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Conserved domains on  [gi|528312291|emb|CCW33483|]
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polyprotein, partial [Echovirus E18]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ps-ssRNAv_RdRp-like super family cl40470
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
 1168-1370 8.73e-132

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 cd23213:

Pssm-ID: 477363  Cd Length: 453  Bit Score: 413.85  E-value: 8.73e-132
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1168 SKEAGFPVINTPSKTKLEPSVFHHVFEGNKEPAVLRNGDPRLKANFEEAIFSKYIGNVNTHVDEYMMEAVDHYAGQLATL 1247
Cdd:cd23213     1 NKEVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1248 DISTEPMKLEDAVYGTEGLEALDLTTSAGYPYVALGIKKRDILSKRTKDLTKLKECMDKYGLNLPMVTYVKDELRSAEKI 1327
Cdd:cd23213    81 DIDTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKV 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 528312291 1328 AKGKSRLIEASSLNDSVAMRQTFGNLYKTFHLNPGIVTGSAVG 1370
Cdd:cd23213   161 EKGKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVG 203
Pico_P2A pfam00947
Picornavirus core protein 2A; This protein is a protease, involved in cleavage of the ...
 306-432 8.46e-85

Picornavirus core protein 2A; This protein is a protease, involved in cleavage of the polyprotein.


:

Pssm-ID: 395757  Cd Length: 127  Bit Score: 271.95  E-value: 8.46e-85
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291   306 NRHLATHDDWQNCVWEDYNRDLLVSTTTAHGCDTIARCRCTAGVYFCASKNRHYPVCFEGPGLVEVQESEYYPKRYQSHV 385
Cdd:pfam00947    1 NRHLATHEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 528312291   386 LLAAGFSEPGDCGGILRCEHGVIGIVTMGGEGVVGFADVRDLLWLED 432
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVRDLLWLEE 127
Peptidase_C3 super family cl02893
3C cysteine protease (picornain 3C); Picornaviral proteins are expressed as a single ...
 977-1142 2.65e-54

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


The actual alignment was detected with superfamily member pfam00548:

Pssm-ID: 278947  Cd Length: 174  Bit Score: 187.27  E-value: 2.65e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291   977 GPAFEFAVAMMKRNASTVKTEYGEFTML--GIYDRWAVLPRHAKPGPTILMNDQEVGVAD-AKELVDKDGTNLELTLLKL 1053
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291  1054 NRNEKFRDIRGFLAREEAEVNEAVLAINTSKFPNMYIPVGQVTDYGFL-NLGGTPTKRMLMYNFPTRAGQCGGVLMS--- 1129
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVVIAkve 160

                          170
                   ....*....|....
gi 528312291  1130 -TGKVLGIHVGGNG 1142
Cdd:pfam00548  161 gNGKILGMHIAGNG 174
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
 38-209 5.38e-45

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.


:

Pssm-ID: 395026  Cd Length: 170  Bit Score: 160.17  E-value: 5.38e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291    38 PSDTMQTKHVVNFHSRSESTVKNFMGRAACVSMDQ-----YKLNGEETSTDN--FAVWTINI--REMAQLRRKCEMFTYM 108
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVqgerfYTLDSTDWTSLSkgFFWWKLPLalLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291   109 RFDIEMTMVITSSQdqgtqleqdMPVLTHQIMYVPPGGPIPAKVDsYEWQTSTNPSVFWTKG-NAPARMSIPFISVGNAN 187
Cdd:pfam00073   81 RGGLEVTVQFNGSK---------FHQGKLLVAYVPPGAPPPGSRD-YLWQATLNPHQFWNLGlNSSARLSVPYISIAHYY 150

                          170       180
                   ....*....|....*....|..
gi 528312291   188 SLFYDGwsHFTQDGTyGYTTLN 209
Cdd:pfam00073  151 STFYDG--NWTLVVA-GWVPLN 169
RNA_helicase pfam00910
RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...
 661-759 2.28e-42

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.


:

Pssm-ID: 459992  Cd Length: 102  Bit Score: 150.06  E-value: 2.28e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291   661 LLLHGSPGAGKSVATNLIGRSLAEKLN---SSVYSLPPDPDHFDGYKQQAVVIMDDLCQNPDGKDVSLFCQMVSSVDFVP 737
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKKLGlpkDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 528312291   738 PMAALEEKGILFTSPFVLASTN 759
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102
Pico_P2B super family cl03260
Picornavirus 2B protein; Poliovirus infection leads to drastic alterations in membrane ...
 437-536 1.44e-29

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


The actual alignment was detected with superfamily member pfam01552:

Pssm-ID: 279840  Cd Length: 101  Bit Score: 113.58  E-value: 1.44e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291   437 QGVKDYVEQLGNAFGSGFTNQICEQVNVLKESLIGQDSILEKSLKALVKIISALVIVVRNHDDLVTITATLALIGCTSSP 516
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTQQISDKIKELTNFINPTSKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|
gi 528312291   517 WRWLKQKVSQYYGIPMAERQ 536
Cdd:pfam01552   81 WQFLKEKACAVLEIPYVHKQ 100
P3A super family cl07374
Poliovirus 3A protein like; This domain is found in positive-strand RNA viruses. The 3A ...
 866-926 1.68e-14

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.


The actual alignment was detected with superfamily member pfam08727:

Pssm-ID: 400873  Cd Length: 59  Bit Score: 69.38  E-value: 1.68e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 528312291   866 GPPVYREIKISVaPETPPPPAIADLLKSVDSEAVREYCKEKGWLVpEINSTLQIEKHVSRA 926
Cdd:pfam08727    1 AIFQGIDLKIDI-KTSPPPEAIADLLQAVDSPEIIDYCEDKGWIV-NIPAECQIERDIGIA 59
 
Name Accession Description Interval E-value
Enterovirus_RdRp cd23213
RNA-dependent RNA polymerase (RdRp) in the Enterovirus genus of positive-sense single-stranded ...
 1168-1370 8.73e-132

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: 413.85  E-value: 8.73e-132
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1168 SKEAGFPVINTPSKTKLEPSVFHHVFEGNKEPAVLRNGDPRLKANFEEAIFSKYIGNVNTHVDEYMMEAVDHYAGQLATL 1247
Cdd:cd23213     1 NKEVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1248 DISTEPMKLEDAVYGTEGLEALDLTTSAGYPYVALGIKKRDILSKRTKDLTKLKECMDKYGLNLPMVTYVKDELRSAEKI 1327
Cdd:cd23213    81 DIDTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKV 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 528312291 1328 AKGKSRLIEASSLNDSVAMRQTFGNLYKTFHLNPGIVTGSAVG 1370
Cdd:cd23213   161 EKGKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVG 203
Pico_P2A pfam00947
Picornavirus core protein 2A; This protein is a protease, involved in cleavage of the ...
 306-432 8.46e-85

Picornavirus core protein 2A; This protein is a protease, involved in cleavage of the polyprotein.


Pssm-ID: 395757  Cd Length: 127  Bit Score: 271.95  E-value: 8.46e-85
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291   306 NRHLATHDDWQNCVWEDYNRDLLVSTTTAHGCDTIARCRCTAGVYFCASKNRHYPVCFEGPGLVEVQESEYYPKRYQSHV 385
Cdd:pfam00947    1 NRHLATHEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 528312291   386 LLAAGFSEPGDCGGILRCEHGVIGIVTMGGEGVVGFADVRDLLWLED 432
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVRDLLWLEE 127
Peptidase_C3 pfam00548
3C cysteine protease (picornain 3C); Picornaviral proteins are expressed as a single ...
 977-1142 2.65e-54

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


Pssm-ID: 278947  Cd Length: 174  Bit Score: 187.27  E-value: 2.65e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291   977 GPAFEFAVAMMKRNASTVKTEYGEFTML--GIYDRWAVLPRHAKPGPTILMNDQEVGVAD-AKELVDKDGTNLELTLLKL 1053
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291  1054 NRNEKFRDIRGFLAREEAEVNEAVLAINTSKFPNMYIPVGQVTDYGFL-NLGGTPTKRMLMYNFPTRAGQCGGVLMS--- 1129
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVVIAkve 160

                          170
                   ....*....|....
gi 528312291  1130 -TGKVLGIHVGGNG 1142
Cdd:pfam00548  161 gNGKILGMHIAGNG 174
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
 38-209 5.38e-45

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.


Pssm-ID: 395026  Cd Length: 170  Bit Score: 160.17  E-value: 5.38e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291    38 PSDTMQTKHVVNFHSRSESTVKNFMGRAACVSMDQ-----YKLNGEETSTDN--FAVWTINI--REMAQLRRKCEMFTYM 108
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVqgerfYTLDSTDWTSLSkgFFWWKLPLalLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291   109 RFDIEMTMVITSSQdqgtqleqdMPVLTHQIMYVPPGGPIPAKVDsYEWQTSTNPSVFWTKG-NAPARMSIPFISVGNAN 187
Cdd:pfam00073   81 RGGLEVTVQFNGSK---------FHQGKLLVAYVPPGAPPPGSRD-YLWQATLNPHQFWNLGlNSSARLSVPYISIAHYY 150

                          170       180
                   ....*....|....*....|..
gi 528312291   188 SLFYDGwsHFTQDGTyGYTTLN 209
Cdd:pfam00073  151 STFYDG--NWTLVVA-GWVPLN 169
RNA_helicase pfam00910
RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...
 661-759 2.28e-42

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.


Pssm-ID: 459992  Cd Length: 102  Bit Score: 150.06  E-value: 2.28e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291   661 LLLHGSPGAGKSVATNLIGRSLAEKLN---SSVYSLPPDPDHFDGYKQQAVVIMDDLCQNPDGKDVSLFCQMVSSVDFVP 737
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKKLGlpkDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 528312291   738 PMAALEEKGILFTSPFVLASTN 759
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 58-249 1.87e-35

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


Pssm-ID: 119412  Cd Length: 178  Bit Score: 133.29  E-value: 1.87e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291   58 VKNFMGRAACVSMDQYKLNgeeTSTDNFAVWTIN------IREMAQLRRKCEMFTYMRFDIEMTMVITSSQdqgtqleqd 131
Cdd:cd00205     1 VESFADRPTTVGTNNWNSS---ASGTQLFQWKLSpalgflLLQNTPLGALLSYFTYWRGDLEVTVQFNGSK--------- 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291  132 MPVLTHQIMYVPPGGPIPAKvDSYEWQTSTNPSVFW-TKGNAPARMSIPFISVGNANSLFYDGWShftqdgtygytTLNA 210
Cdd:cd00205    69 FHTGRLLVAYVPPGAPAPTT-GDTRWQATLNPHVIWdLGTNSSVTFVVPYVSPTPYRSTRYDGYG-----------PLNS 136

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 528312291  211 MGKLYIKHVNKSSPHQITST---IRVYFKPKHIKAWVPRPPR 249
Cdd:cd00205   137 FGTLVVRVLTPLTVPSGAPTtvdITVYVRAGDFELYGPRPPR 178
Pico_P2B pfam01552
Picornavirus 2B protein; Poliovirus infection leads to drastic alterations in membrane ...
 437-536 1.44e-29

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


Pssm-ID: 279840  Cd Length: 101  Bit Score: 113.58  E-value: 1.44e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291   437 QGVKDYVEQLGNAFGSGFTNQICEQVNVLKESLIGQDSILEKSLKALVKIISALVIVVRNHDDLVTITATLALIGCTSSP 516
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTQQISDKIKELTNFINPTSKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|
gi 528312291   517 WRWLKQKVSQYYGIPMAERQ 536
Cdd:pfam01552   81 WQFLKEKACAVLEIPYVHKQ 100
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
 1185-1370 8.82e-17

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: 84.77  E-value: 8.82e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291  1185 EPSVFHHVFEGNKEPAVLRNGDPRLKANFEeaIFSKYIGNVN------THVDEYMME------AVDHYAGQLATLDISTE 1252
Cdd:pfam00680    1 SPTERHLVAIPAYVPASLGPEDPRWARSYL--NTDPYVDDIKkysrpkLPGPADERDkllnrsAAKMVLSELRGVPKKAN 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291  1253 PMKLEDAVY-GTEGLEALDLTTSAGYPYVALGIKKRDI---LSKRTKDLT---KLKECMDKYGLNLPMV----TYVKDEL 1321
Cdd:pfam00680   79 STLIVYRAIdGVEQIDPLNWDTSAGYPYVGLGGKKGDLiehLKDGTEARElaeRLAADWEVLQNGTPLKlvyqTCLKDEL 158

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 528312291  1322 RSAEKIAKGKSRLIEASSLNDSVAMRQTFGNLYKTFHLNPGIVTgSAVG 1370
Cdd:pfam00680  159 RPLEKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHP-IQVG 206
P3A pfam08727
Poliovirus 3A protein like; This domain is found in positive-strand RNA viruses. The 3A ...
 866-926 1.68e-14

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.


Pssm-ID: 400873  Cd Length: 59  Bit Score: 69.38  E-value: 1.68e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 528312291   866 GPPVYREIKISVaPETPPPPAIADLLKSVDSEAVREYCKEKGWLVpEINSTLQIEKHVSRA 926
Cdd:pfam08727    1 AIFQGIDLKIDI-KTSPPPEAIADLLQAVDSPEIIDYCEDKGWIV-NIPAECQIERDIGIA 59
 
Name Accession Description Interval E-value
Enterovirus_RdRp cd23213
RNA-dependent RNA polymerase (RdRp) in the Enterovirus genus of positive-sense single-stranded ...
 1168-1370 8.73e-132

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: 413.85  E-value: 8.73e-132
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1168 SKEAGFPVINTPSKTKLEPSVFHHVFEGNKEPAVLRNGDPRLKANFEEAIFSKYIGNVNTHVDEYMMEAVDHYAGQLATL 1247
Cdd:cd23213     1 NKEVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1248 DISTEPMKLEDAVYGTEGLEALDLTTSAGYPYVALGIKKRDILSKRTKDLTKLKECMDKYGLNLPMVTYVKDELRSAEKI 1327
Cdd:cd23213    81 DIDTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKV 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 528312291 1328 AKGKSRLIEASSLNDSVAMRQTFGNLYKTFHLNPGIVTGSAVG 1370
Cdd:cd23213   161 EKGKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVG 203
Pico_P2A pfam00947
Picornavirus core protein 2A; This protein is a protease, involved in cleavage of the ...
 306-432 8.46e-85

Picornavirus core protein 2A; This protein is a protease, involved in cleavage of the polyprotein.


Pssm-ID: 395757  Cd Length: 127  Bit Score: 271.95  E-value: 8.46e-85
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291   306 NRHLATHDDWQNCVWEDYNRDLLVSTTTAHGCDTIARCRCTAGVYFCASKNRHYPVCFEGPGLVEVQESEYYPKRYQSHV 385
Cdd:pfam00947    1 NRHLATHEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 528312291   386 LLAAGFSEPGDCGGILRCEHGVIGIVTMGGEGVVGFADVRDLLWLED 432
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVRDLLWLEE 127
Peptidase_C3 pfam00548
3C cysteine protease (picornain 3C); Picornaviral proteins are expressed as a single ...
 977-1142 2.65e-54

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


Pssm-ID: 278947  Cd Length: 174  Bit Score: 187.27  E-value: 2.65e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291   977 GPAFEFAVAMMKRNASTVKTEYGEFTML--GIYDRWAVLPRHAKPGPTILMNDQEVGVAD-AKELVDKDGTNLELTLLKL 1053
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291  1054 NRNEKFRDIRGFLAREEAEVNEAVLAINTSKFPNMYIPVGQVTDYGFL-NLGGTPTKRMLMYNFPTRAGQCGGVLMS--- 1129
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVVIAkve 160

                          170
                   ....*....|....
gi 528312291  1130 -TGKVLGIHVGGNG 1142
Cdd:pfam00548  161 gNGKILGMHIAGNG 174
Rabovirus_RdRp cd23230
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Rabovirus of ...
 1259-1370 6.98e-49

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: 178.54  E-value: 6.98e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1259 AVYGTEGLEALDLTTSAGYPYVALGIKKRDILSKRTKDLTKLKECMDKYGLNLPMVTYVKDELRSAEKIAKGKSRLIEAS 1338
Cdd:cd23230     1 AAYGIENLEGLDLNTSAGYPYVLNGIKKRDILDPETRDTTKLQECLDKYGVDLPFVTYLKDELRPLEKIKKGKTRLIECS 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 528312291 1339 SLNDSVAMRQTFGNLYKTFHLNPGIVTGSAVG 1370
Cdd:cd23230    81 SMNDTIRMKMMFGRLFATYHRNPGPITGSAVG 112
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
 38-209 5.38e-45

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.


Pssm-ID: 395026  Cd Length: 170  Bit Score: 160.17  E-value: 5.38e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291    38 PSDTMQTKHVVNFHSRSESTVKNFMGRAACVSMDQ-----YKLNGEETSTDN--FAVWTINI--REMAQLRRKCEMFTYM 108
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVqgerfYTLDSTDWTSLSkgFFWWKLPLalLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291   109 RFDIEMTMVITSSQdqgtqleqdMPVLTHQIMYVPPGGPIPAKVDsYEWQTSTNPSVFWTKG-NAPARMSIPFISVGNAN 187
Cdd:pfam00073   81 RGGLEVTVQFNGSK---------FHQGKLLVAYVPPGAPPPGSRD-YLWQATLNPHQFWNLGlNSSARLSVPYISIAHYY 150

                          170       180
                   ....*....|....*....|..
gi 528312291   188 SLFYDGwsHFTQDGTyGYTTLN 209
Cdd:pfam00073  151 STFYDG--NWTLVVA-GWVPLN 169
Sapelovirus_RdRp cd23218
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Sapelovirus of ...
 1258-1370 2.48e-43

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: 162.38  E-value: 2.48e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1258 DAVYGTEGLEALDLTTSAGYPYVALGIKKRDILSKRTKDLTKLKECMDKYGLNLPMVTYVKDELRSAEKIAKGKSRLIEA 1337
Cdd:cd23218     1 DVVYGIDNLEGLDLNTSAGYPYNTMGIRKKDLIPPRGEPLSPLLKALDLHGYDLPFTTYLKDELRPKEKVKMGKTRLIEC 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 528312291 1338 SSLNDSVAMRQTFGNLYKTFHLNPGIVTGSAVG 1370
Cdd:cd23218    81 SSLNDTIRMKRIFGRLFQTFHKNPGTYTGSAVG 113
ps-ssRNA_Picornaviridae cd23193
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Picornaviridae of ...
 1259-1370 1.90e-42

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: 159.25  E-value: 1.90e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1259 AVYGTEGLEALDLTTSAGYPYVALGIKKRDILSKRTKDLT-----KLKECMDKYGLNLPMVTYVKDELRSAEKIAKGKSR 1333
Cdd:cd23193     1 AINGIDGLDPIDLNTSPGYPYTTQGLRRRDLIDNDKGGVSplleeEEQVLLDLDGPDVVFTTFLKDELRPKEKVKAGKTR 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 528312291 1334 LIEASSLNDSVAMRQTFGNLYKTFHLNPGIVTGSAVG 1370
Cdd:cd23193    81 VIEAAPLDYVIAGRMVFGRLFAQFHSNPGILTGSAVG 117
RNA_helicase pfam00910
RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...
 661-759 2.28e-42

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.


Pssm-ID: 459992  Cd Length: 102  Bit Score: 150.06  E-value: 2.28e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291   661 LLLHGSPGAGKSVATNLIGRSLAEKLN---SSVYSLPPDPDHFDGYKQQAVVIMDDLCQNPDGKDVSLFCQMVSSVDFVP 737
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKKLGlpkDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 528312291   738 PMAALEEKGILFTSPFVLASTN 759
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 58-249 1.87e-35

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


Pssm-ID: 119412  Cd Length: 178  Bit Score: 133.29  E-value: 1.87e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291   58 VKNFMGRAACVSMDQYKLNgeeTSTDNFAVWTIN------IREMAQLRRKCEMFTYMRFDIEMTMVITSSQdqgtqleqd 131
Cdd:cd00205     1 VESFADRPTTVGTNNWNSS---ASGTQLFQWKLSpalgflLLQNTPLGALLSYFTYWRGDLEVTVQFNGSK--------- 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291  132 MPVLTHQIMYVPPGGPIPAKvDSYEWQTSTNPSVFW-TKGNAPARMSIPFISVGNANSLFYDGWShftqdgtygytTLNA 210
Cdd:cd00205    69 FHTGRLLVAYVPPGAPAPTT-GDTRWQATLNPHVIWdLGTNSSVTFVVPYVSPTPYRSTRYDGYG-----------PLNS 136

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 528312291  211 MGKLYIKHVNKSSPHQITST---IRVYFKPKHIKAWVPRPPR 249
Cdd:cd00205   137 FGTLVVRVLTPLTVPSGAPTtvdITVYVRAGDFELYGPRPPR 178
Dicipivirus_RdRp cd23222
RNA-dependent RNA polymerase (RdRp) in the genus Dicipivirus of positive-sense single-stranded ...
 1185-1370 3.75e-31

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: 128.55  E-value: 3.75e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1185 EPSVFHHVFEGNKEPAVLRNGDPRLKA--NFEEAIFSKYIGNVNTHVDEyMMEAVDHYAGQLATLdISTE---PMKLEDA 1259
Cdd:cd23222     1 KPSPVYGVYPVTKEPAPLKPTDRRIDEgvDFNEPVFGKYGADMKEPFRN-LDVGRDVVIARLKKV-LPNKkfaPCTVSEA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1260 VYGTEGLEALDLTTSAGYPYVALGIKKRDI--------LSKRTKDLTKLKECmDKYGLNLPMVTYVKDELRSAEKIAKGK 1331
Cdd:cd23222    79 LNGKDGLPKLDLKQASGYPYNLSAIKRKHLiesdkdgfLTATPKLLADIEES-KKHPEKFPYTSFLKDELRSVKKVKAGK 157

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 528312291 1332 SRLIEASSLNDSVAMRQTFGNLYKTFHLNPGIVTGSAVG 1370
Cdd:cd23222   158 TRVVEAGSLPVIVEGRMIFGNLFAYFNTHPGFETMAAVG 196
Pico_P2B pfam01552
Picornavirus 2B protein; Poliovirus infection leads to drastic alterations in membrane ...
 437-536 1.44e-29

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


Pssm-ID: 279840  Cd Length: 101  Bit Score: 113.58  E-value: 1.44e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291   437 QGVKDYVEQLGNAFGSGFTNQICEQVNVLKESLIGQDSILEKSLKALVKIISALVIVVRNHDDLVTITATLALIGCTSSP 516
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTQQISDKIKELTNFINPTSKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|
gi 528312291   517 WRWLKQKVSQYYGIPMAERQ 536
Cdd:pfam01552   81 WQFLKEKACAVLEIPYVHKQ 100
Mischivirus_RdRp cd23227
RNA-dependent RNA polymerase (RdRp) in the genus Mischivirus of positive-sense single-stranded ...
 1174-1370 1.71e-29

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: 123.90  E-value: 1.71e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1174 PVINTPSKTKLEPSVFHHVFEGNKEPAVLRNGDPRLK--ANFEEAIFSKYIGNVNTHVDEY--MMEavdHYAGQLAT-LD 1248
Cdd:cd23227    10 PRIHVPRKTKLRKSPAYPIFKPDAGPAVLSKNDPRLAegVDFDKQVFSKHSANQKEYPKAFrrMAR---WYADRVFTyLG 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1249 ISTEPMKLEDAVYGTEGLEALDLTTSAGYPYVALGIKKRDILSKRTKDLTK--LKECMDKYG----LNLPMVTYVKDELR 1322
Cdd:cd23227    87 KDNGPLSVKDAIKGIDNLDAMDPTTSPGLPYSAAGIKRTDLLDFDTGEIISpaLRAEYNKYVsgdySDHVFQTFLKDEIR 166

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 528312291 1323 SAEKIAKGKSRLIEASSLNDSVAMRQTFGNLYKTFHLNPGIVTGSAVG 1370
Cdd:cd23227   167 SEEKIKAGKTRIVDVPSLAHVIIGRVLLGKFCSKFQASPGTELGSAIG 214
Cardiovirus_RdRp cd23211
RNA-dependent RNA polymerase (RdRp) in the Cardiovirus genus of positive-sense single-stranded ...
 1174-1370 9.77e-29

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: 121.49  E-value: 9.77e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1174 PVINTPSKTKLEPSVFHHVFEGNKEPAVLRNGDPRLKANFEEAIFSKYIGNVNTHVDEYMMEAVDHYAGQLATLDISTEP 1253
Cdd:cd23211    10 PVVHVPRKTKLRRTVAHPVFQPKFEPAVLSKYDPRTDKDVDEVAFSKHTTNQESLPPVFRMVAKEYANRVFTLLGKDNGR 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1254 MKLEDAVYGTEGLEALDLTTSAGYPYVALGIKKRDILSKRTKDLTK-LKECMDKYGL----NLPMVTYVKDELRSAEKIA 1328
Cdd:cd23211    90 LTVEQAVLGLEGMDPMEKDTSPGLPYTQQGLRRTDVVDFETATMIPfLAEAHRKMVEgdysDVVYQSFLKDEIRPIEKVQ 169

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 528312291 1329 KGKSRLIEASSLNDSVAMRQTFGNLYKTFHLNPGIVTGSAVG 1370
Cdd:cd23211   170 AAKTRIVDVPPFEHCILGRQLLGRFASKFQTNPGLELGSAIG 211
Cosavirus_RdRp cd23226
RNA-dependent RNA polymerase (RdRp) in the genus Cosavirus of positive-sense single-stranded ...
 1174-1370 7.58e-25

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: 109.72  E-value: 7.58e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1174 PVINTPSKTKLEPSVFHHVFEGNKEPAVLRNGDPRLK--ANFEEAIFSKYIGNV----NTHVDEYMMEAVDHYAGQLATL 1247
Cdd:cd23226    10 PRVHVPRQSKLKRTNATYPATGKYGPAVLSKNDPRLDpdVDFDKVIFSKHVANVvideDTSFWNALKMSAQIYAEKFKGV 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1248 DIStePMKLEDAVYGTEGLEALDLTTSAGYPYVALGIKKRDILSKRTKDlTKLKECMDKYGLN----LPMVTYVKDELRS 1323
Cdd:cd23226    90 DFS--PLTVEEAILGIPGLDRMDPNTASGLPYTKTRRQMIDFQEGKILD-PELQERLDTWLSGkqpeMLYQTFLKDEIRP 166

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 528312291 1324 AEKIAKGKSRLIEASSLNDSVAMRQTFGNLYKTFHLNPGIVTGSAVG 1370
Cdd:cd23226   167 IEKVKAGKTRIIDVTPLDHVLAFRIVLGRFMAHFHNNYGFELGSAVG 213
Aphthovirus_RdRp cd23210
RNA-dependent RNA polymerase (RdRp) in the Aphthovirus genus of positive-sense single-stranded ...
 1176-1370 1.75e-24

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: 108.50  E-value: 1.75e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1176 INTPSKTKLEPSVFHHVFEGNKEPAVLRNGDPRLK--ANFEEAIFSKYIGNVNTHVDE--YMMEAVDHYAGQL-ATLDIS 1250
Cdd:cd23210     6 VHVMRKTKLAPTVAHGVFNPEFGPAALSNKDPRLNegVVLDEVIFSKHKGDTKMSAEDkaLFRRCAADYASRLhSVLGTA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1251 TEPMKLEDAVYGTEGLEALDLTTSAGYPYVALGIKKRDIL---SKRTKDLTKL-KECMDKYGLNLPMVTYVKDELRSAEK 1326
Cdd:cd23210    86 NAPLSIYEAIKGVDGLDAMEPDTAPGLPWALQGKRRGALIdfeNGTVGPEVEAaLKLMEKREYKFACQTFLKDEIRPMEK 165

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 528312291 1327 IAKGKSRLIEASSLNDSVAMRQTFGNLYKTFHLNPGIVTGSAVG 1370
Cdd:cd23210   166 VRAGKTRIVDVLPVEHILYTRMMIGRFCAQMHSNNGPQIGSAVG 209
Megrivirus_RdRp cd23223
RNA-dependent RNA polymerase (RdRp) in the genus Megrivirus of positive-sense single-stranded ...
 1190-1370 2.16e-20

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: 95.68  E-value: 2.16e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1190 HHVFEGNKEPAVLRNGDPRLK--ANFEEAIFSKYIGNVN--THVDEYMMEAVDHYAGQLATLDISTEPM-KLEDAVYGTE 1264
Cdd:cd23223     2 YGAFPVTHGPAALTNKDKRLEegVDLDDVMFSKHVPDHPgwPTLEPAMSYVVEDLMHKLGFSKDEPVPMwTLEQAINGEG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1265 GLEALDLTTSAGYPYVALGIKKRDILS------KRTKDLTKLKECMDKYGLNLPMVTYVKDELRSAEKIAKGKSRLIEAS 1338
Cdd:cd23223    82 VMDGIDMGQSPGYPYNAQGRSRRSFFEwngekwQPTEELKKEVDHALKDPDDFYFSTFLKDELRPLEKVKAGKTRLVDGD 161

                         170       180       190
                  ....*....|....*....|....*....|..
gi 528312291 1339 SLNDSVAMRQTFGNLYKTFHLNPGIVTGSAVG 1370
Cdd:cd23223   162 SLPRILAMRMVFGPLFEAMLRKNGPEIHSAVG 193
Teschovirus_RdRp cd23212
RNA-dependent RNA polymerase (RdRp) in the Teschovirus genus of positive-sense single-stranded ...
 1252-1370 2.71e-19

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: 91.22  E-value: 2.71e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1252 EPMKLEDAVYGTEGLEALDLTTSAGYPYVALGIKKRDILSKRTKDLTKLKECMDKY-GLNLP---MVTYVKDELRSAEKI 1327
Cdd:cd23212     9 EPLSVREAVEGIDGLDPMDMDKSPGLPYVKKGLRRTDLWNPKTGPSIELMAEINRYlDYNYDkhvFLTFLKDELRPKEKV 88

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 528312291 1328 AKGKSRLIEASSLNDSVAMRQTFGNLYKTFHLNPGIVTGSAVG 1370
Cdd:cd23212    89 QAGKTRVIDVAGFGHAIVGRMLFGRLFAFFHKNPGWNTGSAVG 131
Kobuvirus_RdRp cd23214
RNA-dependent RNA polymerase (RdRp) in the Kobuvirus genus of positive-sense single-stranded ...
 1174-1370 2.33e-18

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: 89.90  E-value: 2.33e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1174 PVINTPSKTKLEPSVFHHVFEGNKEPAVLRNGDPRLK--ANFEEAIFSKYIGNVNTHVDEYMMEAVDHYAGQLATLdIST 1251
Cdd:cd23214     1 PGVNVNRKSRLGPSPAYGAFPVKKQPAPLTQKDDRLEdgIRLDDQLFLKHNKGDMDEPWPGLEAAADLYFSKFPTM-IRT 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1252 epMKLEDAVYGTEGLEALDLTTSAGYPYVALGIKKRDILSKRTKDL----TKLKECMDKYGLNLPMV--TYVKDELRSAE 1325
Cdd:cd23214    80 --LTQEEAINGTPNLEGLDMNQAAGYPWNTMGRSRRSLFVEVQPGIyvpkPELQAEIDKTLEDPDYFysTFLKDELRPTA 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 528312291 1326 KIAKGKSRLIEASSLNDSVAMRQTFGNLYKTFHLNPGiVTGSAVG 1370
Cdd:cd23214   158 KVTLGLTRVVEAAPIHAIVAGRMLLGGLIEYMQARPG-KHGSAVG 201
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
 1185-1370 8.82e-17

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: 84.77  E-value: 8.82e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291  1185 EPSVFHHVFEGNKEPAVLRNGDPRLKANFEeaIFSKYIGNVN------THVDEYMME------AVDHYAGQLATLDISTE 1252
Cdd:pfam00680    1 SPTERHLVAIPAYVPASLGPEDPRWARSYL--NTDPYVDDIKkysrpkLPGPADERDkllnrsAAKMVLSELRGVPKKAN 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291  1253 PMKLEDAVY-GTEGLEALDLTTSAGYPYVALGIKKRDI---LSKRTKDLT---KLKECMDKYGLNLPMV----TYVKDEL 1321
Cdd:pfam00680   79 STLIVYRAIdGVEQIDPLNWDTSAGYPYVGLGGKKGDLiehLKDGTEARElaeRLAADWEVLQNGTPLKlvyqTCLKDEL 158

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 528312291  1322 RSAEKIAKGKSRLIEASSLNDSVAMRQTFGNLYKTFHLNPGIVTgSAVG 1370
Cdd:pfam00680  159 RPLEKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHP-IQVG 206
Rosavirus_RdRp cd23221
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Rosavirus of ...
 1259-1370 1.63e-16

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: 83.05  E-value: 1.63e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1259 AVYGTEGLEALDLTTSAGYPYVALGIKKRDILS-------KRTKDLTKLKECMDKYGLNlPMVTYVKDELRSAEKIAKGK 1331
Cdd:cd23221     1 AINGIDNMDGLDMNQSPGVPYVSEGVSRRSLFDcvdgqwvPRERLASDIAQVSGDPSLG-HFATFLKDELRSTEKVAAGK 79

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 528312291 1332 SRLIEASSLNDSVAMRQTFGNLYKTFHLNPGIVTGSAVG 1370
Cdd:cd23221    80 TRVVEAGSLPHIIVGRKIFGNLFALFNSNPGFQTMCAVG 118
Hepatovirus_RdRp cd23215
RNA-dependent RNA polymerase (RdRp) in the genus Hepatovirus of positive-sense single-stranded ...
 1249-1370 2.66e-16

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: 83.36  E-value: 2.66e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1249 ISTEPMKLEDAVYGTEGLEALDLTTSAGYPYVALGIKKRDI---------------LSKRTK-DLTKLKECMDkygLNLP 1312
Cdd:cd23215    60 LYDEFFDLEQAITGVPGMDAINMDSSPGYPYVQEKLTKSDLiwlddngellgmhprLAQRILfNLTMMDNGND---LDVV 136

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 528312291 1313 MVTYVKDELRSAEKIAKGKSRLIEASSLNDSVAMRQTFGNLYKTFHLNPGIVTGSAVG 1370
Cdd:cd23215   137 YTTCPKDELRPLEKVLESKTRAIDACPLDFTIICRMFWGPAISYFQLNPGFHTGVAVG 194
Parechovirus_RdRp cd23217
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Parechovirus of ...
 1259-1370 9.09e-16

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: 80.68  E-value: 9.09e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1259 AVYGTEGLEALDLTTSAGYPYVALGIKKRDILS-----------KRTKDLTKlkecmDKYGLNLP---MVTYVKDELRSA 1324
Cdd:cd23217     1 AVLGTSHLNSLDLSTSPGYKYVKSGYKKRDLLSlepfsvspqleKDVKDKLH-----AVYKGNQPttiFNACLKDELRKL 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 528312291 1325 EKIAKGKSRLIEASSLNDSVAMRQTFGNLYKTFHLNPGIVTGSAVG 1370
Cdd:cd23217    76 DKIAQGKTRCIEACSIDYVIAYRVVMSSLYEAIYQTPCQELGLAVG 121
P3A pfam08727
Poliovirus 3A protein like; This domain is found in positive-strand RNA viruses. The 3A ...
 866-926 1.68e-14

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.


Pssm-ID: 400873  Cd Length: 59  Bit Score: 69.38  E-value: 1.68e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 528312291   866 GPPVYREIKISVaPETPPPPAIADLLKSVDSEAVREYCKEKGWLVpEINSTLQIEKHVSRA 926
Cdd:pfam08727    1 AIFQGIDLKIDI-KTSPPPEAIADLLQAVDSPEIIDYCEDKGWIV-NIPAECQIERDIGIA 59
Mosavirus_RdRp cd23225
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Mosavirus of ...
 1267-1370 1.49e-13

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: 74.18  E-value: 1.49e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1267 EALDLTTSAGYPYVALGIKKRDILSKRTKD-------LTKLKECMDKY--GLNLP-MVTYVKDELRSAEKIAKGKSRLIE 1336
Cdd:cd23225    10 DAMDMTKAVGYPYCLDSIKRLDLVEIKETEngkvylpTERLVEETEKFftGEEKPkFVTFLKDEVRSNEKIKQGKTRIVD 89

                          90       100       110
                  ....*....|....*....|....*....|....
gi 528312291 1337 ASSLNDSVAMRQTFGNLYKTFHLNPGIVTGSAVG 1370
Cdd:cd23225    90 ASPFPYAIAGRMVMQNFMSNMMRCNGTEVGSAVG 123
Fipivirus_RdRp cd23229
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Fipivirus of ...
 1260-1370 6.72e-12

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: 6.72e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1260 VYGTEGLEALDLTTSAGYPYVALGIKKRDILS----KRTKDLTKLKECMDKY-------GLNLPMVTYV---KDELRSAE 1325
Cdd:cd23229     2 VEGIPGMEGLDMKTSAGYPWCEQNQKKKDKIKllagKNFLVRPLREVVHIVVdwyimppDMPKPEIKYVvylKDELLSSD 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 528312291 1326 KIAKGKSRLIEASSLNDSVAMRQTFGNLYKTFHL-NP--GIVTGSAVG 1370
Cdd:cd23229    82 KVKMGRTRWICAAPVQLVCAWKKVFGRAIAAIHLeSVtdGKSTGCAVG 129
Passerivirus_RdRp cd23224
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Passerivirus of ...
 1258-1370 1.35e-11

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: 68.19  E-value: 1.35e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1258 DAVYGTEGLEALDLTTSAGYPYvALGIKKRDILSK----RTKDLTKLKE----CMDKygLNLPMVTYVKDELRSAEKIAK 1329
Cdd:cd23224     1 EAINGTPLLDGLDMKQSPGYPW-SLTTNRRSLFTQdetgKYYPVPELEEavlaCLEN--PDYFYTTHLKDELRPVEKALA 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 528312291 1330 GKSRLIEASSLNDSVAMRQTFGNLYKTFHLNPGiVTGSAVG 1370
Cdd:cd23224    78 GKTRLIEAAPIHAIIAGRMLLGGLFEYMHARPG-EHGSAVG 117
ps-ssRNAv-Picornavirales cd23169
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of ...
 1314-1370 4.55e-10

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: 62.61  E-value: 4.55e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 528312291 1314 VTYVKDELRSAEKIAKGKSRLIEASSLNDSVAMRQTFGNLYKTFHLNPgIVTGSAVG 1370
Cdd:cd23169     4 VDCLKDELRPIEKVKAGKTRLFSASPLDYTIAFRKYFGDFIAAFQKNR-IKLEHAVG 59
Limnipivirus_RdRp cd23228
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Limnipivirus of ...
 1265-1370 1.02e-09

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: 62.20  E-value: 1.02e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1265 GLEALDLTTSAGYPYVALGIKKRD---ILSKRT--------KDLTKLKECMDKYGLNLPMVTYV-KDELRSAEKIAKGKS 1332
Cdd:cd23228     6 GTNPIDKNTSPGLKYTRDGLKKSDlytIDEDGNvvvsdmlrADVEAWEELIQSGGYPTTLFTAClKDELRSDEKVALGKT 85

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 528312291 1333 RLIEASSLNDSVAMRQTFGNLYKTFHLNPGIVTGSAVG 1370
Cdd:cd23228    86 RVIEAAELDYVVAYRMYMSSIYSDLYNAYAGDTGIAAG 123
Kunsagivirus_RdRp cd23219
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Kunsagivirus of ...
 1256-1370 1.12e-09

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: 1.12e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1256 LEDAVYGTegLEALDLTTSAGYPYValGIKKRD-------ILSKRTK-DLTKLKECMDKYGLN-LPMVTYVKDELRSAEK 1326
Cdd:cd23219     1 IEEAVFDT--VTPMDHTASAGPKYP--GTKRSElidfqnrIISDRLRnDVLELQFRGTSGGAGeVKFSSFLKDELRPLSK 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 528312291 1327 IAKGKSRLIEASSLNDSVAMRQTFGNLYKTFHLNPGIVTGSAVG 1370
Cdd:cd23219    77 IRSGDTRVVECSSLDYTVAFRMQFLRVLQMCYGSDPTLTGLAPG 120
RNA_dep_RNAP cd01699
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
 1301-1370 1.53e-09

RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage. RdRp catalyzes synthesis of the RNA strand complementary to a given RNA template. RdRps of many viruses are products of processing of polyproteins. Some RdRps consist of one polypeptide chain, and others are complexes of several subunits. The domain organization and the 3D structure of the catalytic center of a wide range of RdRps, including those with a low overall sequence homology, are conserved. The catalytic center is formed by several motifs containing a number of conserved amino acid residues. This subfamily represents the RNA-dependent RNA polymerases from all positive-strand RNA eukaryotic viruses with no DNA stage.


Pssm-ID: 238843 [Multi-domain]  Cd Length: 278  Bit Score: 60.76  E-value: 1.53e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1301 KECMDKYGLNLPMVTYVKDELRSAEKIAKGKSRLIEASSLNDSVAMRQTFGNLYKTFHLNpGIVTGSAVG 1370
Cdd:cd01699     8 LEDLPLIRPDLVFTTFLKDELRPLEKVEAGKTRLIQPRPLDYNIALRMYLGPFEAKLMKN-RGGLPIAVG 76
Crohivirus_RdRp cd23232
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Crohivirus of ...
 1256-1370 1.76e-09

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: 61.27  E-value: 1.76e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1256 LEDAVYGTEGLEALDLTTSAGYPYVALGIKKRDILSKRT--------KDLTKLKECMDKYG-LNLPMVTYVKDELRSAEK 1326
Cdd:cd23232     1 IEEACFEEGDEHALDLKTSPGFKYVQMGLKKTDLVNRPNkfihpilrNDVRLIFDEMAKGQmPVVTFTAHLKDELRKLEK 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 528312291 1327 IAKGKSRLIEASSLNDSVAMRQTFGNLYKTFHLNPGIVTGSAVG 1370
Cdd:cd23232    81 IRSGKTRCIEACDFDYTVAHKMMFGTLYKAIYDTPGIITGLAVG 124
Avisivirus_RdRp cd23231
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Avisivirus of ...
 1269-1363 4.72e-08

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: 56.82  E-value: 4.72e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1269 LDLTTSAGYPYValGIKKRDILS-----KRTKDLTKLKECMDKYGLNLPMVTYVKDELRSAEKIAKGKSRLIEASSLNDS 1343
Cdd:cd23231    11 IDWGTSPGDKYK--GKTKAQLVDdkkfkADVMNLVRFNGDPNREPPDVYFTTYLKDELRPKEKAKAGKTRVISAASFDYT 88

                          90       100
                  ....*....|....*....|....*..
gi 528312291 1344 VAMRQTFGNLYKTFHLN-------PGI 1363
Cdd:cd23231    89 IACRMVFGPILRQLFAWgrefgfgPGL 115
Aalivirus_RdRp cd23216
RNA-dependent RNA polymerase (RdRp) in the genus Aalivirus of positive-sense single-stranded ...
 1315-1370 4.77e-08

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: 56.60  E-value: 4.77e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 528312291 1315 TYVKDELRSAEKIAKGKSRLIEASSLNDSVAMRQTFGNLYKTFHLNPGIVTGSAVG 1370
Cdd:cd23216    53 TYLKDELRSIEKIANGNTRAIEAANFDHVVAWRQVMGNIVKQLFSDHDRVTGFAPG 108
Aquamavirus_RdRp cd23220
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Aquamavirus of ...
 1256-1341 2.80e-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: 44.70  E-value: 2.80e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 528312291 1256 LEDAVYGTEGLEALDLTTSAGYPyvalGIKKRDILSKRT----KDLTKLKECMDKYGLNLPMVTYVKDELRSAEKIAKGK 1331
Cdd:cd23220     1 LNEAINSSESPLNFNGTAGAKYP----GMNRRQLLLPLNpqvrDDVVKLAGDVGNGTATVVFETFMKDELRPKEKIESGK 76

                          90
                  ....*....|
gi 528312291 1332 SRLIEASSLN 1341
Cdd:cd23220    77 TRIVESCPLD 86
Caliciviridae_RdRp cd23192
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Caliciviridae of ...
 1318-1354 5.37e-04

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: 43.79  E-value: 5.37e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 528312291 1318 KDELRSAEKIAKGKSRLIEASSLNDSVAMRQTFGNLY 1354
Cdd:cd23192     8 KDELRPVEKIAEGKRRLLWGCDVGVTLVAAAAFGPVA 44
Dicistroviridae_RdRp cd23194
RNA-dependent RNA polymerase (RdRp) in the family Dicistroviridae of positive-sense ...
 1318-1351 1.25e-03

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: 42.49  E-value: 1.25e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 528312291 1318 KDELRSAEKIAKGKSRLIEASSLNDSVAMRQTFG 1351
Cdd:cd23194    13 KDERRPIEKVDAGKTRVFSAGPMDYTIAFRMYFL 46
 
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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