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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643 1170 SKDAGFPVINTPSKTKLEPSVFHQVFEGSKEPAVLRNGDPRLKANFEEAIFSKYIGNVNTHVDEYMQEAVDHYAGQLATL 1249
Cdd:cd23213     1 NKEVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643 1250 DISTEPMRLEDAVYGTEGLEALDLTTSAGYPYVTLGIKKRDILSKKTKDLTRLKECMDKYGLNLPMVTYVKDELRSAEKV 1329
Cdd:cd23213    81 DIDTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKV 160

                         170       180       190
                  ....*....|....*....|....*....|..
gi 302127643 1330 AKGKSRLIEASSLNDSVAMRQTFGNLYKTFHL 1361
Cdd:cd23213   161 EKGKSRLIEASSLNDSVAMRMTFGNLYATFHL 192

3C cysteine protease (picornain 3C); Picornaviral proteins are expressed as a single polyprotein which is cleaved by the viral 3C cysteine protease.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643   979 GPAFEFAVAMMKRNASMVKTEYGEFTML--GIYDRWAVLPRHAKPGPTILMNDQEVGVLD-AKELVDKDGTNLELTLLKL 1055
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643  1056 NRNEKFRDIRGFLAKEEVEVSEAVLAINTSKFPNMYIPVGQVTDYGFL-NLGGTPTKRMLMYNFPTRAGQCGGVLMS--- 1131
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVVIAkve 160

                          170
                   ....*....|....
gi 302127643  1132 -TGKVLGIHVGGNG 1144
Cdd:pfam00548  161 gNGKILGMHIAGNG 174

RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in a variety of single stranded RNA viruses.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643   663 LLLHGSPGAGKSVATNLIGRSLAEKLN---SSVYSLPPDPDHFDGYKQQAVVIMDDLCQNPDGKDVSLFCQMVSSVDFVP 739
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKKLGlpkDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 302127643   740 PMAALEEKGILFTSPFVLASTN 761
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

Poliovirus 3A protein like; This domain is found in positive-strand RNA viruses. The 3A protein is a critical component of the poliovirus replication complex, and is also an inhibitor of host cell ER to Golgi transport.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 302127643   868 GPPVYREIKISVaPETPPPPAIADLLKSVDSEVVREYCKERGWLVpEVNSTLQIEKHVSRA 928
Cdd:pfam08727    1 AIFQGIDLKIDI-KTSPPPEAIADLLQAVDSPEIIDYCEDKGWIV-NIPAECQIERDIGIA 59

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643 1170 SKDAGFPVINTPSKTKLEPSVFHQVFEGSKEPAVLRNGDPRLKANFEEAIFSKYIGNVNTHVDEYMQEAVDHYAGQLATL 1249
Cdd:cd23213     1 NKEVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643 1250 DISTEPMRLEDAVYGTEGLEALDLTTSAGYPYVTLGIKKRDILSKKTKDLTRLKECMDKYGLNLPMVTYVKDELRSAEKV 1329
Cdd:cd23213    81 DIDTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKV 160

                         170       180       190
                  ....*....|....*....|....*....|..
gi 302127643 1330 AKGKSRLIEASSLNDSVAMRQTFGNLYKTFHL 1361
Cdd:cd23213   161 EKGKSRLIEASSLNDSVAMRMTFGNLYATFHL 192

3C cysteine protease (picornain 3C); Picornaviral proteins are expressed as a single polyprotein which is cleaved by the viral 3C cysteine protease.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643   979 GPAFEFAVAMMKRNASMVKTEYGEFTML--GIYDRWAVLPRHAKPGPTILMNDQEVGVLD-AKELVDKDGTNLELTLLKL 1055
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643  1056 NRNEKFRDIRGFLAKEEVEVSEAVLAINTSKFPNMYIPVGQVTDYGFL-NLGGTPTKRMLMYNFPTRAGQCGGVLMS--- 1131
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVVIAkve 160

                          170
                   ....*....|....
gi 302127643  1132 -TGKVLGIHVGGNG 1144
Cdd:pfam00548  161 gNGKILGMHIAGNG 174

RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in a variety of single stranded RNA viruses.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643   663 LLLHGSPGAGKSVATNLIGRSLAEKLN---SSVYSLPPDPDHFDGYKQQAVVIMDDLCQNPDGKDVSLFCQMVSSVDFVP 739
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKKLGlpkDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 302127643   740 PMAALEEKGILFTSPFVLASTN 761
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

Picornavirus 2B protein; Poliovirus infection leads to drastic alterations in membrane permeability late during infection. Proteins 2B and 2BC enhance membrane permeability.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643   439 QGVKDYVEQLGNAFGSGFTNQICEQVNLLKESLIGQDSTLEKSLKALVKIISALVIVVRNHEDLITVTATLALIGCTSSP 518
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTQQISDKIKELTNFINPTSKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|
gi 302127643   519 WRWLKQKVSQYFGVPMAERQ 538
Cdd:pfam01552   81 WQFLKEKACAVLEIPYVHKQ 100

Poliovirus 3A protein like; This domain is found in positive-strand RNA viruses. The 3A protein is a critical component of the poliovirus replication complex, and is also an inhibitor of host cell ER to Golgi transport.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 302127643   868 GPPVYREIKISVaPETPPPPAIADLLKSVDSEVVREYCKERGWLVpEVNSTLQIEKHVSRA 928
Cdd:pfam08727    1 AIFQGIDLKIDI-KTSPPPEAIADLLQAVDSPEIIDYCEDKGWIV-NIPAECQIERDIGIA 59

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643 1170 SKDAGFPVINTPSKTKLEPSVFHQVFEGSKEPAVLRNGDPRLKANFEEAIFSKYIGNVNTHVDEYMQEAVDHYAGQLATL 1249
Cdd:cd23213     1 NKEVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643 1250 DISTEPMRLEDAVYGTEGLEALDLTTSAGYPYVTLGIKKRDILSKKTKDLTRLKECMDKYGLNLPMVTYVKDELRSAEKV 1329
Cdd:cd23213    81 DIDTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKV 160

                         170       180       190
                  ....*....|....*....|....*....|..
gi 302127643 1330 AKGKSRLIEASSLNDSVAMRQTFGNLYKTFHL 1361
Cdd:cd23213   161 EKGKSRLIEASSLNDSVAMRMTFGNLYATFHL 192

3C cysteine protease (picornain 3C); Picornaviral proteins are expressed as a single polyprotein which is cleaved by the viral 3C cysteine protease.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643   979 GPAFEFAVAMMKRNASMVKTEYGEFTML--GIYDRWAVLPRHAKPGPTILMNDQEVGVLD-AKELVDKDGTNLELTLLKL 1055
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643  1056 NRNEKFRDIRGFLAKEEVEVSEAVLAINTSKFPNMYIPVGQVTDYGFL-NLGGTPTKRMLMYNFPTRAGQCGGVLMS--- 1131
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVVIAkve 160

                          170
                   ....*....|....
gi 302127643  1132 -TGKVLGIHVGGNG 1144
Cdd:pfam00548  161 gNGKILGMHIAGNG 174

RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in a variety of single stranded RNA viruses.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643   663 LLLHGSPGAGKSVATNLIGRSLAEKLN---SSVYSLPPDPDHFDGYKQQAVVIMDDLCQNPDGKDVSLFCQMVSSVDFVP 739
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKKLGlpkDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 302127643   740 PMAALEEKGILFTSPFVLASTN 761
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA animal viruses with icosahedral capsids composed of 60 copies each of 4 virus encoded proteins; alignment includes picornaviridae, like poliovirus, hepatitis A virus, rhinovirus, foot-and-mouth disease virus and encephalomyocarditis virus; common structure is an 8-stranded beta sandwich

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643   64 VENFLSRSACVYIVEYKTrdDTPDKMYDSWVIN------TRQVAQLRRKLEFFTYVRFDVEVTFVITSvqddstrqnTDT 137
Cdd:cd00205     1 VESFADRPTTVGTNNWNS--SASGTQLFQWKLSpalgflLLQNTPLGALLSYFTYWRGDLEVTVQFNG---------SKF 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643  138 PALTHQIMYVPPGGPIPQAvDDYNWQTSTNPSVFWTEGSAPP-RMSIPFMSVGNAYSNFYDGWShfsqtgvygfnTLNNM 216
Cdd:cd00205    70 HTGRLLVAYVPPGAPAPTT-GDTRWQATLNPHVIWDLGTNSSvTFVVPYVSPTPYRSTRYDGYG-----------PLNSF 137

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 302127643  217 GKLYFRHVNDKTI---SPITSKVRIYFKPKHVKAWVPRPPR 254
Cdd:cd00205   138 GTLVVRVLTPLTVpsgAPTTVDITVYVRAGDFELYGPRPPR 178

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643 1261 AVYGTEGLEALDLTTSAGYPYVTLGIKKRDILSKKTKDLT-----RLKECMDKYGLNLPMVTYVKDELRSAEKVAKGKSR 1335
Cdd:cd23193     1 AINGIDGLDPIDLNTSPGYPYTTQGLRRRDLIDNDKGGVSplleeEEQVLLDLDGPDVVFTTFLKDELRPKEKVKAGKTR 80

                          90       100
                  ....*....|....*....|....*
gi 302127643 1336 LIEASSLNDSVAMRQTFGNLYKTFH 1360
Cdd:cd23193    81 VIEAAPLDYVIAGRMVFGRLFAQFH 105

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643 1187 EPSVFHQVFEGSKEPAVLRNGDPRLKA--NFEEAIFSKYIGNVNTHVDEyMQEAVDHYAGQLATLdISTE---PMRLEDA 1261
Cdd:cd23222     1 KPSPVYGVYPVTKEPAPLKPTDRRIDEgvDFNEPVFGKYGADMKEPFRN-LDVGRDVVIARLKKV-LPNKkfaPCTVSEA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643 1262 VYGTEGLEALDLTTSAGYPYVTLGIKKRDI--------LSKKTKDLTRLKECmDKYGLNLPMVTYVKDELRSAEKVAKGK 1333
Cdd:cd23222    79 LNGKDGLPKLDLKQASGYPYNLSAIKRKHLiesdkdgfLTATPKLLADIEES-KKHPEKFPYTSFLKDELRSVKKVKAGK 157

                         170       180
                  ....*....|....*....|....*..
gi 302127643 1334 SRLIEASSLNDSVAMRQTFGNLYKTFH 1360
Cdd:cd23222   158 TRVVEAGSLPVIVEGRMIFGNLFAYFN 184

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643 1176 PVINTPSKTKLEPSVFHQVFEGSKEPAVLRNGDPRLKANFEEAIFSKYIGNVnthvdEYMQEAVDHYAGQLA-----TLD 1250
Cdd:cd23211    10 PVVHVPRKTKLRRTVAHPVFQPKFEPAVLSKYDPRTDKDVDEVAFSKHTTNQ-----ESLPPVFRMVAKEYAnrvftLLG 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643 1251 ISTEPMRLEDAVYGTEGLEALDLTTSAGYPYVTLGIKKRDILSKKTKDLT-----RLKECMDKYGLNLPMVTYVKDELRS 1325
Cdd:cd23211    85 KDNGRLTVEQAVLGLEGMDPMEKDTSPGLPYTQQGLRRTDVVDFETATMIpflaeAHRKMVEGDYSDVVYQSFLKDEIRP 164

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 302127643 1326 AEKVAKGKSRLIEASSLNDSVAMRQTFGNLYKTFH 1360
Cdd:cd23211   165 IEKVQAAKTRIVDVPPFEHCILGRQLLGRFASKFQ 199

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643 1176 PVINTPSKTKLEPSVFHQVFEGSKEPAVLRNGDPRLK--ANFEEAIFSKYIGNV----NTHVDEYMQEAVDHYAGQLATL 1249
Cdd:cd23226    10 PRVHVPRQSKLKRTNATYPATGKYGPAVLSKNDPRLDpdVDFDKVIFSKHVANVvideDTSFWNALKMSAQIYAEKFKGV 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643 1250 DIStePMRLEDAVYGTEGLEALDLTTSAGYPYVTLGIKKRDILSKKTKDlTRLKECMDKYGLN----LPMVTYVKDELRS 1325
Cdd:cd23226    90 DFS--PLTVEEAILGIPGLDRMDPNTASGLPYTKTRRQMIDFQEGKILD-PELQERLDTWLSGkqpeMLYQTFLKDEIRP 166

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 302127643 1326 AEKVAKGKSRLIEASSLNDSVAMRQTFGNLYKTFHL 1361
Cdd:cd23226   167 IEKVKAGKTRIIDVTPLDHVLAFRIVLGRFMAHFHN 202

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643 1176 PVINTPSKTKLEPSVFHQVFEGSKEPAVLRNGDPRLK--ANFEEAIFSKYIGNVNTHVDEYMQEAVDHYAGQLATLdIST 1253
Cdd:cd23214     1 PGVNVNRKSRLGPSPAYGAFPVKKQPAPLTQKDDRLEdgIRLDDQLFLKHNKGDMDEPWPGLEAAADLYFSKFPTM-IRT 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643 1254 epMRLEDAVYGTEGLEALDLTTSAGYPYVTLGIKKRDILSKKTKDL----TRLKECMDKYGLNLPMV--TYVKDELRSAE 1327
Cdd:cd23214    80 --LTQEEAINGTPNLEGLDMNQAAGYPWNTMGRSRRSLFVEVQPGIyvpkPELQAEIDKTLEDPDYFysTFLKDELRPTA 157

                         170       180
                  ....*....|....*....|....*...
gi 302127643 1328 KVAKGKSRLIEASSLNDSVAMRQTFGNL 1355
Cdd:cd23214   158 KVTLGLTRVVEAAPIHAIVAGRMLLGGL 185

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643 1254 EPMRLEDAVYGTEGLEALDLTTSAGYPYVTLGIKKRDILSKKTKDLTRLKECMDKY-GLNLP---MVTYVKDELRSAEKV 1329
Cdd:cd23212     9 EPLSVREAVEGIDGLDPMDMDKSPGLPYVKKGLRRTDLWNPKTGPSIELMAEINRYlDYNYDkhvFLTFLKDELRPKEKV 88

                          90       100       110
                  ....*....|....*....|....*....|.
gi 302127643 1330 AKGKSRLIEASSLNDSVAMRQTFGNLYKTFH 1360
Cdd:cd23212    89 QAGKTRVIDVAGFGHAIVGRMLFGRLFAFFH 119

Poliovirus 3A protein like; This domain is found in positive-strand RNA viruses. The 3A protein is a critical component of the poliovirus replication complex, and is also an inhibitor of host cell ER to Golgi transport.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 302127643   868 GPPVYREIKISVaPETPPPPAIADLLKSVDSEVVREYCKERGWLVpEVNSTLQIEKHVSRA 928
Cdd:pfam08727    1 AIFQGIDLKIDI-KTSPPPEAIADLLQAVDSPEIIDYCEDKGWIV-NIPAECQIERDIGIA 59

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643 1262 VYGTEGLEALDLTTSAGYPYVTLGIKKRDILS----KKTKDLTRLKECMDKY-------GLNLPMVTYV---KDELRSAE 1327
Cdd:cd23229     2 VEGIPGMEGLDMKTSAGYPWCEQNQKKKDKIKllagKNFLVRPLREVVHIVVdwyimppDMPKPEIKYVvylKDELLSSD 81

                          90       100       110
                  ....*....|....*....|....*....|....
gi 302127643 1328 KVAKGKSRLIEASSLNDSVAMRQTFGNLYKTFHL 1361
Cdd:cd23229    82 KVKMGRTRWICAAPVQLVCAWKKVFGRAIAAIHL 115

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643 1269 EALDLTTSAGYPYVTLGIKKRDILSKKTKD-------LTRLKECMDKY--GLNLP-MVTYVKDELRSAEKVAKGKSRLIE 1338
Cdd:cd23225    10 DAMDMTKAVGYPYCLDSIKRLDLVEIKETEngkvylpTERLVEETEKFftGEEKPkFVTFLKDEVRSNEKIKQGKTRIVD 89

                          90
                  ....*....|....*..
gi 302127643 1339 ASSLNDSVAMRQTFGNL 1355
Cdd:cd23225    90 ASPFPYAIAGRMVMQNF 106

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643 1267 GLEALDLTTSAGYPYVTLGIKKRD---ILSKKT--------KDLTRLKECMDKYGLNLPMVTYV-KDELRSAEKVAKGKS 1334
Cdd:cd23228     6 GTNPIDKNTSPGLKYTRDGLKKSDlytIDEDGNvvvsdmlrADVEAWEELIQSGGYPTTLFTAClKDELRSDEKVALGKT 85

                          90       100
                  ....*....|....*....|....*.
gi 302127643 1335 RLIEASSLNDSVAMRQTFGNLYKTFH 1360
Cdd:cd23228    86 RVIEAAELDYVVAYRMYMSSIYSDLY 111

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 302127643 1316 VTYVKDELRSAEKVAKGKSRLIEASSLNDSVAMRQTFGNLYKTFH 1360
Cdd:cd23169     4 VDCLKDELRPIEKVKAGKTRLFSASPLDYTIAFRKYFGDFIAAFQ 48

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127643 1271 LDLTTSAGYPYVtlGIKKRDILSKKT-----KDLTRLKECMDKYGLNLPMVTYVKDELRSAEKVAKGKSRLIEASSLNDS 1345
Cdd:cd23231    11 IDWGTSPGDKYK--GKTKAQLVDDKKfkadvMNLVRFNGDPNREPPDVYFTTYLKDELRPKEKAKAGKTRVISAASFDYT 88

                          90
                  ....*....|..
gi 302127643 1346 VAMRQTFGNLYK 1357
Cdd:cd23231    89 IACRMVFGPILR 100