12

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Kunsagivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Kunsagivirus genus within the family Picornaviridae, order Picornavirales. The Kunsagivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. Kunsagivirus is a new picornavirus genus containing a three species. Viral RNA of kunsagivirus A1 was detected in feces of an apparently healthy European roller (Coracias garrulus), of kunsagivirus B1 (bat kunsagivirus) in feces of the fruit bat Eidolon helvum, and of kunsagivirus C1 (bakunsavirus) in wild baboons (Papio cynocephalus). RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. 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: 438069  Cd Length: 346  Bit Score: 61.81  E-value: 6.29e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764   2 LPSCAFRIVEKHLERLIGDERVT-RYIETIRHSRHVFGNETYEMIGGNPSGCVGTSIINTIINNV-CVLSALIQHPDFsp 79
Cdd:cd23219  150 LPLQVMHRVAQLISNLTPDPQVSmRLFQPIIISTHIVGSYEVVVEGGMPSGCPITTIMNSVCNVVmTSYAMLLLDPDS-- 227

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 371491764  80 eSFRILAYGDDVIYGCDPPIHPSFIKEFYDEHTPLVVTPANKTDTF----PEnstiyDVTFLKR 139
Cdd:cd23219  228 -DFWPVAYGDDNIVSTRKPIDTELFCSILNEEFGMILTGADKTTTVqavpPM-----SVDFLKR 285
Parechovirus_RdRp cd23217
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Parechovirus of ...
 28-139 1.62e-11

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Parechovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the Parechovirus genus within the family Picornaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. The Parechovirus genus is comprised of six species, Parechovirus A (formerly named Human parechovirus), Parechovirus B (formerly named Ljungan virus), Parechovirus C (Sebokele virus) and Parechovirus D (ferret parechovirus), Parechovirus E (falcon parechovirus) and Parechovirus F (gecko parechovirus). Humans, ferrets, and various rodents serve as natural hosts. Human parechoviruses may cause gastrointestinal or respiratory illness in infants, and have been implicated in cases of myocarditis and encephalitis. Human parechoviruses replicate in the respiratory and gastrointestinal tract. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. 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: 438067  Cd Length: 371  Bit Score: 60.65  E-value: 1.62e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764  28 ETIRHSRHVFGNETYEMIGGNPSGCVGTSIINTIIN-NVCVLSALIQHPDFspeSFRILAYGDDVIYGCDPPIHPSFIKE 106
Cdd:cd23217  178 KPVINSDHVVMDERWLVHGGMPSGSPCTTVLNSICNlLVCIYLAYLQSPGI---ECLPIVYGDDVIFSVSSEIDPEYLVS 254

                         90       100       110
                 ....*....|....*....|....*....|...
gi 371491764 107 FYDEHTPLVVTPANKtDTFPENSTIYDVTFLKR 139
Cdd:cd23217  255 SAADSFGMEVTGSDK-DEPPSLLPRMEVEFLKR 286
Crohivirus_RdRp cd23232
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Crohivirus of ...
 32-139 4.62e-10

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Crohivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Crohivirus genus within the family Picornaviridae, order Picornavirales. The Crohivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. Crohivirus is a new genus containing two species, Crohivirus A and Crohivirus B. Crohivirus A (Crohivirus 1, CroV-1) is a novel picornavirus found the lesser red musk shrew (Crocidura hirta) which is found in southern Africa. The genome sequence is most closely related to the parechoviruses. Crohivirus B consists of a virus which has been found in the straw-colored fruit bat (Eidolon helvum). RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. 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: 438082  Cd Length: 373  Bit Score: 56.65  E-value: 4.62e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764  32 HSRHVFGNETYEMIGGNPSGCVGTSIINTIINNVCVLSALIQHPDfspESFRILAYGDDVIYGCDPPIHPSFIKEFYDEH 111
Cdd:cd23232  185 ESVHLVLDQKWNVSGGMPSGSPCTTVLNSVCNLIVSSTIADMCTE---GDFKILVYGDDLIISSTAPLDCDRFKTLVELH 261

                         90       100
                 ....*....|....*....|....*...
gi 371491764 112 TPLVVTPANKTDTFpENSTIYDVTFLKR 139
Cdd:cd23232  262 YGMEVTPGDKGDEF-KVKDREQVSFLKR 288
Aalivirus_RdRp cd23216
RNA-dependent RNA polymerase (RdRp) in the genus Aalivirus of positive-sense single-stranded ...
 32-139 1.55e-09

RNA-dependent RNA polymerase (RdRp) in the genus Aalivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Aalivirus genus within the family Picornaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. Aalivirus is a new picornavirus found in ducks in China. It is most closely related to duck hepatitis A virus (genus Avihepatovirus) and to avisivirus A1 (genus Avisivirus). The name "aalivirus" is derived from Avihepatovirus/Avisivirus-like virus. RdRps are multi-domain proteins that play a pivotal role in enterovirus replication. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. 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: 438066  Cd Length: 337  Bit Score: 55.06  E-value: 1.55e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764  32 HSRHVFGNETYEMIGGNPSGCVGTSIINTIInNVCVLSALIQHPDFSPESFRILAYGDDVIYGCDP-----PiHPSFIKE 106
Cdd:cd23216  169 YSTNVVSDETWFVEGGMCSGSPCTTVLNTIC-NLLVNTTILLSEGIQPDNFYIAAYGDDTIISVDGlssslP-DPKIMQQ 246

                         90       100       110
                 ....*....|....*....|....*....|...
gi 371491764 107 FYDEHTPLVVTPANKTDTFPENsTIYDVTFLKR 139
Cdd:cd23216  247 KYKEWFGMTVTSADKGSEITWD-TRNHVQFLKR 278
ps-ssRNAv_RdRp-like cd23167
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
 42-95 1.14e-08

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: 48.87  E-value: 1.14e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 371491764  42 YEMIGGNPSGCVGTSIINTIINNVCVLSALIQHPDFSP--ESFRILAYGDDVIYGC 95
Cdd:cd23167   17 DLLKAGQPSGSPNTSADNSLINLLLARLALRKACGRAEflNSVGILVYGDDSLVSV 72
Limnipivirus_RdRp cd23228
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Limnipivirus of ...
 21-141 1.54e-08

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Limnipivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Limnipivirus genus within the family Picornaviridae, order Picornavirales. The Limnipivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. This genus contains three species, Limnipivirus A (bluegill picornavirus 1), Limnipivirus B (carp picornavirus 1) and Limnipivirus C (fathead minnow picornavirus 1). Limnipiviruses infect freshwater fishes. The virus can be grown in various fish cell lines. Experimental infection of bluegills with bluegill picornavirus induces morbidity (inflammation and redness at the base of fins, exophthalmia, abdomen distension, internal hemorrhaging and ascites) and mortality. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. 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: 438078  Cd Length: 390  Bit Score: 52.19  E-value: 1.54e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764  21 ERVTRYIETIRHSRHVFGNETYEMIGGNPSGCVGTSIINTIINNVCVLSALIQH---------PDFSPESFRILAYGDDV 91
Cdd:cd23228  175 DLVRRLHETVIISKHLVVDEDWTVKGGMPSGSPCTTVLNCICNLLVLEYAFLVHfgvyedddgVGLPQCDYLSVVYGDDC 254

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 371491764  92 IYGCD-PPIHPSFiKEFYDEHTPLVVTPANKT-DTFpeNSTIYDVTFLKRWF 141
Cdd:cd23228  255 IVAYNgMEMGLAF-AETIEDTFGMEVTPASKVgDHF--NVELHEVEFLKRKF 303
Secoviridae_RdRp cd23196
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Secoviridae of ...
 34-142 2.00e-06

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Secoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Secoviridae, order Picornavirales. Members of the family Secoviridae are non-enveloped viruses with mono- or bipartite (RNA-1 and RNA-2) linear (+)ssRNA genomes of 9 to 13.7 kilobases in total. Secoviruses are related to picornaviruses and are classified in the order Picornavirales. The majority of known members infect dicotyledonous plants and many are important plant pathogens (e.g., grapevine fanleaf virus and rice tungro spherical virus). The Secoviridae includes 8 genera (Comovirus, Fabavirus, Nepovirus, Cheravirus, Sadwavirus, Torradovirus, Sequivirus, and Waikavirus) as well as unassigned species (strawberry latent ringspot virus-MEN 454, strawberry mottle virus-Thompson, black raspberry necrosis virus- 1, chocolate lily virus A-KP2, and Dioscorea mosaic associated virus-goiana). RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. 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: 438046  Cd Length: 309  Bit Score: 45.84  E-value: 2.00e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764  34 RHVFGNETYEMIGGNPSGCVGTSIINTIINNV--------CVLSALIQHPDfspESFRILAYGDDVIYGCDPPIHPSF-- 103
Cdd:cd23196  130 RSICGRQVYMVRGGMPSGCALTVIINSIFNEIliryvyrkVVPRPARNNFN---KYVRLVVYGDDNLISVKEEIIPYFdg 206

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 371491764 104 --IKEFYDEHTPLVVTPANKTDTFPENSTIYDVTFLKRWFV 142
Cdd:cd23196  207 pvIKKEMAKVGVTITDGTDKTSPTLERKPLESLDFLKRGFR 247
ps-ssRNAv_Astroviridae_RdRp cd23172
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Astroviridae of ...
 40-111 6.96e-06

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Astroviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Astroviridae, order, Stellavirales. Astrovirus has a non-segmented, (+)ssRNA genome within a non-enveloped icosahedral capsid. The family Astroviridae comprises two genera, Mamastrovirus, which infect mammals, and Avastrovirus, which infect birds. Astroviruses have been isolated from stools from a wide variety of mammals and birds. Human astroviruses have been shown to be an important cause of gastroenteritis in young children. Duck astrovirus causes an often-fatal hepatitis in ducklings. Astroviruses infecting turkeys, guinea fowl and chickens affect multiple organs, including the kidney and thymus. 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: 438022  Cd Length: 243  Bit Score: 44.00  E-value: 6.96e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764  40 ETYEMIGGNPSGCVGTSIINTIIN-------NVCVLSALIQHPDFSPESFRILAYGDDVI--YGCDPPIHPSFIKEFYDE 110
Cdd:cd23172  140 EVTRVTKGNPSGQISTTMDNCMVNtfltafeFAYVYGPKTGTLKELWDNYDTIVYGDDRLsgYPSLPDPYVERVVDMYKD 219


                 .
gi 371491764 111 H 111
Cdd:cd23172  220 V 220
Avisivirus_RdRp cd23231
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Avisivirus of ...
 39-139 8.00e-05

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Avisivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Avisivirus genus within the family Picornaviridae, order Picornavirales. The Avisivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. Avisivirus is a picornavirus genus containing three species Avisivirus A, Avisivirus B and Avisivirus C. The name Avisivirus is derived from Avihepato sister-clade. Turkeys serve as natural hosts. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. 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: 438081  Cd Length: 362  Bit Score: 41.41  E-value: 8.00e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764  39 NETYEMIGGNPSGCVGTSIINTIINNV-CVLSALIQHPDFSpESFrILAYGDDVIYGCDPPIHPSFIKEFYDEHTPLVVT 117
Cdd:cd23231  182 DEVWYVYGGMPSGSPWTTTLNTICNLLmCYTYLLDMGHCWS-ETF-VVAYGDDVVISANIKHNLEGIEQWFKTKFGATVT 259

                         90       100
                 ....*....|....*....|..
gi 371491764 118 PANKTDTFpENSTIYDVTFLKR 139
Cdd:cd23231  260 PSDKQGKI-TWTTKNNMEFLKR 280
Nora-virus_RdRp cd23200
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in a novel picorna-like ...
 25-145 5.85e-04

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in a novel picorna-like Drosophila virus, Nora virus; This group contains the catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the unclassified Nora virus, a new picorna-like virus family. Nora virus has a (+)ssRNA genome followed by a poly(A) tail. Unlike other picorna-like viruses, the genome has four open reading frames (ORFs). One ORF encodes a picornavirus-like cassette of proteins for virus replication, including an iflavirus-like RdRp and a helicase that is related to those of mammalian picornaviruses. The three other ORFs are not closely related to any previously described viruses. Nora virus is present as a persistent infection in several tested laboratory stocks and wild-caught flies. 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: 438050  Cd Length: 306  Bit Score: 38.75  E-value: 5.85e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764  25 RYIETIRH-SRHVFGNET-YEMIGGNPSGCVGTSIINTIINNVCVLSA------LIQHPDFSpESFRILAYGDDVIYgcd 96
Cdd:cd23200  120 RAVEELDAiDTYVVDYQTvYKTNRGNKSGSYTTTIDNCLANDIYGLYAwvkttgLRSLWDYR-QNVSSVAFGDDIIK--- 195

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764  97 ppihpSFIKEFYDEH-----------TPLVVTPANKTDTFPENSTIYDVTFLKRWFVPDD 145
Cdd:cd23200  196 -----SVSDEYKDKYnyctyrdvlnaTGHIMTPGSKDGEEKPFTSFENLQFLKRGFKLEN 250
Aquamavirus_RdRp cd23220
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Aquamavirus of ...
 33-144 7.27e-04

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Aquamavirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Aquamavirus genus within the family Picornaviridae, order Picornavirales. The Aquamavirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. Aquamavirus is a genus containing a single species, Aquamavirus A. This species consists of the previously named seal picornavirus 1, now to be called seal aquamavirus A1. Recently other aquamaviruses have been discovered in bears and seals (unassigned aquamaviruses). RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. 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: 438070  Cd Length: 338  Bit Score: 38.53  E-value: 7.27e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764  33 SRHVFGNETYEMIGGNPSGCVGTSIINTIINnvcVLSALIQHPDFSPESFRILAYGDDVIYGCDPPIHPSFIKEFYDEHT 112
Cdd:cd23220  177 SHHWHNNVVDLVLGGMPSGAPCTSVLNSIVN---VLMARYICALMDIDYPVMVAYGDDNVVSFDEEIDIERMVSLYKTEF 253

                         90       100       110
                 ....*....|....*....|....*....|....
gi 371491764 113 PLVVTPANKTdtfPENSTIYDVTFLKRW--FVPD 144
Cdd:cd23220  254 GVTATNHDKT---PVPRPMANPVFLKRRlrFNPD 284
Solinviviridae_RdRp cd23199
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Solinviviridae of ...
 28-141 8.28e-04

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Solinviviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Solinviviridae, order Picornavirales. Solinviviridae is a family of picorna/calici-like viruses with non-segmented, linear, (+)ssRNA genomes of approximately 10-11 kb. Members of two species within the family infect ants but related unclassified virus sequences derive from a large variety of insects and other arthropods. Phylogenetic analysis of RdRp amino acid sequences shows that members of the two classified solinvivirus species form part of a large and very diverse group of arthropod-infecting viruses within the picorna/calici-like group of viruses. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg (viral protein genome-linked)-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. 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: 438049  Cd Length: 323  Bit Score: 38.49  E-value: 8.28e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371491764  28 ETIRHSRHVFGNETYEMIGGNPSGCVGTSIINTIINNVCVLSALI-----------QHPDFSPESFRILAYGDDVIYGCD 96
Cdd:cd23199  134 QTIIDRIQVSGNSILLVHGGMPSGCVPTAPLNSKVNDIMIYTAYVnilrradrgdiTSYRYYRDLVCRLFYGDDVIIAVD 213

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 371491764  97 PPIHPSFIKEFYDEHTP----LVVTPANKTDTFPENSTIYDVTFLKRWF 141
Cdd:cd23199  214 DSIADIFNCQTLSEEMKilfgMNMTDGSKSDIIPKFETIETLSFISRFF 262
RdRP_4 pfam02123
Viral RNA-directed RNA-polymerase; This family includes RNA-dependent RNA polymerase proteins ...
 38-110 3.92e-03

Viral RNA-directed RNA-polymerase; This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.


Pssm-ID: 280316  Cd Length: 465  Bit Score: 36.28  E-value: 3.92e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 371491764   38 GNETYEMIGGNPSGCVGTSIINTIINnvCVLSALIQHPDFSPESFriLAYGDDVIYGCDPPIHPSFIKEFYDE 110
Cdd:pfam02123 352 TLLAQRVPGTLKSGHRATTFINSVLN--CAYAELAGAPWADVPTS--IHMGDDVLEGLRTPADATSLLDKYAR 420
ps-ssRNAv_Potyviridae_RdRp cd23175
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Potyviridae of ...
 46-107 5.95e-03

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


Pssm-ID: 438025  Cd Length: 236  Bit Score: 35.50  E-value: 5.95e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 371491764  46 GGNPSGCVGTSIINTIINNVCVLSALIQH---PDFSPESFRILAYGDDVIYGCdPPIHPSFIKEF 107
Cdd:cd23175  145 KGNNSGQPSTVVDNTLMVMIAMYYALLKLgidFEEIDERCVFFCNGDDLLIAV-SPEHEHILDTF 208
 
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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