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 302127661 1170 SKEAGFPVINTPSKTKLEPSVFHQVFDGNKEPAVLRNGDPRLKANFEEAIFSKYIGNVHTHVDEYMMEAVDHYAGQLATL 1249
Cdd:cd23213     1 NKEVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127661 1250 DISTEPMRLEDAVYGTEGLEALDLTTSAGYPYVALGIKKRDILSKKTRDLTKLKECMDKYGLNLPMVTYVKDELRSAEKV 1329
Cdd:cd23213    81 DIDTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKV 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 302127661 1330 AKGKSRLIEASSLNDSVAMRQTFGNLYKTFHMNPGIVTGSAVGCTP 1375
Cdd:cd23213   161 EKGKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDP 206

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 302127661   979 GPAFEFAVAMMKRNASTVKTEYGEFTML--GIYDRWAVLPRHAKPGPTILMNDQEVGVVD-AKELVDKDGTNLELTLLKL 1055
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127661  1056 NRNEKFRDIRGFLAREEAEINEAVLAINTSKFPNMYIPVGQVTDYGFL-NLGGTPTKRMLMYNFPTRAGQCGGVLMS--- 1131
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVVIAkve 160

                          170
                   ....*....|....
gi 302127661  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 302127661   663 LLLHGSPGAGKSVATNLIGRSLAEKLN---SSVYSLPPDPDHFDGYKQQAVVIMDDLCQNPDGKDVSLFCQMVSSVDFVP 739
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKKLGlpkDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 302127661   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 302127661   868 GPPVYREIKISVaPETPPPPAIADLLKSVDSEAVRVYCKEKGWLVpEVNSTLQIEKHVSRA 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 302127661 1170 SKEAGFPVINTPSKTKLEPSVFHQVFDGNKEPAVLRNGDPRLKANFEEAIFSKYIGNVHTHVDEYMMEAVDHYAGQLATL 1249
Cdd:cd23213     1 NKEVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127661 1250 DISTEPMRLEDAVYGTEGLEALDLTTSAGYPYVALGIKKRDILSKKTRDLTKLKECMDKYGLNLPMVTYVKDELRSAEKV 1329
Cdd:cd23213    81 DIDTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKV 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 302127661 1330 AKGKSRLIEASSLNDSVAMRQTFGNLYKTFHMNPGIVTGSAVGCTP 1375
Cdd:cd23213   161 EKGKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDP 206

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 302127661   979 GPAFEFAVAMMKRNASTVKTEYGEFTML--GIYDRWAVLPRHAKPGPTILMNDQEVGVVD-AKELVDKDGTNLELTLLKL 1055
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127661  1056 NRNEKFRDIRGFLAREEAEINEAVLAINTSKFPNMYIPVGQVTDYGFL-NLGGTPTKRMLMYNFPTRAGQCGGVLMS--- 1131
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVVIAkve 160

                          170
                   ....*....|....
gi 302127661  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 302127661   663 LLLHGSPGAGKSVATNLIGRSLAEKLN---SSVYSLPPDPDHFDGYKQQAVVIMDDLCQNPDGKDVSLFCQMVSSVDFVP 739
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKKLGlpkDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 302127661   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 302127661   439 QGVKDYVEQLGNAFGSGFTNQICEQVNLLKESLVGQDSILEKSLKALVKIISALVIVVRNHDDLITVTATLALIGCTSSP 518
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTQQISDKIKELTNFINPTSKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|
gi 302127661   519 WRWLKKKVSQYYGIPMAERQ 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 302127661   868 GPPVYREIKISVaPETPPPPAIADLLKSVDSEAVRVYCKEKGWLVpEVNSTLQIEKHVSRA 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 302127661 1170 SKEAGFPVINTPSKTKLEPSVFHQVFDGNKEPAVLRNGDPRLKANFEEAIFSKYIGNVHTHVDEYMMEAVDHYAGQLATL 1249
Cdd:cd23213     1 NKEVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127661 1250 DISTEPMRLEDAVYGTEGLEALDLTTSAGYPYVALGIKKRDILSKKTRDLTKLKECMDKYGLNLPMVTYVKDELRSAEKV 1329
Cdd:cd23213    81 DIDTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKV 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 302127661 1330 AKGKSRLIEASSLNDSVAMRQTFGNLYKTFHMNPGIVTGSAVGCTP 1375
Cdd:cd23213   161 EKGKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDP 206

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 302127661   979 GPAFEFAVAMMKRNASTVKTEYGEFTML--GIYDRWAVLPRHAKPGPTILMNDQEVGVVD-AKELVDKDGTNLELTLLKL 1055
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127661  1056 NRNEKFRDIRGFLAREEAEINEAVLAINTSKFPNMYIPVGQVTDYGFL-NLGGTPTKRMLMYNFPTRAGQCGGVLMS--- 1131
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVVIAkve 160

                          170
                   ....*....|....
gi 302127661  1132 -TGKVLGIHVGGNG 1144
Cdd:pfam00548  161 gNGKILGMHIAGNG 174

picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by clustalw. If a representative set is used for a seed, many so-called members are not recognized. The family should probably be split up into sub-families. Capsid proteins of picornaviruses. Picornaviruses are non-enveloped plus-strand ssRNA animal viruses with icosahedral capsids. They include rhinovirus (common cold) and poliovirus. Common structure is an 8-stranded beta sandwich. Variations (one or two extra strands) occur.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127661    44 PSDTIQTRHVKNYHVRSESSVENFLSRSACV--------YIVEYKTRDDTPDKMYDSWVINT--RQVAQLRRKLEFFTYV 113
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVqpdvqgerFYTLDSTDWTSLSKGFFWWKLPLalLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127661   114 RFDVEVTFVITSvqddstrqnTDTPALTHQIMYVPPGGPIPQAVdDYNWQTSTNPSVFWTEG-NAPPRMSIPFMSVGNAY 192
Cdd:pfam00073   81 RGGLEVTVQFNG---------SKFHQGKLLVAYVPPGAPPPGSR-DYLWQATLNPHQFWNLGlNSSARLSVPYISIAHYY 150

                          170       180
                   ....*....|....*....|...
gi 302127661   193 SNFYDGwsHFSQTGVyGFNTLNN 215
Cdd:pfam00073  151 STFYDG--NWTLVVA-GWVPLNY 170

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 302127661 1261 AVYGTEGLEALDLTTSAGYPYVALGIKKRDILSKKTRDLT-----KLKECMDKYGLNLPMVTYVKDELRSAEKVAKGKSR 1335
Cdd:cd23193     1 AINGIDGLDPIDLNTSPGYPYTTQGLRRRDLIDNDKGGVSplleeEEQVLLDLDGPDVVFTTFLKDELRPKEKVKAGKTR 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 302127661 1336 LIEASSLNDSVAMRQTFGNLYKTFHMNPGIVTGSAVGCTP 1375
Cdd:cd23193    81 VIEAAPLDYVIAGRMVFGRLFAQFHSNPGILTGSAVGCNP 120

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 302127661   64 VENFLSRSACVYIVEYKTrdDTPDKMYDSWVIN------TRQVAQLRRKLEFFTYVRFDVEVTFVITSvqddstrqnTDT 137
Cdd:cd00205     1 VESFADRPTTVGTNNWNS--SASGTQLFQWKLSpalgflLLQNTPLGALLSYFTYWRGDLEVTVQFNG---------SKF 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127661  138 PALTHQIMYVPPGGPIPQAvDDYNWQTSTNPSVFWTEG-NAPPRMSIPFMSVGNAYSNFYDGWShfsqtgvygfnTLNNM 216
Cdd:cd00205    70 HTGRLLVAYVPPGAPAPTT-GDTRWQATLNPHVIWDLGtNSSVTFVVPYVSPTPYRSTRYDGYG-----------PLNSF 137

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 302127661  217 GKLYFRHVNDKTI---SPITSKVRIYFKPKHVKAWVPRPPR 254
Cdd:cd00205   138 GTLVVRVLTPLTVpsgAPTTVDITVYVRAGDFELYGPRPPR 178

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127661 1176 PVINTPSKTKLEPSVFHQVFDGNKEPAVLRNGDPRLK--ANFEEAIFSKYIGNVHTHVDEY--MMEavdHYAGQLAT-LD 1250
Cdd:cd23227    10 PRIHVPRKTKLRKSPAYPIFKPDAGPAVLSKNDPRLAegVDFDKQVFSKHSANQKEYPKAFrrMAR---WYADRVFTyLG 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127661 1251 ISTEPMRLEDAVYGTEGLEALDLTTSAGYPYVALGIKKRDILSKKTRDLTK--LKECMDKYG----LNLPMVTYVKDELR 1324
Cdd:cd23227    87 KDNGPLSVKDAIKGIDNLDAMDPTTSPGLPYSAAGIKRTDLLDFDTGEIISpaLRAEYNKYVsgdySDHVFQTFLKDEIR 166

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 302127661 1325 SAEKVAKGKSRLIEASSLNDSVAMRQTFGNLYKTFHMNPGIVTGSAVGCTP 1375
Cdd:cd23227   167 SEEKIKAGKTRIVDVPSLAHVIIGRVLLGKFCSKFQASPGTELGSAIGCNP 217

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 302127661   439 QGVKDYVEQLGNAFGSGFTNQICEQVNLLKESLVGQDSILEKSLKALVKIISALVIVVRNHDDLITVTATLALIGCTSSP 518
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTQQISDKIKELTNFINPTSKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|
gi 302127661   519 WRWLKKKVSQYYGIPMAERQ 538
Cdd:pfam01552   81 WQFLKEKACAVLEIPYVHKQ 100

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127661 1178 INTPSKTKLEPSVFHQVFDGNKEPAVLRNGDPRLK--ANFEEAIFSKYIGNVHTHVDE--YMMEAVDHYAGQL-ATLDIS 1252
Cdd:cd23210     6 VHVMRKTKLAPTVAHGVFNPEFGPAALSNKDPRLNegVVLDEVIFSKHKGDTKMSAEDkaLFRRCAADYASRLhSVLGTA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127661 1253 TEPMRLEDAVYGTEGLEALDLTTSAGYPYVALGIKKRDILSKKTRDL---TKL-KECMDKYGLNLPMVTYVKDELRSAEK 1328
Cdd:cd23210    86 NAPLSIYEAIKGVDGLDAMEPDTAPGLPWALQGKRRGALIDFENGTVgpeVEAaLKLMEKREYKFACQTFLKDEIRPMEK 165

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 302127661 1329 VAKGKSRLIEASSLNDSVAMRQTFGNLYKTFHMNPGIVTGSAVGCTP 1375
Cdd:cd23210   166 VRAGKTRIVDVLPVEHILYTRMMIGRFCAQMHSNNGPQIGSAVGCNP 212

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 302127661 1176 PVINTPSKTKLEPSVFHQVFDGNKEPAVLRNGDPRLK--ANFEEAIFSKYIGNVHTHVDEYMMEAVDHYAGQLATLdIST 1253
Cdd:cd23214     1 PGVNVNRKSRLGPSPAYGAFPVKKQPAPLTQKDDRLEdgIRLDDQLFLKHNKGDMDEPWPGLEAAADLYFSKFPTM-IRT 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127661 1254 epMRLEDAVYGTEGLEALDLTTSAGYPYVALGIKKRDILSKKTRDL----TKLKECMDKYGLNLPMV--TYVKDELRSAE 1327
Cdd:cd23214    80 --LTQEEAINGTPNLEGLDMNQAAGYPWNTMGRSRRSLFVEVQPGIyvpkPELQAEIDKTLEDPDYFysTFLKDELRPTA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 302127661 1328 KVAKGKSRLIEASSLNDSVAMRQTFGNLYKTFHMNPGiVTGSAVGCTP 1375
Cdd:cd23214   158 KVTLGLTRVVEAAPIHAIVAGRMLLGGLIEYMQARPG-KHGSAVGCNP 204

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127661 1261 AVYGTEGLEALDLTTSAGYPYVALGIKKRDILS-------KKTRDLTKLKECMDKYGLNlPMVTYVKDELRSAEKVAKGK 1333
Cdd:cd23221     1 AINGIDNMDGLDMNQSPGVPYVSEGVSRRSLFDcvdgqwvPRERLASDIAQVSGDPSLG-HFATFLKDELRSTEKVAAGK 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 302127661 1334 SRLIEASSLNDSVAMRQTFGNLYKTFHMNPGIVTGSAVGCTP 1375
Cdd:cd23221    80 TRVVEAGSLPHIIVGRKIFGNLFALFNSNPGFQTMCAVGCDP 121

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 302127661 1261 AVYGTEGLEALDLTTSAGYPYVALGIKKRDILSKKTRDLTKLKECMDK------YGLNLP---MVTYVKDELRSAEKVAK 1331
Cdd:cd23217     1 AVLGTSHLNSLDLSTSPGYKYVKSGYKKRDLLSLEPFSVSPQLEKDVKdklhavYKGNQPttiFNACLKDELRKLDKIAQ 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 302127661 1332 GKSRLIEASSLNDSVAMRQTFGNLYKTFHMNPGIVTGSAVGCTP 1375
Cdd:cd23217    81 GKTRCIEACSIDYVIAYRVVMSSLYEAIYQTPCQELGLAVGMNP 124

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 302127661 1269 EALDLTTSAGYPYVALGIKKRDILSKKTRD-------LTKLKECMDKY--GLNLP-MVTYVKDELRSAEKVAKGKSRLIE 1338
Cdd:cd23225    10 DAMDMTKAVGYPYCLDSIKRLDLVEIKETEngkvylpTERLVEETEKFftGEEKPkFVTFLKDEVRSNEKIKQGKTRIVD 89

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 302127661 1339 ASSLNDSVAMRQTFGNLYKTFHMNPGIVTGSAVGCTP 1375
Cdd:cd23225    90 ASPFPYAIAGRMVMQNFMSNMMRCNGTEVGSAVGCDP 126

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 302127661   868 GPPVYREIKISVaPETPPPPAIADLLKSVDSEAVRVYCKEKGWLVpEVNSTLQIEKHVSRA 928
Cdd:pfam08727    1 AIFQGIDLKIDI-KTSPPPEAIADLLQAVDSPEIIDYCEDKGWIV-NIPAECQIERDIGIA 59

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 302127661 1303 KECMDKYGLNLPMVTYVKDELRSAEKVAKGKSRLIEASSLNDSVAMRQTFGNLYKTFHMNpGIVTGSAVGCTP 1375
Cdd:cd01699     8 LEDLPLIRPDLVFTTFLKDELRPLEKVEAGKTRLIQPRPLDYNIALRMYLGPFEAKLMKN-RGGLPIAVGINP 79

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 302127661 1267 GLEALDLTTSAGYPYVALGIKKRDI----------LSKKTR-DLTKLKECMDKYGLNLPMVTYV-KDELRSAEKVAKGKS 1334
Cdd:cd23228     6 GTNPIDKNTSPGLKYTRDGLKKSDLytidedgnvvVSDMLRaDVEAWEELIQSGGYPTTLFTAClKDELRSDEKVALGKT 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 302127661 1335 RLIEASSLNDSVAMRQTFGNLYKTFHMNPGIVTGSAVGCTP 1375
Cdd:cd23228    86 RVIEAAELDYVVAYRMYMSSIYSDLYNAYAGDTGIAAGINP 126