NCBI Conserved Domain Search

Conserved domains on [gi|130486|sp|P12916|]

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RecName: Full=Genome polyprotein; Contains: RecName: Full=P1; Contains: RecName: Full=Capsid protein VP0; AltName: Full=VP4-VP2; Contains: RecName: Full=Capsid protein VP4; AltName: Full=P1A; AltName: Full=Virion protein 4; Contains: RecName: Full=Capsid protein VP2; AltName: Full=P1B; AltName: Full=Virion protein 2; Contains: RecName: Full=Capsid protein VP3; AltName: Full=P1C; AltName: Full=Virion protein 3; Contains: RecName: Full=Capsid protein VP1; AltName: Full=P1D; AltName: Full=Virion protein 1; Contains: RecName: Full=P2; Contains: RecName: Full=Protease 2A; Short=P2A; AltName: Full=Picornain 2A; AltName: Full=Protein 2A; Contains: RecName: Full=Protein 2B; Short=P2B; Contains: RecName: Full=Protein 2C; Short=P2C; Contains: RecName: Full=P3; Contains: RecName: Full=Protein 3AB; Co

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 ...

1708-2157

0e+00

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: 829.09 E-value: 0e+00

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1708 ECGLPTIHTPSKTKLQPSVFYDVFPGSKEPAVSRDNDPRLKVNFKEALFSKYKGNTECSLNQHMEIAIAHYSAQLITLDI 1787
Cdd:cd23213    3 EVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATLDI 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1788 DSKPIALEDSVFGIEGLEALDLNTSAGFPYVTMGIKKRDLINNKTKDISRLKEALDKYGVDLPMITFLKDELRKKEKISA 1867
Cdd:cd23213   83 DTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKVEK 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1868 GKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPETFWSKIPVMLDGdCIMAFDYTNYDGSIHPVWFQAL 1947
Cdd:cd23213  163 GKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDG-SLFAFDYTGYDASLSPVWFRAL 241

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1948 KKVLE--NLSFQSNLIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKNIDLDKLKIIAYGDD 2025
Cdd:cd23213  242 KMVLEkgYSEEAVSLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYGDD 321

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   2026 VIFSYKYTLDMEAIANEGKKYGLTITPADKSTEFKKLDYNNVTFLKRGFKQDEKHTFLIHPTFPVEEIYESIRWTKKPSQ 2105
Cdd:cd23213  322 VIASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDPRN 401

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|..
gi 130486   2106 MQEHVLSLCHLMWHNGRKVYEDFSSKIRSVSAGRALYIPPYDLLKHEWYEKF 2157
Cdd:cd23213  402 TQDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453

Pico_P2A

pfam00947

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

873-998

1.74e-75

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

Pssm-ID: 395757 Cd Length: 127 Bit Score: 246.52 E-value: 1.74e-75

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486      873 NLHLFN-SEMHDSILVSYSSDLIIYRTNTTGDDYIPSCNCTEATYYCKHKNRYYPIKVTPHDWYEIQESEYYPKHIQYNL 951
Cdd:pfam00947    1 NRHLAThEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 130486      952 LIGEGPCEPGDCGGKLLCRHGVIGIITAGGEGHVAFTDLRQFQCAEE 998
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVRDLLWLEE 127

Rhv

pfam00073

picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...

93-300

4.38e-64

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: 215.64 E-value: 4.38e-64

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486       93 TSQDVANAVVGYGVWPHYLTPQDATAIDKPTQPDTSSNRFYTLESKHWNGDSKGW-WWKLPDALKEMGIFGENMYYHFLG 171
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFfWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486      172 RSGYTVHVQCNASKFHQGTLLVAMIPEHQlasakngsvtagynlTHPGEAgrvvgqqrdanlrqpsddswlnfdgTLLGN 251
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPPGA---------------PPPGSR-------------------------DYLWQ 120

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 130486      252 LLIFPHQFINLRSNNSATLIVPYVNAVPMDSMLRHNNWSLVIIPISPLR 300
Cdd:pfam00073  121 ATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGNWTLVVAGWVPLN 169

Peptidase_C3 super family

cl02893

3C cysteine protease (picornain 3C); Picornaviral proteins are expressed as a single ...

1515-1680

1.87e-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: 188.04 E-value: 1.87e-54

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486     1515 GPEEEFGRSILKNNTCVITTDNGKFTGL--GIYDRTLIIPTHADPGREVQVNGIHTKVLD-SYDLYNRDGVKLEITVIQL 1591
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486     1592 DRNEKFRDIRKYIPETEDDYPECNLALSANQVEPTIIKVGDVVSYGNI-LLSGNQTARMLKYNYPTKSGYCGGVLYKI-- 1668
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVVIAKve 160

                          170
                   ....*....|....
gi 130486     1669 --GQILGIHVGGNG 1680
Cdd:pfam00548  161 gnGKILGMHIAGNG 174

Rhv

pfam00073

picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...

360-525

2.93e-53

Pssm-ID: 395026 Cd Length: 170 Bit Score: 184.44 E-value: 2.93e-53

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486      360 YHPTKEISIPGEVKNLIEMCQVDTLIPVNNVGTNVGNISMYTVQLGNQMDMAQEVFAIKVDItsQPLATTLIGEIASYYT 439
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFFWWKLPL--ALLSMGLLGRLLRYHT 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486      440 HWTGSLRFSFMFCGTANTTLKLLLAYTPPGIDKPATR---KDAMLGTHVVWDVGLQSTISLVVPWVSASHFRLTANDK-- 514
Cdd:pfam00073   79 YYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRdylWQATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGnw 158

                          170
                   ....*....|..
gi 130486      515 -YSMAGYITCWY 525
Cdd:pfam00073  159 tLVVAGWVPLNY 170

Rhv

pfam00073

picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...

617-769

7.02e-50

Pssm-ID: 395026 Cd Length: 170 Bit Score: 174.81 E-value: 7.02e-50

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486      617 PEDAIETRYVMTSQTRDEMSIESFLGRSGCVH-----ISRIKVDYNDYNGVNKNFTTWKITL--QEMAQIRRKFELFTYV 689
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQpdvqgERFYTLDSTDWTSLSKGFFWWKLPLalLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486      690 RFDSEVTLVPCiagrGDDIGHVVMQYMYVPPGAPIPKTRnDFSWQSGTNMSIFWQHG-QPFPRFSLPFLSIASAYYMFYD 768
Cdd:pfam00073   81 RGGLEVTVQFN----GSKFHQGKLLVAYVPPGAPPPGSR-DYLWQATLNPHQFWNLGlNSSARLSVPYISIAHYYSTFYD 155


                   .
gi 130486      769 G 769
Cdd:pfam00073  156 G 156

Pico_P2B super family

cl03260

Picornavirus 2B protein; Poliovirus infection leads to drastic alterations in membrane ...

999-1095

2.21e-45

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: 159.42 E-value: 2.21e-45

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486      999 QGITDYIHMLGEAFGNGFV----DSVKEQINAINPINSISKKVIKWLLRIISAMVIIIRNSSDPQTIIATLTLIGCNGSP 1074
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTqqisDKIKELTNFINPTSKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|.
gi 130486     1075 WRFLKEKFCKWTQLTYIHKES 1095
Cdd:pfam01552   81 WQFLKEKACAVLEIPYVHKQG 101

Pico_P1A

pfam02226

Picornavirus coat protein (VP4); VP1, VP2, VP3 and VP4 for the basic unit that forms the ...

2-69

2.05e-41

Picornavirus coat protein (VP4); VP1, VP2, VP3 and VP4 for the basic unit that forms the icosahedral coat of picornaviruses. Five symmetry-related N termini of coat protein VP4 form a ten-stranded, antiparallel beta barrel around the base of the icosahedral fivefold axis.

Pssm-ID: 308053 Cd Length: 68 Bit Score: 146.75 E-value: 2.05e-41

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 130486        2 GAQVSRQNVGTHSTQNSVSNGSSLNYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 69
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 68

RNA_helicase

pfam00910

RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...

1214-1310

5.68e-40

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: 143.90 E-value: 5.68e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486     1214 VMIHGPPGTGKSITTNFLARMI-----TNESDVYSLPPDPKYFDGYDNQSVVIMDDIMQNPDGEDMTLFCQMVSSVTFIP 1288
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALlkklgLPKDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 130486     1289 PMADLPDKGKPFDSRFVLCSTN 1310
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

P3A super family

cl07374

Poliovirus 3A protein like; This domain is found in positive-strand RNA viruses. The 3A ...

1413-1465

3.36e-20

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: 85.94 E-value: 3.36e-20

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 130486     1413 AIFQG----PISLDAPPPPAIADLLQSVRTPEVIKYCQDNKWIV--PAECQIERDLSIA 1465
Cdd:pfam08727    1 AIFQGidlkIDIKTSPPPEAIADLLQAVDSPEIIDYCEDKGWIVniPAECQIERDIGIA 59

Name

Accession

Description

Interval

E-value

Enterovirus_RdRp

cd23213

RNA-dependent RNA polymerase (RdRp) in the Enterovirus genus of positive-sense single-stranded ...

1708-2157

0e+00

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: 829.09 E-value: 0e+00

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1708 ECGLPTIHTPSKTKLQPSVFYDVFPGSKEPAVSRDNDPRLKVNFKEALFSKYKGNTECSLNQHMEIAIAHYSAQLITLDI 1787
Cdd:cd23213    3 EVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATLDI 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1788 DSKPIALEDSVFGIEGLEALDLNTSAGFPYVTMGIKKRDLINNKTKDISRLKEALDKYGVDLPMITFLKDELRKKEKISA 1867
Cdd:cd23213   83 DTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKVEK 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1868 GKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPETFWSKIPVMLDGdCIMAFDYTNYDGSIHPVWFQAL 1947
Cdd:cd23213  163 GKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDG-SLFAFDYTGYDASLSPVWFRAL 241

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1948 KKVLE--NLSFQSNLIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKNIDLDKLKIIAYGDD 2025
Cdd:cd23213  242 KMVLEkgYSEEAVSLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYGDD 321

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   2026 VIFSYKYTLDMEAIANEGKKYGLTITPADKSTEFKKLDYNNVTFLKRGFKQDEKHTFLIHPTFPVEEIYESIRWTKKPSQ 2105
Cdd:cd23213  322 VIASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDPRN 401

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|..
gi 130486   2106 MQEHVLSLCHLMWHNGRKVYEDFSSKIRSVSAGRALYIPPYDLLKHEWYEKF 2157
Cdd:cd23213  402 TQDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453

Pico_P2A

pfam00947

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

873-998

1.74e-75

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

Pssm-ID: 395757 Cd Length: 127 Bit Score: 246.52 E-value: 1.74e-75

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486      873 NLHLFN-SEMHDSILVSYSSDLIIYRTNTTGDDYIPSCNCTEATYYCKHKNRYYPIKVTPHDWYEIQESEYYPKHIQYNL 951
Cdd:pfam00947    1 NRHLAThEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 130486      952 LIGEGPCEPGDCGGKLLCRHGVIGIITAGGEGHVAFTDLRQFQCAEE 998
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVRDLLWLEE 127

Rhv

pfam00073

picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...

93-300

4.38e-64

Pssm-ID: 395026 Cd Length: 170 Bit Score: 215.64 E-value: 4.38e-64

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486       93 TSQDVANAVVGYGVWPHYLTPQDATAIDKPTQPDTSSNRFYTLESKHWNGDSKGW-WWKLPDALKEMGIFGENMYYHFLG 171
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFfWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486      172 RSGYTVHVQCNASKFHQGTLLVAMIPEHQlasakngsvtagynlTHPGEAgrvvgqqrdanlrqpsddswlnfdgTLLGN 251
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPPGA---------------PPPGSR-------------------------DYLWQ 120

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 130486      252 LLIFPHQFINLRSNNSATLIVPYVNAVPMDSMLRHNNWSLVIIPISPLR 300
Cdd:pfam00073  121 ATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGNWTLVVAGWVPLN 169

Peptidase_C3

pfam00548

3C cysteine protease (picornain 3C); Picornaviral proteins are expressed as a single ...

1515-1680

1.87e-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: 188.04 E-value: 1.87e-54

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486     1515 GPEEEFGRSILKNNTCVITTDNGKFTGL--GIYDRTLIIPTHADPGREVQVNGIHTKVLD-SYDLYNRDGVKLEITVIQL 1591
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486     1592 DRNEKFRDIRKYIPETEDDYPECNLALSANQVEPTIIKVGDVVSYGNI-LLSGNQTARMLKYNYPTKSGYCGGVLYKI-- 1668
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVVIAKve 160

                          170
                   ....*....|....
gi 130486     1669 --GQILGIHVGGNG 1680
Cdd:pfam00548  161 gnGKILGMHIAGNG 174

Rhv

pfam00073

picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...

360-525

2.93e-53

Pssm-ID: 395026 Cd Length: 170 Bit Score: 184.44 E-value: 2.93e-53

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486      360 YHPTKEISIPGEVKNLIEMCQVDTLIPVNNVGTNVGNISMYTVQLGNQMDMAQEVFAIKVDItsQPLATTLIGEIASYYT 439
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFFWWKLPL--ALLSMGLLGRLLRYHT 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486      440 HWTGSLRFSFMFCGTANTTLKLLLAYTPPGIDKPATR---KDAMLGTHVVWDVGLQSTISLVVPWVSASHFRLTANDK-- 514
Cdd:pfam00073   79 YYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRdylWQATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGnw 158

                          170
                   ....*....|..
gi 130486      515 -YSMAGYITCWY 525
Cdd:pfam00073  159 tLVVAGWVPLNY 170

RdRP_1

pfam00680

Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...

1724-2134

1.43e-50

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: 186.85 E-value: 1.43e-50

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486     1724 PSVFYDVFPGSKEPAVSRDNDPRL--KVNFKEALF---SKYK-----GNTECSLNQHMEIAIAHYSAQLITLDIDSKPIA 1793
Cdd:pfam00680    2 PTERHLVAIPAYVPASLGPEDPRWarSYLNTDPYVddiKKYSrpklpGPADERDKLLNRSAAKMVLSELRGVPKKANSTL 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486     1794 LEDSVF-GIEGLEALDLNTSAGFPYVTMGIKKRDLIN----NKTKDI--SRLKEALDKY--GVDLPMI--TFLKDELRKK 1862
Cdd:pfam00680   82 IVYRAIdGVEQIDPLNWDTSAGYPYVGLGGKKGDLIEhlkdGTEARElaERLAADWEVLqnGTPLKLVyqTCLKDELRPL 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486     1863 EKISAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTgSAVGCDPetFWSKIPVMLD-----GDCIMAFDYTNYDG 1937
Cdd:pfam00680  162 EKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHP-IQVGINP--FDRGWPRLLRrlarfGDYVYELDYSGFDS 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486     1938 SIHPVWFQALKKVL-------ENLSFQSNLIDRLCYSKH-LFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAY 2009
Cdd:pfam00680  239 SVPPWLIRFAFEILrellgfpSNVKEWRAILELLIYTPIaLPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYALLKSL 318

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486     2010 KNIDL------DKLKIIAYGDDVIFSYKYTLD--MEAIANEGKKYGLTITPADKSTEFKKlDYNNVTFLKRGFKQDEkht 2081
Cdd:pfam00680  319 ENDGPrvcnldKYFDFFTYGDDSLVAVSPDFDpvLDRLSPHLKELGLTITPAKKTFPVSR-ELEEVSFLKRTFRKTP--- 394

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|...
gi 130486     2082 FLIHPTFPVEEIYESIRWTKKPSQMQEHVLSLCHLMWHNGRKVYEDFSSKIRS 2134
Cdd:pfam00680  395 GGYRPPLDRKRILAQLEYIRSKPVPSGQLENIRAYASHHGYEFYRDLLYRFVE 447

Rhv

pfam00073

picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...

617-769

7.02e-50

Pssm-ID: 395026 Cd Length: 170 Bit Score: 174.81 E-value: 7.02e-50

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486      617 PEDAIETRYVMTSQTRDEMSIESFLGRSGCVH-----ISRIKVDYNDYNGVNKNFTTWKITL--QEMAQIRRKFELFTYV 689
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQpdvqgERFYTLDSTDWTSLSKGFFWWKLPLalLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486      690 RFDSEVTLVPCiagrGDDIGHVVMQYMYVPPGAPIPKTRnDFSWQSGTNMSIFWQHG-QPFPRFSLPFLSIASAYYMFYD 768
Cdd:pfam00073   81 RGGLEVTVQFN----GSKFHQGKLLVAYVPPGAPPPGSR-DYLWQATLNPHQFWNLGlNSSARLSVPYISIAHYYSTFYD 155


                   .
gi 130486      769 G 769
Cdd:pfam00073  156 G 156

Pico_P2B

pfam01552

Picornavirus 2B protein; Poliovirus infection leads to drastic alterations in membrane ...

999-1095

2.21e-45

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: 159.42 E-value: 2.21e-45

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486      999 QGITDYIHMLGEAFGNGFV----DSVKEQINAINPINSISKKVIKWLLRIISAMVIIIRNSSDPQTIIATLTLIGCNGSP 1074
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTqqisDKIKELTNFINPTSKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|.
gi 130486     1075 WRFLKEKFCKWTQLTYIHKES 1095
Cdd:pfam01552   81 WQFLKEKACAVLEIPYVHKQG 101

rhv_like

cd00205

Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...

375-559

5.98e-43

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: 155.25 E-value: 5.98e-43

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486    375 LIEMCQVDTLIPVNNVGTNvgnismytvqlgnqmDMAQEVFAIKVDITSQPL--ATTLIGEIASYYTHWTGSLRFSFMFC 452
Cdd:cd00205    1 VESFADRPTTVGTNNWNSS---------------ASGTQLFQWKLSPALGFLllQNTPLGALLSYFTYWRGDLEVTVQFN 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486    453 GTANTTLKLLLAYTPPGIDKPA---TRKDAMLGTHVVWDVGLQSTISLVVPWVSASHFRLTANDKY---SMAGYITCWYQ 526
Cdd:cd00205   66 GSKFHTGRLLVAYVPPGAPAPTtgdTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDGYgplNSFGTLVVRVL 145

                        170       180       190
                 ....*....|....*....|....*....|...
gi 130486    527 TNLVVPPNTPQTADMLCFVSAcKDFCLRMARDT 559
Cdd:cd00205  146 TPLTVPSGAPTTVDITVYVRA-GDFELYGPRPP 177

Pico_P1A

pfam02226

Picornavirus coat protein (VP4); VP1, VP2, VP3 and VP4 for the basic unit that forms the ...

2-69

2.05e-41

Pssm-ID: 308053 Cd Length: 68 Bit Score: 146.75 E-value: 2.05e-41

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 130486        2 GAQVSRQNVGTHSTQNSVSNGSSLNYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 69
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 68

RNA_helicase

pfam00910

RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...

1214-1310

5.68e-40

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: 143.90 E-value: 5.68e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486     1214 VMIHGPPGTGKSITTNFLARMI-----TNESDVYSLPPDPKYFDGYDNQSVVIMDDIMQNPDGEDMTLFCQMVSSVTFIP 1288
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALlkklgLPKDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 130486     1289 PMADLPDKGKPFDSRFVLCSTN 1310
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

rhv_like

cd00205

Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...

125-329

6.06e-37

Pssm-ID: 119412 Cd Length: 178 Bit Score: 138.30 E-value: 6.06e-37

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486    125 PDTSSNRFYTLESKHWNG---DSKGWWWKLPDA----LKEMGIFGENMYYHFLGRSGYTVHVQCNASKFHQGTLLVAMIP 197
Cdd:cd00205    1 VESFADRPTTVGTNNWNSsasGTQLFQWKLSPAlgflLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486    198 EHQLASAKNGSvtagynlthpgeagrvvgqqrdanlrqpsddswlnfdgtlLGNLLIFPHQFINLRSNNSATLIVPYVNA 277
Cdd:cd00205   81 PGAPAPTTGDT----------------------------------------RWQATLNPHVIWDLGTNSSVTFVVPYVSP 120

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 130486    278 VPMDSMLRH------NNWSLVIIPISPLRSETTSSNIRPITVSISPMCAEFSGARAKN 329
Cdd:cd00205  121 TPYRSTRYDgygplnSFGTLVVRVLTPLTVPSGAPTTVDITVYVRAGDFELYGPRPPR 178

rhv_like

cd00205

Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...

637-825

3.07e-35

Pssm-ID: 119412 Cd Length: 178 Bit Score: 133.29 E-value: 3.07e-35

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486    637 IESFLGRSGCVHISRIKVDYNDyngvnKNFTTWKITLQE------MAQIRRKFELFTYVRFDSEVTLVPCiagrGDDIGH 710
Cdd:cd00205    1 VESFADRPTTVGTNNWNSSASG-----TQLFQWKLSPALgflllqNTPLGALLSYFTYWRGDLEVTVQFN----GSKFHT 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486    711 VVMQYMYVPPGAPIPKTrNDFSWQSGTNMSIFWQHG-QPFPRFSLPFLSIASAYYMFYDGYDgdnssskygsiVTNDMGT 789
Cdd:cd00205   72 GRLLVAYVPPGAPAPTT-GDTRWQATLNPHVIWDLGtNSSVTFVVPYVSPTPYRSTRYDGYG-----------PLNSFGT 139

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 130486    790 ICSRIVTEKQ---EHPVVITTHIYHKAKHTKAWCPRPPR 825
Cdd:cd00205  140 LVVRVLTPLTvpsGAPTTVDITVYVRAGDFELYGPRPPR 178

P3A

pfam08727

Poliovirus 3A protein like; This domain is found in positive-strand RNA viruses. The 3A ...

1413-1465

3.36e-20

Pssm-ID: 400873 Cd Length: 59 Bit Score: 85.94 E-value: 3.36e-20

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 130486     1413 AIFQG----PISLDAPPPPAIADLLQSVRTPEVIKYCQDNKWIV--PAECQIERDLSIA 1465
Cdd:pfam08727    1 AIFQGidlkIDIKTSPPPEAIADLLQAVDSPEIIDYCEDKGWIVniPAECQIERDIGIA 59

DEXXQc_SF1

cd18043

DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...

1213-1270

4.82e-04

DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are nucleic acid motor proteins that couple ATP hydrolysis to translocation along with the concomitant unwinding of DNA or RNA. This is central to many aspects of cellular DNA and RNA metabolism and accordingly, they are implicated in a wide range of nucleic acid processing events including DNA replication, recombination, and repair as well as many aspects of RNA metabolism. Superfamily 1 helicases are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

Pssm-ID: 350801 [Multi-domain] Cd Length: 127 Bit Score: 42.18 E-value: 4.82e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1213 AVMIHGPPGTGKS-----ITTNFLAR----------------------MITNESDVYSLPPDPKYFDgydnqsVVIMDDI 1265
Cdd:cd18043   16 NVVIQGPPGTGKSqtianIIANALARgkrvlfvsekkaaldvvrfpcwIMSPLSVSQYLPLNRNLFD------LVIFDEA 89


                 ....*
gi 130486   1266 MQNPD 1270
Cdd:cd18043   90 SQIPI 94

CDC6

COG1474

Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];

1214-1252

4.86e-03

Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];

Pssm-ID: 441083 [Multi-domain] Cd Length: 389 Bit Score: 41.76 E-value: 4.86e-03

                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 130486   1214 VMIHGPPGTGKSITTNFLARMITNESDVYSLPPDPKYFD 1252
Cdd:COG1474   54 VLIYGPTGTGKTAVAKYVLEELEEEAEERGVDVRVVYVN 92

Name

Accession

Description

Interval

E-value

Enterovirus_RdRp

cd23213

RNA-dependent RNA polymerase (RdRp) in the Enterovirus genus of positive-sense single-stranded ...

1708-2157

0e+00

Pssm-ID: 438063 Cd Length: 453 Bit Score: 829.09 E-value: 0e+00

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1708 ECGLPTIHTPSKTKLQPSVFYDVFPGSKEPAVSRDNDPRLKVNFKEALFSKYKGNTECSLNQHMEIAIAHYSAQLITLDI 1787
Cdd:cd23213    3 EVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATLDI 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1788 DSKPIALEDSVFGIEGLEALDLNTSAGFPYVTMGIKKRDLINNKTKDISRLKEALDKYGVDLPMITFLKDELRKKEKISA 1867
Cdd:cd23213   83 DTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKVEK 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1868 GKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPETFWSKIPVMLDGdCIMAFDYTNYDGSIHPVWFQAL 1947
Cdd:cd23213  163 GKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDG-SLFAFDYTGYDASLSPVWFRAL 241

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1948 KKVLE--NLSFQSNLIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKNIDLDKLKIIAYGDD 2025
Cdd:cd23213  242 KMVLEkgYSEEAVSLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYGDD 321

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   2026 VIFSYKYTLDMEAIANEGKKYGLTITPADKSTEFKKLDYNNVTFLKRGFKQDEKHTFLIHPTFPVEEIYESIRWTKKPSQ 2105
Cdd:cd23213  322 VIASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDPRN 401

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|..
gi 130486   2106 MQEHVLSLCHLMWHNGRKVYEDFSSKIRSVSAGRALYIPPYDLLKHEWYEKF 2157
Cdd:cd23213  402 TQDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453

Sapelovirus_RdRp

cd23218

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Sapelovirus of ...

1796-2157

1.00e-164

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: 509.83 E-value: 1.00e-164

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1796 DSVFGIEGLEALDLNTSAGFPYVTMGIKKRDLINNKTKDISRLKEALDKYGVDLPMITFLKDELRKKEKISAGKTRVIEA 1875
Cdd:cd23218    1 DVVYGIDNLEGLDLNTSAGYPYNTMGIRKKDLIPPRGEPLSPLLKALDLHGYDLPFTTYLKDELRPKEKVKMGKTRLIEC 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1876 SSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPETFWSKIPVMLDGDCIMAFDYTNYDGSIHPVWFQALKKVLENLS 1955
Cdd:cd23218   81 SSLNDTIRMKRIFGRLFQTFHKNPGTYTGSAVGCNPDVHWSKFAEEGGMDNVCAFDYTNWDASLSPFWFDALKLFLSKLG 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1956 FQSN---LIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKNIDLDKLKIIAYGDDVIFSYKY 2032
Cdd:cd23218  161 YSERdivLIDHLCYSNHIFKNEGYKVAGGMPSGCSGTSIFNSIINNIVVRTLVLLVYKGINLDELRILCYGDDLLVAYPY 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   2033 TLDMEAIANEGKKYGLTITPADKSTEF---KKLdyNNVTFLKRGFKQDEKHTFLIHPTFPVEEIYESIRWTKKPSQMQEH 2109
Cdd:cd23218  241 PLDPNVLADLGKSLGLTMTPADKSDTFqgcTKL--TEVTFLKRSFVFDEEFPFLCHPVFPMEEVHESIRWTRNASTTQEH 318

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*...
gi 130486   2110 VLSLCHLMWHNGRKVYEDFSSKIRSVSAGRALYIPPYDLLKHEWYEKF 2157
Cdd:cd23218  319 VTSLCLLAWHNGEEVYEEFCEKIRSVPVGRALILPPYSQLRRSWLDMF 366

Rabovirus_RdRp

cd23230

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Rabovirus of ...

1797-2157

1.13e-161

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: 501.34 E-value: 1.13e-161

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1797 SVFGIEGLEALDLNTSAGFPYVTMGIKKRDLINNKTKDISRLKEALDKYGVDLPMITFLKDELRKKEKISAGKTRVIEAS 1876
Cdd:cd23230    1 AAYGIENLEGLDLNTSAGYPYVLNGIKKRDILDPETRDTTKLQECLDKYGVDLPFVTYLKDELRPLEKIKKGKTRLIECS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1877 SINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPETFWSKIPVMLDGDcIMAFDYTNYDGSIHPVWFQALKKVLENLSF 1956
Cdd:cd23230   81 SMNDTIRMKMMFGRLFATYHRNPGPITGSAVGCNPDIHWTKFRAEMHGE-IIAFDYSNYDASLNKVWFECLKMVLKNFGF 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1957 QS-NLIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKNIDLDKLKIIAYGDDVIFSYKYTLD 2035
Cdd:cd23230  160 KDlRPIDHIIRSRHIYKGIEYDVEGGMPSGCSGTSIFNSIINNIIIMTLVLDAYKGIDLEQLKIIAYGDDVIVTYPYPLD 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   2036 MEAIANEGKKYGLTITPADKSTEFKKLDYNNVTFLKRGFKQDEKHTFLIHPTFPVEEIYESIRWTKKPSQMQEHVLSLCH 2115
Cdd:cd23230  240 AALLADCGKKYGLKMTPPDKSAEFKNVTWEDVTFLKRRFKPAKHYPFLIHPVFDQQEILESLRWTRNPAHTQEHVRSLAE 319

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|..
gi 130486   2116 LMWHNGRKVYEDFSSKIRSVSAGRALYIPPYDLLKHEWYEKF 2157
Cdd:cd23230  320 LAWHSGRKSYEEFCNLVKSTNVGKACILPPYESFKRMWLDQF 361

ps-ssRNA_Picornaviridae

cd23193

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Picornaviridae of ...

1798-2133

1.51e-138

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: 436.21 E-value: 1.51e-138

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1798 VFGIEGLEALDLNTSAGFPYVTMGIKKRDLINNKTKDIS-----RLKEALDKYGVDLPMITFLKDELRKKEKISAGKTRV 1872
Cdd:cd23193    2 INGIDGLDPIDLNTSPGYPYTTQGLRRRDLIDNDKGGVSplleeEEQVLLDLDGPDVVFTTFLKDELRPKEKVKAGKTRV 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1873 IEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPETFWSKIPVMLDGDCIMAFDYTNYDGSIHPVWFQALKKVLE 1952
Cdd:cd23193   82 IEAAPLDYVIAGRMVFGRLFAQFHSNPGILTGSAVGCNPDTDWTRLFASLKQDNVYDLDYSGFDASLSSQLFEAAVEVLA 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1953 NLS----FQSNLIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKnIDLDKLKIIAYGDDVIF 2028
Cdd:cd23193  162 ECHgdpeLVLRYLEPIINSKHVVGDERYTVEGGMPSGCPCTSILNSICNNLVVRYALLETGK-FDPDEYYILAYGDDVLV 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   2029 SYKYTLDMEAIANEGKKY-GLTITPADKSTEFKKLDYNNVTFLKRGFKQDEkHTFLIHPTFPVEEIYESIRWTKKPSQMQ 2107
Cdd:cd23193  241 STDEPIDPSDLAEFYKKYfGMTVTPADKSSDFPESSPIEDVFLKRRFFVPD-GTFLIHPVMDLETLEQSLMWCGRGGFFQ 319

                        330       340
                 ....*....|....*....|....*.
gi 130486   2108 EHVLSLCHLMWHNGRKVYEDFSSKIR 2133
Cdd:cd23193  320 QLLSSLCELALHHGPEEYERLVSKVR 345

Mischivirus_RdRp

cd23227

RNA-dependent RNA polymerase (RdRp) in the genus Mischivirus of positive-sense single-stranded ...

1712-2157

3.45e-82

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: 279.14 E-value: 3.45e-82

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1712 PTIHTPSKTKLQPSVFYDVFPGSKEPAVSRDNDPRLK--VNFKEALFSKYKGNtECSLNQHMEIAIAHYSAQLIT-LDID 1788
Cdd:cd23227   10 PRIHVPRKTKLRKSPAYPIFKPDAGPAVLSKNDPRLAegVDFDKQVFSKHSAN-QKEYPKAFRRMARWYADRVFTyLGKD 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1789 SKPIALEDSVFGIEGLEALDLNTSAGFPYVTMGIKKRDLINNKTKDISR--LKEALDKYG----VDLPMITFLKDELRKK 1862
Cdd:cd23227   89 NGPLSVKDAIKGIDNLDAMDPTTSPGLPYSAAGIKRTDLLDFDTGEIISpaLRAEYNKYVsgdySDHVFQTFLKDEIRSE 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1863 EKISAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPETFWSKIPVML-DGDCIMAFDYTNYDGSIHP 1941
Cdd:cd23227  169 EKIKAGKTRIVDVPSLAHVIIGRVLLGKFCSKFQASPGTELGSAIGCNPDWDWTYFAHQLmERQWCYDIDYSNFDSTHGT 248

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1942 VWFQALKKVL---ENlSFQSNLID---RLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKNIDLD 2015
Cdd:cd23227  249 GMFELLIDCFftpEN-GFSPAVAPylrSLAFSKHAWMDKRYKIEGGLPSGCSATSVLNTVMNNIIIRALLSLTYKNFHPE 327

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   2016 KLKIIAYGDDVIFSYKYTLD---MEAIANEGKKYGLTItpADKSTEFKKLD-YNNVTFLKRGFKQDEKHTFLIHPTFPVE 2091
Cdd:cd23227  328 DVLVLAYGDDLLVASDYQLDfnrVREKAAEHTLYKLTT--ANKAPDFPETStLLDCQFLKRKFVLHSTRNFIWRPVMDVT 405

                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 130486   2092 EIyESIRWTKKPSQMQEHVLSLCHLMWHNGRKVYEDFSSKIRSVSagraLYIPPYDLLKHEWYEKF 2157
Cdd:cd23227  406 NL-KTMLSFYKPNTLSEKLLSVAQLAFHSGYTVYEELFAPFKELQ----MTVPSWWYLEHEWEHNF 466

Cardiovirus_RdRp

cd23211

RNA-dependent RNA polymerase (RdRp) in the Cardiovirus genus of positive-sense single-stranded ...

1712-2157

7.68e-82

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: 278.26 E-value: 7.68e-82

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1712 PTIHTPSKTKLQPSVFYDVFPGSKEPAVSRDNDPRLKVNFKEALFSKYKGNTEcSLNQHMEIAIAHYSAQLIT-LDIDSK 1790
Cdd:cd23211   10 PVVHVPRKTKLRRTVAHPVFQPKFEPAVLSKYDPRTDKDVDEVAFSKHTTNQE-SLPPVFRMVAKEYANRVFTlLGKDNG 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1791 PIALEDSVFGIEGLEALDLNTSAGFPYVTMGIKKRDLINNKTKD-ISRLKEALDKYGV----DLPMITFLKDELRKKEKI 1865
Cdd:cd23211   89 RLTVEQAVLGLEGMDPMEKDTSPGLPYTQQGLRRTDVVDFETATmIPFLAEAHRKMVEgdysDVVYQSFLKDEIRPIEKV 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1866 SAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPETFWSKIPVMLDG-DCIMAFDYTNYDGSIHPVWF 1944
Cdd:cd23211  169 QAAKTRIVDVPPFEHCILGRQLLGRFASKFQTNPGLELGSAIGCDPDVDWTAFAVALSGfKYVYDVDYSNFDSTHSTAMF 248

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1945 QALkkvLENLSFQSNLIDR--------LCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKNIDLDK 2016
Cdd:cd23211  249 ELL---IENFFTEENGFDPrigeylrsLAVSRHAYEERRVLIRGGLPSGCAATSMLNTIMNNIIIRAGLYLTYKNFEFDD 325

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   2017 LKIIAYGDDVIFSYKYTLDMEAIANEGKKYGLTITPADKSTEFKKLDY-NNVTFLKRGFKQDEkhTFLIHPTFPvEEIYE 2095
Cdd:cd23211  326 IKVLSYGDDLLVATNYQIDFNLVKARLAKFGYKITPANKTSTFPLTSTlEDVVFLKRKFVKEN--SYLYRPVMD-RENLK 402

                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 130486   2096 SIRWTKKPSQMQEHVLSLCHLMWHNGRKVYEDFSSKIRSVsagrALYIPPYDLLKHEWYEKF 2157
Cdd:cd23211  403 AMLSYYRPGTLKEKLTSIALLAVHSGKQVYDEIFAPFREV----GIVVPTYESVLYRWLSLF 460

Cosavirus_RdRp

cd23226

RNA-dependent RNA polymerase (RdRp) in the genus Cosavirus of positive-sense single-stranded ...

1712-2157

2.25e-81

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: 276.90 E-value: 2.25e-81

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1712 PTIHTPSKTKLQ-PSVFYDVFPgSKEPAVSRDNDPRLK--VNFKEALFSKYKGNTECSLNQHMEIAIAhYSAQLIT---L 1785
Cdd:cd23226   10 PRVHVPRQSKLKrTNATYPATG-KYGPAVLSKNDPRLDpdVDFDKVIFSKHVANVVIDEDTSFWNALK-MSAQIYAekfK 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1786 DIDSKPIALEDSVFGIEGLEALDLNTSAGFPYVTMgikKRDLINNKTKDI------SRLKEALDKYGVDLPMITFLKDEL 1859
Cdd:cd23226   88 GVDFSPLTVEEAILGIPGLDRMDPNTASGLPYTKT---RRQMIDFQEGKIldpelqERLDTWLSGKQPEMLYQTFLKDEI 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1860 RKKEKISAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPETFWSKIPVMLDG-DCIMAFDYTNYDGS 1938
Cdd:cd23226  165 RPIEKVKAGKTRIIDVTPLDHVLAFRIVLGRFMAHFHNNYGFELGSAVGCDPDVAWANFGFALSSkKYQYDFDYSNFDAS 244

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1939 IHPVWFQALKKVL--ENLSFQ---SNLIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKNID 2013
Cdd:cd23226  245 HSESIFELLKQFVftKDNGFDhrcSLMIDSLVTSTHCYEDQRMTIRGGLPSGTSGTSVINTIINNIIFKAALYHTYSNFE 324

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   2014 LDKLKIIAYGDDVIFSYKYTLDMEAIANEGKKYGLTITPADKSTEFKKLDYNNVTFLKRGFKqdeKHTFLIHPTFPVEEI 2093
Cdd:cd23226  325 WDDVQMLAYGDDIVAASDCLLDLDRVKYFMALIGYKITPADKGEKFIPKDMQNIQFLKRSFR---KVAGVWAPIMDLENL 401

                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 130486   2094 YESIRWTkKPSQMQEHVLSLCHLMWHNGRKVYEdfssKIRSVSAGRALYIPPYDLLKHEWYEKF 2157
Cdd:cd23226  402 QAMLSWY-KPGTLQEKLDSVARLAHFCGEKVYD----HLFTTFVKDGFQIKPWKQLHFEWLNRF 460

Dicipivirus_RdRp

cd23222

RNA-dependent RNA polymerase (RdRp) in the genus Dicipivirus of positive-sense single-stranded ...

1723-2153

3.78e-79

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: 269.92 E-value: 3.78e-79

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1723 QPSVFYDVFPGSKEPAVSRDNDPRLK--VNFKEALFSKYKGNTEC---SLNQHMEIAIAHYSAQLITldiDSKPIAL-ED 1796
Cdd:cd23222    1 KPSPVYGVYPVTKEPAPLKPTDRRIDegVDFNEPVFGKYGADMKEpfrNLDVGRDVVIARLKKVLPN---KKFAPCTvSE 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1797 SVFGIEGLEALDLNTSAGFPYVTMGIKKRDLINN--------KTKDISRLKEAlDKYGVDLPMITFLKDELRKKEKISAG 1868
Cdd:cd23222   78 ALNGKDGLPKLDLKQASGYPYNLSAIKRKHLIESdkdgfltaTPKLLADIEES-KKHPEKFPYTSFLKDELRSVKKVKAG 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1869 KTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPETFWSKI-PVMLDGDCIMAFDYTNYDGSIHPVWFQAL 1947
Cdd:cd23222  157 KTRVVEAGSLPVIVEGRMIFGNLFAYFNTHPGFETMAAVGCDPEVCWTDWyYKMREKAHTWDYDYTGFDGSIPSCSFDAL 236

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1948 KKVL----ENLSFQSNLIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKNIDLDKLKIIAYG 2023
Cdd:cd23222  237 ADLLcefvENEDDVRRYISNIKNSYHAYDGNLYLIEGAMPSGCAGTSVFNCLINAMLCFSCFMDLEPEMDPFEPLLIAYG 316

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   2024 DDVIFSYKYTLDMEAIANEGKK-YGLTITPADKSTEFK-KLDYNNVTFLKRGFKQDEKHTfLIHPTFPVEEIYESIRWTK 2101
Cdd:cd23222  317 DDILVSSDHDLFPSRVSEWMKAnTTFKITPADKGEIFNdDSDVSDVRFLKRLFVEDPVCE-LIHPVIETETLEPSLNWCH 395

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 130486   2102 KpSQMQEHVLSLCHLMWHNGRKVYEDFSSKIRSVSAGRALYIP---PYDLLKHEW 2153
Cdd:cd23222  396 E-GEFETKVDAISMLAFHHGPEYYRDWCKKLTDICEERNISPPglkPYSVHRNRW 449

Pico_P2A

pfam00947

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

873-998

1.74e-75

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

Pssm-ID: 395757 Cd Length: 127 Bit Score: 246.52 E-value: 1.74e-75

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486      873 NLHLFN-SEMHDSILVSYSSDLIIYRTNTTGDDYIPSCNCTEATYYCKHKNRYYPIKVTPHDWYEIQESEYYPKHIQYNL 951
Cdd:pfam00947    1 NRHLAThEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 130486      952 LIGEGPCEPGDCGGKLLCRHGVIGIITAGGEGHVAFTDLRQFQCAEE 998
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVRDLLWLEE 127

Megrivirus_RdRp

cd23223

RNA-dependent RNA polymerase (RdRp) in the genus Megrivirus of positive-sense single-stranded ...

1728-2132

2.33e-73

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: 252.46 E-value: 2.33e-73

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1728 YDVFPGSKEPAVSRDNDPRLK--VNFKEALFSKYKGNTEC--SLNQHMEIAIAHYSAQLITLDIDSKPI-ALEDSVFGIE 1802
Cdd:cd23223    2 YGAFPVTHGPAALTNKDKRLEegVDLDDVMFSKHVPDHPGwpTLEPAMSYVVEDLMHKLGFSKDEPVPMwTLEQAINGEG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1803 GLEALDLNTSAGFPYVTMGIKKR---DLINNKTKDISRLKEALD---KYGVDLPMITFLKDELRKKEKISAGKTRVIEAS 1876
Cdd:cd23223   82 VMDGIDMGQSPGYPYNAQGRSRRsffEWNGEKWQPTEELKKEVDhalKDPDDFYFSTFLKDELRPLEKVKAGKTRLVDGD 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1877 SINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPETFWSKIPVMLDGDC---IMAFDYTNYDGSIHPVWFQALKKVLEN 1953
Cdd:cd23223  162 SLPRILAMRMVFGPLFEAMLRKNGPEIHSAVGCNPDTDWTRYYHEMGPDSfpyCFDLDYSCFDSTEPKIAFRLMAKYLKP 241

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1954 LsFQSNL---IDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAykNIDLDKLKIIAYGDDVIFSY 2030
Cdd:cd23223  242 Y-FSVDVtpfFEALATSKHVYGDKAYEMEGGMPSGCVGTSMFNCINNSAFIVSALIAL--KISPEDCAWICYGDDVIIST 318

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   2031 KYTLDMEAIAN-EGKKYGLTITPADKSTEFKKLD-YNNVTFLKRGFKQDEKHTFLIHPTFPVEEIYESIRW-TKKPsqMQ 2107
Cdd:cd23223  319 DEKALSKRIADfYHKNTNLVVTPASKSGDFPETStIYDVTFLKRFFQPDSHYPHLIHPYMPLEHLEQSVMWqTDGP--FQ 396

                        410       420
                 ....*....|....*....|....*
gi 130486   2108 EHVLSLCHLMWHNGRKVYEDFSSKI 2132
Cdd:cd23223  397 QKLDSLCLLAFHAGGPDYREFVDAI 421

Aphthovirus_RdRp

cd23210

RNA-dependent RNA polymerase (RdRp) in the Aphthovirus genus of positive-sense single-stranded ...

1714-2156

1.48e-71

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: 248.32 E-value: 1.48e-71

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1714 IHTPSKTKLQPSVFYDVFPGSKEPAVSRDNDPRLK--VNFKEALFSKYKGNTECSL-NQHMEIAIAHYSAQLI--TLDID 1788
Cdd:cd23210    6 VHVMRKTKLAPTVAHGVFNPEFGPAALSNKDPRLNegVVLDEVIFSKHKGDTKMSAeDKALFRRCAADYASRLhsVLGTA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1789 SKPIALEDSVFGIEGLEALDLNTSAGFPYVTMGIKKRDLI---NNKTKDISRL-KEALDKYGVDLPMITFLKDELRKKEK 1864
Cdd:cd23210   86 NAPLSIYEAIKGVDGLDAMEPDTAPGLPWALQGKRRGALIdfeNGTVGPEVEAaLKLMEKREYKFACQTFLKDEIRPMEK 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1865 ISAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPETFWSKIPVMLDG-DCIMAFDYTNYDGSiHPVw 1943
Cdd:cd23210  166 VRAGKTRIVDVLPVEHILYTRMMIGRFCAQMHSNNGPQIGSAVGCNPDVDWQRFGTHFAQyRNVWDVDYSAFDAN-HCS- 243

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1944 fQALKKVLE-----NLSFQSN---LIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKNIDLD 2015
Cdd:cd23210  244 -DAMNIMFEevfrtEFGFHPNaewILKTLVNTEHAYENKRITVEGGMPSGCSATSIINTILNNIYVLYALRRHYEGVELD 322

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   2016 KLKIIAYGDDVIFSYKYTLDMEAIANEGKKYGLTITPADKSTEFKKLDY--NNVTFLKRGFKQDEKHTFLiHPTFPVEEI 2093
Cdd:cd23210  323 TYTMISYGDDIVVASDYDLDFEALKPHFKSLGQTITPADKSDKGFVLGHsiTDVTFLKRHFHMDYGTGFY-KPVMASKTL 401

                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 130486   2094 yESIRWTKKPSQMQEHVLSLCHLMWHNG----RKVYEDFSSkirsvsagrALYIPPYDLLKHEWYEK 2156
Cdd:cd23210  402 -EAILSFARRGTIQEKLISVAGLAVHSGpdeyRRLFEPFQG---------LFEIPSYRSLYLRWVNA 458

Rosavirus_RdRp

cd23221

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Rosavirus of ...

1800-2157

3.49e-70

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: 241.36 E-value: 3.49e-70

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1800 GIEGLEALDLNTSAGFPYVTMGIKKR---DLINNKTKDISRLKEALDKYGVDLPM---ITFLKDELRKKEKISAGKTRVI 1873
Cdd:cd23221    4 GIDNMDGLDMNQSPGVPYVSEGVSRRslfDCVDGQWVPRERLASDIAQVSGDPSLghfATFLKDELRSTEKVAAGKTRVV 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1874 EASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPETFWSKIPVMLDGDC-IMAFDYTNYDGSIHPVWFQALKKVLE 1952
Cdd:cd23221   84 EAGSLPHIIVGRKIFGNLFALFNSNPGFQTMCAVGCDPDVTWTELYHPLSAKTyVFDYDYSGFDGSVPSCCFDALADLLA 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1953 NLSFQSN----LIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKNIDLDKLKIIAYGDDVIF 2028
Cdd:cd23221  164 DFVEGEEdvrkYISSLKTSFHHYKGKLWRLDGAMPSGCCGTSVFNSLINAMLLFSAFSQICPDFRASEPLLVAYGDDVLV 243

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   2029 SYKYTLDMEAIAN-EGKKYGLTITPADKSTEFK-KLDYNNVTFLKRGFKQDEKHTFLIHPTFPVEEIYESIRWtKKPSQM 2106
Cdd:cd23221  244 GTDQPLFPSKVAEwVNSHTTFRITPADKGSVFNdESDIHSVQFLKRHFTPDPDFPALIHPTIDPDTYEQSVMW-QRTGDF 322

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....
gi 130486   2107 QEHVLSLCHLMWHNGRKVYEDFSSKI--RSVSAGRAL-YIPPYDLLKHEWYEKF 2157
Cdd:cd23221  323 QETVNSLALLVFHRGPKSYSRWCESVtrKCVDGGYPPpFFPPFSLLRHQWLKKF 376

ps-ssRNAv-Picornavirales

cd23169

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of ...

1852-2133

6.35e-70

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: 237.88 E-value: 6.35e-70

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1852 ITFLKDELRKKEKISAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPGvVTGSAVGCDPE-TFWSKIPVML--DGDCIM 1928
Cdd:cd23169    4 VDCLKDELRPIEKVKAGKTRLFSASPLDYTIAFRKYFGDFIAAFQKNRI-KLEHAVGINPDsVEWTRLYRRLlkKGPNIF 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1929 AFDYTNYDGSIHPVWFQALKKVL----------ENLSFQSNLIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINN 1998
Cdd:cd23169   83 AGDYSNFDGSLPPDVMEAAFDIIndwydeyvddEDERVRKVLFEELINTIHLVGNLVYQVHGGNPSGNPLTTIINSIVNL 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1999 IIIRTLVLDAYKNIDLDK----LKIIAYGDDVIFS----YKYTLDMEAIANEGKKYGLTITPADKSTEFKKLD-YNNVTF 2069
Cdd:cd23169  163 LYIRYAWLRITGLTSLSDfkknVRLVTYGDDVIISvsdeVKDEFNFVTISEFLKELGITYTDADKSGDIVPYRpLEEVTF 242

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 130486   2070 LKRGFKQDEKHtFLIHPTFPVEEIYESIRWTKKPSQMQE---HVLSLCHLMWH-NGRKVYEDFSSKIR 2133
Cdd:cd23169  243 LKRGFRPHPTP-GLVLAPLDLESIEEQLNWTRKEDDLLEatiENARAALLLAFgHGPEYYNKFRQKLN 309

Mosavirus_RdRp

cd23225

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Mosavirus of ...

1805-2156

1.48e-68

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: 236.73 E-value: 1.48e-68

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1805 EALDLNTSAGFPYVTMGIKKRDLINNKTKD-------ISRLKEALDKY--GVDLP-MITFLKDELRKKEKISAGKTRVIE 1874
Cdd:cd23225   10 DAMDMTKAVGYPYCLDSIKRLDLVEIKETEngkvylpTERLVEETEKFftGEEKPkFVTFLKDEVRSNEKIKQGKTRIVD 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1875 ASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPETFWSKIPVMLDGDCIMAFDYTNYDgSIHP-VWFQALKK--VL 1951
Cdd:cd23225   90 ASPFPYAIAGRMVMQNFMSNMMRCNGTEVGSAVGCDPDTEWTRYFFELCDRYVFDLDYKAFD-STHPtAMFNLLAErfFT 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1952 ENLSFQSN----LIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYK--NIDLDKLKIIAYGDD 2025
Cdd:cd23225  169 ERNGFDQQavriFLNGLSDSDHVYEGKHFRIRGGLPSGCPCTSILNTVINNIIVRAAILGAYQidTVDFQKFRMLAYGDD 248

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   2026 VIFSYKYTL---DMEAIANEGKKYglTITPADKSTEF-KKLDYNNVTFLKRGFKQDEKHTFLIHPTFPVEEIYESIRWTk 2101
Cdd:cd23225  249 VVYATPQPIkpqDLADWLHANTNY--KVTPASKAGTFpEESTIWDVTFLKRSFKPDEDHGHLIRPVMAVGNLKQMLSFM- 325

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 130486   2102 KPSQMQEHVLSLCHLMWHNGRKVYEDFSSKIRSVSAGRAlyIPPYDLLKHEWYEK 2156
Cdd:cd23225  326 RPGTFPDKVRSVAGLAVHCGEEDYNQLADAVALYVPGVS--MPAYKYMKACWYAK 378

Kobuvirus_RdRp

cd23214

RNA-dependent RNA polymerase (RdRp) in the Kobuvirus genus of positive-sense single-stranded ...

1712-2153

1.88e-65

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: 230.50 E-value: 1.88e-65

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1712 PTIHTPSKTKLQPSVFYDVFPGSKEPAVSRDNDPRLK--VNFKEALFSKYKGNTECSLNQHMEIAIAHYSAQLITLdidS 1789
Cdd:cd23214    1 PGVNVNRKSRLGPSPAYGAFPVKKQPAPLTQKDDRLEdgIRLDDQLFLKHNKGDMDEPWPGLEAAADLYFSKFPTM---I 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1790 KPIALEDSVFGIEGLEALDLNTSAGFPYVTMGIKKRDLINNKTKDI----SRLKEALDKYGVDLPMI--TFLKDELRKKE 1863
Cdd:cd23214   78 RTLTQEEAINGTPNLEGLDMNQAAGYPWNTMGRSRRSLFVEVQPGIyvpkPELQAEIDKTLEDPDYFysTFLKDELRPTA 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1864 KISAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVvTGSAVGCDPETFWSKIPVML-DGDCIMAFDYTNYDGSIHPV 1942
Cdd:cd23214  158 KVTLGLTRVVEAAPIHAIVAGRMLLGGLIEYMQARPGK-HGSAVGCNPDLHWTKFFYKFcHYPQVFDLDYKCFDATLPSC 236

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1943 WFQALKKVLENLSFQ---SNLIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTlVLDAYKNIDLDKLKI 2019
Cdd:cd23214  237 AFRIVEDHLERLTGDervTRYIESIRHSHHVYGNETYEMIGGNPSGCVGTSIINTIINNICVLS-ALIQHPDFSPESFRI 315

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   2020 IAYGDDVIFSYKYTLDMEAIANEGKKYG-LTITPADKSTEFKKLD-YNNVTFLKRGFKQDEKHTFLIHPTFPVEEIYESI 2097
Cdd:cd23214  316 LAYGDDVIYGCDPPIHPSFIKEFYDKHTpLVVTPANKGSDFPETStIYDVTFLKRWFVPDDIRPFYIHPVMDPDTYEQSV 395

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 130486   2098 RWTKKpSQMQEHVLSLCHLMWHNGRKVYEDFSSKIRSVSAGRALYIP---PYDLLKHEW 2153
Cdd:cd23214  396 MWLRD-GDFQDLVTSLCYLAFHSGPKTYDRWCTRVRDQVMKTTGFPPtflPYSYLQTRW 453

Teschovirus_RdRp

cd23212

RNA-dependent RNA polymerase (RdRp) in the Teschovirus genus of positive-sense single-stranded ...

1790-2126

9.10e-65

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: 224.88 E-value: 9.10e-65

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1790 KPIALEDSVFGIEGLEALDLNTSAGFPYVTMGIKKRDLINNKTKDISRLKEALDKYgVDLP-----MITFLKDELRKKEK 1864
Cdd:cd23212    9 EPLSVREAVEGIDGLDPMDMDKSPGLPYVKKGLRRTDLWNPKTGPSIELMAEINRY-LDYNydkhvFLTFLKDELRPKEK 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1865 ISAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPETFWSKIPVMLDGDCIMAFDYTNYDGSIHPVWF 1944
Cdd:cd23212   88 VQAGKTRVIDVAGFGHAIVGRMLFGRLFAFFHKNPGWNTGSAVGVNPDLAWTQIFYTAPSRNVLAMDYSGFDASHTSGMF 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1945 QALKKVLENLSF---QSNLIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKnidlDKLKIIA 2021
Cdd:cd23212  168 CILKHFLTTLGYgtlQLSYIDSLCYSKHHWDDETYRLDGGLPSGCSGTTIFNTIMNNIVARAAASYAAE----GPVGILC 243

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   2022 YGDDVIFSYKYTLDMEAIANEGKKYGLTITPADKSTEFKKLDYNNVTFLKRGFKQDEKhtfLIHPTFPVEEIYESIRWTk 2101
Cdd:cd23212  244 YGDDILVSSPEKFPVSDWLEFYSKTPYKVTAADKSEQIDWRDITQCTFLKRGFVLDGS---LVRPVMEEQHLAELLKWA- 319

                        330       340
                 ....*....|....*....|....*
gi 130486   2102 KPSQMQEHVLSLCHLMWHNGRKVYE 2126
Cdd:cd23212  320 RPGTLQAKLLSIAQLAFHLPRQAYD 344

Rhv

pfam00073

picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...

93-300

4.38e-64

Pssm-ID: 395026 Cd Length: 170 Bit Score: 215.64 E-value: 4.38e-64

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486       93 TSQDVANAVVGYGVWPHYLTPQDATAIDKPTQPDTSSNRFYTLESKHWNGDSKGW-WWKLPDALKEMGIFGENMYYHFLG 171
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFfWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486      172 RSGYTVHVQCNASKFHQGTLLVAMIPEHQlasakngsvtagynlTHPGEAgrvvgqqrdanlrqpsddswlnfdgTLLGN 251
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPPGA---------------PPPGSR-------------------------DYLWQ 120

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 130486      252 LLIFPHQFINLRSNNSATLIVPYVNAVPMDSMLRHNNWSLVIIPISPLR 300
Cdd:pfam00073  121 ATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGNWTLVVAGWVPLN 169

RNA_dep_RNAP

cd01699

RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...

1838-2100

4.63e-61

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: 211.37 E-value: 4.63e-61

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1838 LKEALDKYGV------DLPMITFLKDELRKKEKISAGKTRVIEASSINDTILFRTTFGNLFSKFHLNpGVVTGSAVGCDP 1911
Cdd:cd01699    1 LEKAVESLEDlplirpDLVFTTFLKDELRPLEKVEAGKTRLIQPRPLDYNIALRMYLGPFEAKLMKN-RGGLPIAVGINP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1912 E-TFWSKIPVMLD--GDCIMAFDYTNYDGSIHPVWFQALKKVLENLS------FQSNLIDRLCYS-KHLFKSTYYEVAGG 1981
Cdd:cd01699   80 YsRDWTILANKLRsfSPVAIALDYSRFDSSLSPQLLEAEHSIYNALYddddelERRNLLRSLTNNsLHIGFNEVYKVRGG 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1982 VPSGCSGTSIFNTMINNIIIRTLVLDAYKNIDLDKLKIIAYGDDVIFSYK---YTLDMEAIANEGKKYGLTITPADKS-T 2057
Cdd:cd01699  160 RPSGDPLTSIGNSIINCILVRYAFRKLGGKSFFKNVRLLNYGDDCLLSVEkadDKFNLETLAEWLKEYGLTMTDEDKVeS 239

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 130486   2058 EFKKLdyNNVTFLKRGFKQDEkhTFLIHPTFPVEEIYESIRWT 2100
Cdd:cd01699  240 PFRPL--EEVEFLKRRFVLDE--GGGWRAPLDPSSILSKLSWS 278

Fipivirus_RdRp

cd23229

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Fipivirus of ...

1798-2153

2.47e-57

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: 204.66 E-value: 2.47e-57

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1798 VFGIEGLEALDLNTSAGFPYVTMGIKKRDLIN---NKTKDISRLKEALDKYGVDLPM-----------ITFLKDELRKKE 1863
Cdd:cd23229    2 VEGIPGMEGLDMKTSAGYPWCEQNQKKKDKIKllaGKNFLVRPLREVVHIVVDWYIMppdmpkpeikyVVYLKDELLSSD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1864 KISAGKTRVIEASSINDTILFRTTFGNLFSKFHL-NP--GVVTGSAVGCDPETFWSKIPVMLDGDCIMAFDYTNYDGSIH 1940
Cdd:cd23229   82 KVKMGRTRWICAAPVQLVCAWKKVFGRAIAAIHLeSVtdGKSTGCAVGMDPETAWTDIALARPGWPVIALDYSNFDGSLQ 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1941 PVWFQALKKVLENLS-FQSNLIDRLC----YSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINnIIIRTLVLDAYKNIDL- 2014
Cdd:cd23229  162 SFVITGAVRILGYIAgLPDGQSYRLAefvyDVKQIVGKYLYTTVGPLPSGCPSTSIIGSLCN-VLMLLYTLSHATGQRYs 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   2015 ---DKLKIIAYGDDVIF----SYKYTLDMEAIANEgKKYGLTITPA-DKSTEFKKLDYNNVTFLKRGFKQDEKHTFLIHP 2086
Cdd:cd23229  241 afrDWMHVVTYGDDVLVfvhpEVVVVLDTLAHEMY-LVFGVTATDAtDKRAPPQLRELSNVTFLKRGFRQCSSVPFLVHP 319

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 130486   2087 TFPVEEIYESIRWTKKPSQMQEHVLSLCHLMWHNGRKVYEDF------SSKIRSVSAGRALY--IPPYDLLKHEW 2153
Cdd:cd23229  320 TMDKSTIYQMLAWKRKGTTLAENVKCAAEFMMHHGEEEYEDFvgvvkeCSTLIGVDQRSKVYeeLCSYAELHDHW 394

Peptidase_C3

pfam00548

3C cysteine protease (picornain 3C); Picornaviral proteins are expressed as a single ...

1515-1680

1.87e-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: 188.04 E-value: 1.87e-54

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486     1515 GPEEEFGRSILKNNTCVITTDNGKFTGL--GIYDRTLIIPTHADPGREVQVNGIHTKVLD-SYDLYNRDGVKLEITVIQL 1591
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486     1592 DRNEKFRDIRKYIPETEDDYPECNLALSANQVEPTIIKVGDVVSYGNI-LLSGNQTARMLKYNYPTKSGYCGGVLYKI-- 1668
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVVIAKve 160

                          170
                   ....*....|....
gi 130486     1669 --GQILGIHVGGNG 1680
Cdd:pfam00548  161 gnGKILGMHIAGNG 174

Rhv

pfam00073

picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...

360-525

2.93e-53

Pssm-ID: 395026 Cd Length: 170 Bit Score: 184.44 E-value: 2.93e-53

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486      360 YHPTKEISIPGEVKNLIEMCQVDTLIPVNNVGTNVGNISMYTVQLGNQMDMAQEVFAIKVDItsQPLATTLIGEIASYYT 439
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFFWWKLPL--ALLSMGLLGRLLRYHT 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486      440 HWTGSLRFSFMFCGTANTTLKLLLAYTPPGIDKPATR---KDAMLGTHVVWDVGLQSTISLVVPWVSASHFRLTANDK-- 514
Cdd:pfam00073   79 YYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRdylWQATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGnw 158

                          170
                   ....*....|..
gi 130486      515 -YSMAGYITCWY 525
Cdd:pfam00073  159 tLVVAGWVPLNY 170

RdRP_1

pfam00680

Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...

1724-2134

1.43e-50

Pssm-ID: 425815 Cd Length: 450 Bit Score: 186.85 E-value: 1.43e-50

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486     1724 PSVFYDVFPGSKEPAVSRDNDPRL--KVNFKEALF---SKYK-----GNTECSLNQHMEIAIAHYSAQLITLDIDSKPIA 1793
Cdd:pfam00680    2 PTERHLVAIPAYVPASLGPEDPRWarSYLNTDPYVddiKKYSrpklpGPADERDKLLNRSAAKMVLSELRGVPKKANSTL 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486     1794 LEDSVF-GIEGLEALDLNTSAGFPYVTMGIKKRDLIN----NKTKDI--SRLKEALDKY--GVDLPMI--TFLKDELRKK 1862
Cdd:pfam00680   82 IVYRAIdGVEQIDPLNWDTSAGYPYVGLGGKKGDLIEhlkdGTEARElaERLAADWEVLqnGTPLKLVyqTCLKDELRPL 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486     1863 EKISAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTgSAVGCDPetFWSKIPVMLD-----GDCIMAFDYTNYDG 1937
Cdd:pfam00680  162 EKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHP-IQVGINP--FDRGWPRLLRrlarfGDYVYELDYSGFDS 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486     1938 SIHPVWFQALKKVL-------ENLSFQSNLIDRLCYSKH-LFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAY 2009
Cdd:pfam00680  239 SVPPWLIRFAFEILrellgfpSNVKEWRAILELLIYTPIaLPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYALLKSL 318

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486     2010 KNIDL------DKLKIIAYGDDVIFSYKYTLD--MEAIANEGKKYGLTITPADKSTEFKKlDYNNVTFLKRGFKQDEkht 2081
Cdd:pfam00680  319 ENDGPrvcnldKYFDFFTYGDDSLVAVSPDFDpvLDRLSPHLKELGLTITPAKKTFPVSR-ELEEVSFLKRTFRKTP--- 394

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|...
gi 130486     2082 FLIHPTFPVEEIYESIRWTKKPSQMQEHVLSLCHLMWHNGRKVYEDFSSKIRS 2134
Cdd:pfam00680  395 GGYRPPLDRKRILAQLEYIRSKPVPSGQLENIRAYASHHGYEFYRDLLYRFVE 447

Rhv

pfam00073

picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...

617-769

7.02e-50

Pssm-ID: 395026 Cd Length: 170 Bit Score: 174.81 E-value: 7.02e-50

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486      617 PEDAIETRYVMTSQTRDEMSIESFLGRSGCVH-----ISRIKVDYNDYNGVNKNFTTWKITL--QEMAQIRRKFELFTYV 689
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQpdvqgERFYTLDSTDWTSLSKGFFWWKLPLalLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486      690 RFDSEVTLVPCiagrGDDIGHVVMQYMYVPPGAPIPKTRnDFSWQSGTNMSIFWQHG-QPFPRFSLPFLSIASAYYMFYD 768
Cdd:pfam00073   81 RGGLEVTVQFN----GSKFHQGKLLVAYVPPGAPPPGSR-DYLWQATLNPHQFWNLGlNSSARLSVPYISIAHYYSTFYD 155


                   .
gi 130486      769 G 769
Cdd:pfam00073  156 G 156

Passerivirus_RdRp

cd23224

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Passerivirus of ...

1796-2155

1.03e-49

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: 182.21 E-value: 1.03e-49

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1796 DSVFGIEGLEALDLNTSAGFPYvTMGIKKRDLINN----KTKDISRLKEALDK--YGVDLPMITFLKDELRKKEKISAGK 1869
Cdd:cd23224    1 EAINGTPLLDGLDMKQSPGYPW-SLTTNRRSLFTQdetgKYYPVPELEEAVLAclENPDYFYTTHLKDELRPVEKALAGK 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1870 TRVIEASSINDTILFRTTFGNLFSKFHLNPGVVtGSAVGCDPETFWSKIPVMLDGDC-IMAFDYTNYDGSIHPVWFQALK 1948
Cdd:cd23224   80 TRLIEAAPIHAIIAGRMLLGGLFEYMHARPGEH-GSAVGCDPDYHWTPFFHSFDEFSqVWALDYSCFDSTLPSCCFDLIA 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1949 KVLENL---------SFQSNLIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLdAYKNIDLDKLKI 2019
Cdd:cd23224  159 QKLAKIitpgegiapDAIVKYIRSISISKHVFGNEAYLMVGGNPSGCVGTSILNSMINNCVLISAFL-TQKDFNPNQMRI 237

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   2020 IAYGDDVIFSYKYTLDMEAIAN-EGKKYGLTITPADKSTEFKklDYN---NVTFLKRGFKQDEKHTFLIHPTFPVEEIYE 2095
Cdd:cd23224  238 LTYGDDVLYATNPPIHPRVVKKfFDENTTLIVTPATKAGDFP--DEStiwDVTFLKRYFVPDEIRPWYVHPVIEPATYEQ 315

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 130486   2096 SIRWTKKpSQMQEHVLSLCHLMWHNGRKVYEDFSSKIRSVSAGRALY--IPPYDLLKHEWYE 2155
Cdd:cd23224  316 SVMWTRG-GDFQDVVTSLSFLAHHAGPTNYMIWEEKVRKAAAAKGVSlnILPYSYLQHRWML 376

Hepatovirus_RdRp

cd23215

RNA-dependent RNA polymerase (RdRp) in the genus Hepatovirus of positive-sense single-stranded ...

1791-2154

1.75e-48

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: 181.20 E-value: 1.75e-48

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1791 PIALEDSVFGIEGLEALDLNTSAGFPYVTMGIKKRDLI----NNKTKDI-SRLKEALD------KYGVDLPMI--TFLKD 1857
Cdd:cd23215   64 FFDLEQAITGVPGMDAINMDSSPGYPYVQEKLTKSDLIwlddNGELLGMhPRLAQRILfnltmmDNGNDLDVVytTCPKD 143

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1858 ELRKKEKISAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPETFWSKI-PVMLD-GDCIMAFDYTNY 1935
Cdd:cd23215  144 ELRPLEKVLESKTRAIDACPLDFTIICRMFWGPAISYFQLNPGFHTGVAVGIDPDRDWDALfKTMIRfGDYGIDLDFSSF 223

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1936 DGSIHPVWFQALKKVLENLS-----FQSNLIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYK 2010
Cdd:cd23215  224 DASLSPFMIREACRVLSELSgvpdhQGQALINTIIYSKHLLYNLCYHVCGSMPSGSPCTSLLNSIVNNVNLYYVFSKIFK 303

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   2011 NIDL---DKLKIIAYGDDVIFSYKYTLDME-------AIANEGKKYGLTITPADKStEFKKLDYNNVTFLKRGFKQDEKH 2080
Cdd:cd23215  304 KSPVffyDAVKFLCYGDDVLIVFSRDLEIKnldklgqRIQDEFKLLGMTATSADKG-EPQVVPVSELTFLKRSFNLIEDR 382

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 130486   2081 tflIHPTFPVEEIYESIRWTKKPSQMQEHVLSLCHLMWHNGRKVYEDFSSKIRSVSAGRALyipPYDLLKHEWY 2154
Cdd:cd23215  383 ---FRPAISEKTIWSLVAWQRSNAEFEQNLDTACWFAFMHGYDFYQNFYLQLQSCLEKEMI---DYRLKSYEWW 450

Pico_P2B

pfam01552

Picornavirus 2B protein; Poliovirus infection leads to drastic alterations in membrane ...

999-1095

2.21e-45

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: 159.42 E-value: 2.21e-45

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486      999 QGITDYIHMLGEAFGNGFV----DSVKEQINAINPINSISKKVIKWLLRIISAMVIIIRNSSDPQTIIATLTLIGCNGSP 1074
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTqqisDKIKELTNFINPTSKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|.
gi 130486     1075 WRFLKEKFCKWTQLTYIHKES 1095
Cdd:pfam01552   81 WQFLKEKACAVLEIPYVHKQG 101

Dicistroviridae_RdRp

cd23194

RNA-dependent RNA polymerase (RdRp) in the family Dicistroviridae of positive-sense ...

1854-2133

7.11e-44

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: 163.05 E-value: 7.11e-44

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1854 FLKDELRKKEKISAGKTRVIEASSINDTILFRTTFGNLFSkfHLNPG-VVTGSAVGCDPETF-WSKIPVML--DGDCIMA 1929
Cdd:cd23194   11 TLKDERRPIEKVDAGKTRVFSAGPMDYTIAFRMYFLGFVA--HLMRNrIDNEIAVGTNVYSLdWDKLARKLlsKGDKVIA 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1930 FDYTNYDGSIHPvwfQALKKVLE------NLSFQSNLIDR-----LCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINN 1998
Cdd:cd23194   89 GDFSNFDGSLNP---QILWAILDiinewyDDGEENALIRRvlwedIVNSVHICGGYVYQWTHSQPSGNPLTAIINSIYNS 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1999 IIIRTLVLDAYKNIDLDKLK-------IIAYGDDVIFS----YKYTLDMEAIANEGKKYGLTITPADKSTE---FKKLDy 2064
Cdd:cd23194  166 IIMRYVYLLLTKEAGLMTMSdfnkhvsMVSYGDDNVINvsdeVSEWFNQLTITEAMAEIGMTYTDETKTGEivpYRSLE- 244

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 130486   2065 nNVTFLKRGFKQDEKHTFLIHPtFPVEEIYESIRWTKKPSQMQE----------HVLSLcHlmwhnGRKVYEDFSSKIR 2133
Cdd:cd23194  245 -EVSFLKRGFRYDDDLGRWVAP-LDLDTILEMPNWVRKGKDPEEitkqnvenalRELSL-H-----GEEVFDKWAPKIR 315

rhv_like

cd00205

Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...

375-559

5.98e-43

Pssm-ID: 119412 Cd Length: 178 Bit Score: 155.25 E-value: 5.98e-43

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486    375 LIEMCQVDTLIPVNNVGTNvgnismytvqlgnqmDMAQEVFAIKVDITSQPL--ATTLIGEIASYYTHWTGSLRFSFMFC 452
Cdd:cd00205    1 VESFADRPTTVGTNNWNSS---------------ASGTQLFQWKLSPALGFLllQNTPLGALLSYFTYWRGDLEVTVQFN 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486    453 GTANTTLKLLLAYTPPGIDKPA---TRKDAMLGTHVVWDVGLQSTISLVVPWVSASHFRLTANDKY---SMAGYITCWYQ 526
Cdd:cd00205   66 GSKFHTGRLLVAYVPPGAPAPTtgdTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDGYgplNSFGTLVVRVL 145

                        170       180       190
                 ....*....|....*....|....*....|...
gi 130486    527 TNLVVPPNTPQTADMLCFVSAcKDFCLRMARDT 559
Cdd:cd00205  146 TPLTVPSGAPTTVDITVYVRA-GDFELYGPRPP 177

Parechovirus_RdRp

cd23217

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Parechovirus of ...

1797-2151

1.21e-41

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: 158.49 E-value: 1.21e-41

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1797 SVFGIEGLEALDLNTSAGFPYVTMGIKKRDLINNKTKDISRLKEALDK------YGVDLP---MITFLKDELRKKEKISA 1867
Cdd:cd23217    1 AVLGTSHLNSLDLSTSPGYKYVKSGYKKRDLLSLEPFSVSPQLEKDVKdklhavYKGNQPttiFNACLKDELRKLDKIAQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1868 GKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPETFWS-KIPVMLDGDciMAFDYTNYDGSIHPVWFQA 1946
Cdd:cd23217   81 GKTRCIEACSIDYVIAYRVVMSSLYEAIYQTPCQELGLAVGMNPWTDWDfMINALNPYN--YGLDYSSYDGSLSEMLMWE 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1947 LKKVLENLSFQSNLIDRL----CYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLvldAY-KNIDLDKLKIIa 2021
Cdd:cd23217  159 AVEVLAYCHESPDLVMQLhkpvINSDHVVMDERWLVHGGMPSGSPCTTVLNSICNLLVCIYL---AYlQSPGIECLPIV- 234

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   2022 YGDDVIFSYKYTLDMEAIANEGKK-YGLTITPADKSTEFKKLDYNNVTFLKRGFKQDEKHTFLIHpTFPVEEIYESIRWT 2100
Cdd:cd23217  235 YGDDVIFSVSSEIDPEYLVSSAADsFGMEVTGSDKDEPPSLLPRMEVEFLKRTTGYFPGSTYKVG-ALDLETMEQHIMWM 313

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 130486   2101 KK----PSQMQEHVLSLChlmwHNGRKVYEDFSSKIRSVSAGRALYIPPYDLLKH 2151
Cdd:cd23217  314 KNlstfPQQLQSFENELC----LHGKDIYDDYKKIFNPYLKEWNITMDDYDVVIH 364

Pico_P1A

pfam02226

Picornavirus coat protein (VP4); VP1, VP2, VP3 and VP4 for the basic unit that forms the ...

2-69

2.05e-41

Pssm-ID: 308053 Cd Length: 68 Bit Score: 146.75 E-value: 2.05e-41

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 130486        2 GAQVSRQNVGTHSTQNSVSNGSSLNYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 69
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 68

Crohivirus_RdRp

cd23232

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Crohivirus of ...

1794-2147

4.38e-41

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: 156.80 E-value: 4.38e-41

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1794 LEDSVFGIEGLEALDLNTSAGFPYVTMGIKKRDLIN-NK-------TKDISRLKEALDKYG-VDLPMITFLKDELRKKEK 1864
Cdd:cd23232    1 IEEACFEEGDEHALDLKTSPGFKYVQMGLKKTDLVNrPNkfihpilRNDVRLIFDEMAKGQmPVVTFTAHLKDELRKLEK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1865 ISAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPETFWSKIPVMLDgDCIMAFDYTNYDGSIHPVWF 1944
Cdd:cd23232   81 IRSGKTRCIEACDFDYTVAHKMMFGTLYKAIYDTPGIITGLAVGMNPWKDWELIQQSLF-KYNYDFDYKTFDGSLSRELM 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1945 QALKKVLENLSFQSNLIDRL----CYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKNidldKLKII 2020
Cdd:cd23232  160 LHAVDILSACVENDEMAKLMlsvvVESVHLVLDQKWNVSGGMPSGSPCTTVLNSVCNLIVSSTIADMCTEG----DFKIL 235

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   2021 AYGDDVIFSYKYTLDMEAIANEGK-KYGLTITPADKSTEFKKLDYNNVTFLKRGFKQDEKHTFLIHpTFPVEEIYESIRW 2099
Cdd:cd23232  236 VYGDDLIISSTAPLDCDRFKTLVElHYGMEVTPGDKGDEFKVKDREQVSFLKRVTRKFPGTNYRVG-ALDLDTVKQHLMW 314

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*...
gi 130486   2100 TKKPSQMQEHVLSLCHLMWHNGRKVYEDFSSKIRSVSAGRALYIPPYD 2147
Cdd:cd23232  315 CKSYSSFKQQLDSALMEVAMHGEETYNGFLTEIKTKLDKFKIYPPKFK 362

RNA_helicase

pfam00910

RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...

1214-1310

5.68e-40

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: 143.90 E-value: 5.68e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486     1214 VMIHGPPGTGKSITTNFLARMI-----TNESDVYSLPPDPKYFDGYDNQSVVIMDDIMQNPDGEDMTLFCQMVSSVTFIP 1288
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALlkklgLPKDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 130486     1289 PMADLPDKGKPFDSRFVLCSTN 1310
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

Kunsagivirus_RdRp

cd23219

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Kunsagivirus of ...

1794-2126

5.67e-37

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: 143.85 E-value: 5.67e-37

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1794 LEDSVFgiEGLEALDLNTSAGFPYVtmGIKKRDLINNKTKDIS-RLKE-------ALDKYGVD-LPMITFLKDELRKKEK 1864
Cdd:cd23219    1 IEEAVF--DTVTPMDHTASAGPKYP--GTKRSELIDFQNRIISdRLRNdvlelqfRGTSGGAGeVKFSSFLKDELRPLSK 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1865 ISAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPET-FWSKIPVMLDGDciMAFDYTNYDGSIHPVW 1943
Cdd:cd23219   77 IRSGDTRVVECSSLDYTVAFRMQFLRVLQMCYGSDPTLTGLAPGMNVYTdMLPLCTSLYDYN--LCLDFSKYDSRLPLQV 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1944 FQALKKVLENLS----FQSNLIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKNIDldkLKI 2019
Cdd:cd23219  155 MHRVAQLISNLTpdpqVSMRLFQPIIISTHIVGSYEVVVEGGMPSGCPITTIMNSVCNVVMTSYAMLLLDPDSD---FWP 231

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   2020 IAYGDDVIFSYKYTLDMEA---IANEgkKYGLTITPADKSTEFKKLDYNNVTFLKRGFKQDEKHTFLIhPTFPVEEIYES 2096
Cdd:cd23219  232 VAYGDDNIVSTRKPIDTELfcsILNE--EFGMILTGADKTTTVQAVPPMSVDFLKRRLRYTPEFPLPV-PVLPLDSMLSR 308

                        330       340       350
                 ....*....|....*....|....*....|
gi 130486   2097 IRWTKKPSQMQEHVLSLCHLMWHNGRKVYE 2126
Cdd:cd23219  309 ICWCKGETEFKDQLESFSYELALYGQEVYE 338

rhv_like

cd00205

Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...

125-329

6.06e-37

Pssm-ID: 119412 Cd Length: 178 Bit Score: 138.30 E-value: 6.06e-37

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486    125 PDTSSNRFYTLESKHWNG---DSKGWWWKLPDA----LKEMGIFGENMYYHFLGRSGYTVHVQCNASKFHQGTLLVAMIP 197
Cdd:cd00205    1 VESFADRPTTVGTNNWNSsasGTQLFQWKLSPAlgflLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486    198 EHQLASAKNGSvtagynlthpgeagrvvgqqrdanlrqpsddswlnfdgtlLGNLLIFPHQFINLRSNNSATLIVPYVNA 277
Cdd:cd00205   81 PGAPAPTTGDT----------------------------------------RWQATLNPHVIWDLGTNSSVTFVVPYVSP 120

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 130486    278 VPMDSMLRH------NNWSLVIIPISPLRSETTSSNIRPITVSISPMCAEFSGARAKN 329
Cdd:cd00205  121 TPYRSTRYDgygplnSFGTLVVRVLTPLTVPSGAPTTVDITVYVRAGDFELYGPRPPR 178

Avisivirus_RdRp

cd23231

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Avisivirus of ...

1807-2147

5.81e-36

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: 141.57 E-value: 5.81e-36

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1807 LDLNTSAGFPYvtMGIKKRDLINNKT--KDISRLKEA---LDKYGVDLPMITFLKDELRKKEKISAGKTRVIEASSINDT 1881
Cdd:cd23231   11 IDWGTSPGDKY--KGKTKAQLVDDKKfkADVMNLVRFngdPNREPPDVYFTTYLKDELRPKEKAKAGKTRVISAASFDYT 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1882 ILFRTTFGNLFSKFHLNpGVVTGSAVGCDPETFWSKIPVMLDGDCImAFDYTNYDGSIHPVWFQALKKVLENLSFQSNLI 1961
Cdd:cd23231   89 IACRMVFGPILRQLFAW-GREFGFGPGLNPYTHFDELYDKILPFVI-CLDYSGFDGSLSSELMFHAAQVIACFSEKPEAI 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1962 DRLCY----SKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDayKNIDLDKLKIIAYGDDVIFSYKYTLDME 2037
Cdd:cd23231  167 MASAEltigSTERVSDEVWYVYGGMPSGSPWTTTLNTICNLLMCYTYLLD--MGHCWSETFVVAYGDDVVISANIKHNLE 244

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   2038 AIANEGK-KYGLTITPADKSTEFKKLDYNNVTFLKRGFKQDEkhtFL--IHPTFPVEEIYESIRWTKkpSQMQEHVLSLC 2114
Cdd:cd23231  245 GIEQWFKtKFGATVTPSDKQGKITWTTKNNMEFLKRRPKQLD---FLpkIVGALDLDNMLDRIQWTK--GHFQDQLNSFY 319

                        330       340       350
                 ....*....|....*....|....*....|....*
gi 130486   2115 HLMWHNGRKVYEDfsskIRSVSAGRA--LYIPPYD 2147
Cdd:cd23231  320 LELALHGRETYNE----IRAKLAPRApqLVHPTYA 350

Limnipivirus_RdRp

cd23228

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Limnipivirus of ...

1803-2148

2.35e-35

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: 140.40 E-value: 2.35e-35

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1803 GLEALDLNTSAGFPYVTMGIKKRDL--INNK---------TKDISRLKEALDKYG-VDLPMITFLKDELRKKEKISAGKT 1870
Cdd:cd23228    6 GTNPIDKNTSPGLKYTRDGLKKSDLytIDEDgnvvvsdmlRADVEAWEELIQSGGyPTTLFTACLKDELRSDEKVALGKT 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1871 RVIEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPETFWSKIPVMLDG-DCIMAFDYTNYDGSIHPVWFQALKK 1949
Cdd:cd23228   86 RVIEAAELDYVVAYRMYMSSIYSDLYNAYAGDTGIAAGINPPADGHRLREELSQyDSFLALDYSRFDGSLPEMLMRAAVE 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1950 VLENLSFQSNLIDRL----CYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDA----YKNIDLDKLK--- 2018
Cdd:cd23228  166 ILADLHEDPDLVRRLhetvIISKHLVVDEDWTVKGGMPSGSPCTTVLNCICNLLVLEYAFLVHfgvyEDDDGVGLPQcdy 245

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   2019 -IIAYGDDVIFSY---KYTLDM-EAIANegkKYGLTITPADKSTEFKKLDYNNVTFLKRGF-KQDEKHTFLIHPTFPVEE 2092
Cdd:cd23228  246 lSVVYGDDCIVAYngmEMGLAFaETIED---TFGMEVTPASKVGDHFNVELHEVEFLKRKFfAFETEEYDRIALRLSENT 322

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 130486   2093 IYESIRWTKKPSQMQEHVLSLCHLMWHNGRKVYEDFSSKIRSVSAGRALYI--PPYDL 2148
Cdd:cd23228  323 IVQSLMWMRNLKTFPDQVQSLMMELSAWGKEKYDKLRDTCKRRLAKQNLQVtvPGYDI 380

rhv_like

cd00205

Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...

637-825

3.07e-35

Pssm-ID: 119412 Cd Length: 178 Bit Score: 133.29 E-value: 3.07e-35

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486    637 IESFLGRSGCVHISRIKVDYNDyngvnKNFTTWKITLQE------MAQIRRKFELFTYVRFDSEVTLVPCiagrGDDIGH 710
Cdd:cd00205    1 VESFADRPTTVGTNNWNSSASG-----TQLFQWKLSPALgflllqNTPLGALLSYFTYWRGDLEVTVQFN----GSKFHT 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486    711 VVMQYMYVPPGAPIPKTrNDFSWQSGTNMSIFWQHG-QPFPRFSLPFLSIASAYYMFYDGYDgdnssskygsiVTNDMGT 789
Cdd:cd00205   72 GRLLVAYVPPGAPAPTT-GDTRWQATLNPHVIWDLGtNSSVTFVVPYVSPTPYRSTRYDGYG-----------PLNSFGT 139

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 130486    790 ICSRIVTEKQ---EHPVVITTHIYHKAKHTKAWCPRPPR 825
Cdd:cd00205  140 LVVRVLTPLTvpsGAPTTVDITVYVRAGDFELYGPRPPR 178

Aalivirus_RdRp

cd23216

RNA-dependent RNA polymerase (RdRp) in the genus Aalivirus of positive-sense single-stranded ...

1807-2134

1.78e-30

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: 124.78 E-value: 1.78e-30

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1807 LDLNTSAGFPYvtMGIKKRDLINNktkdiSRLKEALDKYGVDLP--MITFLKDELRKKEKISAGKTRVIEASSINDTILF 1884
Cdd:cd23216   12 IDWQTSPGLKY--KGRTKADLVQD-----PKFKEDVKEILAGKPtfFTTYLKDELRSIEKIANGNTRAIEAANFDHVVAW 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1885 RTTFGNLFSKFHLNPGVVTGSAVGCDPETFWSKIPVMLDGDcIMAFDYTNYDGSIHPVWFQALKKVLENLSFQSNLIDRL 1964
Cdd:cd23216   85 RQVMGNIVKQLFSDHDRVTGFAPGMNPYTHFDSLMDQVKWN-VLALDFKKFDGSLSPQVMEEAVDILASFHDMPQMVVDI 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1965 ----CYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDayKNIDLDKLKIIAYGDDVIFS---YKYTLDME 2037
Cdd:cd23216  164 hkhtIYSTNVVSDETWFVEGGMCSGSPCTTVLNTICNLLVNTTILLS--EGIQPDNFYIAAYGDDTIISvdgLSSSLPDP 241

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   2038 AIANEGKK--YGLTITPADKSTEFKKLDYNNVTFLKR--GFKQDEKHTFLIhptFPVEEIYESIRWTKkpSQMQEHVLSL 2113
Cdd:cd23216  242 KIMQQKYKewFGMTVTSADKGSEITWDTRNHVQFLKRrpGFFPGTQKVVGV---LDLESMMEHIAWTK--GSFQDQLNSF 316

                        330       340
                 ....*....|....*....|.
gi 130486   2114 CHLMWHNGRKVYEDFSSKIRS 2134
Cdd:cd23216  317 YQELVLHGEQVYMTVRQTLKS 337

Marnaviridae_RdRp

cd23195

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Marnaviridae of ...

1855-2133

8.37e-27

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Marnaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Marnaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. They are mono- or dicistronic, have a polyadenylate tail and have conserved motifs for RNA helicase, RdRp, and structural protein domains. The first RNA virus isolated and characterized that infects a marine protist was Heterosigma akashiwo RNA virus (HaRNAV) in the genus Marnavirus, that infects the toxic bloom-forming Raphidophyte alga, Heterosigma akashiwo. Recently, it has undergone a major taxonomic revision and now includes 20 species within 7 genera, which include Bacillarnavirus, Kusarnavirus, Labyrnavirus, Locarnavirus, Marnavirus, Salisharnavirus, and Sogarnavirus. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438045 Cd Length: 310 Bit Score: 113.31 E-value: 8.37e-27

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1855 LKDELRKKEKisaGKTRVIEASSINDTILFRTTFGNLFSKFHLNPgVVTGSAVGCD---PEtfWSKIPVML---DGDCIM 1928
Cdd:cd23195    7 LKDEPTKLTK---DKVRVFQAAPVALQLLVRKYFLPIARFLQMNP-LLSECAVGINaqsPE--WEELYEHLtkfGEDRII 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1929 AFDYTNYDGSIHPVWFQALKKVLENLSFQS------------NLIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMI 1996
Cdd:cd23195   81 AGDYSKYDKRMSAQLILAAFKILIDIAAKSggyseedlkimrGIATDIAYPLVDFNGDLIQFFGSNPSGHPLTVIINSIV 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1997 NNIIIRTLVLDAYKNIDL----DKLKIIAYGDDVIFSYK---YTLDMEAIANEGKKYGLTITPADKSTEFKK-LDYNNVT 2068
Cdd:cd23195  161 NSLYMRYAYYSLYPEKEVppfrDVVALMTYGDDNIMSVSpgyPWFNHTSIAEFLAKIGIKYTMADKEAESVPfIHISEAD 240

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 130486   2069 FLKRGFKQDEKHtFLIHPtfPVEE--IYESIRWTKKPS------QMQEHVLSLCHLMWHNGRKVYEDFSSKIR 2133
Cdd:cd23195  241 FLKRKFVFDPEL-GVYVG--PLDEdsIFKSLHCYLKSKvltpeeQAAQNIDGALREWFFHGREVYEKRREQLK 310

Caliciviridae_RdRp

cd23192

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Caliciviridae of ...

1855-2078

8.37e-27

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: 113.13 E-value: 8.37e-27

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1855 LKDELRKKEKISAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPGvVTGSAVGCDPETfwSKIPVM----LDGDCIMAF 1930
Cdd:cd23192    7 LKDELRPVEKIAEGKRRLLWGCDVGVTLVAAAAFGPVADALKAVCP-TGPIAVGINMDS--EDVEVIferlSGFRYHYCL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1931 DYTNYDGSIHPVWFQALKKVLENLSFQSNLIDRLCYSKH-----LFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLV 2005
Cdd:cd23192   84 DYSKWDSTQSPAVTAAAIDILADLSEETPLRDSVVETLSsppmgIFDDVIFVTKRGLPSGMPFTSVINSLNHWLLFSAAV 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   2006 LDAYK-------NIdLDKLKIIAYGDDVIFSYK--YTLDMEAIANEGKKYGLTITPADKSTEFKKLDYNNVTFLKRGFKQ 2076
Cdd:cd23192  164 LKAYElvgiytgNV-FDEADFFTYGDDGVYAMPpaTASVMDEIIENLKSYGLKPTAADKTENPDIPPLQGPVFLKRTFVR 242


                 ..
gi 130486   2077 DE 2078
Cdd:cd23192  243 TP 244

Aquamavirus_RdRp

cd23220

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Aquamavirus of ...

1807-2125

1.74e-24

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: 107.10 E-value: 1.74e-24

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1807 LDLNTSAGFPYVtmGIKKRDLIN--NKT--KDISRLKEALDKYGVDLPMITFLKDELRKKEKISAGKTRVIEASSINDTI 1882
Cdd:cd23220   12 LNFNGTAGAKYP--GMNRRQLLLplNPQvrDDVVKLAGDVGNGTATVVFETFMKDELRPKEKIESGKTRIVESCPLDYLL 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1883 LFRTTFGNLFSKFHLNPGVVTGSAVGCDPETFWSKIpVMLDGDCIMAFDYTNYDGSIHPVWFQALKKVLENLSFQSNLID 1962
Cdd:cd23220   90 LYRMVMLKSMIWWYNSDCIKTGVAPGMNVYTDFVPM-VKQFKKIKYCLDFSAYDSTLSDEILAAGVEVLACTSAVPSYVR 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1963 RL----CYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVldayKNIDLDKLKIIAYGDDVIFSYKYTLDMEA 2038
Cdd:cd23220  169 KLhapiICSHHWHNNVVDLVLGGMPSGAPCTSVLNSIVNVLMARYIC----ALMDIDYPVMVAYGDDNVVSFDEEIDIER 244

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   2039 IAN-EGKKYGLTITPADKSTEFKKLdyNNVTFLKRG--FKQDEKHTFlihPTFPVEEIYESIRWTKKPSQMQEHVLSLCH 2115
Cdd:cd23220  245 MVSlYKTEFGVTATNHDKTPVPRPM--ANPVFLKRRlrFNPDLNIQF---PVLPLGEMIDRMCWTRGPEHLSDQTFSFAI 319

                        330
                 ....*....|
gi 130486   2116 LMWHNGRKVY 2125
Cdd:cd23220  320 ELAGYGKQVY 329

P3A

pfam08727

Poliovirus 3A protein like; This domain is found in positive-strand RNA viruses. The 3A ...

1413-1465

3.36e-20

Pssm-ID: 400873 Cd Length: 59 Bit Score: 85.94 E-value: 3.36e-20

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 130486     1413 AIFQG----PISLDAPPPPAIADLLQSVRTPEVIKYCQDNKWIV--PAECQIERDLSIA 1465
Cdd:pfam08727    1 AIFQGidlkIDIKTSPPPEAIADLLQAVDSPEIIDYCEDKGWIVniPAECQIERDIGIA 59

Secoviridae_RdRp

cd23196

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Secoviridae of ...

1845-2078

1.41e-16

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Secoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Secoviridae, order Picornavirales. Members of the family Secoviridae are non-enveloped viruses with mono- or bipartite (RNA-1 and RNA-2) linear (+)ssRNA genomes of 9 to 13.7 kilobases in total. Secoviruses are related to picornaviruses and are classified in the order Picornavirales. The majority of known members infect dicotyledonous plants and many are important plant pathogens (e.g., grapevine fanleaf virus and rice tungro spherical virus). The Secoviridae includes 8 genera (Comovirus, Fabavirus, Nepovirus, Cheravirus, Sadwavirus, Torradovirus, Sequivirus, and Waikavirus) as well as unassigned species (strawberry latent ringspot virus-MEN 454, strawberry mottle virus-Thompson, black raspberry necrosis virus- 1, chocolate lily virus A-KP2, and Dioscorea mosaic associated virus-goiana). RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438046 Cd Length: 309 Bit Score: 82.82 E-value: 1.41e-16

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1845 YGVDLPmitflKDELRKKEK-ISAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTgSAVGCDPETF-WSKIPVML 1922
Cdd:cd23196    2 NCVECP-----KDERLKKRKvLEKPKTRLFDVLPMEYNLLLRKYFLNFVRFIQANRHRLP-CQVGINPYSReWTTLYDRL 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1923 --DGDCIMAFDYTNYDG----SIHPVWFQALKKVL---ENLSFQSNLIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFN 1993
Cdd:cd23196   76 aeKSDTALNCDYSRFDGllshQVYVWIADMINRLYgdgDEAKARRNLLMMFCGRRSICGRQVYMVRGGMPSGCALTVIIN 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1994 TMINNIIIR----TLVLDAYKNIDLDKLKIIAYGDDVIFSYKYTL----DMEAIANEGKKYGLTITPA-DKST---EFKK 2061
Cdd:cd23196  156 SIFNEILIRyvyrKVVPRPARNNFNKYVRLVVYGDDNLISVKEEIipyfDGPVIKKEMAKVGVTITDGtDKTSptlERKP 235

                        250
                 ....*....|....*..
gi 130486   2062 LDynNVTFLKRGFKQDE 2078
Cdd:cd23196  236 LE--SLDFLKRGFRVQS 250

Nora-virus_RdRp

cd23200

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in a novel picorna-like ...

1855-2133

2.62e-13

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in a novel picorna-like Drosophila virus, Nora virus; This group contains the catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the unclassified Nora virus, a new picorna-like virus family. Nora virus has a (+)ssRNA genome followed by a poly(A) tail. Unlike other picorna-like viruses, the genome has four open reading frames (ORFs). One ORF encodes a picornavirus-like cassette of proteins for virus replication, including an iflavirus-like RdRp and a helicase that is related to those of mammalian picornaviruses. The three other ORFs are not closely related to any previously described viruses. Nora virus is present as a persistent infection in several tested laboratory stocks and wild-caught flies. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438050 Cd Length: 306 Bit Score: 73.03 E-value: 2.62e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1855 LKDELRKKEKISAGKTRVIEASSINDTILFRTTFGNLFSKFHlNPGVVTGSAVGCDPE--------TFWSKIPVMLDGdc 1926
Cdd:cd23200    7 LKDQPIKIAQAKSGRTRVFHCIPVDLILFSGALYGPYKEAYT-KAGLKCYHAVGIDPKsvgwqqlaTYMTKHPNYFDA-- 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1927 imafDYTNYDGSIHPVWFQALKKVlenlsfQSNLIDRLCYSKH----------------LFKSTYYEVAGGVPSGCSGTS 1990
Cdd:cd23200   84 ----DYKNYDKYLHRQVFKAVRKI------QRSVIQQVCPDKWdkaraveeldaidtyvVDYQTVYKTNRGNKSGSYTTT 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1991 IFNTMINNII-----IRTLVLDAYKNIdLDKLKIIAYGDDVIFS----YKYTLDMEAIANEGKKYGLTITPADKSTEFKK 2061
Cdd:cd23200  154 IDNCLANDIYglyawVKTTGLRSLWDY-RQNVSSVAFGDDIIKSvsdeYKDKYNYCTYRDVLNATGHIMTPGSKDGEEKP 232

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 130486   2062 LDY-NNVTFLKRGFKQDEKHTF--LIHPTFPVEEIYESIRWTKKPSQ---MQEHVLSLchLMWhnGRKVYEDFSSKIR 2133
Cdd:cd23200  233 FTSfENLQFLKRGFKLENGMVLapLLQRSIEGPFVWTDIREDQITVWvnlVQEQLIEA--ALW--GEEYYNELCQKLK 306

Iflaviridae_RdRp

cd23197

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Iflaviridae of ...

1850-2128

1.32e-12

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Iflaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Iflaviridae, order Picornavirales. Iflaviridae is a family of small non-enveloped viruses with (+)ssRNA genomes of approximately 9-11 kilobases in length encoding a single polyprotein. All members infect arthropod hosts with the majority infecting insects. Beneficial and pest insects serve as hosts and infections can be symptomless (Nilaparvata lugens honeydew virus 1), cause developmental abnormalities (deformed wing virus, Varroa destructor virus 1, sacbrood virus), behavioral changes (deformed wing virus, Varroa destructor virus 1, slow bee paralysis virus, sacbrood virus) and premature mortality (deformed wing virus, Varroa destructor virus 1, slow bee paralysis virus, infectious flacherie virus, sacbrood virus). 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: 438047 Cd Length: 319 Bit Score: 71.05 E-value: 1.32e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1850 PMITFLKDELRKKEKI-SAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPgVVTGSAVGCDPETF-WSKI--PVMLDGD 1925
Cdd:cd23197    7 VYWAHLKDELRPSEKLrRFGGTRVFSVPPLELVLNSRRFLLPFMDAFQSFP-IEAHHAIGLNPNSGdWRRLrdTLLEKGP 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1926 CIMAFDYTNYDGSIHPVWFQALKKVLENLSFQ--------SNLIDRLCYSKH----LFKSTYYEVAGGVPSGCSGTSIFN 1993
Cdd:cd23197   86 CLLQMDYKNYSDAIPKECVAKAFHIIVDYYRKwhcltveiENALKTLFLDTAdaelLVYGDVFKVNNGVLAGHPMTSVVN 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1994 TMINniiirtLVLDAYKNIDLDKLK---------IIAYGDDVIFSYKYTL----DMEAIANEGKKYGLTITPADKSTEFK 2060
Cdd:cd23197  166 SVVN------LILMNYMWIKITRRRaseffkltyIIVMGDDVVISLPKQLteefDCRKICAEFAKYDIKVTDSEKNLTGE 239

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 130486   2061 KLDYNNV---TFLKRGFKQDEKHTFLIHPTFPVEEIYESIRWTKKPSQMQEHVLSLCH----LMWHNGRKVYEDF 2128
Cdd:cd23197  240 PKPYDSFdkfEFLSRGFSDCDAYPDITFAPVKTIALFDCPLWISKGQDEEEQTIQAIQagllLAFDHGPEFFGKY 314

Polycipiviridae_RdRp

cd23198

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Polycipiviridae of ...

1854-2132

5.86e-12

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Polycipiviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Polycipiviridae (polycistronic picorna-like viruses), order Picornavirales. Polycipiviridae is a family of picorna-like viruses with non-segmented, linear, (+)ssRNA genomes of approximately 10-12 kb. Their genomes are polycistronic, with four (or more) consecutive 5'-proximal open reading frames (ORFs) encoding structural (and possibly other) proteins and a long 3' ORF encoding the replication polyprotein. Members of species within the family are typically found in ants, with Apple picorna-like virus 1 and the unnamed Polycipiviridae virus in fruit bat stool as exceptions. 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: 438048 Cd Length: 317 Bit Score: 68.98 E-value: 5.86e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1854 FLKDELRKKEKI-----SAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPE--------TFWSKIPV 1920
Cdd:cd23198    6 FPKDELRPIYKAlgdpqTPPKTRSVTCMNVYYILAWRRVTLDFWASMHRAADGNFPFCPGINPEgpdwnrlyHYLNRHPN 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1921 MLDgdcimaFDYTNYDGSIHPVWFQALKKVLENL------SFQSNLIDRL------CYSKhlFKSTYYEVAGGVPSGCSG 1988
Cdd:cd23198   86 AVD------FDVSNWDGHLPAELFYAVLDIIKTVlglkpnSPNAKVIYSIltevmnCHIQ--FEDIIYQKLRGLISGFPG 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1989 TSIFNTMINNIIIRTLVLDAYKNIDLDK--------LKIIAYGDDVIFSY----KYTLDMEAIANEGKKYGLTITPADKS 2056
Cdd:cd23198  158 TAEVNTLAHWLLIYYIYLYLAQNTIYDMtitaflrnVSAIFYGDDIIITIsdeiLHWFNGKTIQRMYEEHGYPVTSAAKD 237

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   2057 TE--FKKlDYNNVTFLKRGFKQdekhtflIHPTF-----PVEEIYESIRWTKKPS----QMQEHVLSLCHLMWHNGRKVY 2125
Cdd:cd23198  238 TEipESK-PLSDCQFLKSSWNP-------ILPGYyirkmDIEVVYDLVYWVRAKEhprdQFYSNYHDALRILFGHGEQVF 309


                 ....*..
gi 130486   2126 EDFSSKI 2132
Cdd:cd23198  310 EAFREQV 316

ps-ssRNAv_RdRp-like

cd23167

conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...

1927-2030

1.34e-08

Pssm-ID: 438017 [Multi-domain] Cd Length: 73 Bit Score: 53.50 E-value: 1.34e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1927 IMAFDYTNYDGSIHPVWFQAlkkvlenlsfqsnlidrlcyskhlfkstyyevagGVPSGCSGTSIFNTMINNIIIRTLVL 2006
Cdd:cd23167    2 VVESDYSGFDSSISPDLLKA----------------------------------GQPSGSPNTSADNSLINLLLARLALR 47

                         90       100
                 ....*....|....*....|....*
gi 130486   2007 DAYKNIDLDK-LKIIAYGDDVIFSY 2030
Cdd:cd23167   48 KACGRAEFLNsVGILVYGDDSLVSV 72

RdRP_4

pfam02123

Viral RNA-directed RNA-polymerase; This family includes RNA-dependent RNA polymerase proteins ...

1862-2066

2.53e-08

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

Pssm-ID: 280316 Cd Length: 465 Bit Score: 59.01 E-value: 2.53e-08

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486     1862 KEKISAGKTRvieassindTILFRTTFGNLFSKFHLNPG--VVTGSAVGCDPET-----FWSKIPVMLDGDCIMAFDYTN 1934
Cdd:pfam02123  236 SMKLEHGKSR---------AIYACDTRSYLAFEYLLAPVekAWANKSVILNPGEgdisgFDWSVQDWKRGGVSLMLDYDD 306

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486     1935 YDgSIHPVWfqALKKVLENL-----SFQSNLIDRLCYSkhlFKSTY---------YEVAGGVPSGCSGTSIFNTMINNII 2000
Cdd:pfam02123  307 FN-SQHSTE--SMRAVFERLrrrlpDEPAEAADWLVCS---MDSMYqlsdgtllaQRVPGTLKSGHRATTFINSVLNCAY 380

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 130486     2001 IRTLVLDAyknidLDKLKIIAYGDDVIFSYKYTLDMEAIANEGKKYGLTITPA-----DKSTEFKKLDYNN 2066
Cdd:pfam02123  381 AELAGAPW-----ADVPTSIHMGDDVLEGLRTPADATSLLDKYARLGFKVNPSkqsvgHTIAEFLRVAFCS 446

ps-ssRNAv_Nodaviridae_RdRp

cd23173

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Nodaviridae of ...

1931-2074

1.76e-07

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Nodaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Nodaviridae, order Nodamuvirales. The family name Nodaviridae, derives from the Japanese village of Nodamura where Nodamura virus was first isolated from Culex tritaeniorhynchus mosquitoes. Virions are non-enveloped and spherical in shape with icosahedral symmetry and diameters ranging from 25 to 33 nm. The members of the two genera in this family infect insects (Alphanodavirus) or fish (Betanodavirus). Alphanodavirus infection results in the stunting, paralysis and death of the insect host. The infection of fish by betanodaviruses such as striped jack nervous necrosis virus or red-spotted grouper nervous necrosis virus causes neural necrosis, encephalopathy or retinopathy and is associated with behavioral abnormalities and high mortality, posing significant problems for marine aquaculture. The genome consists of two molecules of (+)ssRNA: RNA1 and RNA2. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438023 Cd Length: 236 Bit Score: 54.44 E-value: 1.76e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1931 DYTNYDGSIHPvWFQALKKVL------------ENLSFQSNLIDRLCYSKHLFKstyYEVAGGVPSGCSGTSIFNTMINN 1998
Cdd:cd23173   89 DYSRFDGTISE-WLRRNVEFAaylrwfhpeyraELLKLLDAEINCPARTKTGVK---YDPGVSRLSGSPTTTDGNTIINA 164

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1999 II----IRTLVLD---AYKNIDLdklkiiAYGDDVIFSYKYTLDMEAIAnegKKYGLTITpADKSTEfkkldYNNVTFLK 2071
Cdd:cd23173  165 FVsycaLRETGYSpeeAFALLGL------YYGDDGLSDNLPAEALEKVA---KDLGLKLK-IEVVRP-----GQPVTFLG 229


                 ...
gi 130486   2072 RGF 2074
Cdd:cd23173  230 RVF 232

ps-ssRNAv_Astroviridae_RdRp

cd23172

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Astroviridae of ...

1854-2035

5.50e-07

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Astroviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Astroviridae, order, Stellavirales. Astrovirus has a non-segmented, (+)ssRNA genome within a non-enveloped icosahedral capsid. The family Astroviridae comprises two genera, Mamastrovirus, which infect mammals, and Avastrovirus, which infect birds. Astroviruses have been isolated from stools from a wide variety of mammals and birds. Human astroviruses have been shown to be an important cause of gastroenteritis in young children. Duck astrovirus causes an often-fatal hepatitis in ducklings. Astroviruses infecting turkeys, guinea fowl and chickens affect multiple organs, including the kidney and thymus. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438022 Cd Length: 243 Bit Score: 52.86 E-value: 5.50e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1854 FLKDELRKKEKISAGKTRVIEASsinDTILFRttFGNLF-----SKFHLNPGVvTGSAVGCDPetFWSKIPVMLD----- 1923
Cdd:cd23172    7 FLKKEILKKEKIEDGDIRQILCP---DPIFAR--IGARFeqdqnNLMKERTLT-NEGQVGWSP--FYGGFDARVRrlgsk 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1924 GDCIMAFDYTNYDGSIhPVW---------FQAL--------KKVLENLSfqSNLIDRLCyskhLFKS-TYYEVAGGVPSG 1985
Cdd:cd23172   79 GNYFVEFDWTRFDGTI-PAElfrhirklrWSFLdpekteenRKVYDWYV--HNLLNRYV----LLPTgEVTRVTKGNPSG 151

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 130486   1986 CSGTSIFNTMInNIIIRTLVLdAY----KNIDLDKL----KIIAYGDDVIFSYKYTLD 2035
Cdd:cd23172  152 QISTTMDNCMV-NTFLTAFEF-AYvygpKTGTLKELwdnyDTIVYGDDRLSGYPSLPD 207

ps-ssRNAv_Potyviridae_RdRp

cd23175

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Potyviridae of ...

1854-2064

2.77e-04

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

Pssm-ID: 438025 Cd Length: 236 Bit Score: 44.75 E-value: 2.77e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1854 FLKDELRKKEKISAGKTRVIEASSInDTIL----FRTTFGNLFSKFHLN-PgvvtgSAVG-------CDpeTFWSKIPvm 1921
Cdd:cd23175    9 SLKAELRPIEKVEANKTRTFTAAPI-DTLLggkvCVDDFNNQFYSLHLKaP-----WTVGitkfyggWD--KLLRKLP-- 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1922 lDG----DCimafDYTNYDGSIHPVWFQALKKV--------------LENLSFQsnlidrLCYSK-HLFKSTYYEVAGGV 1982
Cdd:cd23175   79 -DGwvycDA----DGSQFDSSLTPYLINAVLRIrlhfmedwdigeqmLRNLYTE------IVYTPiLTPDGTIVKKFKGN 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1983 PSGCSGTSIFNTMINNI-----IIRTLVldAYKNIDlDKLKIIAYGDDVIFS----YKYTLDmeAIANEGKKYGLTITPA 2053
Cdd:cd23175  148 NSGQPSTVVDNTLMVMIamyyaLLKLGI--DFEEID-ERCVFFCNGDDLLIAvspeHEHILD--TFSSSFSELGLNYDFS 222

                        250
                 ....*....|.
gi 130486   2054 DKSTEFKKLDY 2064
Cdd:cd23175  223 SRTRDKEELWF 233

DEXXQc_SF1

cd18043

DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...

1213-1270

4.82e-04

Pssm-ID: 350801 [Multi-domain] Cd Length: 127 Bit Score: 42.18 E-value: 4.82e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486   1213 AVMIHGPPGTGKS-----ITTNFLAR----------------------MITNESDVYSLPPDPKYFDgydnqsVVIMDDI 1265
Cdd:cd18043   16 NVVIQGPPGTGKSqtianIIANALARgkrvlfvsekkaaldvvrfpcwIMSPLSVSQYLPLNRNLFD------LVIFDEA 89


                 ....*
gi 130486   1266 MQNPD 1270
Cdd:cd18043   90 SQIPI 94

Calici_coat

pfam00915

Calicivirus coat protein;

425-532

7.85e-04

Calicivirus coat protein;

Pssm-ID: 459994 Cd Length: 291 Bit Score: 43.73 E-value: 7.85e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 130486      425 PLATTLIGEIASYYTHWTGSLRFSFMFCGTANTTLKLLLAYTPPGIDkPATRKDAMLGTHVVWDVGLQSTISLVVPWVSA 504
Cdd:pfam00915   90 PHLNPFLLHLSQMYNGWSGGMRVRFMVAGSGVFGGKLAASVIPPGVE-PITSASMLQFPHVLFDARQLEPVIFTIPDLRN 168

                           90       100
                   ....*....|....*....|....*...
gi 130486      505 SHFRLTANDKYSMAgyITCWYQTNLVVP 532
Cdd:pfam00915  169 TLFHNMDRNTDTTR--LVIMVYNPLINP 194

CDC6

COG1474

Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];

1214-1252

4.86e-03

Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];

Pssm-ID: 441083 [Multi-domain] Cd Length: 389 Bit Score: 41.76 E-value: 4.86e-03

                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 130486   1214 VMIHGPPGTGKSITTNFLARMITNESDVYSLPPDPKYFD 1252
Cdd:COG1474   54 VLIYGPTGTGKTAVAKYVLEELEEEAEERGVDVRVVYVN 92

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