NCBI Conserved Domain Search

Conserved domains on [gi|2099547072|gb|UBI50867|]

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polyprotein [rhinovirus A61]

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 ...

1709-2160

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: 819.08 E-value: 0e+00

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1709 VHECGYPTIHTPAKTKLQPSVFFDVFEGSKEPAVLTEKDPRLTTDFNQALFSKYKGNVECNMSEHMQVAISHYSAQLMTL 1788
Cdd:cd23213      1 NKEVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1789 DIDPSNITLEESVFGTEGLEALDLNTSAGFPYIGMGIRKRDLINNSTKDITKLKMALDKYGVDLPMVTFLKDELRKKEKI 1868
Cdd:cd23213     81 DIDTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKV 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1869 MAGKTRVIEASSINDTIAFRMTYGKLFSSFHRNPGIVTGSAVGCDPETFWSKIPVMLDGeCIMAFDYTNYDGSIHPIWFE 1948
Cdd:cd23213    161 EKGKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDG-SLFAFDYTGYDASLSPVWFR 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1949 ALKQVLTNLSFEHR--LIDRLCKSKHIFKDTYYEVEGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKYIDLDKLKIIAYG 2026
Cdd:cd23213    240 ALKMVLEKGYSEEAvsLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYG 319

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2027 DDVIFSYKYPLDMEAIAAEGNKYGLTITPADKSDTFKKLDYSSVTFLKRGFKQDDKYPFLIHPTFPISEIHESIRWTKKP 2106
Cdd:cd23213    320 DDVIASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDP 399

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2099547072 2107 SQMQEHVLSLCHLMWHNGRDVYKEFERKIRSVSAGRALYIPPYDLLLHEWYEKF 2160
Cdd:cd23213    400 RNTQDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453

Pico_P2A

pfam00947

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

876-1001

1.70e-71

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

Pssm-ID: 395757 Cd Length: 127 Bit Score: 234.97 E-value: 1.70e-71

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  876 NLHLFN-SEAHDSILVSYSSDLVIYRTNTVGDDFIPTCDCTQATYYCRHKNRYYPITVTSHDWYEIQESEYYPKHIQYNL 954
Cdd:pfam00947    1 NRHLAThEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 2099547072  955 LIGEGPCEPGDCGGKLLCKHGVIGIITAGGEGHVAFVDLRHFLCAEE 1001
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVRDLLWLEE 127

Rhv

pfam00073

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

93-301

9.71e-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: 214.48 E-value: 9.71e-64

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072   93 TSQDVANAVVGYGVWPHYLTPQDATAIDKPSKPDTSSNRFYTLESQTWTNESKGW-WWKLPDALKDMGIFGENMFYHFLG 171
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFfWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  172 RSGYTVHVQCNASKFHQGTLLVAMIPEHQlatavggsvsagynyTHPGEKgrdvgklnresnprqpsddnwlnfdgTLLG 251
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPPGA---------------PPPGSR--------------------------DYLW 119

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 2099547072  252 NLTIFPHQFINLRSNNSATIIVPYVNAVPMDSMLRHNNWSLVIIPICELR 301
Cdd:pfam00073  120 QATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGNWTLVVAGWVPLN 169

Peptidase_C3 super family

cl02893

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

1518-1683

4.68e-58

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: 198.44 E-value: 4.68e-58

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1518 GPEEEFGRSLIKHNTCIVTTDNGKFTGL--GIYDKLMILPTHADPGKEIYINGIATRVSD-SYDMYNKQGIKLEITAVLL 1594
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1595 DRNEKFRDIRKYIPEREDDYPECNLALVANQPEPTIISVGDVISYGNI-LLSGNQTARMLKYNYPTKSGYCGGVLYKI-- 1671
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVVIAKve 160

                          170
                   ....*....|....
gi 2099547072 1672 --GQIIGIHVGGNG 1683
Cdd:pfam00548  161 gnGKILGMHIAGNG 174

Rhv

pfam00073

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

358-523

1.94e-49

Pssm-ID: 395026 Cd Length: 170 Bit Score: 173.65 E-value: 1.94e-49

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  358 YHPTKEISIPGQVRNLVELCQVDTLIPINNTEANIRNKNMYTVQLGGEPDPTTPVFTIRVDIASqpLATTLIGEISSYYT 437
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFFWWKLPLAL--LSMGLLGRLLRYHT 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  438 HWTGSVRFSFMFCGSALTTLKLLIAYTPPGIRVPRSR---KEAMLGTHLIWDVGLQSTVSMVVPWVSASHYRNTTPD--- 511
Cdd:pfam00073   79 YYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRdylWQATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDgnw 158

                          170
                   ....*....|..
gi 2099547072  512 TYSLAGFITCWY 523
Cdd:pfam00073  159 TLVVAGWVPLNY 170

Rhv

pfam00073

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

615-767

3.45e-46

Pssm-ID: 395026 Cd Length: 170 Bit Score: 164.41 E-value: 3.45e-46

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  615 PEDMIETRYVQTSQTRDEMSIESFLGRSGCIHMSTLN-----INYDNYDDSIENFKVWKINL--QEMAQIRRKFELFTYA 687
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGerfytLDSTDWTSLSKGFFWWKLPLalLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  688 RFDSEITIVPCvagqGGDIGHVVMQYMYVPPGAPTPEKRnDFTWQSGTNASVFWQHG-QAYPRFSLPFLSIASAYYMFYD 766
Cdd:pfam00073   81 RGGLEVTVQFN----GSKFHQGKLLVAYVPPGAPPPGSR-DYLWQATLNPHQFWNLGlNSSARLSVPYISIAHYYSTFYD 155


                   .
gi 2099547072  767 G 767
Cdd:pfam00073  156 G 156

Pico_P2B super family

cl03260

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

1002-1098

2.87e-44

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: 155.95 E-value: 2.87e-44

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1002 QGVTDYIHMLGEAFGNGFV----DSVKDHVNAINPINNISKKVIKWLLRIVSAMVIIIRNSSDPQTVVATLTLIGCSGSP 1077
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTqqisDKIKELTNFINPTSKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|.
gi 2099547072 1078 WRFLKEKFCKWTQLTYIHKES 1098
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

1.48e-40

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: 144.44 E-value: 1.48e-40

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2099547072    2 GAQVSRQNVGTHSTQNSVSNGSSLNYFNINYFKDAASSGASKLEFSQDPSKFTDPVKDVLEKGIPTLQ 69
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 68

RNA_helicase

pfam00910

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

1217-1313

1.03e-39

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: 143.13 E-value: 1.03e-39

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1217 VMIHGSPGTGKSITTNFLARMI-----TNESDIYSLPPDPKYFDGYDQQSVVIMDDIMQNPDGEDMALFCQMVSSVTFIP 1291
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALlkklgLPKDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 2099547072 1292 PMADLPDKGKPFDSRFVLCSTN 1313
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

P3A super family

cl07374

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

1416-1466

3.58e-18

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: 80.16 E-value: 3.58e-18

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2099547072 1416 AIFQGpISMEV-----PPPPAITDLLRSVKTPEVIKYCEDNKWI--IPADCKIERDLN 1466
Cdd:pfam08727    1 AIFQG-IDLKIdiktsPPPEAIADLLQAVDSPEIIDYCEDKGWIvnIPAECQIERDIG 57

Name

Accession

Description

Interval

E-value

Enterovirus_RdRp

cd23213

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

1709-2160

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: 819.08 E-value: 0e+00

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1709 VHECGYPTIHTPAKTKLQPSVFFDVFEGSKEPAVLTEKDPRLTTDFNQALFSKYKGNVECNMSEHMQVAISHYSAQLMTL 1788
Cdd:cd23213      1 NKEVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1789 DIDPSNITLEESVFGTEGLEALDLNTSAGFPYIGMGIRKRDLINNSTKDITKLKMALDKYGVDLPMVTFLKDELRKKEKI 1868
Cdd:cd23213     81 DIDTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKV 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1869 MAGKTRVIEASSINDTIAFRMTYGKLFSSFHRNPGIVTGSAVGCDPETFWSKIPVMLDGeCIMAFDYTNYDGSIHPIWFE 1948
Cdd:cd23213    161 EKGKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDG-SLFAFDYTGYDASLSPVWFR 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1949 ALKQVLTNLSFEHR--LIDRLCKSKHIFKDTYYEVEGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKYIDLDKLKIIAYG 2026
Cdd:cd23213    240 ALKMVLEKGYSEEAvsLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYG 319

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2027 DDVIFSYKYPLDMEAIAAEGNKYGLTITPADKSDTFKKLDYSSVTFLKRGFKQDDKYPFLIHPTFPISEIHESIRWTKKP 2106
Cdd:cd23213    320 DDVIASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDP 399

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2099547072 2107 SQMQEHVLSLCHLMWHNGRDVYKEFERKIRSVSAGRALYIPPYDLLLHEWYEKF 2160
Cdd:cd23213    400 RNTQDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453

Pico_P2A

pfam00947

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

876-1001

1.70e-71

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

Pssm-ID: 395757 Cd Length: 127 Bit Score: 234.97 E-value: 1.70e-71

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  876 NLHLFN-SEAHDSILVSYSSDLVIYRTNTVGDDFIPTCDCTQATYYCRHKNRYYPITVTSHDWYEIQESEYYPKHIQYNL 954
Cdd:pfam00947    1 NRHLAThEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 2099547072  955 LIGEGPCEPGDCGGKLLCKHGVIGIITAGGEGHVAFVDLRHFLCAEE 1001
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVRDLLWLEE 127

Rhv

pfam00073

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

93-301

9.71e-64

Pssm-ID: 395026 Cd Length: 170 Bit Score: 214.48 E-value: 9.71e-64

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072   93 TSQDVANAVVGYGVWPHYLTPQDATAIDKPSKPDTSSNRFYTLESQTWTNESKGW-WWKLPDALKDMGIFGENMFYHFLG 171
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFfWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  172 RSGYTVHVQCNASKFHQGTLLVAMIPEHQlatavggsvsagynyTHPGEKgrdvgklnresnprqpsddnwlnfdgTLLG 251
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPPGA---------------PPPGSR--------------------------DYLW 119

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 2099547072  252 NLTIFPHQFINLRSNNSATIIVPYVNAVPMDSMLRHNNWSLVIIPICELR 301
Cdd:pfam00073  120 QATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGNWTLVVAGWVPLN 169

Peptidase_C3

pfam00548

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

1518-1683

4.68e-58

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: 198.44 E-value: 4.68e-58

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1518 GPEEEFGRSLIKHNTCIVTTDNGKFTGL--GIYDKLMILPTHADPGKEIYINGIATRVSD-SYDMYNKQGIKLEITAVLL 1594
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1595 DRNEKFRDIRKYIPEREDDYPECNLALVANQPEPTIISVGDVISYGNI-LLSGNQTARMLKYNYPTKSGYCGGVLYKI-- 1671
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVVIAKve 160

                          170
                   ....*....|....
gi 2099547072 1672 --GQIIGIHVGGNG 1683
Cdd:pfam00548  161 gnGKILGMHIAGNG 174

Rhv

pfam00073

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

358-523

1.94e-49

Pssm-ID: 395026 Cd Length: 170 Bit Score: 173.65 E-value: 1.94e-49

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  358 YHPTKEISIPGQVRNLVELCQVDTLIPINNTEANIRNKNMYTVQLGGEPDPTTPVFTIRVDIASqpLATTLIGEISSYYT 437
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFFWWKLPLAL--LSMGLLGRLLRYHT 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  438 HWTGSVRFSFMFCGSALTTLKLLIAYTPPGIRVPRSR---KEAMLGTHLIWDVGLQSTVSMVVPWVSASHYRNTTPD--- 511
Cdd:pfam00073   79 YYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRdylWQATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDgnw 158

                          170
                   ....*....|..
gi 2099547072  512 TYSLAGFITCWY 523
Cdd:pfam00073  159 TLVVAGWVPLNY 170

RdRP_1

pfam00680

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

1727-2137

6.79e-49

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: 181.84 E-value: 6.79e-49

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1727 PSVFFDVFEGSKEPAVLTEKDPR-----LTTDFNQALFSKYK-----GNVECNMSEHMQVAISHYSAQLMTLD-IDPSNI 1795
Cdd:pfam00680    2 PTERHLVAIPAYVPASLGPEDPRwarsyLNTDPYVDDIKKYSrpklpGPADERDKLLNRSAAKMVLSELRGVPkKANSTL 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1796 TLEESVFGTEGLEALDLNTSAGFPYIGMGIRKRDLIN----NSTKDI--TKLKMALDKY--GVDLPMV--TFLKDELRKK 1865
Cdd:pfam00680   82 IVYRAIDGVEQIDPLNWDTSAGYPYVGLGGKKGDLIEhlkdGTEARElaERLAADWEVLqnGTPLKLVyqTCLKDELRPL 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1866 EKIMAGKTRVIEASSINDTIAFRMTYGKLFSSFHRNPGIVTgSAVGCDPetFWSKIPVMLD-----GECIMAFDYTNYDG 1940
Cdd:pfam00680  162 EKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHP-IQVGINP--FDRGWPRLLRrlarfGDYVYELDYSGFDS 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1941 SIHPIWFEALKQVLT-------NLSFEHRLIDRLCKSKH-IFKDTYYEVEGGVPSGCSGTSIFNTMINNIIIRTLVL--- 2009
Cdd:pfam00680  239 SVPPWLIRFAFEILRellgfpsNVKEWRAILELLIYTPIaLPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYALLksl 318

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2010 --DAYKYIDLDKLKI-IAYGDDVIFSYKYPLD--MEAIAAEGNKYGLTITPADKS-DTFKKLDysSVTFLKRGFKQDdky 2083
Cdd:pfam00680  319 enDGPRVCNLDKYFDfFTYGDDSLVAVSPDFDpvLDRLSPHLKELGLTITPAKKTfPVSRELE--EVSFLKRTFRKT--- 393

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2099547072 2084 PFLIHPTFPISEIHESIRWTKKPSQMQEHVLSLCHLMWHNGRDVYKEFERKIRS 2137
Cdd:pfam00680  394 PGGYRPPLDRKRILAQLEYIRSKPVPSGQLENIRAYASHHGYEFYRDLLYRFVE 447

Rhv

pfam00073

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

615-767

3.45e-46

Pssm-ID: 395026 Cd Length: 170 Bit Score: 164.41 E-value: 3.45e-46

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  615 PEDMIETRYVQTSQTRDEMSIESFLGRSGCIHMSTLN-----INYDNYDDSIENFKVWKINL--QEMAQIRRKFELFTYA 687
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGerfytLDSTDWTSLSKGFFWWKLPLalLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  688 RFDSEITIVPCvagqGGDIGHVVMQYMYVPPGAPTPEKRnDFTWQSGTNASVFWQHG-QAYPRFSLPFLSIASAYYMFYD 766
Cdd:pfam00073   81 RGGLEVTVQFN----GSKFHQGKLLVAYVPPGAPPPGSR-DYLWQATLNPHQFWNLGlNSSARLSVPYISIAHYYSTFYD 155


                   .
gi 2099547072  767 G 767
Cdd:pfam00073  156 G 156

Pico_P2B

pfam01552

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

1002-1098

2.87e-44

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: 155.95 E-value: 2.87e-44

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1002 QGVTDYIHMLGEAFGNGFV----DSVKDHVNAINPINNISKKVIKWLLRIVSAMVIIIRNSSDPQTVVATLTLIGCSGSP 1077
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTqqisDKIKELTNFINPTSKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|.
gi 2099547072 1078 WRFLKEKFCKWTQLTYIHKES 1098
Cdd:pfam01552   81 WQFLKEKACAVLEIPYVHKQG 101

rhv_like

cd00205

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

373-558

5.81e-41

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: 149.85 E-value: 5.81e-41

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  373 LVELCQVDTLIPINNTeanirnknmytvqlgGEPDPTTPVFTIRVDIASQPL--ATTLIGEISSYYTHWTGSVRFSFMFC 450
Cdd:cd00205      1 VESFADRPTTVGTNNW---------------NSSASGTQLFQWKLSPALGFLllQNTPLGALLSYFTYWRGDLEVTVQFN 65

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  451 GSALTTLKLLIAYTPPGIRVP---RSRKEAMLGTHLIWDVGLQSTVSMVVPWVSASHYRNTTPDTYSLA---GFITCWYQ 524
Cdd:cd00205     66 GSKFHTGRLLVAYVPPGAPAPttgDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDGYGPLnsfGTLVVRVL 145

                          170       180       190
                   ....*....|....*....|....*....|....
gi 2099547072  525 TKLVVPPNTASTADMLCFVSGcKDFCLRMARDTN 558
Cdd:cd00205    146 TPLTVPSGAPTTVDITVYVRA-GDFELYGPRPPR 178

Pico_P1A

pfam02226

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

2-69

1.48e-40

Pssm-ID: 308053 Cd Length: 68 Bit Score: 144.44 E-value: 1.48e-40

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2099547072    2 GAQVSRQNVGTHSTQNSVSNGSSLNYFNINYFKDAASSGASKLEFSQDPSKFTDPVKDVLEKGIPTLQ 69
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 68

RNA_helicase

pfam00910

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

1217-1313

1.03e-39

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: 143.13 E-value: 1.03e-39

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1217 VMIHGSPGTGKSITTNFLARMI-----TNESDIYSLPPDPKYFDGYDQQSVVIMDDIMQNPDGEDMALFCQMVSSVTFIP 1291
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALlkklgLPKDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 2099547072 1292 PMADLPDKGKPFDSRFVLCSTN 1313
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

rhv_like

cd00205

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

125-329

3.29e-35

Pssm-ID: 119412 Cd Length: 178 Bit Score: 133.29 E-value: 3.29e-35

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  125 PDTSSNRFYTLESQTWT---NESKGWWWKLPDA----LKDMGIFGENMFYHFLGRSGYTVHVQCNASKFHQGTLLVAMIP 197
Cdd:cd00205      1 VESFADRPTTVGTNNWNssaSGTQLFQWKLSPAlgflLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  198 EHQLATAvggsvsagynythpgekgrdvgklnresnprqpsddnwlnfDGTLLGNLTIFPHQFINLRSNNSATIIVPYVN 277
Cdd:cd00205     81 PGAPAPT-----------------------------------------TGDTRWQATLNPHVIWDLGTNSSVTFVVPYVS 119

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2099547072  278 AVPMDSMLRH------NNWSLVIIPICELR-GSGVDLTIPITISISPMCAEFSGARANS 329
Cdd:cd00205    120 PTPYRSTRYDgygplnSFGTLVVRVLTPLTvPSGAPTTVDITVYVRAGDFELYGPRPPR 178

rhv_like

cd00205

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

635-823

1.19e-34

Pssm-ID: 119412 Cd Length: 178 Bit Score: 131.75 E-value: 1.19e-34

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  635 IESFLGRSGCIHMSTlninyDNYDDSIENFKVWKINLQE------MAQIRRKFELFTYARFDSEITIVPCvagqgGDIGH 708
Cdd:cd00205      1 VESFADRPTTVGTNN-----WNSSASGTQLFQWKLSPALgflllqNTPLGALLSYFTYWRGDLEVTVQFN-----GSKFH 70

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  709 -VVMQYMYVPPGAPTPEKrNDFTWQSGTNASVFWQHGQAYP-RFSLPFLSIASAYYMFYDGYDgdsestrygtsVTNDMG 786
Cdd:cd00205     71 tGRLLVAYVPPGAPAPTT-GDTRWQATLNPHVIWDLGTNSSvTFVVPYVSPTPYRSTRYDGYG-----------PLNSFG 138

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 2099547072  787 ALCFRIVTE-----QHTNQVKITtrIYHKAKHVKVWCPRPPR 823
Cdd:cd00205    139 TLVVRVLTPltvpsGAPTTVDIT--VYVRAGDFELYGPRPPR 178

P3A

pfam08727

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

1416-1466

3.58e-18

Pssm-ID: 400873 Cd Length: 59 Bit Score: 80.16 E-value: 3.58e-18

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2099547072 1416 AIFQGpISMEV-----PPPPAITDLLRSVKTPEVIKYCEDNKWI--IPADCKIERDLN 1466
Cdd:pfam08727    1 AIFQG-IDLKIdiktsPPPEAIADLLQAVDSPEIIDYCEDKGWIvnIPAECQIERDIG 57

DEXXQc_SF1

cd18043

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

1204-1273

7.19e-03

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: 38.72 E-value: 7.19e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1204 TIIKQKKRSEpvAVMIHGSPGTGKS-----ITTNFLAR----------------------MITNESDIYSLPPDPKYFDg 1256
Cdd:cd18043      6 AAIISARNGK--NVVIQGPPGTGKSqtianIIANALARgkrvlfvsekkaaldvvrfpcwIMSPLSVSQYLPLNRNLFD- 82

                           90
                   ....*....|....*..
gi 2099547072 1257 ydqqsVVIMDDIMQNPD 1273
Cdd:cd18043     83 -----LVIFDEASQIPI 94

Name

Accession

Description

Interval

E-value

Enterovirus_RdRp

cd23213

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

1709-2160

0e+00

Pssm-ID: 438063 Cd Length: 453 Bit Score: 819.08 E-value: 0e+00

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1709 VHECGYPTIHTPAKTKLQPSVFFDVFEGSKEPAVLTEKDPRLTTDFNQALFSKYKGNVECNMSEHMQVAISHYSAQLMTL 1788
Cdd:cd23213      1 NKEVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1789 DIDPSNITLEESVFGTEGLEALDLNTSAGFPYIGMGIRKRDLINNSTKDITKLKMALDKYGVDLPMVTFLKDELRKKEKI 1868
Cdd:cd23213     81 DIDTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKV 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1869 MAGKTRVIEASSINDTIAFRMTYGKLFSSFHRNPGIVTGSAVGCDPETFWSKIPVMLDGeCIMAFDYTNYDGSIHPIWFE 1948
Cdd:cd23213    161 EKGKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDG-SLFAFDYTGYDASLSPVWFR 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1949 ALKQVLTNLSFEHR--LIDRLCKSKHIFKDTYYEVEGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKYIDLDKLKIIAYG 2026
Cdd:cd23213    240 ALKMVLEKGYSEEAvsLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYG 319

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2027 DDVIFSYKYPLDMEAIAAEGNKYGLTITPADKSDTFKKLDYSSVTFLKRGFKQDDKYPFLIHPTFPISEIHESIRWTKKP 2106
Cdd:cd23213    320 DDVIASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDP 399

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2099547072 2107 SQMQEHVLSLCHLMWHNGRDVYKEFERKIRSVSAGRALYIPPYDLLLHEWYEKF 2160
Cdd:cd23213    400 RNTQDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453

Sapelovirus_RdRp

cd23218

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

1801-2160

2.95e-165

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: 511.37 E-value: 2.95e-165

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1801 VFGTEGLEALDLNTSAGFPYIGMGIRKRDLINNSTKDITKLKMALDKYGVDLPMVTFLKDELRKKEKIMAGKTRVIEASS 1880
Cdd:cd23218      3 VYGIDNLEGLDLNTSAGYPYNTMGIRKKDLIPPRGEPLSPLLKALDLHGYDLPFTTYLKDELRPKEKVKMGKTRLIECSS 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1881 INDTIAFRMTYGKLFSSFHRNPGIVTGSAVGCDPETFWSKIPVMLDGECIMAFDYTNYDGSIHPIWFEALKQVLTNLSFE 1960
Cdd:cd23218     83 LNDTIRMKRIFGRLFQTFHKNPGTYTGSAVGCNPDVHWSKFAEEGGMDNVCAFDYTNWDASLSPFWFDALKLFLSKLGYS 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1961 HR---LIDRLCKSKHIFKDTYYEVEGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKYIDLDKLKIIAYGDDVIFSYKYPL 2037
Cdd:cd23218    163 ERdivLIDHLCYSNHIFKNEGYKVAGGMPSGCSGTSIFNSIINNIVVRTLVLLVYKGINLDELRILCYGDDLLVAYPYPL 242

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2038 DMEAIAAEGNKYGLTITPADKSDTF---KKLdySSVTFLKRGFKQDDKYPFLIHPTFPISEIHESIRWTKKPSQMQEHVL 2114
Cdd:cd23218    243 DPNVLADLGKSLGLTMTPADKSDTFqgcTKL--TEVTFLKRSFVFDEEFPFLCHPVFPMEEVHESIRWTRNASTTQEHVT 320

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*.
gi 2099547072 2115 SLCHLMWHNGRDVYKEFERKIRSVSAGRALYIPPYDLLLHEWYEKF 2160
Cdd:cd23218    321 SLCLLAWHNGEEVYEEFCEKIRSVPVGRALILPPYSQLRRSWLDMF 366

Rabovirus_RdRp

cd23230

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

1800-2160

1.71e-160

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: 498.25 E-value: 1.71e-160

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1800 SVFGTEGLEALDLNTSAGFPYIGMGIRKRDLINNSTKDITKLKMALDKYGVDLPMVTFLKDELRKKEKIMAGKTRVIEAS 1879
Cdd:cd23230      1 AAYGIENLEGLDLNTSAGYPYVLNGIKKRDILDPETRDTTKLQECLDKYGVDLPFVTYLKDELRPLEKIKKGKTRLIECS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1880 SINDTIAFRMTYGKLFSSFHRNPGIVTGSAVGCDPETFWSKIPVMLDGEcIMAFDYTNYDGSIHPIWFEALKQVLTNLSF 1959
Cdd:cd23230     81 SMNDTIRMKMMFGRLFATYHRNPGPITGSAVGCNPDIHWTKFRAEMHGE-IIAFDYSNYDASLNKVWFECLKMVLKNFGF 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1960 -EHRLIDRLCKSKHIFKDTYYEVEGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKYIDLDKLKIIAYGDDVIFSYKYPLD 2038
Cdd:cd23230    160 kDLRPIDHIIRSRHIYKGIEYDVEGGMPSGCSGTSIFNSIINNIIIMTLVLDAYKGIDLEQLKIIAYGDDVIVTYPYPLD 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2039 MEAIAAEGNKYGLTITPADKSDTFKKLDYSSVTFLKRGFKQDDKYPFLIHPTFPISEIHESIRWTKKPSQMQEHVLSLCH 2118
Cdd:cd23230    240 AALLADCGKKYGLKMTPPDKSAEFKNVTWEDVTFLKRRFKPAKHYPFLIHPVFDQQEILESLRWTRNPAHTQEHVRSLAE 319

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|..
gi 2099547072 2119 LMWHNGRDVYKEFERKIRSVSAGRALYIPPYDLLLHEWYEKF 2160
Cdd:cd23230    320 LAWHSGRKSYEEFCNLVKSTNVGKACILPPYESFKRMWLDQF 361

ps-ssRNA_Picornaviridae

cd23193

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

1801-2136

8.82e-139

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: 436.59 E-value: 8.82e-139

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1801 VFGTEGLEALDLNTSAGFPYIGMGIRKRDLINNSTKDIT-----KLKMALDKYGVDLPMVTFLKDELRKKEKIMAGKTRV 1875
Cdd:cd23193      2 INGIDGLDPIDLNTSPGYPYTTQGLRRRDLIDNDKGGVSplleeEEQVLLDLDGPDVVFTTFLKDELRPKEKVKAGKTRV 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1876 IEASSINDTIAFRMTYGKLFSSFHRNPGIVTGSAVGCDPETFWSKIPVMLDGECIMAFDYTNYDGSIHPIWFEALKQVLT 1955
Cdd:cd23193     82 IEAAPLDYVIAGRMVFGRLFAQFHSNPGILTGSAVGCNPDTDWTRLFASLKQDNVYDLDYSGFDASLSSQLFEAAVEVLA 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1956 N-LSFEH---RLIDRLCKSKHIFKDTYYEVEGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKyIDLDKLKIIAYGDDVIF 2031
Cdd:cd23193    162 EcHGDPElvlRYLEPIINSKHVVGDERYTVEGGMPSGCPCTSILNSICNNLVVRYALLETGK-FDPDEYYILAYGDDVLV 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2032 SYKYPLDMEAIAAEGNKY-GLTITPADKSDTFKKLDYSSVTFLKRGFKQDDKYpFLIHPTFPISEIHESIRWTKKPSQMQ 2110
Cdd:cd23193    241 STDEPIDPSDLAEFYKKYfGMTVTPADKSSDFPESSPIEDVFLKRRFFVPDGT-FLIHPVMDLETLEQSLMWCGRGGFFQ 319

                          330       340
                   ....*....|....*....|....*.
gi 2099547072 2111 EHVLSLCHLMWHNGRDVYKEFERKIR 2136
Cdd:cd23193    320 QLLSSLCELALHHGPEEYERLVSKVR 345

Cardiovirus_RdRp

cd23211

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

1715-2160

4.35e-83

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: 281.73 E-value: 4.35e-83

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1715 PTIHTPAKTKLQPSVFFDVFEGSKEPAVLTEKDPRLTTDFNQALFSKYKGNVECNMSEHMQVAISHYSAQLMTLDIDPSN 1794
Cdd:cd23211     10 PVVHVPRKTKLRRTVAHPVFQPKFEPAVLSKYDPRTDKDVDEVAFSKHTTNQESLPPVFRMVAKEYANRVFTLLGKDNGR 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1795 ITLEESVFGTEGLEALDLNTSAGFPYIGMGIRKRDLINNSTKDITKL------KMALDKYGvDLPMVTFLKDELRKKEKI 1868
Cdd:cd23211     90 LTVEQAVLGLEGMDPMEKDTSPGLPYTQQGLRRTDVVDFETATMIPFlaeahrKMVEGDYS-DVVYQSFLKDEIRPIEKV 168

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1869 MAGKTRVIEASSINDTIAFRMTYGKLFSSFHRNPGIVTGSAVGCDPETFWSKIPVMLDG-ECIMAFDYTNYDGSIHPIWF 1947
Cdd:cd23211    169 QAAKTRIVDVPPFEHCILGRQLLGRFASKFQTNPGLELGSAIGCDPDVDWTAFAVALSGfKYVYDVDYSNFDSTHSTAMF 248

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1948 EALKQVLTNLS--FEHRLID---RLCKSKHIFKDTYYEVEGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKYIDLDKLKI 2022
Cdd:cd23211    249 ELLIENFFTEEngFDPRIGEylrSLAVSRHAYEERRVLIRGGLPSGCAATSMLNTIMNNIIIRAGLYLTYKNFEFDDIKV 328

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2023 IAYGDDVIFSYKYPLDMEAIAAEGNKYGLTITPADKSDTFKKLDY-SSVTFLKRGFKQDDkyPFLIHPTFPiSEIHESIR 2101
Cdd:cd23211    329 LSYGDDLLVATNYQIDFNLVKARLAKFGYKITPANKTSTFPLTSTlEDVVFLKRKFVKEN--SYLYRPVMD-RENLKAML 405

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2099547072 2102 WTKKPSQMQEHVLSLCHLMWHNGRDVYKEFERKIRSVsagrALYIPPYDLLLHEWYEKF 2160
Cdd:cd23211    406 SYYRPGTLKEKLTSIALLAVHSGKQVYDEIFAPFREV----GIVVPTYESVLYRWLSLF 460

Cosavirus_RdRp

cd23226

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

1701-2160

5.81e-83

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: 281.52 E-value: 5.81e-83

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1701 GEIVTSKKVhecgyPTIHTPAKTKLQPSVFFDVFEGSKEPAVLTEKDPRLT--TDFNQALFSKYKGNVECNMSEHMQVAI 1778
Cdd:cd23226      1 GQIVNTENG-----PRVHVPRQSKLKRTNATYPATGKYGPAVLSKNDPRLDpdVDFDKVIFSKHVANVVIDEDTSFWNAL 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1779 ShYSAQLMT---LDIDPSNITLEESVFGTEGLEALDLNTSAGFPYIGMgirKRDLINNSTKDI--TKLKMALDKY----G 1849
Cdd:cd23226     76 K-MSAQIYAekfKGVDFSPLTVEEAILGIPGLDRMDPNTASGLPYTKT---RRQMIDFQEGKIldPELQERLDTWlsgkQ 151

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1850 VDLPMVTFLKDELRKKEKIMAGKTRVIEASSINDTIAFRMTYGKLFSSFHRNPGIVTGSAVGCDPETFWSKIPVMLDG-E 1928
Cdd:cd23226    152 PEMLYQTFLKDEIRPIEKVKAGKTRIIDVTPLDHVLAFRIVLGRFMAHFHNNYGFELGSAVGCDPDVAWANFGFALSSkK 231

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1929 CIMAFDYTNYDGSIHPIWFEALKQVLTNLS--FEHR---LIDRLCKSKHIFKDTYYEVEGGVPSGCSGTSIFNTMINNII 2003
Cdd:cd23226    232 YQYDFDYSNFDASHSESIFELLKQFVFTKDngFDHRcslMIDSLVTSTHCYEDQRMTIRGGLPSGTSGTSVINTIINNII 311

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2004 IRTLVLDAYKYIDLDKLKIIAYGDDVIFSYKYPLDMEAIAAEGNKYGLTITPADKSDTFKKLDYSSVTFLKRGFKqddKY 2083
Cdd:cd23226    312 FKAALYHTYSNFEWDDVQMLAYGDDIVAASDCLLDLDRVKYFMALIGYKITPADKGEKFIPKDMQNIQFLKRSFR---KV 388

                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2099547072 2084 PFLIHPTFPISEIHESIRWTkKPSQMQEHVLSLCHLMWHNGRDVY-KEFERKIRSvsagrALYIPPYDLLLHEWYEKF 2160
Cdd:cd23226    389 AGVWAPIMDLENLQAMLSWY-KPGTLQEKLDSVARLAHFCGEKVYdHLFTTFVKD-----GFQIKPWKQLHFEWLNRF 460

Mischivirus_RdRp

cd23227

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

1715-2160

3.40e-78

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: 267.58 E-value: 3.40e-78

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1715 PTIHTPAKTKLQPSVFFDVFEGSKEPAVLTEKDPRLT--TDFNQALFSKYKGNvECNMSEHMQVAISHYSAQLMT-LDID 1791
Cdd:cd23227     10 PRIHVPRKTKLRKSPAYPIFKPDAGPAVLSKNDPRLAegVDFDKQVFSKHSAN-QKEYPKAFRRMARWYADRVFTyLGKD 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1792 PSNITLEESVFGTEGLEALDLNTSAGFPYIGMGIRKRDLINNSTKDITK--LKMALDKYG----VDLPMVTFLKDELRKK 1865
Cdd:cd23227     89 NGPLSVKDAIKGIDNLDAMDPTTSPGLPYSAAGIKRTDLLDFDTGEIISpaLRAEYNKYVsgdySDHVFQTFLKDEIRSE 168

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1866 EKIMAGKTRVIEASSINDTIAFRMTYGKLFSSFHRNPGIVTGSAVGCDPETFWSKIPVML-DGECIMAFDYTNYDGSIHP 1944
Cdd:cd23227    169 EKIKAGKTRIVDVPSLAHVIIGRVLLGKFCSKFQASPGTELGSAIGCNPDWDWTYFAHQLmERQWCYDIDYSNFDSTHGT 248

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1945 IWFEALKQVL--TNLSFEHRLID---RLCKSKHIFKDTYYEVEGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKYIDLDK 2019
Cdd:cd23227    249 GMFELLIDCFftPENGFSPAVAPylrSLAFSKHAWMDKRYKIEGGLPSGCSATSVLNTVMNNIIIRALLSLTYKNFHPED 328

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2020 LKIIAYGDDVIFSYKYPLD---MEAIAAEGNKYGLTItpADKSDTFKKLD-YSSVTFLKRGFKQDDKYPFLIHPTFPISE 2095
Cdd:cd23227    329 VLVLAYGDDLLVASDYQLDfnrVREKAAEHTLYKLTT--ANKAPDFPETStLLDCQFLKRKFVLHSTRNFIWRPVMDVTN 406

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2099547072 2096 IhESIRWTKKPSQMQEHVLSLCHLMWHNGRDVYKEFERKIRSVSagraLYIPPYDLLLHEWYEKF 2160
Cdd:cd23227    407 L-KTMLSFYKPNTLSEKLLSVAQLAFHSGYTVYEELFAPFKELQ----MTVPSWWYLEHEWEHNF 466

Megrivirus_RdRp

cd23223

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

1733-2131

1.46e-74

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: 255.92 E-value: 1.46e-74

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1733 VFEGSKEPAVLTEKDPRLT--TDFNQALFSKYKGNVEC--NMSEHMQVAISHYSAQLMTLDIDPSNI-TLEESVFGTEGL 1807
Cdd:cd23223      4 AFPVTHGPAALTNKDKRLEegVDLDDVMFSKHVPDHPGwpTLEPAMSYVVEDLMHKLGFSKDEPVPMwTLEQAINGEGVM 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1808 EALDLNTSAGFPYIGMGIRKR---DLINNSTKDITKLKMALD---KYGVDLPMVTFLKDELRKKEKIMAGKTRVIEASSI 1881
Cdd:cd23223     84 DGIDMGQSPGYPYNAQGRSRRsffEWNGEKWQPTEELKKEVDhalKDPDDFYFSTFLKDELRPLEKVKAGKTRLVDGDSL 163

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1882 NDTIAFRMTYGKLFSSFHRNPGIVTGSAVGCDPETFWSKI---------PVMLDgecimaFDYTNYDGSIHPIWFEALKQ 1952
Cdd:cd23223    164 PRILAMRMVFGPLFEAMLRKNGPEIHSAVGCNPDTDWTRYyhemgpdsfPYCFD------LDYSCFDSTEPKIAFRLMAK 237

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1953 VLTNLsFEH---RLIDRLCKSKHIFKDTYYEVEGGVPSGCSGTSIFNTMINNIIIRTLVLdAYKyIDLDKLKIIAYGDDV 2029
Cdd:cd23223    238 YLKPY-FSVdvtPFFEALATSKHVYGDKAYEMEGGMPSGCVGTSMFNCINNSAFIVSALI-ALK-ISPEDCAWICYGDDV 314

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2030 IFSYKYPLDMEAIAAEGNK-YGLTITPADKSDTFKKLD-YSSVTFLKRGFKQDDKYPFLIHPTFPISEIHESIRW-TKKP 2106
Cdd:cd23223    315 IISTDEKALSKRIADFYHKnTNLVVTPASKSGDFPETStIYDVTFLKRFFQPDSHYPHLIHPYMPLEHLEQSVMWqTDGP 394

                          410       420
                   ....*....|....*....|....*
gi 2099547072 2107 sqMQEHVLSLCHLMWHNGRDVYKEF 2131
Cdd:cd23223    395 --FQQKLDSLCLLAFHAGGPDYREF 417

Dicipivirus_RdRp

cd23222

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

1726-2156

4.49e-74

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: 255.28 E-value: 4.49e-74

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1726 QPSVFFDVFEGSKEPAVLTEKDPRLT--TDFNQALFSKYKGNVEC---NMSEHMQVAISHYSAQLMTLDIDPSniTLEES 1800
Cdd:cd23222      1 KPSPVYGVYPVTKEPAPLKPTDRRIDegVDFNEPVFGKYGADMKEpfrNLDVGRDVVIARLKKVLPNKKFAPC--TVSEA 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1801 VFGTEGLEALDLNTSAGFPYIGMGIRKRDLI--NNSTKDITKLKMALD-----KYGVDLPMVTFLKDELRKKEKIMAGKT 1873
Cdd:cd23222     79 LNGKDGLPKLDLKQASGYPYNLSAIKRKHLIesDKDGFLTATPKLLADieeskKHPEKFPYTSFLKDELRSVKKVKAGKT 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1874 RVIEASSINDTIAFRMTYGKLFSSFHRNPGIVTGSAVGCDPETFWSKI-PVMLDGECIMAFDYTNYDGSIHPIWFEALKQ 1952
Cdd:cd23222    159 RVVEAGSLPVIVEGRMIFGNLFAYFNTHPGFETMAAVGCDPEVCWTDWyYKMREKAHTWDYDYTGFDGSIPSCSFDALAD 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1953 VL----TNLSFEHRLIDRLCKSKHIFKDTYYEVEGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKYIDLDKLKIIAYGDD 2028
Cdd:cd23222    239 LLcefvENEDDVRRYISNIKNSYHAYDGNLYLIEGAMPSGCAGTSVFNCLINAMLCFSCFMDLEPEMDPFEPLLIAYGDD 318

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2029 VIFSYKYPLDMEAIAAEGNK-YGLTITPADKSDTFK-KLDYSSVTFLKRGFKQDDKYPfLIHPTFPISEIHESIRWTKKp 2106
Cdd:cd23222    319 ILVSSDHDLFPSRVSEWMKAnTTFKITPADKGEIFNdDSDVSDVRFLKRLFVEDPVCE-LIHPVIETETLEPSLNWCHE- 396

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2099547072 2107 SQMQEHVLSLCHLMWHNGRDVYKEFERKIRSVSAGRALYIP---PYDLLLHEW 2156
Cdd:cd23222    397 GEFETKVDAISMLAFHHGPEYYRDWCKKLTDICEERNISPPglkPYSVHRNRW 449

Pico_P2A

pfam00947

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

876-1001

1.70e-71

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

Pssm-ID: 395757 Cd Length: 127 Bit Score: 234.97 E-value: 1.70e-71

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  876 NLHLFN-SEAHDSILVSYSSDLVIYRTNTVGDDFIPTCDCTQATYYCRHKNRYYPITVTSHDWYEIQESEYYPKHIQYNL 954
Cdd:pfam00947    1 NRHLAThEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 2099547072  955 LIGEGPCEPGDCGGKLLCKHGVIGIITAGGEGHVAFVDLRHFLCAEE 1001
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVRDLLWLEE 127

Rosavirus_RdRp

cd23221

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

1803-2160

5.33e-71

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: 243.68 E-value: 5.33e-71

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1803 GTEGLEALDLNTSAGFPYIGMGIRKR---DLINNSTKDITKLKMALDKYGVDLPM---VTFLKDELRKKEKIMAGKTRVI 1876
Cdd:cd23221      4 GIDNMDGLDMNQSPGVPYVSEGVSRRslfDCVDGQWVPRERLASDIAQVSGDPSLghfATFLKDELRSTEKVAAGKTRVV 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1877 EASSINDTIAFRMTYGKLFSSFHRNPGIVTGSAVGCDPETFWSKIPVMLDGEC-IMAFDYTNYDGSIHPIWFEALKQVLT 1955
Cdd:cd23221     84 EAGSLPHIIVGRKIFGNLFALFNSNPGFQTMCAVGCDPDVTWTELYHPLSAKTyVFDYDYSGFDGSVPSCCFDALADLLA 163

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1956 NL----SFEHRLIDRLCKSKHIFKDTYYEVEGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKYIDLDKLKIIAYGDDVIF 2031
Cdd:cd23221    164 DFvegeEDVRKYISSLKTSFHHYKGKLWRLDGAMPSGCCGTSVFNSLINAMLLFSAFSQICPDFRASEPLLVAYGDDVLV 243

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2032 SYKYPLDMEAIAAEGNKY-GLTITPADKSDTFK-KLDYSSVTFLKRGFKQDDKYPFLIHPTFPISEIHESIRWtKKPSQM 2109
Cdd:cd23221    244 GTDQPLFPSKVAEWVNSHtTFRITPADKGSVFNdESDIHSVQFLKRHFTPDPDFPALIHPTIDPDTYEQSVMW-QRTGDF 322

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2099547072 2110 QEHVLSLCHLMWHNGRDVYKEFERKI--RSVSAGRAL-YIPPYDLLLHEWYEKF 2160
Cdd:cd23221    323 QETVNSLALLVFHRGPKSYSRWCESVtrKCVDGGYPPpFFPPFSLLRHQWLKKF 376

Aphthovirus_RdRp

cd23210

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

1717-2159

1.74e-70

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: 245.24 E-value: 1.74e-70

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1717 IHTPAKTKLQPSVFFDVFEGSKEPAVLTEKDPRLT--TDFNQALFSKYKGNVECNMSEH--MQVAISHYSAQLMT-LDID 1791
Cdd:cd23210      6 VHVMRKTKLAPTVAHGVFNPEFGPAALSNKDPRLNegVVLDEVIFSKHKGDTKMSAEDKalFRRCAADYASRLHSvLGTA 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1792 PSNITLEESVFGTEGLEALDLNTSAGFPYIGMGIRKRDLI---NNSTKDITKLKMAL-DKYGVDLPMVTFLKDELRKKEK 1867
Cdd:cd23210     86 NAPLSIYEAIKGVDGLDAMEPDTAPGLPWALQGKRRGALIdfeNGTVGPEVEAALKLmEKREYKFACQTFLKDEIRPMEK 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1868 IMAGKTRVIEASSINDTIAFRMTYGKLFSSFHRNPGIVTGSAVGCDPETFWSKIPVMLDG-ECIMAFDYTNYDGSiHPIw 1946
Cdd:cd23210    166 VRAGKTRIVDVLPVEHILYTRMMIGRFCAQMHSNNGPQIGSAVGCNPDVDWQRFGTHFAQyRNVWDVDYSAFDAN-HCS- 243

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1947 fEALKQVLTNL-SFEH-------RLIDRLCKSKHIFKDTYYEVEGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKYIDLD 2018
Cdd:cd23210    244 -DAMNIMFEEVfRTEFgfhpnaeWILKTLVNTEHAYENKRITVEGGMPSGCSATSIINTILNNIYVLYALRRHYEGVELD 322

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2019 KLKIIAYGDDVIFSYKYPLDMEAIAAEGNKYGLTITPADKSDTFKKLDY--SSVTFLKRGFKQDDKYPFLiHPTFPISEI 2096
Cdd:cd23210    323 TYTMISYGDDIVVASDYDLDFEALKPHFKSLGQTITPADKSDKGFVLGHsiTDVTFLKRHFHMDYGTGFY-KPVMASKTL 401

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2099547072 2097 hESIRWTKKPSQMQEHVLSLCHLMWHNGRDVYkefeRKIRSVSAGrALYIPPYDLLLHEWYEK 2159
Cdd:cd23210    402 -EAILSFARRGTIQEKLISVAGLAVHSGPDEY----RRLFEPFQG-LFEIPSYRSLYLRWVNA 458

Mosavirus_RdRp

cd23225

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

1808-2159

4.77e-69

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: 238.28 E-value: 4.77e-69

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1808 EALDLNTSAGFPYIGMGIRKRDLINNSTKDITKLKMALDK---------YGVDLP-MVTFLKDELRKKEKIMAGKTRVIE 1877
Cdd:cd23225     10 DAMDMTKAVGYPYCLDSIKRLDLVEIKETENGKVYLPTERlveetekffTGEEKPkFVTFLKDEVRSNEKIKQGKTRIVD 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1878 ASSINDTIAFRMTYGKLFSSFHRNPGIVTGSAVGCDPETFWSKIPVMLDGECIMAFDYTNYDgSIHPiwfEALKQVLTNL 1957
Cdd:cd23225     90 ASPFPYAIAGRMVMQNFMSNMMRCNGTEVGSAVGCDPDTEWTRYFFELCDRYVFDLDYKAFD-STHP---TAMFNLLAER 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1958 SFEHR----------LIDRLCKSKHIFKDTYYEVEGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKY--IDLDKLKIIAY 2025
Cdd:cd23225    166 FFTERngfdqqavriFLNGLSDSDHVYEGKHFRIRGGLPSGCPCTSILNTVINNIIVRAAILGAYQIdtVDFQKFRMLAY 245

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2026 GDDVIFSYKYPLDMEAIAAEGNK-YGLTITPADKSDTF-KKLDYSSVTFLKRGFKQDDKYPFLIHPTFPISEIHESIRWT 2103
Cdd:cd23225    246 GDDVVYATPQPIKPQDLADWLHAnTNYKVTPASKAGTFpEESTIWDVTFLKRSFKPDEDHGHLIRPVMAVGNLKQMLSFM 325

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2099547072 2104 kKPSQMQEHVLSLCHLMWHNGRDVYKEFERKIRSVSAGRAlyIPPYDLLLHEWYEK 2159
Cdd:cd23225    326 -RPGTFPDKVRSVAGLAVHCGEEDYNQLADAVALYVPGVS--MPAYKYMKACWYAK 378

ps-ssRNAv-Picornavirales

cd23169

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

1855-2136

9.16e-69

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: 234.80 E-value: 9.16e-69

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1855 VTFLKDELRKKEKIMAGKTRVIEASSINDTIAFRMTYGKLFSSFHRNPgIVTGSAVGCDPE-TFWSKIPVML--DGECIM 1931
Cdd:cd23169      4 VDCLKDELRPIEKVKAGKTRLFSASPLDYTIAFRKYFGDFIAAFQKNR-IKLEHAVGINPDsVEWTRLYRRLlkKGPNIF 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1932 AFDYTNYDGSIHPIWFEALKQVLTNL-----SFEHR-----LIDRLCKSKHIFKDTYYEVEGGVPSGCSGTSIFNTMINN 2001
Cdd:cd23169     83 AGDYSNFDGSLPPDVMEAAFDIINDWydeyvDDEDErvrkvLFEELINTIHLVGNLVYQVHGGNPSGNPLTTIINSIVNL 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2002 IIIRTLVLDAYKYIDLDK----LKIIAYGDDVIFS----YKYPLDMEAIAAEGNKYGLTITPADKSDTFKKLD-YSSVTF 2072
Cdd:cd23169    163 LYIRYAWLRITGLTSLSDfkknVRLVTYGDDVIISvsdeVKDEFNFVTISEFLKELGITYTDADKSGDIVPYRpLEEVTF 242

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2099547072 2073 LKRGFKQDDKyPFLIHPTFPISEIHESIRWTKKPSQMQE---HVLSLCHLMWH-NGRDVYKEFERKIR 2136
Cdd:cd23169    243 LKRGFRPHPT-PGLVLAPLDLESIEEQLNWTRKEDDLLEatiENARAALLLAFgHGPEYYNKFRQKLN 309

Kobuvirus_RdRp

cd23214

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

1715-2156

1.05e-66

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: 233.97 E-value: 1.05e-66

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1715 PTIHTPAKTKLQPSVFFDVFEGSKEPAVLTEKDPRLT--TDFNQALFSKY-KGNVE---CNMSEHMQVAISHYSAQLMTL 1788
Cdd:cd23214      1 PGVNVNRKSRLGPSPAYGAFPVKKQPAPLTQKDDRLEdgIRLDDQLFLKHnKGDMDepwPGLEAAADLYFSKFPTMIRTL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1789 didpsniTLEESVFGTEGLEALDLNTSAGFPYIGMGIRKRDLINNSTKDI----TKLKMALDKYGVDLPMV--TFLKDEL 1862
Cdd:cd23214     81 -------TQEEAINGTPNLEGLDMNQAAGYPWNTMGRSRRSLFVEVQPGIyvpkPELQAEIDKTLEDPDYFysTFLKDEL 153

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1863 RKKEKIMAGKTRVIEASSINDTIAFRMTYGKLFSSFHRNPGiVTGSAVGCDPETFWSKIPVML-DGECIMAFDYTNYDGS 1941
Cdd:cd23214    154 RPTAKVTLGLTRVVEAAPIHAIVAGRMLLGGLIEYMQARPG-KHGSAVGCNPDLHWTKFFYKFcHYPQVFDLDYKCFDAT 232

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1942 IHPIWFEALKQVLTNLSFEHRL---IDRLCKSKHIFKDTYYEVEGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKYiDLD 2018
Cdd:cd23214    233 LPSCAFRIVEDHLERLTGDERVtryIESIRHSHHVYGNETYEMIGGNPSGCVGTSIINTIINNICVLSALIQHPDF-SPE 311

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2019 KLKIIAYGDDVIFSYKYPLDMEAIAAEGNKYG-LTITPADKSDTFKKLD-YSSVTFLKRGFKQDDKYPFLIHPTFPISEI 2096
Cdd:cd23214    312 SFRILAYGDDVIYGCDPPIHPSFIKEFYDKHTpLVVTPANKGSDFPETStIYDVTFLKRWFVPDDIRPFYIHPVMDPDTY 391

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2099547072 2097 HESIRWTKKpSQMQEHVLSLCHLMWHNGRDVYKEFERKIRSVSAGRALYIP---PYDLLLHEW 2156
Cdd:cd23214    392 EQSVMWLRD-GDFQDLVTSLCYLAFHSGPKTYDRWCTRVRDQVMKTTGFPPtflPYSYLQTRW 453

Teschovirus_RdRp

cd23212

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

1795-2131

8.59e-66

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: 227.96 E-value: 8.59e-66

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1795 ITLEESVFGTEGLEALDLNTSAGFPYIGMGIRKRDLINNSTKDITKLKMALDKYgVDLP-----MVTFLKDELRKKEKIM 1869
Cdd:cd23212     11 LSVREAVEGIDGLDPMDMDKSPGLPYVKKGLRRTDLWNPKTGPSIELMAEINRY-LDYNydkhvFLTFLKDELRPKEKVQ 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1870 AGKTRVIEASSINDTIAFRMTYGKLFSSFHRNPGIVTGSAVGCDPETFWSKIPVMLDGECIMAFDYTNYDGSIHPIWFEA 1949
Cdd:cd23212     90 AGKTRVIDVAGFGHAIVGRMLFGRLFAFFHKNPGWNTGSAVGVNPDLAWTQIFYTAPSRNVLAMDYSGFDASHTSGMFCI 169

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1950 LKQVLTNLSF---EHRLIDRLCKSKHIFKDTYYEVEGGVPSGCSGTSIFNTMINNIIIRTlvldAYKYIDLDKLKIIAYG 2026
Cdd:cd23212    170 LKHFLTTLGYgtlQLSYIDSLCYSKHHWDDETYRLDGGLPSGCSGTTIFNTIMNNIVARA----AASYAAEGPVGILCYG 245

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2027 DDVIFSYKYPLDMEAIAAEGNKYGLTITPADKSDTFKKLDYSSVTFLKRGFKQDDKypfLIHPTFPISEIHESIRWTkKP 2106
Cdd:cd23212    246 DDILVSSPEKFPVSDWLEFYSKTPYKVTAADKSEQIDWRDITQCTFLKRGFVLDGS---LVRPVMEEQHLAELLKWA-RP 321

                          330       340
                   ....*....|....*....|....*
gi 2099547072 2107 SQMQEHVLSLCHLMWHNGRDVYKEF 2131
Cdd:cd23212    322 GTLQAKLLSIAQLAFHLPRQAYDRL 346

Rhv

pfam00073

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

93-301

9.71e-64

Pssm-ID: 395026 Cd Length: 170 Bit Score: 214.48 E-value: 9.71e-64

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072   93 TSQDVANAVVGYGVWPHYLTPQDATAIDKPSKPDTSSNRFYTLESQTWTNESKGW-WWKLPDALKDMGIFGENMFYHFLG 171
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFfWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  172 RSGYTVHVQCNASKFHQGTLLVAMIPEHQlatavggsvsagynyTHPGEKgrdvgklnresnprqpsddnwlnfdgTLLG 251
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPPGA---------------PPPGSR--------------------------DYLW 119

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 2099547072  252 NLTIFPHQFINLRSNNSATIIVPYVNAVPMDSMLRHNNWSLVIIPICELR 301
Cdd:pfam00073  120 QATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGNWTLVVAGWVPLN 169

RNA_dep_RNAP

cd01699

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

1851-2103

1.50e-59

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

Pssm-ID: 238843 [Multi-domain] Cd Length: 278 Bit Score: 206.75 E-value: 1.50e-59

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1851 DLPMVTFLKDELRKKEKIMAGKTRVIEASSINDTIAFRMTYGKLFSSFHRNpGIVTGSAVGCDPE-TFWSKIPVMLD--G 1927
Cdd:cd01699     17 DLVFTTFLKDELRPLEKVEAGKTRLIQPRPLDYNIALRMYLGPFEAKLMKN-RGGLPIAVGINPYsRDWTILANKLRsfS 95

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1928 ECIMAFDYTNYDGSIHPIWFEALKQVLTNLS------FEHRLIDRLCKS-KHIFKDTYYEVEGGVPSGCSGTSIFNTMIN 2000
Cdd:cd01699     96 PVAIALDYSRFDSSLSPQLLEAEHSIYNALYddddelERRNLLRSLTNNsLHIGFNEVYKVRGGRPSGDPLTSIGNSIIN 175

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2001 NIIIRTLVLDAYKYIDLDKLKIIAYGDDVIFSYK---YPLDMEAIAAEGNKYGLTITPADKSDT-FKKLdySSVTFLKRG 2076
Cdd:cd01699    176 CILVRYAFRKLGGKSFFKNVRLLNYGDDCLLSVEkadDKFNLETLAEWLKEYGLTMTDEDKVESpFRPL--EEVEFLKRR 253

                          250       260
                   ....*....|....*....|....*..
gi 2099547072 2077 FKQDDkyPFLIHPTFPISEIHESIRWT 2103
Cdd:cd01699    254 FVLDE--GGGWRAPLDPSSILSKLSWS 278

Peptidase_C3

pfam00548

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

1518-1683

4.68e-58

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: 198.44 E-value: 4.68e-58

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1518 GPEEEFGRSLIKHNTCIVTTDNGKFTGL--GIYDKLMILPTHADPGKEIYINGIATRVSD-SYDMYNKQGIKLEITAVLL 1594
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1595 DRNEKFRDIRKYIPEREDDYPECNLALVANQPEPTIISVGDVISYGNI-LLSGNQTARMLKYNYPTKSGYCGGVLYKI-- 1671
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVVIAKve 160

                          170
                   ....*....|....
gi 2099547072 1672 --GQIIGIHVGGNG 1683
Cdd:pfam00548  161 gnGKILGMHIAGNG 174

Fipivirus_RdRp

cd23229

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

1801-2156

5.12e-58

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: 206.58 E-value: 5.12e-58

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1801 VFGTEGLEALDLNTSAGFPYIGMGIRKRDLI--------------NNSTKDITKLKMALDKYGVDLPMVTFLKDELRKKE 1866
Cdd:cd23229      2 VEGIPGMEGLDMKTSAGYPWCEQNQKKKDKIkllagknflvrplrEVVHIVVDWYIMPPDMPKPEIKYVVYLKDELLSSD 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1867 KIMAGKTRVIEASSINDTIAFRMTYGKLFSSFHR-NP--GIVTGSAVGCDPETFWSKIPVMLDGECIMAFDYTNYDGSIH 1943
Cdd:cd23229     82 KVKMGRTRWICAAPVQLVCAWKKVFGRAIAAIHLeSVtdGKSTGCAVGMDPETAWTDIALARPGWPVIALDYSNFDGSLQ 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1944 PIWFEALKQVLTNLSFEH-----RLIDRLCKSKHIFKDTYYEVEGGVPSGCSGTSIFNTMINniiIRTLVLDAYKYIDL- 2017
Cdd:cd23229    162 SFVITGAVRILGYIAGLPdgqsyRLAEFVYDVKQIVGKYLYTTVGPLPSGCPSTSIIGSLCN---VLMLLYTLSHATGQr 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2018 -----DKLKIIAYGDDVIF----SYKYPLDMEAIAAEgNKYGLTITPA-DKSDTFKKLDYSSVTFLKRGFKQDDKYPFLI 2087
Cdd:cd23229    239 ysafrDWMHVVTYGDDVLVfvhpEVVVVLDTLAHEMY-LVFGVTATDAtDKRAPPQLRELSNVTFLKRGFRQCSSVPFLV 317

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2099547072 2088 HPTFPISEIHESIRWTKKPSQMQEHVLSLCHLMWHNGRDVYKEFERKIRS------VSAGRALY--IPPYDLLLHEW 2156
Cdd:cd23229    318 HPTMDKSTIYQMLAWKRKGTTLAENVKCAAEFMMHHGEEEYEDFVGVVKEcstligVDQRSKVYeeLCSYAELHDHW 394

Passerivirus_RdRp

cd23224

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

1799-2158

3.10e-52

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: 189.53 E-value: 3.10e-52

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1799 ESVFGTEGLEALDLNTSAGFPYiGMGIRKRDLINNST----KDITKLKMALDK--YGVDLPMVTFLKDELRKKEKIMAGK 1872
Cdd:cd23224      1 EAINGTPLLDGLDMKQSPGYPW-SLTTNRRSLFTQDEtgkyYPVPELEEAVLAclENPDYFYTTHLKDELRPVEKALAGK 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1873 TRVIEASSINDTIAFRMTYGKLFSSFHRNPGiVTGSAVGCDPETFWSKIPVMLDGEC-IMAFDYTNYDGSIHPIWFE--- 1948
Cdd:cd23224     80 TRLIEAAPIHAIIAGRMLLGGLFEYMHARPG-EHGSAVGCDPDYHWTPFFHSFDEFSqVWALDYSCFDSTLPSCCFDlia 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1949 -ALKQVLTNLSFEH-----RLIDRLCKSKHIFKDTYYEVEGGVPSGCSGTSIFNTMINNIIIRTLVLdAYKYIDLDKLKI 2022
Cdd:cd23224    159 qKLAKIITPGEGIApdaivKYIRSISISKHVFGNEAYLMVGGNPSGCVGTSILNSMINNCVLISAFL-TQKDFNPNQMRI 237

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2023 IAYGDDVIFSYK---YPLDMEAIAAEGNKygLTITPADKSDTFKklDYSS---VTFLKRGFKQDDKYPFLIHPTFPISEI 2096
Cdd:cd23224    238 LTYGDDVLYATNppiHPRVVKKFFDENTT--LIVTPATKAGDFP--DESTiwdVTFLKRYFVPDEIRPWYVHPVIEPATY 313

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2099547072 2097 HESIRWTKKpSQMQEHVLSLCHLMWHNGRDVYKEFERKIRSVSAGRALY--IPPYDLLLHEWYE 2158
Cdd:cd23224    314 EQSVMWTRG-GDFQDVVTSLSFLAHHAGPTNYMIWEEKVRKAAAAKGVSlnILPYSYLQHRWML 376

Rhv

pfam00073

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

358-523

1.94e-49

Pssm-ID: 395026 Cd Length: 170 Bit Score: 173.65 E-value: 1.94e-49

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  358 YHPTKEISIPGQVRNLVELCQVDTLIPINNTEANIRNKNMYTVQLGGEPDPTTPVFTIRVDIASqpLATTLIGEISSYYT 437
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFFWWKLPLAL--LSMGLLGRLLRYHT 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  438 HWTGSVRFSFMFCGSALTTLKLLIAYTPPGIRVPRSR---KEAMLGTHLIWDVGLQSTVSMVVPWVSASHYRNTTPD--- 511
Cdd:pfam00073   79 YYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRdylWQATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDgnw 158

                          170
                   ....*....|..
gi 2099547072  512 TYSLAGFITCWY 523
Cdd:pfam00073  159 TLVVAGWVPLNY 170

RdRP_1

pfam00680

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

1727-2137

6.79e-49

Pssm-ID: 425815 Cd Length: 450 Bit Score: 181.84 E-value: 6.79e-49

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1727 PSVFFDVFEGSKEPAVLTEKDPR-----LTTDFNQALFSKYK-----GNVECNMSEHMQVAISHYSAQLMTLD-IDPSNI 1795
Cdd:pfam00680    2 PTERHLVAIPAYVPASLGPEDPRwarsyLNTDPYVDDIKKYSrpklpGPADERDKLLNRSAAKMVLSELRGVPkKANSTL 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1796 TLEESVFGTEGLEALDLNTSAGFPYIGMGIRKRDLIN----NSTKDI--TKLKMALDKY--GVDLPMV--TFLKDELRKK 1865
Cdd:pfam00680   82 IVYRAIDGVEQIDPLNWDTSAGYPYVGLGGKKGDLIEhlkdGTEARElaERLAADWEVLqnGTPLKLVyqTCLKDELRPL 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1866 EKIMAGKTRVIEASSINDTIAFRMTYGKLFSSFHRNPGIVTgSAVGCDPetFWSKIPVMLD-----GECIMAFDYTNYDG 1940
Cdd:pfam00680  162 EKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHP-IQVGINP--FDRGWPRLLRrlarfGDYVYELDYSGFDS 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1941 SIHPIWFEALKQVLT-------NLSFEHRLIDRLCKSKH-IFKDTYYEVEGGVPSGCSGTSIFNTMINNIIIRTLVL--- 2009
Cdd:pfam00680  239 SVPPWLIRFAFEILRellgfpsNVKEWRAILELLIYTPIaLPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYALLksl 318

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2010 --DAYKYIDLDKLKI-IAYGDDVIFSYKYPLD--MEAIAAEGNKYGLTITPADKS-DTFKKLDysSVTFLKRGFKQDdky 2083
Cdd:pfam00680  319 enDGPRVCNLDKYFDfFTYGDDSLVAVSPDFDpvLDRLSPHLKELGLTITPAKKTfPVSRELE--EVSFLKRTFRKT--- 393

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2099547072 2084 PFLIHPTFPISEIHESIRWTKKPSQMQEHVLSLCHLMWHNGRDVYKEFERKIRS 2137
Cdd:pfam00680  394 PGGYRPPLDRKRILAQLEYIRSKPVPSGQLENIRAYASHHGYEFYRDLLYRFVE 447

Rhv

pfam00073

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

615-767

3.45e-46

Pssm-ID: 395026 Cd Length: 170 Bit Score: 164.41 E-value: 3.45e-46

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  615 PEDMIETRYVQTSQTRDEMSIESFLGRSGCIHMSTLN-----INYDNYDDSIENFKVWKINL--QEMAQIRRKFELFTYA 687
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGerfytLDSTDWTSLSKGFFWWKLPLalLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  688 RFDSEITIVPCvagqGGDIGHVVMQYMYVPPGAPTPEKRnDFTWQSGTNASVFWQHG-QAYPRFSLPFLSIASAYYMFYD 766
Cdd:pfam00073   81 RGGLEVTVQFN----GSKFHQGKLLVAYVPPGAPPPGSR-DYLWQATLNPHQFWNLGlNSSARLSVPYISIAHYYSTFYD 155


                   .
gi 2099547072  767 G 767
Cdd:pfam00073  156 G 156

Hepatovirus_RdRp

cd23215

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

1795-2157

9.96e-45

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: 170.03 E-value: 9.96e-45

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1795 ITLEESVFGTEGLEALDLNTSAGFPYIGMGIRKRDLI----NNSTKDIT---------KLKMALDKYGVDLPMVTFLKDE 1861
Cdd:cd23215     65 FDLEQAITGVPGMDAINMDSSPGYPYVQEKLTKSDLIwlddNGELLGMHprlaqrilfNLTMMDNGNDLDVVYTTCPKDE 144

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1862 LRKKEKIMAGKTRVIEASSINDTIAFRMTYGKLFSSFHRNPGIVTGSAVGCDPETFWSKI-PVMLD-GECIMAFDYTNYD 1939
Cdd:cd23215    145 LRPLEKVLESKTRAIDACPLDFTIICRMFWGPAISYFQLNPGFHTGVAVGIDPDRDWDALfKTMIRfGDYGIDLDFSSFD 224

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1940 GSIHPIWFEALKQVLTNLS-----FEHRLIDRLCKSKHIFKDTYYEVEGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKY 2014
Cdd:cd23215    225 ASLSPFMIREACRVLSELSgvpdhQGQALINTIIYSKHLLYNLCYHVCGSMPSGSPCTSLLNSIVNNVNLYYVFSKIFKK 304

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2015 IDL---DKLKIIAYGDDVIFSYKYPLDME-------AIAAEGNKYGLTITPADKSDTfKKLDYSSVTFLKRGFKQ-DDKy 2083
Cdd:cd23215    305 SPVffyDAVKFLCYGDDVLIVFSRDLEIKnldklgqRIQDEFKLLGMTATSADKGEP-QVVPVSELTFLKRSFNLiEDR- 382

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2099547072 2084 pflIHPTFPISEIHESIRWTKKPSQMQEHVLSLCHLMWHNGRDVYKEFERKIRSVSAGRALyipPYDLLLHEWY 2157
Cdd:cd23215    383 ---FRPAISEKTIWSLVAWQRSNAEFEQNLDTACWFAFMHGYDFYQNFYLQLQSCLEKEMI---DYRLKSYEWW 450

Pico_P2B

pfam01552

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

1002-1098

2.87e-44

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: 155.95 E-value: 2.87e-44

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1002 QGVTDYIHMLGEAFGNGFV----DSVKDHVNAINPINNISKKVIKWLLRIVSAMVIIIRNSSDPQTVVATLTLIGCSGSP 1077
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTqqisDKIKELTNFINPTSKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|.
gi 2099547072 1078 WRFLKEKFCKWTQLTYIHKES 1098
Cdd:pfam01552   81 WQFLKEKACAVLEIPYVHKQG 101

Dicistroviridae_RdRp

cd23194

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

1857-2136

1.26e-43

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: 162.28 E-value: 1.26e-43

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1857 FLKDELRKKEKIMAGKTRVIEASSINDTIAFRMTYGKLFSSFHRNPgIVTGSAVGCDPETF-WSKIPVML--DGECIMAF 1933
Cdd:cd23194     11 TLKDERRPIEKVDAGKTRVFSAGPMDYTIAFRMYFLGFVAHLMRNR-IDNEIAVGTNVYSLdWDKLARKLlsKGDKVIAG 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1934 DYTNYDGSIHP-IWFEALKQV--LTNLSFEHRLIDR-----LCKSKHIFKDTYYEVEGGVPSGCSGTSIFNTMINNIIIR 2005
Cdd:cd23194     90 DFSNFDGSLNPqILWAILDIIneWYDDGEENALIRRvlwedIVNSVHICGGYVYQWTHSQPSGNPLTAIINSIYNSIIMR 169

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2006 ---TLVLDAYKYIDL----DKLKIIAYGDDVIFS----YKYPLDMEAIAAEGNKYGLTITPADKSDT---FKKLDysSVT 2071
Cdd:cd23194    170 yvyLLLTKEAGLMTMsdfnKHVSMVSYGDDNVINvsdeVSEWFNQLTITEAMAEIGMTYTDETKTGEivpYRSLE--EVS 247

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2099547072 2072 FLKRGFKQDDKYPFLIHPtFPISEIHESIRWTKKPSQMQE----------HVLSLcHlmwhnGRDVYKEFERKIR 2136
Cdd:cd23194    248 FLKRGFRYDDDLGRWVAP-LDLDTILEMPNWVRKGKDPEEitkqnvenalRELSL-H-----GEEVFDKWAPKIR 315

Parechovirus_RdRp

cd23217

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

1800-2154

9.85e-43

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: 161.57 E-value: 9.85e-43

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1800 SVFGTEGLEALDLNTSAGFPYIGMGIRKRDLINNS--------TKDITKLKMALdkYGVDLP---MVTFLKDELRKKEKI 1868
Cdd:cd23217      1 AVLGTSHLNSLDLSTSPGYKYVKSGYKKRDLLSLEpfsvspqlEKDVKDKLHAV--YKGNQPttiFNACLKDELRKLDKI 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1869 MAGKTRVIEASSINDTIAFRMTYGKLFSSFHRNPGIVTGSAVGCDPETFWS-KIPVMLDGEciMAFDYTNYDGSIHPIWF 1947
Cdd:cd23217     79 AQGKTRCIEACSIDYVIAYRVVMSSLYEAIYQTPCQELGLAVGMNPWTDWDfMINALNPYN--YGLDYSSYDGSLSEMLM 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1948 EALKQVLTNLSFEHRLIDRLCK----SKHIFKDTYYEVEGGVPSGCSGTSIFNTMINNIIIRTLvldAY-KYIDLDKLKI 2022
Cdd:cd23217    157 WEAVEVLAYCHESPDLVMQLHKpvinSDHVVMDERWLVHGGMPSGSPCTTVLNSICNLLVCIYL---AYlQSPGIECLPI 233

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2023 IaYGDDVIFSYKYPLDMEAIAAE-GNKYGLTITPADKSDTFKKLDYSSVTFLKRGFKqddkypFLIHPTFPI-----SEI 2096
Cdd:cd23217    234 V-YGDDVIFSVSSEIDPEYLVSSaADSFGMEVTGSDKDEPPSLLPRMEVEFLKRTTG------YFPGSTYKVgaldlETM 306

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2099547072 2097 HESIRWTKK----PSQMQEHVLSLChlmwHNGRDVYKEFERKIRSVSAGRALYIPPYDLLLH 2154
Cdd:cd23217    307 EQHIMWMKNlstfPQQLQSFENELC----LHGKDIYDDYKKIFNPYLKEWNITMDDYDVVIH 364

Crohivirus_RdRp

cd23232

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

1797-2150

8.49e-42

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: 158.73 E-value: 8.49e-42

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1797 LEESVFGTEGLEALDLNTSAGFPYIGMGIRKRDLINNST--------KDITKLKMALDKYG-VDLPMVTFLKDELRKKEK 1867
Cdd:cd23232      1 IEEACFEEGDEHALDLKTSPGFKYVQMGLKKTDLVNRPNkfihpilrNDVRLIFDEMAKGQmPVVTFTAHLKDELRKLEK 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1868 IMAGKTRVIEASSINDTIAFRMTYGKLFSSFHRNPGIVTGSAVGCDPETFWSKIPVMLDgECIMAFDYTNYDGSIHPIWF 1947
Cdd:cd23232     81 IRSGKTRCIEACDFDYTVAHKMMFGTLYKAIYDTPGIITGLAVGMNPWKDWELIQQSLF-KYNYDFDYKTFDGSLSRELM 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1948 EALKQVLTNLS----FEHRLIDRLCKSKHIFKDTYYEVEGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKyidlDKLKII 2023
Cdd:cd23232    160 LHAVDILSACVendeMAKLMLSVVVESVHLVLDQKWNVSGGMPSGSPCTTVLNSVCNLIVSSTIADMCTE----GDFKIL 235

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2024 AYGDDVIFSYKYPLDMEAIA-AEGNKYGLTITPADKSDTFKKLDYSSVTFLKRGFKQDDKYPFLIHpTFPISEIHESIRW 2102
Cdd:cd23232    236 VYGDDLIISSTAPLDCDRFKtLVELHYGMEVTPGDKGDEFKVKDREQVSFLKRVTRKFPGTNYRVG-ALDLDTVKQHLMW 314

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*...
gi 2099547072 2103 TKKPSQMQEHVLSLCHLMWHNGRDVYKEFERKIRSVSAGRALYIPPYD 2150
Cdd:cd23232    315 CKSYSSFKQQLDSALMEVAMHGEETYNGFLTEIKTKLDKFKIYPPKFK 362

rhv_like

cd00205

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

373-558

5.81e-41

Pssm-ID: 119412 Cd Length: 178 Bit Score: 149.85 E-value: 5.81e-41

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  373 LVELCQVDTLIPINNTeanirnknmytvqlgGEPDPTTPVFTIRVDIASQPL--ATTLIGEISSYYTHWTGSVRFSFMFC 450
Cdd:cd00205      1 VESFADRPTTVGTNNW---------------NSSASGTQLFQWKLSPALGFLllQNTPLGALLSYFTYWRGDLEVTVQFN 65

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  451 GSALTTLKLLIAYTPPGIRVP---RSRKEAMLGTHLIWDVGLQSTVSMVVPWVSASHYRNTTPDTYSLA---GFITCWYQ 524
Cdd:cd00205     66 GSKFHTGRLLVAYVPPGAPAPttgDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDGYGPLnsfGTLVVRVL 145

                          170       180       190
                   ....*....|....*....|....*....|....
gi 2099547072  525 TKLVVPPNTASTADMLCFVSGcKDFCLRMARDTN 558
Cdd:cd00205    146 TPLTVPSGAPTTVDITVYVRA-GDFELYGPRPPR 178

Kunsagivirus_RdRp

cd23219

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

1797-2128

7.13e-41

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: 155.41 E-value: 7.13e-41

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1797 LEESVFGTegLEALDLNTSAGFPYigMGIRKRDLINNSTK--------DITKLKMALDKYGVD-LPMVTFLKDELRKKEK 1867
Cdd:cd23219      1 IEEAVFDT--VTPMDHTASAGPKY--PGTKRSELIDFQNRiisdrlrnDVLELQFRGTSGGAGeVKFSSFLKDELRPLSK 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1868 IMAGKTRVIEASSINDTIAFRMTYGKLFSSFHRNPGIVTGSAVGCDPETFWSKIPVMLdGECIMAFDYTNYDGSIHPIWF 1947
Cdd:cd23219     77 IRSGDTRVVECSSLDYTVAFRMQFLRVLQMCYGSDPTLTGLAPGMNVYTDMLPLCTSL-YDYNLCLDFSKYDSRLPLQVM 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1948 EALKQVLTNLS----FEHRLIDRLCKSKHIFKDTYYEVEGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKYIDldkLKII 2023
Cdd:cd23219    156 HRVAQLISNLTpdpqVSMRLFQPIIISTHIVGSYEVVVEGGMPSGCPITTIMNSVCNVVMTSYAMLLLDPDSD---FWPV 232

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2024 AYGDDVIFSYKYPLDMEA---IAAEgnKYGLTITPADKSDTFKKLDYSSVTFLKRGFKQDDKYPFLIhPTFPISEIHESI 2100
Cdd:cd23219    233 AYGDDNIVSTRKPIDTELfcsILNE--EFGMILTGADKTTTVQAVPPMSVDFLKRRLRYTPEFPLPV-PVLPLDSMLSRI 309

                          330       340
                   ....*....|....*....|....*...
gi 2099547072 2101 RWTKKPSQMQEHVLSLCHLMWHNGRDVY 2128
Cdd:cd23219    310 CWCKGETEFKDQLESFSYELALYGQEVY 337

Pico_P1A

pfam02226

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

2-69

1.48e-40

Pssm-ID: 308053 Cd Length: 68 Bit Score: 144.44 E-value: 1.48e-40

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2099547072    2 GAQVSRQNVGTHSTQNSVSNGSSLNYFNINYFKDAASSGASKLEFSQDPSKFTDPVKDVLEKGIPTLQ 69
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 68

RNA_helicase

pfam00910

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

1217-1313

1.03e-39

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: 143.13 E-value: 1.03e-39

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1217 VMIHGSPGTGKSITTNFLARMI-----TNESDIYSLPPDPKYFDGYDQQSVVIMDDIMQNPDGEDMALFCQMVSSVTFIP 1291
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALlkklgLPKDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 2099547072 1292 PMADLPDKGKPFDSRFVLCSTN 1313
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

Avisivirus_RdRp

cd23231

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

1810-2150

1.12e-37

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: 146.57 E-value: 1.12e-37

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1810 LDLNTSAGFPYIGMgiRKRDLINNST--KDITKLKMA---LDKYGVDLPMVTFLKDELRKKEKIMAGKTRVIEASSINDT 1884
Cdd:cd23231     11 IDWGTSPGDKYKGK--TKAQLVDDKKfkADVMNLVRFngdPNREPPDVYFTTYLKDELRPKEKAKAGKTRVISAASFDYT 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1885 IAFRMTYGKLFSSFHRNpGIVTGSAVGCDPETFWSKIPVMLDGECImAFDYTNYDGSIHPIWFEALKQVLTNLSFEHRLI 1964
Cdd:cd23231     89 IACRMVFGPILRQLFAW-GREFGFGPGLNPYTHFDELYDKILPFVI-CLDYSGFDGSLSSELMFHAAQVIACFSEKPEAI 166

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1965 DRLCK----SKHIFKDTYYEVEGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKyiDLDKLKIIAYGDDVIFSYKYPLDME 2040
Cdd:cd23231    167 MASAEltigSTERVSDEVWYVYGGMPSGSPWTTTLNTICNLLMCYTYLLDMGH--CWSETFVVAYGDDVVISANIKHNLE 244

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2041 AIAAE-GNKYGLTITPADKSDTFKKLDYSSVTFLKRGFKQDDKYPFLIHpTFPISEIHESIRWTKkpSQMQEHVLSLCHL 2119
Cdd:cd23231    245 GIEQWfKTKFGATVTPSDKQGKITWTTKNNMEFLKRRPKQLDFLPKIVG-ALDLDNMLDRIQWTK--GHFQDQLNSFYLE 321

                          330       340       350
                   ....*....|....*....|....*....|...
gi 2099547072 2120 MWHNGRDVYKEFERKIrsvsAGRA--LYIPPYD 2150
Cdd:cd23231    322 LALHGRETYNEIRAKL----APRApqLVHPTYA 350

rhv_like

cd00205

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

125-329

3.29e-35

Pssm-ID: 119412 Cd Length: 178 Bit Score: 133.29 E-value: 3.29e-35

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  125 PDTSSNRFYTLESQTWT---NESKGWWWKLPDA----LKDMGIFGENMFYHFLGRSGYTVHVQCNASKFHQGTLLVAMIP 197
Cdd:cd00205      1 VESFADRPTTVGTNNWNssaSGTQLFQWKLSPAlgflLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  198 EHQLATAvggsvsagynythpgekgrdvgklnresnprqpsddnwlnfDGTLLGNLTIFPHQFINLRSNNSATIIVPYVN 277
Cdd:cd00205     81 PGAPAPT-----------------------------------------TGDTRWQATLNPHVIWDLGTNSSVTFVVPYVS 119

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2099547072  278 AVPMDSMLRH------NNWSLVIIPICELR-GSGVDLTIPITISISPMCAEFSGARANS 329
Cdd:cd00205    120 PTPYRSTRYDgygplnSFGTLVVRVLTPLTvPSGAPTTVDITVYVRAGDFELYGPRPPR 178

Limnipivirus_RdRp

cd23228

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

1806-2151

6.22e-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: 139.24 E-value: 6.22e-35

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1806 GLEALDLNTSAGFPYIGMGIRKRDL--INNS---------TKDITKLKMALDKYG-VDLPMVTFLKDELRKKEKIMAGKT 1873
Cdd:cd23228      6 GTNPIDKNTSPGLKYTRDGLKKSDLytIDEDgnvvvsdmlRADVEAWEELIQSGGyPTTLFTACLKDELRSDEKVALGKT 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1874 RVIEASSINDTIAFRMTYGKLFSSFHRNPGIVTGSAVGCDPETFWSKIPVMLDG-ECIMAFDYTNYDGSIHPIWFEALKQ 1952
Cdd:cd23228     86 RVIEAAELDYVVAYRMYMSSIYSDLYNAYAGDTGIAAGINPPADGHRLREELSQyDSFLALDYSRFDGSLPEMLMRAAVE 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1953 VLTNLSFEHRLIDRLCK----SKHIFKDTYYEVEGGVPSGCSGTSIFNTMINNIIIRTLVLDA----YKYIDLDKLK--- 2021
Cdd:cd23228    166 ILADLHEDPDLVRRLHEtviiSKHLVVDEDWTVKGGMPSGSPCTTVLNCICNLLVLEYAFLVHfgvyEDDDGVGLPQcdy 245

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2022 -IIAYGDDVIFSYKYPlDMEAIAAEG--NKYGLTITPADKSDTFKKLDYSSVTFLKRGF-----KQDDKypflIHPTFPI 2093
Cdd:cd23228    246 lSVVYGDDCIVAYNGM-EMGLAFAETieDTFGMEVTPASKVGDHFNVELHEVEFLKRKFfafetEEYDR----IALRLSE 320

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2094 SEIHESIRWTKKPSQMQEHVLSLCHLMWHNGRDVYKEFERKIRSVSAGRALYI--PPYDL 2151
Cdd:cd23228    321 NTIVQSLMWMRNLKTFPDQVQSLMMELSAWGKEKYDKLRDTCKRRLAKQNLQVtvPGYDI 380

rhv_like

cd00205

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

635-823

1.19e-34

Pssm-ID: 119412 Cd Length: 178 Bit Score: 131.75 E-value: 1.19e-34

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  635 IESFLGRSGCIHMSTlninyDNYDDSIENFKVWKINLQE------MAQIRRKFELFTYARFDSEITIVPCvagqgGDIGH 708
Cdd:cd00205      1 VESFADRPTTVGTNN-----WNSSASGTQLFQWKLSPALgflllqNTPLGALLSYFTYWRGDLEVTVQFN-----GSKFH 70

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  709 -VVMQYMYVPPGAPTPEKrNDFTWQSGTNASVFWQHGQAYP-RFSLPFLSIASAYYMFYDGYDgdsestrygtsVTNDMG 786
Cdd:cd00205     71 tGRLLVAYVPPGAPAPTT-GDTRWQATLNPHVIWDLGTNSSvTFVVPYVSPTPYRSTRYDGYG-----------PLNSFG 138

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 2099547072  787 ALCFRIVTE-----QHTNQVKITtrIYHKAKHVKVWCPRPPR 823
Cdd:cd00205    139 TLVVRVLTPltvpsGAPTTVDIT--VYVRAGDFELYGPRPPR 178

Aalivirus_RdRp

cd23216

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

1810-2137

1.71e-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: 1.71e-30

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1810 LDLNTSAGFPYIGMgiRKRDLINN-STKDITKLKMAldkyGVDLPMVTFLKDELRKKEKIMAGKTRVIEASSINDTIAFR 1888
Cdd:cd23216     12 IDWQTSPGLKYKGR--TKADLVQDpKFKEDVKEILA----GKPTFFTTYLKDELRSIEKIANGNTRAIEAANFDHVVAWR 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1889 MTYGKLFSSFHRNPGIVTGSAVGCDPETFWSKIPVMLDGEcIMAFDYTNYDGSIHPIWFEALKQVLTNLSFEHRLIDRLC 1968
Cdd:cd23216     86 QVMGNIVKQLFSDHDRVTGFAPGMNPYTHFDSLMDQVKWN-VLALDFKKFDGSLSPQVMEEAVDILASFHDMPQMVVDIH 164

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1969 K----SKHIFKDTYYEVEGGVPSGCSGTSIFNTMINNIIIRTLVLDayKYIDLDKLKIIAYGDDVIFSYK-YPLDMEAIA 2043
Cdd:cd23216    165 KhtiySTNVVSDETWFVEGGMCSGSPCTTVLNTICNLLVNTTILLS--EGIQPDNFYIAAYGDDTIISVDgLSSSLPDPK 242

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2044 AEGNKY----GLTITPADKSDTFKKLDYSSVTFLKR--GFKQDDKYpflIHPTFPISEIHESIRWTKkpSQMQEHVLSLC 2117
Cdd:cd23216    243 IMQQKYkewfGMTVTSADKGSEITWDTRNHVQFLKRrpGFFPGTQK---VVGVLDLESMMEHIAWTK--GSFQDQLNSFY 317

                          330       340
                   ....*....|....*....|
gi 2099547072 2118 HLMWHNGRDVYKEFERKIRS 2137
Cdd:cd23216    318 QELVLHGEQVYMTVRQTLKS 337

Aquamavirus_RdRp

cd23220

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

1797-2134

2.18e-26

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: 112.88 E-value: 2.18e-26

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1797 LEESVFGTEglEALDLNTSAGFPYIGMGIRKR-DLINNSTKD-ITKLKMALDKYGVDLPMVTFLKDELRKKEKIMAGKTR 1874
Cdd:cd23220      1 LNEAINSSE--SPLNFNGTAGAKYPGMNRRQLlLPLNPQVRDdVVKLAGDVGNGTATVVFETFMKDELRPKEKIESGKTR 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1875 VIEASSINDTIAFRMTYGKLFSSFHRNPGIVTGSAVGCDPETFWSKIpVMLDGECIMAFDYTNYDGSIHPIWFEALKQVL 1954
Cdd:cd23220     79 IVESCPLDYLLLYRMVMLKSMIWWYNSDCIKTGVAPGMNVYTDFVPM-VKQFKKIKYCLDFSAYDSTLSDEILAAGVEVL 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1955 ----TNLSFEHRLIDRLCKSKHIFKDTYYEVEGGVPSGCSGTSIFNTMINNIIIRTLVldayKYIDLDKLKIIAYGDDVI 2030
Cdd:cd23220    158 actsAVPSYVRKLHAPIICSHHWHNNVVDLVLGGMPSGAPCTSVLNSIVNVLMARYIC----ALMDIDYPVMVAYGDDNV 233

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2031 FSYKYPLDM-EAIAAEGNKYGLTITPADKSDTFKKLdySSVTFLKRG--FKQDDKYPFlihPTFPISEIHESIRWTKKPS 2107
Cdd:cd23220    234 VSFDEEIDIeRMVSLYKTEFGVTATNHDKTPVPRPM--ANPVFLKRRlrFNPDLNIQF---PVLPLGEMIDRMCWTRGPE 308

                          330       340
                   ....*....|....*....|....*..
gi 2099547072 2108 QMQEHVLSLCHLMWHNGRDVYKEFERK 2134
Cdd:cd23220    309 HLSDQTFSFAIELAGYGKQVYTHIRDA 335

Caliciviridae_RdRp

cd23192

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

1858-2109

5.82e-26

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: 110.82 E-value: 5.82e-26

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1858 LKDELRKKEKIMAGKTRVIEASSINDTIAFRMTYGKLFSSFHRNPGiVTGSAVGCDPETfwSKIPVM----LDGECIMAF 1933
Cdd:cd23192      7 LKDELRPVEKIAEGKRRLLWGCDVGVTLVAAAAFGPVADALKAVCP-TGPIAVGINMDS--EDVEVIferlSGFRYHYCL 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1934 DYTNYDGSIHPIWFEALKQVLTNLSFEHRLIDRLCKSKH-----IFKDTYYEVEGGVPSGCSGTSIFNTMINNIIIRTLV 2008
Cdd:cd23192     84 DYSKWDSTQSPAVTAAAIDILADLSEETPLRDSVVETLSsppmgIFDDVIFVTKRGLPSGMPFTSVINSLNHWLLFSAAV 163

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2009 LDAYKYIDL------DKLKIIAYGDDVIFSYK--YPLDMEAIAAEGNKYGLTITPADKSDTFKKLDYSSVTFLKRGFKQD 2080
Cdd:cd23192    164 LKAYELVGIytgnvfDEADFFTYGDDGVYAMPpaTASVMDEIIENLKSYGLKPTAADKTENPDIPPLQGPVFLKRTFVRT 243

                          250       260
                   ....*....|....*....|....*....
gi 2099547072 2081 dkyPFLIHPTFPISEIHESIRWTKKPSQM 2109
Cdd:cd23192    244 ---PGGWRALLDRSSILRQLYWVKGPNTH 269

Marnaviridae_RdRp

cd23195

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

1858-2131

2.36e-23

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: 102.91 E-value: 2.36e-23

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1858 LKDELRKKEKimaGKTRVIEASSINDTIAFRMTYGKLFSSFHRNPgIVTGSAVGCD---PEtfWSKIPVML---DGECIM 1931
Cdd:cd23195      7 LKDEPTKLTK---DKVRVFQAAPVALQLLVRKYFLPIARFLQMNP-LLSECAVGINaqsPE--WEELYEHLtkfGEDRII 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1932 AFDYTNYDGSIHPIW----FEALKQVLT---NLSFEHRLIDR-----LCKSKHIFKDTYYEVEGGVPSGCSGTSIFNTMI 1999
Cdd:cd23195     81 AGDYSKYDKRMSAQLilaaFKILIDIAAksgGYSEEDLKIMRgiatdIAYPLVDFNGDLIQFFGSNPSGHPLTVIINSIV 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2000 NNIIIRTLVLDAYKYIDL----DKLKIIAYGDDVIFSYK--YPL-DMEAIAAEGNKYGLTITPADKSDTFKK-LDYSSVT 2071
Cdd:cd23195    161 NSLYMRYAYYSLYPEKEVppfrDVVALMTYGDDNIMSVSpgYPWfNHTSIAEFLAKIGIKYTMADKEAESVPfIHISEAD 240

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2099547072 2072 FLKRGFKQDDKyPFLIHPtfPISE--IHESIRWTKKPS------QMQEHVLSLCHLMWHNGRDVYKEF 2131
Cdd:cd23195    241 FLKRKFVFDPE-LGVYVG--PLDEdsIFKSLHCYLKSKvltpeeQAAQNIDGALREWFFHGREVYEKR 305

P3A

pfam08727

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

1416-1466

3.58e-18

Pssm-ID: 400873 Cd Length: 59 Bit Score: 80.16 E-value: 3.58e-18

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2099547072 1416 AIFQGpISMEV-----PPPPAITDLLRSVKTPEVIKYCEDNKWI--IPADCKIERDLN 1466
Cdd:pfam08727    1 AIFQG-IDLKIdiktsPPPEAIADLLQAVDSPEIIDYCEDKGWIvnIPAECQIERDIG 57

Iflaviridae_RdRp

cd23197

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

1858-2114

3.02e-14

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: 76.06 E-value: 3.02e-14

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1858 LKDELRKKEKIMA-GKTRVIEASSINDTIAFRMTYGKLFSSFHRNPgIVTGSAVGCDPETF-WSKI--PVMLDGECIMAF 1933
Cdd:cd23197     12 LKDELRPSEKLRRfGGTRVFSVPPLELVLNSRRFLLPFMDAFQSFP-IEAHHAIGLNPNSGdWRRLrdTLLEKGPCLLQM 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1934 DYTNYDGSIHPIWFEALKQVLTNLSFEHR--------LIDRLC----KSKHIFKDTYYEVEGGVPSGCSGTSIFNTMINn 2001
Cdd:cd23197     91 DYKNYSDAIPKECVAKAFHIIVDYYRKWHcltveienALKTLFldtaDAELLVYGDVFKVNNGVLAGHPMTSVVNSVVN- 169

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2002 iiirtLVLDAYKYIDLDKLK---------IIAYGDDVIFSYKYPL----DMEAIAAEGNKYGLTITPADKSDTFKKLDYS 2068
Cdd:cd23197    170 -----LILMNYMWIKITRRRaseffkltyIIVMGDDVVISLPKQLteefDCRKICAEFAKYDIKVTDSEKNLTGEPKPYD 244

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*....
gi 2099547072 2069 SV---TFLKRGFKQDDKYPFLIHPTFPISEIHESIRWTKKPSQMQEHVL 2114
Cdd:cd23197    245 SFdkfEFLSRGFSDCDAYPDITFAPVKTIALFDCPLWISKGQDEEEQTI 293

Secoviridae_RdRp

cd23196

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

1848-2081

3.35e-14

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: 75.88 E-value: 3.35e-14

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1848 YGVDLPmvtflKDELRKKEKIMAG-KTRVIEASSINDTIAFRMTYGKlFSSFHRNPGIVTGSAVGCDPETF-WSKIPVML 1925
Cdd:cd23196      2 NCVECP-----KDERLKKRKVLEKpKTRLFDVLPMEYNLLLRKYFLN-FVRFIQANRHRLPCQVGINPYSReWTTLYDRL 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1926 --DGECIMAFDYTNYDGSIHpiwfealKQVLTNLSfehRLIDRLCKSKH-----------------IFKDTYYEVEGGVP 1986
Cdd:cd23196     76 aeKSDTALNCDYSRFDGLLS-------HQVYVWIA---DMINRLYGDGDeakarrnllmmfcgrrsICGRQVYMVRGGMP 145

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1987 SGCSGTSIFNTMINNIIIRTlvldAYKYI-------DLDKL-KIIAYGDD-------VIFSYkypLDMEAIAAEGNKYGL 2051
Cdd:cd23196    146 SGCALTVIINSIFNEILIRY----VYRKVvprparnNFNKYvRLVVYGDDnlisvkeEIIPY---FDGPVIKKEMAKVGV 218

                          250       260       270
                   ....*....|....*....|....*....|....
gi 2099547072 2052 TITP-ADKSD---TFKKLdySSVTFLKRGFKQDD 2081
Cdd:cd23196    219 TITDgTDKTSptlERKPL--ESLDFLKRGFRVQS 250

Nora-virus_RdRp

cd23200

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

1858-2136

2.53e-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: 2.53e-13

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1858 LKDELRKKEKIMAGKTRVIEASSINDTIAFRMTYGKLFSSFHRnPGIVTGSAVGCDPETF-WSKIPV-MLDGECIMAFDY 1935
Cdd:cd23200      7 LKDQPIKIAQAKSGRTRVFHCIPVDLILFSGALYGPYKEAYTK-AGLKCYHAVGIDPKSVgWQQLATyMTKHPNYFDADY 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1936 TNYDGSIHPIWFEALKQVLTNlsfehrLIDRLCKSKHI-------FKD---------TYYEVEGGVPSGCSGTSIFNTMI 1999
Cdd:cd23200     86 KNYDKYLHRQVFKAVRKIQRS------VIQQVCPDKWDkaraveeLDAidtyvvdyqTVYKTNRGNKSGSYTTTIDNCLA 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2000 NNI------IIRTLVLDAYKYidLDKLKIIAYGDDVIFS----YKYPLDMEAIAAEGNKYGLTITPADKSDTFKKLDY-S 2068
Cdd:cd23200    160 NDIyglyawVKTTGLRSLWDY--RQNVSSVAFGDDIIKSvsdeYKDKYNYCTYRDVLNATGHIMTPGSKDGEEKPFTSfE 237

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2099547072 2069 SVTFLKRGFKQDDKY---PFL---IHPTFPISEIHESiRWTKKPSQMQEHVLSLchLMWhnGRDVYKEFERKIR 2136
Cdd:cd23200    238 NLQFLKRGFKLENGMvlaPLLqrsIEGPFVWTDIRED-QITVWVNLVQEQLIEA--ALW--GEEYYNELCQKLK 306

Polycipiviridae_RdRp

cd23198

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

1857-2135

2.49e-10

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: 64.36 E-value: 2.49e-10

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1857 FLKDELRKKEKIMAG-----KTRVIEASSINDTIAFRMTYGKLFSSFHR--------NPGIvtgsavgcDPE-------- 1915
Cdd:cd23198      6 FPKDELRPIYKALGDpqtppKTRSVTCMNVYYILAWRRVTLDFWASMHRaadgnfpfCPGI--------NPEgpdwnrly 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1916 TFWSKIPVMLDgecimaFDYTNYDGSIHPIWFEALKQVLTNL------SFEHRLIDRL------CkskHI-FKDTYYEVE 1982
Cdd:cd23198     78 HYLNRHPNAVD------FDVSNWDGHLPAELFYAVLDIIKTVlglkpnSPNAKVIYSIltevmnC---HIqFEDIIYQKL 148

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1983 GGVPSGCSGTSIFNTMINNIIIrtlvldAYKYIDLDKLKI--------------IAYGDDVIFSY----KYPLDMEAIAA 2044
Cdd:cd23198    149 RGLISGFPGTAEVNTLAHWLLI------YYIYLYLAQNTIydmtitaflrnvsaIFYGDDIIITIsdeiLHWFNGKTIQR 222

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 2045 EGNKYGLTITPADK-SDTFKKLDYSSVTFLKRGFKQddkypflIHPTFPISEIHESI--------RWTKKP-SQMQEHVL 2114
Cdd:cd23198    223 MYEEHGYPVTSAAKdTEIPESKPLSDCQFLKSSWNP-------ILPGYYIRKMDIEVvydlvywvRAKEHPrDQFYSNYH 295

                          330       340
                   ....*....|....*....|.
gi 2099547072 2115 SLCHLMWHNGRDVYKEFERKI 2135
Cdd:cd23198    296 DALRILFGHGEQVFEAFREQV 316

RdRP_4

pfam02123

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

1865-2077

3.21e-09

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: 61.71 E-value: 3.21e-09

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1865 KEKIMAGKTRVIEASSINDTIAFRMTYG---KLF--SSFHRNPGivTGSAVGcdpetFWSKIPVMLDGECIMAFDYTNYD 1939
Cdd:pfam02123  236 SMKLEHGKSRAIYACDTRSYLAFEYLLApveKAWanKSVILNPG--EGDISG-----FDWSVQDWKRGGVSLMLDYDDFN 308

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1940 gSIHPIW-----FEALKQVLTNlsFEHRLIDRLCKS-KHIF-----KDTYYEVEGGVPSGCSGTSIFNTMINNIIIRTLV 2008
Cdd:pfam02123  309 -SQHSTEsmravFERLRRRLPD--EPAEAADWLVCSmDSMYqlsdgTLLAQRVPGTLKSGHRATTFINSVLNCAYAELAG 385

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2099547072 2009 LDAykyidLDKLKIIAYGDDVIFSYKYPLDMEAIAAEGNKYGLTITPADKSDTFKKLDYSSVTFLKRGF 2077
Cdd:pfam02123  386 APW-----ADVPTSIHMGDDVLEGLRTPADATSLLDKYARLGFKVNPSKQSVGHTIAEFLRVAFCSHEV 449

ps-ssRNAv_Nodaviridae_RdRp

cd23173

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

1934-2077

1.77e-08

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: 57.52 E-value: 1.77e-08

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1934 DYTNYDGSIHpiwfEALKQVLTN------LSFEHR-----LIDRL----CKSKHIFKdtyYEVEGGVPSGCSGTSIFNTM 1998
Cdd:cd23173     89 DYSRFDGTIS----EWLRRNVEFaaylrwFHPEYRaellkLLDAEincpARTKTGVK---YDPGVSRLSGSPTTTDGNTI 161

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1999 INNIIIRTlvldAYKYIDLDK----LKI-IAYGDDVIFSYKYPLDMEAIAAegnKYGLTItpadKSDTFKklDYSSVTFL 2073
Cdd:cd23173    162 INAFVSYC----ALRETGYSPeeafALLgLYYGDDGLSDNLPAEALEKVAK---DLGLKL----KIEVVR--PGQPVTFL 228


                   ....
gi 2099547072 2074 KRGF 2077
Cdd:cd23173    229 GRVF 232

ps-ssRNAv_RdRp-like

cd23167

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

1930-2033

3.92e-08

Pssm-ID: 438017 [Multi-domain] Cd Length: 73 Bit Score: 51.96 E-value: 3.92e-08

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1930 IMAFDYTNYDGSIHPIWFEAlkqvltnlsfehrlidrlckskhifkdtyyevegGVPSGCSGTSIFNTMINNIIIRTLVL 2009
Cdd:cd23167      2 VVESDYSGFDSSISPDLLKA----------------------------------GQPSGSPNTSADNSLINLLLARLALR 47

                           90       100
                   ....*....|....*....|....*
gi 2099547072 2010 DAYKYIDLDK-LKIIAYGDDVIFSY 2033
Cdd:cd23167     48 KACGRAEFLNsVGILVYGDDSLVSV 72

Calici_coat

pfam00915

Calicivirus coat protein;

384-512

3.59e-05

Calicivirus coat protein;

Pssm-ID: 459994 Cd Length: 291 Bit Score: 47.97 E-value: 3.59e-05

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072  384 PINNTEANIRNKNMYTVQLGGEPDPTTPVftirvdiasqplattligeISSYYTHWTGSVRFSFMFCGSALTTLKLLIAY 463
Cdd:pfam00915   70 SQNWSTIEPQGKVLFDQSLGPHLNPFLLH-------------------LSQMYNGWSGGMRVRFMVAGSGVFGGKLAASV 130

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 2099547072  464 TPPGIRvPRSRKEAMLGTHLIWDVGLQSTVSMVVPWVSASHYRNTTPDT 512
Cdd:pfam00915  131 IPPGVE-PITSASMLQFPHVLFDARQLEPVIFTIPDLRNTLFHNMDRNT 178

Solinviviridae_RdRp

cd23199

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

1909-2078

4.49e-04

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Solinviviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Solinviviridae, order Picornavirales. Solinviviridae is a family of picorna/calici-like viruses with non-segmented, linear, (+)ssRNA genomes of approximately 10-11 kb. Members of two species within the family infect ants but related unclassified virus sequences derive from a large variety of insects and other arthropods. Phylogenetic analysis of RdRp amino acid sequences shows that members of the two classified solinvivirus species form part of a large and very diverse group of arthropod-infecting viruses within the picorna/calici-like group of viruses. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg (viral protein genome-linked)-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438049 Cd Length: 323 Bit Score: 44.65 E-value: 4.49e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1909 AVGCDPETFWSKIPVMLDG-ECIMAFDYTNYDGSIHPIWFEALKQVLTNL-------------SFEHRLidrlckskHIF 1974
Cdd:cd23199     72 AVGCNPYATFHKFATKFFKfKNFFSCDYKNFDRTIPKCVFEDFRDMLIQAnphmkneiyacfqTIIDRI--------QVS 143

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1975 KDTYYEVEGGVPSGCSGTSIFNTMINNI--------IIRTLVLDAYKYIDLDKLKI--IAYGDDVIFSYKypldmEAIAA 2044
Cdd:cd23199    144 GNSILLVHGGMPSGCVPTAPLNSKVNDImiytayvnILRRADRGDITSYRYYRDLVcrLFYGDDVIIAVD-----DSIAD 218

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 2099547072 2045 EGNK----------YGLTITPADKSDTFKKLD-YSSVTFLKRGFK 2078
Cdd:cd23199    219 IFNCqtlseemkilFGMNMTDGSKSDIIPKFEtIETLSFISRFFR 263

ps-ssRNAv_EoPV-like_RdRp

cd23171

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

1844-2078

5.20e-04

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the positive-sense single-stranded RNA [(+)ssRNA] picorna-like virus Ectropis obliqua, and related viruses; This group contains the catalytic core domain of RdRp of Ectropis obliqua picorna-like virus (EoPV), and related viruses. EoPV is an insect (+)ssRNA virus that causes a lethal granulosis infection of larvae of the tea looper (Ectropis obliqua), and related insect-infecting iflaviruses. Ectropis obliqua, a species of moth, is one of the most destructive pest insects on tea plants throughout growing areas of this crop in southern China. The EoPV genome contains a single large ORF encoding the capsid proteins at the 5' terminus of the genome with the non-structural proteins at the 3' end of the genome. This organization is similar to typical mammalian 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: 438021 Cd Length: 239 Bit Score: 44.12 E-value: 5.20e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1844 ALDKYGVdLPMVTFL---KDELRKkekimAGK-TRVIEASSINDTIAFRMTYGKLFSSF-HRNPGIvtgsAVGCD-PETF 1917
Cdd:cd23171      4 ELRKRAV-LPPTTFMdfpKDELLK-----PGKdTRLINGAPLHHTLDMRRYLMEFFAAItTINNKI----AVGIDvHSGD 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1918 WSKIPVMLDGecIMAFDYTNYDGSIHPIWFEALKQVLTNLSFEHR------------LIDRLCKSKHIFKDTYYEVEGGV 1985
Cdd:cd23171     74 WALIHGGADD--VVDEDYSGFGPGFHSQWLDVIRRIAVAWCKHHKtvdpeyenvvrcLIRELQNAYHVAGDLVYQVLCGS 151

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1986 PSGCSGTSIFNTMINniIIRTLVLDAYKYIDLDKL---KIIAYGDDVIFS---YKYPLDMEAIAAegnkYGLTITPADKS 2059
Cdd:cd23171    152 PSGAFATDRINSLAN--LCYHCLCYLRKYGTLTGFwshYLLVYGDDTRRRetaYTGDEFQDCMAS----IGITVNRDKSG 225

                          250
                   ....*....|....*....
gi 2099547072 2060 DTfkkldyssvTFLKRGFK 2078
Cdd:cd23171    226 VT---------SFLKRQFI 235

ps-ssRNAv_Potyviridae_RdRp

cd23175

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

1857-1884

4.67e-03

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

Pssm-ID: 438025 Cd Length: 236 Bit Score: 40.90 E-value: 4.67e-03

                           10        20
                   ....*....|....*....|....*...
gi 2099547072 1857 FLKDELRKKEKIMAGKTRVIEASSInDT 1884
Cdd:cd23175      9 SLKAELRPIEKVEANKTRTFTAAPI-DT 35

DEXXQc_SF1

cd18043

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

1204-1273

7.19e-03

Pssm-ID: 350801 [Multi-domain] Cd Length: 127 Bit Score: 38.72 E-value: 7.19e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547072 1204 TIIKQKKRSEpvAVMIHGSPGTGKS-----ITTNFLAR----------------------MITNESDIYSLPPDPKYFDg 1256
Cdd:cd18043      6 AAIISARNGK--NVVIQGPPGTGKSqtianIIANALARgkrvlfvsekkaaldvvrfpcwIMSPLSVSQYLPLNRNLFD- 82

                           90
                   ....*....|....*..
gi 2099547072 1257 ydqqsVVIMDDIMQNPD 1273
Cdd:cd18043     83 -----LVIFDEASQIPI 94

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