NCBI Conserved Domain Search

Conserved domains on [gi|254942204|gb|ACT89355|]

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polyprotein [rhinovirus A101]

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 ...

1707-2157

0e+00

conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense single-stranded RNA [(+)ssRNA] viruses and closely related viruses; This family contains the catalytic core domain of RdRp of RNA viruses which belong to Group IV of the Baltimore classification system, and are a group of related viruses that have positive-sense (+), single-stranded (ss) genomes made of ribonucleic acid (RNA). RdRp (also known as RNA replicase) catalyzes the replication of RNA from an RNA template; specifically, it catalyzes the synthesis of the RNA strand complementary to a given RNA template. The Baltimore Classification is divided into 7 classes, 3 of which include RNA viruses: Group IV (+) RNA viruses, Group III double-stranded (ds) RNA viruses, and Group V negative-sense (-) RNA viruses. Baltimore groups of viruses differ with respect to the nature of their genome (i.e., the nucleic acid form that is packaged into virions) and correspond to distinct strategies of genome replication and expression. (+) viral RNA is similar to mRNA and thus can be immediately translated by the host cell. (+)ssRNA viruses can also produce (+) copies of the genome from (-) strands of an intermediate dsRNA genome. This acts as both a transcription and a replication process since the replicated RNA is also mRNA. RdRps belong to the expansive class of polymerases containing so-called palm catalytic domains along with the accessory fingers and thumb domains. All RdRps also have six conserved structural motifs (A-F), located in its majority in the palm subdomain (A-E motifs) and the F motif is located on the finger subdomain. All these motifs have been shown to be implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. In addition to Group IV viruses, this model also includes Picobirnaviruses (PBVs), members of the family Picobirnaviridae of dsRNA viruses (Baltimore classification Group III), which are bi-segmented dsRNA viruses. The phylogenetic tree of the RdRps of RNA viruses (realm Riboviria) showed that picobirnaviruses are embedded in the branch of diverse (+)RNA viruses; sometimes they are collectively referred to as the picornavirus supergroup. RdRps of members of the family Permutatetraviridae, a distinct group of RNA viruses that encompass a circular permutation within the RdRp palm domain, are not included in this model.

The actual alignment was detected with superfamily member cd23213:

Pssm-ID: 477363 Cd Length: 453 Bit Score: 736.26 E-value: 0e+00

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1707 VKEINLYSIHTPSKTKLQPSVFHDIFPGEKAPVVLSPKDPRLLVDLDGAIFSKYKGNKNVELTDNMVTAAAHYAAQLATL 1786
Cdd:cd23213     1 NKEVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1787 DINPEPISLEESVYGIEGLEALDLHTSAGYPYTAHGIKKKDLI-PKDRNLAKLKCAMEKYGLDLPMITFLKDELRKPEKI 1865
Cdd:cd23213    81 DIDTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILnKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1866 CSGKTRIIEASSLNDTVQFRMVFGNLFSTFHKNPGTITGSAVGCDPEVFWSKIPLMLDGdCLMAFDYTNYDGSLHPIWFE 1945
Cdd:cd23213   161 EKGKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDG-SLFAFDYTGYDASLSPVWFR 239

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1946 LLKKIL--DELGFPGDMVRKLCNSKHIYKTSYYEVEGGMPSGCAGTSIFNTMINNVIIRTLVLDTYKHINLDKLKILAYG 2023
Cdd:cd23213   240 ALKMVLekGYSEEAVSLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYG 319

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2024 DDVLFSYPFELDMAELASEGVKYGLTITPADKSDKFQKLTYENATFLKRGFKPDEKHSFLIHPIYPVSEVQESIRWTKNP 2103
Cdd:cd23213   320 DDVIASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDP 399

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....
gi 254942204 2104 RNMQEHVLSLCHLLWHSGRDKYDQFVAKIRSVSAGRALYIPPYELLCHEWYDKF 2157
Cdd:cd23213   400 RNTQDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453

Pico_P2A

pfam00947

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

873-999

7.15e-67

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

Pssm-ID: 395757 Cd Length: 127 Bit Score: 221.87 E-value: 7.15e-67

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204   873 NLHLCNPEDLDDSVLICYSSDLVIYRTNTKGDDYIPVCNCTEATYYCKHKDRYFPVNVKKHQWYEIQESEYYPKHIQYNI 952
Cdd:pfam00947    1 NRHLATHEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 254942204   953 LIGEGPCTPGDCGGKLLCKHGVIGIVTAGGENHVAFIDLRDFHVADE 999
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVRDLLWLEE 127

Rhv

pfam00073

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

93-300

6.36e-60

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: 203.70 E-value: 6.36e-60

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204    93 TSQDVANAVVGYGVWPQYLPDDDASAIDKPTHPDTSSNRFYTLESKEWKSDSKGW-WWKLPDALKNMGIFGENLFYHFLG 171
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFfWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204   172 RAGYTVHVQCNASKFHQGALVVAAIPEHQlayigsenvsvgykhTHPGESgrtlndrennnsqqptdeswlncdgTLLGN 251
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPPGA---------------PPPGSR-------------------------DYLWQ 120

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 254942204   252 ITIFPHQFINLRSNNSATLILPYVNAVPMDSMVRHNNWSIVIIPVSPLQ 300
Cdd:pfam00073  121 ATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGNWTLVVAGWVPLN 169

Peptidase_C3 super family

cl02893

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

1516-1681

6.97e-55

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: 189.58 E-value: 6.97e-55

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  1516 GPQEEFGRSLIKHNSCVVTTCNGKFTGL--GIYDNVMIIPTHADAGTQVEIDGIKTNVVD-SYDLCNSQGVKLEITVLKL 1592
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  1593 KRNEKFRDIRKYIPETEDDYPECCLALVANQVEPTIIEVGDCLSYGNI-LLSGNQTARMIKYNYPTKSGYCGGILYKI-- 1669
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVVIAKve 160

                          170
                   ....*....|....
gi 254942204  1670 --GLVLGIHVGGNG 1681
Cdd:pfam00548  161 gnGKILGMHIAGNG 174

Rhv

pfam00073

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

358-523

2.64e-49

Pssm-ID: 395026 Cd Length: 170 Bit Score: 173.27 E-value: 2.64e-49

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204   358 FHPTKEIFIPGRVTNLSEICQVDSMIPINNTVASHKRVSMYAVRVGVQTAPAREVFAIPVDVASqpLATTLIGEIASYYT 437
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFFWWKLPLAL--LSMGLLGRLLRYHT 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204   438 HWTGSIRFSFMFCGTANTSLKLLVAYTPPGVPKPDSRTK---AMLGTHVVWDVGLQSTVSMVVPWVSASHYRLTTPD--- 511
Cdd:pfam00073   79 YYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRDYlwqATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDgnw 158

                          170
                   ....*....|..
gi 254942204   512 TYSKAGYITSWY 523
Cdd:pfam00073  159 TLVVAGWVPLNY 170

Rhv

pfam00073

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

615-769

1.98e-45

Pssm-ID: 395026 Cd Length: 170 Bit Score: 162.10 E-value: 1.98e-45

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204   615 PEDTVETRYVITDQTRDEMSVESFLGRSGCISEMHTivehGEGVY-------NAVDKNFTKWKITL--KEMAQIRRKCEL 685
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQ----GERFYtldstdwTSLSKGFFWWKLPLalLSMGLLGRLLRY 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204   686 FTYLRFDSEITIVPTiagqGNDIGHVVLQYMFVPPGAPIPTKRdDYTWQSGTNASVFWQQG-QTYPRFTIPFMSIASAYY 764
Cdd:pfam00073   77 HTYYRGGLEVTVQFN----GSKFHQGKLLVAYVPPGAPPPGSR-DYLWQATLNPHQFWNLGlNSSARLSVPYISIAHYYS 151


                   ....*
gi 254942204   765 MFYDG 769
Cdd:pfam00073  152 TFYDG 156

Pico_P2B super family

cl03260

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

1000-1096

8.56e-43

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: 152.10 E-value: 8.56e-43

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  1000 QGITDYIHTLGEAFGAGFV----DNIKDQIQAINPINRITSKIVKWIIRIISAVTIIIRNSADPHTIVATLALIGCSGSP 1075
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTqqisDKIKELTNFINPTSKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|.
gi 254942204  1076 WRFIKEKVCNWLQLSYIHKES 1096
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

1.05e-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: 144.82 E-value: 1.05e-40

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 254942204     2 GAQVSRQNVGTHSTQNAVSNGSSLNYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLTKGIPTLQ 69
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 68

RNA_helicase

pfam00910

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

1215-1311

4.71e-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: 141.20 E-value: 4.71e-39

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  1215 VLFHGEPGTGKSIATSILARMI-----TTESDIYSLPPSPKYFDGYDQQSVVIMDDIMQNPSGEDMSLFCQMVSSVPFIP 1289
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALlkklgLPKDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 254942204  1290 PMADLPDKGKPFSSDYVLASTN 1311
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

P3A super family

cl07374

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

1413-1466

5.27e-17

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: 76.69 E-value: 5.27e-17

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 254942204  1413 AIFQG---PIDVVNKPPPPAILDLLKSVRNPDVIKYCEENKWIV--PADCKLERDLNYA 1466
Cdd:pfam08727    1 AIFQGidlKIDIKTSPPPEAIADLLQAVDSPEIIDYCEDKGWIVniPAECQIERDIGIA 59

SpoVK super family

cl33891

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...

1191-1236

2.17e-03

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];

The actual alignment was detected with superfamily member COG0464:

Pssm-ID: 440232 [Multi-domain] Cd Length: 397 Bit Score: 42.98 E-value: 2.17e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 254942204 1191 KRIKELLKRSEMILRTAKRTEPVGVLFHGEPGTGKSIATSILARMI 1236
Cdd:COG0464   170 RELVALPLKRPELREEYGLPPPRGLLLYGPPGTGKTLLARALAGEL 215

Name

Accession

Description

Interval

E-value

Enterovirus_RdRp

cd23213

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

1707-2157

0e+00

RNA-dependent RNA polymerase (RdRp) in the Enterovirus genus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Enterovirus genus within the family Picornaviridae, order Picornavirales. Enteroviruses have small, non-enveloped (+)ssRNA genomes, and replicate within the gastrointestinal tract or other mucosal surfaces. The genus Enterovirus has been divided into 15 species based on genetic divergence (EV A-L and Rhinovirus A-C), and its major members include poliovirus, coxsackievirus and rhinovirus. More than 100 enterovirus types have been associated with several human diseases, all of which are classified into four species (Enterovirus A, Enterovirus B, Enterovirus C, and Enterovirus D). RdRps are multi-domain proteins that play a pivotal role in enterovirus replication. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of enteroviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438063 Cd Length: 453 Bit Score: 736.26 E-value: 0e+00

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1707 VKEINLYSIHTPSKTKLQPSVFHDIFPGEKAPVVLSPKDPRLLVDLDGAIFSKYKGNKNVELTDNMVTAAAHYAAQLATL 1786
Cdd:cd23213     1 NKEVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1787 DINPEPISLEESVYGIEGLEALDLHTSAGYPYTAHGIKKKDLI-PKDRNLAKLKCAMEKYGLDLPMITFLKDELRKPEKI 1865
Cdd:cd23213    81 DIDTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILnKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1866 CSGKTRIIEASSLNDTVQFRMVFGNLFSTFHKNPGTITGSAVGCDPEVFWSKIPLMLDGdCLMAFDYTNYDGSLHPIWFE 1945
Cdd:cd23213   161 EKGKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDG-SLFAFDYTGYDASLSPVWFR 239

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1946 LLKKIL--DELGFPGDMVRKLCNSKHIYKTSYYEVEGGMPSGCAGTSIFNTMINNVIIRTLVLDTYKHINLDKLKILAYG 2023
Cdd:cd23213   240 ALKMVLekGYSEEAVSLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYG 319

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2024 DDVLFSYPFELDMAELASEGVKYGLTITPADKSDKFQKLTYENATFLKRGFKPDEKHSFLIHPIYPVSEVQESIRWTKNP 2103
Cdd:cd23213   320 DDVIASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDP 399

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....
gi 254942204 2104 RNMQEHVLSLCHLLWHSGRDKYDQFVAKIRSVSAGRALYIPPYELLCHEWYDKF 2157
Cdd:cd23213   400 RNTQDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453

Pico_P2A

pfam00947

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

873-999

7.15e-67

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

Pssm-ID: 395757 Cd Length: 127 Bit Score: 221.87 E-value: 7.15e-67

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204   873 NLHLCNPEDLDDSVLICYSSDLVIYRTNTKGDDYIPVCNCTEATYYCKHKDRYFPVNVKKHQWYEIQESEYYPKHIQYNI 952
Cdd:pfam00947    1 NRHLATHEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 254942204   953 LIGEGPCTPGDCGGKLLCKHGVIGIVTAGGENHVAFIDLRDFHVADE 999
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVRDLLWLEE 127

Rhv

pfam00073

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

93-300

6.36e-60

Pssm-ID: 395026 Cd Length: 170 Bit Score: 203.70 E-value: 6.36e-60

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204    93 TSQDVANAVVGYGVWPQYLPDDDASAIDKPTHPDTSSNRFYTLESKEWKSDSKGW-WWKLPDALKNMGIFGENLFYHFLG 171
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFfWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204   172 RAGYTVHVQCNASKFHQGALVVAAIPEHQlayigsenvsvgykhTHPGESgrtlndrennnsqqptdeswlncdgTLLGN 251
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPPGA---------------PPPGSR-------------------------DYLWQ 120

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 254942204   252 ITIFPHQFINLRSNNSATLILPYVNAVPMDSMVRHNNWSIVIIPVSPLQ 300
Cdd:pfam00073  121 ATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGNWTLVVAGWVPLN 169

Peptidase_C3

pfam00548

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

1516-1681

6.97e-55

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: 189.58 E-value: 6.97e-55

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  1516 GPQEEFGRSLIKHNSCVVTTCNGKFTGL--GIYDNVMIIPTHADAGTQVEIDGIKTNVVD-SYDLCNSQGVKLEITVLKL 1592
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  1593 KRNEKFRDIRKYIPETEDDYPECCLALVANQVEPTIIEVGDCLSYGNI-LLSGNQTARMIKYNYPTKSGYCGGILYKI-- 1669
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVVIAKve 160

                          170
                   ....*....|....
gi 254942204  1670 --GLVLGIHVGGNG 1681
Cdd:pfam00548  161 gnGKILGMHIAGNG 174

RdRP_1

pfam00680

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

1725-2134

1.33e-52

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: 192.63 E-value: 1.33e-52

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  1725 PSVFHDIFPGEKAPVVLSPKDPRL---LVDLDGAI--FSKYKGNKNVELTDNMVTAAAHYAAQLATLDINP-----EPIS 1794
Cdd:pfam00680    2 PTERHLVAIPAYVPASLGPEDPRWarsYLNTDPYVddIKKYSRPKLPGPADERDKLLNRSAAKMVLSELRGvpkkaNSTL 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  1795 LEESVY-GIEGLEALDLHTSAGYPYTAHGIKKKDLI------PKDRNLA-KLKCAMEKYGLDLPM----ITFLKDELRKP 1862
Cdd:pfam00680   82 IVYRAIdGVEQIDPLNWDTSAGYPYVGLGGKKGDLIehlkdgTEARELAeRLAADWEVLQNGTPLklvyQTCLKDELRPL 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  1863 EKICSGKTRIIEASSLNDTVQFRMVFGNLFSTFHKNPGtITGSAVGCDPevFWSKIPLMLD-----GDCLMAFDYTNYDG 1937
Cdd:pfam00680  162 EKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNG-FHPIQVGINP--FDRGWPRLLRrlarfGDYVYELDYSGFDS 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  1938 SLHPIWFELLKKILDEL-GFP------GDMVRKLCNSKH-IYKTSYYEVEGGMPSGCAGTSIFNTMINNVIIRTLVL--- 2006
Cdd:pfam00680  239 SVPPWLIRFAFEILRELlGFPsnvkewRAILELLIYTPIaLPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYALLksl 318

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  2007 --DTYKHINLDKLKILA-YGDDVLF--SYPFELDMAELASEGVKYGLTITPADKSDKFQKlTYENATFLKRGFKPDEkhs 2081
Cdd:pfam00680  319 enDGPRVCNLDKYFDFFtYGDDSLVavSPDFDPVLDRLSPHLKELGLTITPAKKTFPVSR-ELEEVSFLKRTFRKTP--- 394

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|...
gi 254942204  2082 FLIHPIYPVSEVQESIRWTKNPRNMQEHVLSLCHLLWHSGRDKYDQFVAKIRS 2134
Cdd:pfam00680  395 GGYRPPLDRKRILAQLEYIRSKPVPSGQLENIRAYASHHGYEFYRDLLYRFVE 447

Rhv

pfam00073

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

358-523

2.64e-49

Pssm-ID: 395026 Cd Length: 170 Bit Score: 173.27 E-value: 2.64e-49

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204   358 FHPTKEIFIPGRVTNLSEICQVDSMIPINNTVASHKRVSMYAVRVGVQTAPAREVFAIPVDVASqpLATTLIGEIASYYT 437
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFFWWKLPLAL--LSMGLLGRLLRYHT 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204   438 HWTGSIRFSFMFCGTANTSLKLLVAYTPPGVPKPDSRTK---AMLGTHVVWDVGLQSTVSMVVPWVSASHYRLTTPD--- 511
Cdd:pfam00073   79 YYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRDYlwqATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDgnw 158

                          170
                   ....*....|..
gi 254942204   512 TYSKAGYITSWY 523
Cdd:pfam00073  159 TLVVAGWVPLNY 170

Rhv

pfam00073

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

615-769

1.98e-45

Pssm-ID: 395026 Cd Length: 170 Bit Score: 162.10 E-value: 1.98e-45

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204   615 PEDTVETRYVITDQTRDEMSVESFLGRSGCISEMHTivehGEGVY-------NAVDKNFTKWKITL--KEMAQIRRKCEL 685
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQ----GERFYtldstdwTSLSKGFFWWKLPLalLSMGLLGRLLRY 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204   686 FTYLRFDSEITIVPTiagqGNDIGHVVLQYMFVPPGAPIPTKRdDYTWQSGTNASVFWQQG-QTYPRFTIPFMSIASAYY 764
Cdd:pfam00073   77 HTYYRGGLEVTVQFN----GSKFHQGKLLVAYVPPGAPPPGSR-DYLWQATLNPHQFWNLGlNSSARLSVPYISIAHYYS 151


                   ....*
gi 254942204   765 MFYDG 769
Cdd:pfam00073  152 TFYDG 156

Pico_P2B

pfam01552

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

1000-1096

8.56e-43

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: 152.10 E-value: 8.56e-43

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  1000 QGITDYIHTLGEAFGAGFV----DNIKDQIQAINPINRITSKIVKWIIRIISAVTIIIRNSADPHTIVATLALIGCSGSP 1075
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTqqisDKIKELTNFINPTSKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|.
gi 254942204  1076 WRFIKEKVCNWLQLSYIHKES 1096
Cdd:pfam01552   81 WQFLKEKACAVLEIPYVHKQG 101

rhv_like

cd00205

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

373-558

9.88e-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: 149.08 E-value: 9.88e-41

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  373 LSEICQVDSMIPINNTVASHKRVSMYAVRVgvqtaparevfaiPVDVASQPLATTLIGEIASYYTHWTGSIRFSFMFCGT 452
Cdd:cd00205     1 VESFADRPTTVGTNNWNSSASGTQLFQWKL-------------SPALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGS 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  453 ANTSLKLLVAYTPPGVPKP---DSRTKAMLGTHVVWDVGLQSTVSMVVPWVSASHYRLTT---PDTYSKAGYITSWYQTN 526
Cdd:cd00205    68 KFHTGRLLVAYVPPGAPAPttgDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRydgYGPLNSFGTLVVRVLTP 147

                         170       180       190
                  ....*....|....*....|....*....|..
gi 254942204  527 FVVPPCTPKTADIICFVSGcKDFCLRMARDTN 558
Cdd:cd00205   148 LTVPSGAPTTVDITVYVRA-GDFELYGPRPPR 178

Pico_P1A

pfam02226

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

2-69

1.05e-40

Pssm-ID: 308053 Cd Length: 68 Bit Score: 144.82 E-value: 1.05e-40

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 254942204     2 GAQVSRQNVGTHSTQNAVSNGSSLNYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLTKGIPTLQ 69
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 68

RNA_helicase

pfam00910

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

1215-1311

4.71e-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: 141.20 E-value: 4.71e-39

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  1215 VLFHGEPGTGKSIATSILARMI-----TTESDIYSLPPSPKYFDGYDQQSVVIMDDIMQNPSGEDMSLFCQMVSSVPFIP 1289
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALlkklgLPKDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 254942204  1290 PMADLPDKGKPFSSDYVLASTN 1311
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

rhv_like

cd00205

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

635-825

6.89e-38

Pssm-ID: 119412 Cd Length: 178 Bit Score: 140.99 E-value: 6.89e-38

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  635 VESFLGRSGCISEMHTIVEHGEGVYNAVDKNFTKWKITLKeMAQIRRKCELFTYLRFDSEITIVPTiagqGNDIGHVVLQ 714
Cdd:cd00205     1 VESFADRPTTVGTNNWNSSASGTQLFQWKLSPALGFLLLQ-NTPLGALLSYFTYWRGDLEVTVQFN----GSKFHTGRLL 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  715 YMFVPPGAPIPTKrDDYTWQSGTNASVFWQ-QGQTYPRFTIPFMSIASAYYMFYDGYEddtpnskygavVTNDMGTLCVR 793
Cdd:cd00205    76 VAYVPPGAPAPTT-GDTRWQATLNPHVIWDlGTNSSVTFVVPYVSPTPYRSTRYDGYG-----------PLNSFGTLVVR 143

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 254942204  794 IVTEQQANTVHITS---RVYHKAKHISAWCPRPPR 825
Cdd:cd00205   144 VLTPLTVPSGAPTTvdiTVYVRAGDFELYGPRPPR 178

rhv_like

cd00205

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

125-328

1.01e-33

Pssm-ID: 119412 Cd Length: 178 Bit Score: 129.05 E-value: 1.01e-33

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  125 PDTSSNRFYTLESKEWK---SDSKGWWWKLPDA----LKNMGIFGENLFYHFLGRAGYTVHVQCNASKFHQGALVVAAIP 197
Cdd:cd00205     1 VESFADRPTTVGTNNWNssaSGTQLFQWKLSPAlgflLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  198 EHQLAYIgsenvsvgykhthpgesgrtlndrennnsqqptdeswlncDGTLLGNITIFPHQFINLRSNNSATLILPYVNA 277
Cdd:cd00205    81 PGAPAPT----------------------------------------TGDTRWQATLNPHVIWDLGTNSSVTFVVPYVSP 120

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 254942204  278 VPMDSMVRH------NNWSIVIIPVSPLQTIEGTP-YVPITLSISPMASEFSGARNTS 328
Cdd:cd00205   121 TPYRSTRYDgygplnSFGTLVVRVLTPLTVPSGAPtTVDITVYVRAGDFELYGPRPPR 178

P3A

pfam08727

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

1413-1466

5.27e-17

Pssm-ID: 400873 Cd Length: 59 Bit Score: 76.69 E-value: 5.27e-17

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 254942204  1413 AIFQG---PIDVVNKPPPPAILDLLKSVRNPDVIKYCEENKWIV--PADCKLERDLNYA 1466
Cdd:pfam08727    1 AIFQGidlKIDIKTSPPPEAIADLLQAVDSPEIIDYCEDKGWIVniPAECQIERDIGIA 59

SpoVK

COG0464

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...

1191-1236

2.17e-03

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];

Pssm-ID: 440232 [Multi-domain] Cd Length: 397 Bit Score: 42.98 E-value: 2.17e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 254942204 1191 KRIKELLKRSEMILRTAKRTEPVGVLFHGEPGTGKSIATSILARMI 1236
Cdd:COG0464   170 RELVALPLKRPELREEYGLPPPRGLLLYGPPGTGKTLLARALAGEL 215

Name

Accession

Description

Interval

E-value

Enterovirus_RdRp

cd23213

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

1707-2157

0e+00

Pssm-ID: 438063 Cd Length: 453 Bit Score: 736.26 E-value: 0e+00

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1707 VKEINLYSIHTPSKTKLQPSVFHDIFPGEKAPVVLSPKDPRLLVDLDGAIFSKYKGNKNVELTDNMVTAAAHYAAQLATL 1786
Cdd:cd23213     1 NKEVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1787 DINPEPISLEESVYGIEGLEALDLHTSAGYPYTAHGIKKKDLI-PKDRNLAKLKCAMEKYGLDLPMITFLKDELRKPEKI 1865
Cdd:cd23213    81 DIDTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILnKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1866 CSGKTRIIEASSLNDTVQFRMVFGNLFSTFHKNPGTITGSAVGCDPEVFWSKIPLMLDGdCLMAFDYTNYDGSLHPIWFE 1945
Cdd:cd23213   161 EKGKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDG-SLFAFDYTGYDASLSPVWFR 239

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1946 LLKKIL--DELGFPGDMVRKLCNSKHIYKTSYYEVEGGMPSGCAGTSIFNTMINNVIIRTLVLDTYKHINLDKLKILAYG 2023
Cdd:cd23213   240 ALKMVLekGYSEEAVSLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYG 319

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2024 DDVLFSYPFELDMAELASEGVKYGLTITPADKSDKFQKLTYENATFLKRGFKPDEKHSFLIHPIYPVSEVQESIRWTKNP 2103
Cdd:cd23213   320 DDVIASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDP 399

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....
gi 254942204 2104 RNMQEHVLSLCHLLWHSGRDKYDQFVAKIRSVSAGRALYIPPYELLCHEWYDKF 2157
Cdd:cd23213   400 RNTQDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453

Sapelovirus_RdRp

cd23218

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

1799-2157

5.41e-162

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: 502.51 E-value: 5.41e-162

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1799 VYGIEGLEALDLHTSAGYPYTAHGIKKKDLIP-KDRNLAKLKCAMEKYGLDLPMITFLKDELRKPEKICSGKTRIIEASS 1877
Cdd:cd23218     3 VYGIDNLEGLDLNTSAGYPYNTMGIRKKDLIPpRGEPLSPLLKALDLHGYDLPFTTYLKDELRPKEKVKMGKTRLIECSS 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1878 LNDTVQFRMVFGNLFSTFHKNPGTITGSAVGCDPEVFWSKIPLMLDGDCLMAFDYTNYDGSLHPIWFELLKKILDELGFP 1957
Cdd:cd23218    83 LNDTIRMKRIFGRLFQTFHKNPGTYTGSAVGCNPDVHWSKFAEEGGMDNVCAFDYTNWDASLSPFWFDALKLFLSKLGYS 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1958 G---DMVRKLCNSKHIYKTSYYEVEGGMPSGCAGTSIFNTMINNVIIRTLVLDTYKHINLDKLKILAYGDDVLFSYPFEL 2034
Cdd:cd23218   163 ErdiVLIDHLCYSNHIFKNEGYKVAGGMPSGCSGTSIFNSIINNIVVRTLVLLVYKGINLDELRILCYGDDLLVAYPYPL 242

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2035 DMAELASEGVKYGLTITPADKSDKFQ---KLTyeNATFLKRGFKPDEKHSFLIHPIYPVSEVQESIRWTKNPRNMQEHVL 2111
Cdd:cd23218   243 DPNVLADLGKSLGLTMTPADKSDTFQgctKLT--EVTFLKRSFVFDEEFPFLCHPVFPMEEVHESIRWTRNASTTQEHVT 320

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*.
gi 254942204 2112 SLCHLLWHSGRDKYDQFVAKIRSVSAGRALYIPPYELLCHEWYDKF 2157
Cdd:cd23218   321 SLCLLAWHNGEEVYEEFCEKIRSVPVGRALILPPYSQLRRSWLDMF 366

Rabovirus_RdRp

cd23230

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

1798-2157

8.15e-157

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: 487.85 E-value: 8.15e-157

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1798 SVYGIEGLEALDLHTSAGYPYTAHGIKKKDLI-PKDRNLAKLKCAMEKYGLDLPMITFLKDELRKPEKICSGKTRIIEAS 1876
Cdd:cd23230     1 AAYGIENLEGLDLNTSAGYPYVLNGIKKRDILdPETRDTTKLQECLDKYGVDLPFVTYLKDELRPLEKIKKGKTRLIECS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1877 SLNDTVQFRMVFGNLFSTFHKNPGTITGSAVGCDPEVFWSKIPLMLDGDcLMAFDYTNYDGSLHPIWFELLKKILDELGF 1956
Cdd:cd23230    81 SMNDTIRMKMMFGRLFATYHRNPGPITGSAVGCNPDIHWTKFRAEMHGE-IIAFDYSNYDASLNKVWFECLKMVLKNFGF 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1957 PgDM--VRKLCNSKHIYKTSYYEVEGGMPSGCAGTSIFNTMINNVIIRTLVLDTYKHINLDKLKILAYGDDVLFSYPFEL 2034
Cdd:cd23230   160 K-DLrpIDHIIRSRHIYKGIEYDVEGGMPSGCSGTSIFNSIINNIIIMTLVLDAYKGIDLEQLKIIAYGDDVIVTYPYPL 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2035 DMAELASEGVKYGLTITPADKSDKFQKLTYENATFLKRGFKPDEKHSFLIHPIYPVSEVQESIRWTKNPRNMQEHVLSLC 2114
Cdd:cd23230   239 DAALLADCGKKYGLKMTPPDKSAEFKNVTWEDVTFLKRRFKPAKHYPFLIHPVFDQQEILESLRWTRNPAHTQEHVRSLA 318

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|...
gi 254942204 2115 HLLWHSGRDKYDQFVAKIRSVSAGRALYIPPYELLCHEWYDKF 2157
Cdd:cd23230   319 ELAWHSGRKSYEEFCNLVKSTNVGKACILPPYESFKRMWLDQF 361

ps-ssRNA_Picornaviridae

cd23193

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

1799-2133

2.60e-132

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: 418.49 E-value: 2.60e-132

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1799 VYGIEGLEALDLHTSAGYPYTAHGIKKKDLIPKD------RNLAKLKCAMEKYGLDLPMITFLKDELRKPEKICSGKTRI 1872
Cdd:cd23193     2 INGIDGLDPIDLNTSPGYPYTTQGLRRRDLIDNDkggvspLLEEEEQVLLDLDGPDVVFTTFLKDELRPKEKVKAGKTRV 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1873 IEASSLNDTVQFRMVFGNLFSTFHKNPGTITGSAVGCDPEVFWSKIPLMLDGDCLMAFDYTNYDGSLHPIWFELLKKIL- 1951
Cdd:cd23193    82 IEAAPLDYVIAGRMVFGRLFAQFHSNPGILTGSAVGCNPDTDWTRLFASLKQDNVYDLDYSGFDASLSSQLFEAAVEVLa 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1952 DELGFP---GDMVRKLCNSKHIYKTSYYEVEGGMPSGCAGTSIFNTMINNVIIRTLVLDTYkHINLDKLKILAYGDDVLF 2028
Cdd:cd23193   162 ECHGDPelvLRYLEPIINSKHVVGDERYTVEGGMPSGCPCTSILNSICNNLVVRYALLETG-KFDPDEYYILAYGDDVLV 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2029 SYPFELDMAELASEGVKY-GLTITPADKSDKFQKLTYENATFLKRGFKPDEkHSFLIHPIYPVSEVQESIRWTKNPRNMQ 2107
Cdd:cd23193   241 STDEPIDPSDLAEFYKKYfGMTVTPADKSSDFPESSPIEDVFLKRRFFVPD-GTFLIHPVMDLETLEQSLMWCGRGGFFQ 319

                         330       340
                  ....*....|....*....|....*.
gi 254942204 2108 EHVLSLCHLLWHSGRDKYDQFVAKIR 2133
Cdd:cd23193   320 QLLSSLCELALHHGPEEYERLVSKVR 345

Mischivirus_RdRp

cd23227

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

1715-2157

4.53e-81

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: 276.06 E-value: 4.53e-81

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1715 IHTPSKTKLQPSVFHDIFPGEKAPVVLSPKDPRLL--VDLDGAIFSKYKGNKNVELTDNMVTAAAHYAAQLATLDINPEP 1792
Cdd:cd23227    12 IHVPRKTKLRKSPAYPIFKPDAGPAVLSKNDPRLAegVDFDKQVFSKHSANQKEYPKAFRRMARWYADRVFTYLGKDNGP 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1793 ISLEESVYGIEGLEALDLHTSAGYPYTAHGIKKKDLIPKDRNL---AKLKCAMEKYG----LDLPMITFLKDELRKPEKI 1865
Cdd:cd23227    92 LSVKDAIKGIDNLDAMDPTTSPGLPYSAAGIKRTDLLDFDTGEiisPALRAEYNKYVsgdySDHVFQTFLKDEIRSEEKI 171

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1866 CSGKTRIIEASSLNDTVQFRMVFGNLFSTFHKNPGTITGSAVGCDPEVFWSKIP--LMLDGDClMAFDYTNYDGSLHPIW 1943
Cdd:cd23227   172 KAGKTRIVDVPSLAHVIIGRVLLGKFCSKFQASPGTELGSAIGCNPDWDWTYFAhqLMERQWC-YDIDYSNFDSTHGTGM 250

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1944 FELLKKIL--DELGFP---GDMVRKLCNSKHIYKTSYYEVEGGMPSGCAGTSIFNTMINNVIIRTLVLDTYKHINLDKLK 2018
Cdd:cd23227   251 FELLIDCFftPENGFSpavAPYLRSLAFSKHAWMDKRYKIEGGLPSGCSATSVLNTVMNNIIIRALLSLTYKNFHPEDVL 330

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2019 ILAYGDDVLFSYPFELD---MAELASEGVKYGLTItpADKSDKFQKL-TYENATFLKRGFKPDEKHSFLIHPIYPVSEVQ 2094
Cdd:cd23227   331 VLAYGDDLLVASDYQLDfnrVREKAAEHTLYKLTT--ANKAPDFPETsTLLDCQFLKRKFVLHSTRNFIWRPVMDVTNLK 408

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 254942204 2095 ESIRWTKnPRNMQEHVLSLCHLLWHSGRDKYDQFVAKIRSVSagraLYIPPYELLCHEWYDKF 2157
Cdd:cd23227   409 TMLSFYK-PNTLSEKLLSVAQLAFHSGYTVYEELFAPFKELQ----MTVPSWWYLEHEWEHNF 466

Cosavirus_RdRp

cd23226

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

1699-2157

6.92e-80

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: 272.66 E-value: 6.92e-80

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1699 GQImtkkdVKEINLYSIHTPSKTKLQPSvfHDIFP--GEKAPVVLSPKDPRLL--VDLDGAIFSKYKGNKNVElTDNMVT 1774
Cdd:cd23226     1 GQI-----VNTENGPRVHVPRQSKLKRT--NATYPatGKYGPAVLSKNDPRLDpdVDFDKVIFSKHVANVVID-EDTSFW 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1775 AAAHYAAQLAT---LDINPEPISLEESVYGIEGLEALDLHTSAGYPYTAhgiKKKDLIP------KDRNL-AKLKCAMEK 1844
Cdd:cd23226    73 NALKMSAQIYAekfKGVDFSPLTVEEAILGIPGLDRMDPNTASGLPYTK---TRRQMIDfqegkiLDPELqERLDTWLSG 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1845 YGLDLPMITFLKDELRKPEKICSGKTRIIEASSLNDTVQFRMVFGNLFSTFHKNPGTITGSAVGCDPEVFWSKIPLMLDG 1924
Cdd:cd23226   150 KQPEMLYQTFLKDEIRPIEKVKAGKTRIIDVTPLDHVLAFRIVLGRFMAHFHNNYGFELGSAVGCDPDVAWANFGFALSS 229

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1925 -DCLMAFDYTNYDGSLHPIWFELLKKIL--DELGFPGD---MVRKLCNSKHIYKTSYYEVEGGMPSGCAGTSIFNTMINN 1998
Cdd:cd23226   230 kKYQYDFDYSNFDASHSESIFELLKQFVftKDNGFDHRcslMIDSLVTSTHCYEDQRMTIRGGLPSGTSGTSVINTIINN 309

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1999 VIIRTLVLDTYKHINLDKLKILAYGDDVLFSYPFELDMaelasEGVKY-----GLTITPADKSDKFQKLTYENATFLKRG 2073
Cdd:cd23226   310 IIFKAALYHTYSNFEWDDVQMLAYGDDIVAASDCLLDL-----DRVKYfmaliGYKITPADKGEKFIPKDMQNIQFLKRS 384

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2074 FKpdeKHSFLIHPIYPVSEVQESIRWTKnPRNMQEHVLSLCHLLWHSGRDKYDQFVAKIrsVSAGraLYIPPYELLCHEW 2153
Cdd:cd23226   385 FR---KVAGVWAPIMDLENLQAMLSWYK-PGTLQEKLDSVARLAHFCGEKVYDHLFTTF--VKDG--FQIKPWKQLHFEW 456


                  ....
gi 254942204 2154 YDKF 2157
Cdd:cd23226   457 LNRF 460

Cardiovirus_RdRp

cd23211

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

1715-2157

4.60e-79

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: 270.17 E-value: 4.60e-79

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1715 IHTPSKTKLQPSVFHDIFPGEKAPVVLSPKDPRLLVDLDGAIFSKYKGNKNVELTDNMVTAAAHYAAQLATLDINPEPIS 1794
Cdd:cd23211    12 VHVPRKTKLRRTVAHPVFQPKFEPAVLSKYDPRTDKDVDEVAFSKHTTNQESLPPVFRMVAKEYANRVFTLLGKDNGRLT 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1795 LEESVYGIEGLEALDLHTSAGYPYTAHGIKKKDLIPKDRN--LAKLKCAMEKYGL----DLPMITFLKDELRKPEKICSG 1868
Cdd:cd23211    92 VEQAVLGLEGMDPMEKDTSPGLPYTQQGLRRTDVVDFETAtmIPFLAEAHRKMVEgdysDVVYQSFLKDEIRPIEKVQAA 171

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1869 KTRIIEASSLNDTVQFRMVFGNLFSTFHKNPGTITGSAVGCDPEVFWSKIPLMLDG-DCLMAFDYTNYDGSLHPIWFELL 1947
Cdd:cd23211   172 KTRIVDVPPFEHCILGRQLLGRFASKFQTNPGLELGSAIGCDPDVDWTAFAVALSGfKYVYDVDYSNFDSTHSTAMFELL 251

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1948 --KKILDELGFP---GDMVRKLCNSKHIYKTSYYEVEGGMPSGCAGTSIFNTMINNVIIRTLVLDTYKHINLDKLKILAY 2022
Cdd:cd23211   252 ieNFFTEENGFDpriGEYLRSLAVSRHAYEERRVLIRGGLPSGCAATSMLNTIMNNIIIRAGLYLTYKNFEFDDIKVLSY 331

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2023 GDDVLFSYPFELDMAELASEGVKYGLTITPADKSDKF-QKLTYENATFLKRGFKpdEKHSFLIHPIYPVSEVQESIRWTK 2101
Cdd:cd23211   332 GDDLLVATNYQIDFNLVKARLAKFGYKITPANKTSTFpLTSTLEDVVFLKRKFV--KENSYLYRPVMDRENLKAMLSYYR 409

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 254942204 2102 nPRNMQEHVLSLCHLLWHSGRDKYDQFVAKIRSVsagrALYIPPYELLCHEWYDKF 2157
Cdd:cd23211   410 -PGTLKEKLTSIALLAVHSGKQVYDEIFAPFREV----GIVVPTYESVLYRWLSLF 460

Dicipivirus_RdRp

cd23222

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

1724-2153

1.96e-76

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: 262.22 E-value: 1.96e-76

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1724 QPSVFHDIFPGEKAPVVLSPKDPRLL--VDLDGAIFSKYKGNKNVELTDNMVTAAAHYAAQLATLDINPEPISL-EESVY 1800
Cdd:cd23222     1 KPSPVYGVYPVTKEPAPLKPTDRRIDegVDFNEPVFGKYGADMKEPFRNLDVGRDVVIARLKKVLPNKKFAPCTvSEALN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1801 GIEGLEALDLHTSAGYPYTAHGIKKKDLIPKDRN-----LAKLKCAME---KYGLDLPMITFLKDELRKPEKICSGKTRI 1872
Cdd:cd23222    81 GKDGLPKLDLKQASGYPYNLSAIKRKHLIESDKDgfltaTPKLLADIEeskKHPEKFPYTSFLKDELRSVKKVKAGKTRV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1873 IEASSLNDTVQFRMVFGNLFSTFHKNPGTITGSAVGCDPEVFWSKI--PLMLDGDcLMAFDYTNYDGSLHPIWFELLKKI 1950
Cdd:cd23222   161 VEAGSLPVIVEGRMIFGNLFAYFNTHPGFETMAAVGCDPEVCWTDWyyKMREKAH-TWDYDYTGFDGSIPSCSFDALADL 239

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1951 LDELGFPGDMVRK----LCNSKHIYKTSYYEVEGGMPSGCAGTSIFNTMINNVIIRTLVLDTYKHINLDKLKILAYGDDV 2026
Cdd:cd23222   240 LCEFVENEDDVRRyisnIKNSYHAYDGNLYLIEGAMPSGCAGTSVFNCLINAMLCFSCFMDLEPEMDPFEPLLIAYGDDI 319

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2027 LFSYPFELDMAELaSEGVKYGLT--ITPADKSDKFQKLT-YENATFLKRGFKPDEKHSfLIHPIYPVSEVQESIRWTkNP 2103
Cdd:cd23222   320 LVSSDHDLFPSRV-SEWMKANTTfkITPADKGEIFNDDSdVSDVRFLKRLFVEDPVCE-LIHPVIETETLEPSLNWC-HE 396

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|...
gi 254942204 2104 RNMQEHVLSLCHLLWHSGRDKYDQFVAKIRSVSAGRALYIP---PYELLCHEW 2153
Cdd:cd23222   397 GEFETKVDAISMLAFHHGPEYYRDWCKKLTDICEERNISPPglkPYSVHRNRW 449

Aphthovirus_RdRp

cd23210

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

1715-2156

1.00e-75

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: 260.26 E-value: 1.00e-75

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1715 IHTPSKTKLQPSVFHDIFPGEKAPVVLSPKDPRLL--VDLDGAIFSKYKGNKNVELTDNMV---TAAAHYAAQLATLDIN 1789
Cdd:cd23210     6 VHVMRKTKLAPTVAHGVFNPEFGPAALSNKDPRLNegVVLDEVIFSKHKGDTKMSAEDKALfrrCAADYASRLHSVLGTA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1790 PEPISLEESVYGIEGLEALDLHTSAGYPYTAHGIKKKDLIPKDRNLAK-----LKCAMEKYGLDLPMITFLKDELRKPEK 1864
Cdd:cd23210    86 NAPLSIYEAIKGVDGLDAMEPDTAPGLPWALQGKRRGALIDFENGTVGpeveaALKLMEKREYKFACQTFLKDEIRPMEK 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1865 ICSGKTRIIEASSLNDTVQFRMVFGNLFSTFHKNPGTITGSAVGCDPEVFWSKIPLMLDG-DCLMAFDYTNYDG-----S 1938
Cdd:cd23210   166 VRAGKTRIVDVLPVEHILYTRMMIGRFCAQMHSNNGPQIGSAVGCNPDVDWQRFGTHFAQyRNVWDVDYSAFDAnhcsdA 245

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1939 LHPIWFELLKkilDELGF-PGD--MVRKLCNSKHIYKTSYYEVEGGMPSGCAGTSIFNTMINNVIIRTLVLDTYKHINLD 2015
Cdd:cd23210   246 MNIMFEEVFR---TEFGFhPNAewILKTLVNTEHAYENKRITVEGGMPSGCSATSIINTILNNIYVLYALRRHYEGVELD 322

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2016 KLKILAYGDDVLFSYPFELDMAELASEGVKYGLTITPADKSDKFQKL--TYENATFLKRGFKPDEKHSFLihpiYPVSEV 2093
Cdd:cd23210   323 TYTMISYGDDIVVASDYDLDFEALKPHFKSLGQTITPADKSDKGFVLghSITDVTFLKRHFHMDYGTGFY----KPVMAS 398

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 254942204 2094 Q--ESIRWTKNPRNMQEHVLSLCHLLWHSGRDKYDQFVAKIRSVsagraLYIPPYELLCHEWYDK 2156
Cdd:cd23210   399 KtlEAILSFARRGTIQEKLISVAGLAVHSGPDEYRRLFEPFQGL-----FEIPSYRSLYLRWVNA 458

Megrivirus_RdRp

cd23223

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

1729-2132

7.29e-73

RNA-dependent RNA polymerase (RdRp) in the genus Megrivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Megrivirus genus within the family Picornaviridae, order Picornavirales. The Megrivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. The genus Megrivirus contains a five species Megrivirus A, Megrivirus B, Megrivirus C, Megrivirus D and Megrivirus E. The name Megrivirus is derived from the turkey genus name Meleagris. Megrivirus A is comprised of turkey hepatitis virus 1 (THV-1), duck megrivirus and goose megrivirus 1. Megrivirus B contains the mesiviruses. Megrivirus D contains harrier picornavirus 1 (HaPV-1). Megrivirus E was found in an Adelie penguin. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438073 Cd Length: 432 Bit Score: 250.92 E-value: 7.29e-73

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1729 HDIFPGEKAPVVLSPKDPRL--LVDLDGAIFSKYKGN----KNVELTDNMVTAAAHYAAQLATLDinPEPI-SLEESVYG 1801
Cdd:cd23223     2 YGAFPVTHGPAALTNKDKRLeeGVDLDDVMFSKHVPDhpgwPTLEPAMSYVVEDLMHKLGFSKDE--PVPMwTLEQAING 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1802 IEGLEALDLHTSAGYPYTAHGIKKKDLIPKDRN-------LAKLKCAMEKYGLDLPMITFLKDELRKPEKICSGKTRIIE 1874
Cdd:cd23223    80 EGVMDGIDMGQSPGYPYNAQGRSRRSFFEWNGEkwqpteeLKKEVDHALKDPDDFYFSTFLKDELRPLEKVKAGKTRLVD 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1875 ASSLNDTVQFRMVFGNLFSTFHKNPGTITGSAVGCDPEVFWSKI---------PLMLDgdclmaFDYTNYDGSLHPIWFE 1945
Cdd:cd23223   160 GDSLPRILAMRMVFGPLFEAMLRKNGPEIHSAVGCNPDTDWTRYyhemgpdsfPYCFD------LDYSCFDSTEPKIAFR 233

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1946 LLKKILDELgF---PGDMVRKLCNSKHIYKTSYYEVEGGMPSGCAGTSIFNTMINNVIIRTLVLDTykHINLDKLKILAY 2022
Cdd:cd23223   234 LMAKYLKPY-FsvdVTPFFEALATSKHVYGDKAYEMEGGMPSGCVGTSMFNCINNSAFIVSALIAL--KISPEDCAWICY 310

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2023 GDDVLFSY---PFELDMAELASEGVKygLTITPADKSDKF-QKLTYENATFLKRGFKPDEKHSFLIHPIYPVSEVQESIR 2098
Cdd:cd23223   311 GDDVIISTdekALSKRIADFYHKNTN--LVVTPASKSGDFpETSTIYDVTFLKRFFQPDSHYPHLIHPYMPLEHLEQSVM 388

                         410       420       430
                  ....*....|....*....|....*....|....*
gi 254942204 2099 W-TKNPrnMQEHVLSLCHLLWHSGRDKYDQFVAKI 2132
Cdd:cd23223   389 WqTDGP--FQQKLDSLCLLAFHAGGPDYREFVDAI 421

Mosavirus_RdRp

cd23225

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

1806-2156

1.38e-71

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: 245.59 E-value: 1.38e-71

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1806 EALDLHTSAGYPYTAHGIKKKDLIP-KDRNLAKLKCAMEK---------YGLDLP-MITFLKDELRKPEKICSGKTRIIE 1874
Cdd:cd23225    10 DAMDMTKAVGYPYCLDSIKRLDLVEiKETENGKVYLPTERlveetekffTGEEKPkFVTFLKDEVRSNEKIKQGKTRIVD 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1875 ASSLNDTVQFRMVFGNLFSTFHKNPGTITGSAVGCDPEVFWSKIPLMLDGDCLMAFDYTNYDgSLHPI-WFELLKK--IL 1951
Cdd:cd23225    90 ASPFPYAIAGRMVMQNFMSNMMRCNGTEVGSAVGCDPDTEWTRYFFELCDRYVFDLDYKAFD-STHPTaMFNLLAErfFT 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1952 DELGFPGDMVRKLCN----SKHIYKTSYYEVEGGMPSGCAGTSIFNTMINNVIIRTLVLDTYK--HINLDKLKILAYGDD 2025
Cdd:cd23225   169 ERNGFDQQAVRIFLNglsdSDHVYEGKHFRIRGGLPSGCPCTSILNTVINNIIVRAAILGAYQidTVDFQKFRMLAYGDD 248

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2026 VLFSYPFEL---DMAELASEGVKYglTITPADKSDKF-QKLTYENATFLKRGFKPDEKHSFLIHPIYPVSEVQESIRWTK 2101
Cdd:cd23225   249 VVYATPQPIkpqDLADWLHANTNY--KVTPASKAGTFpEESTIWDVTFLKRSFKPDEDHGHLIRPVMAVGNLKQMLSFMR 326

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 254942204 2102 nPRNMQEHVLSLCHLLWHSGRDKYDQFVAKIRSVSAGRAlyIPPYELLCHEWYDK 2156
Cdd:cd23225   327 -PGTFPDKVRSVAGLAVHCGEEDYNQLADAVALYVPGVS--MPAYKYMKACWYAK 378

ps-ssRNAv-Picornavirales

cd23169

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

1852-2133

3.87e-67

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: 229.79 E-value: 3.87e-67

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1852 ITFLKDELRKPEKICSGKTRIIEASSLNDTVQFRMVFGNLFSTFHKNPGTiTGSAVGCDPE-VFWSKIP--LMLDGDCLM 1928
Cdd:cd23169     4 VDCLKDELRPIEKVKAGKTRLFSASPLDYTIAFRKYFGDFIAAFQKNRIK-LEHAVGINPDsVEWTRLYrrLLKKGPNIF 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1929 AFDYTNYDGSLHPIWFELLKKIL----DELGFPGD------MVRKLCNSKHIYKTSYYEVEGGMPSGCAGTSIFNTMINN 1998
Cdd:cd23169    83 AGDYSNFDGSLPPDVMEAAFDIIndwyDEYVDDEDervrkvLFEELINTIHLVGNLVYQVHGGNPSGNPLTTIINSIVNL 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1999 VIIRTLVLDTYKHINLDK----LKILAYGDDVLFS----YPFELDMAELASEGVKYGLTITPADKSDKFQKL-TYENATF 2069
Cdd:cd23169   163 LYIRYAWLRITGLTSLSDfkknVRLVTYGDDVIISvsdeVKDEFNFVTISEFLKELGITYTDADKSGDIVPYrPLEEVTF 242

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 254942204 2070 LKRGFKPDEKHSFLIHPIyPVSEVQESIRWTK---NPRNMQEHVLSLCHLLWHS-GRDKYDQFVAKIR 2133
Cdd:cd23169   243 LKRGFRPHPTPGLVLAPL-DLESIEEQLNWTRkedDLLEATIENARAALLLAFGhGPEYYNKFRQKLN 309

Pico_P2A

pfam00947

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

873-999

7.15e-67

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

Pssm-ID: 395757 Cd Length: 127 Bit Score: 221.87 E-value: 7.15e-67

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204   873 NLHLCNPEDLDDSVLICYSSDLVIYRTNTKGDDYIPVCNCTEATYYCKHKDRYFPVNVKKHQWYEIQESEYYPKHIQYNI 952
Cdd:pfam00947    1 NRHLATHEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 254942204   953 LIGEGPCTPGDCGGKLLCKHGVIGIVTAGGENHVAFIDLRDFHVADE 999
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVRDLLWLEE 127

Rosavirus_RdRp

cd23221

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

1798-2157

7.12e-65

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: 225.96 E-value: 7.12e-65

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1798 SVYGIEGLEALDLHTSAGYPYTAHGIKKKDL--------IPKDRnLAK--LKCAME-KYGldlPMITFLKDELRKPEKIC 1866
Cdd:cd23221     1 AINGIDNMDGLDMNQSPGVPYVSEGVSRRSLfdcvdgqwVPRER-LASdiAQVSGDpSLG---HFATFLKDELRSTEKVA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1867 SGKTRIIEASSLNDTVQFRMVFGNLFSTFHKNPGTITGSAVGCDPEVFWSKIPLMLDGDC-LMAFDYTNYDGSLHPIWFE 1945
Cdd:cd23221    77 AGKTRVVEAGSLPHIIVGRKIFGNLFALFNSNPGFQTMCAVGCDPDVTWTELYHPLSAKTyVFDYDYSGFDGSVPSCCFD 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1946 LLKKILDELGFPGDMVRK----LCNSKHIYKTSYYEVEGGMPSGCAGTSIFNTMINNVIIRTLVLDTYKHINLDKLKILA 2021
Cdd:cd23221   157 ALADLLADFVEGEEDVRKyissLKTSFHHYKGKLWRLDGAMPSGCCGTSVFNSLINAMLLFSAFSQICPDFRASEPLLVA 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2022 YGDDVLFSYPFELdMAELASEGVKYGLT--ITPADKSDKFQKLT-YENATFLKRGFKPDEKHSFLIHPIYPVSEVQESIR 2098
Cdd:cd23221   237 YGDDVLVGTDQPL-FPSKVAEWVNSHTTfrITPADKGSVFNDESdIHSVQFLKRHFTPDPDFPALIHPTIDPDTYEQSVM 315

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 254942204 2099 WTKNPrNMQEHVLSLCHLLWHSGRDKYDQFVAKI--RSVSAGRAL-YIPPYELLCHEWYDKF 2157
Cdd:cd23221   316 WQRTG-DFQETVNSLALLVFHRGPKSYSRWCESVtrKCVDGGYPPpFFPPFSLLRHQWLKKF 376

Teschovirus_RdRp

cd23212

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

1791-2130

9.74e-64

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: 221.80 E-value: 9.74e-64

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1791 EPISLEESVYGIEGLEALDLHTSAGYPYTAHGIKKKDLI-PKDRNLAKLKCAMEKYgLDLP-----MITFLKDELRKPEK 1864
Cdd:cd23212     9 EPLSVREAVEGIDGLDPMDMDKSPGLPYVKKGLRRTDLWnPKTGPSIELMAEINRY-LDYNydkhvFLTFLKDELRPKEK 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1865 ICSGKTRIIEASSLNDTVQFRMVFGNLFSTFHKNPGTITGSAVGCDPEVFWSKIPLMLDGDCLMAFDYTNYDGSLHPIWF 1944
Cdd:cd23212    88 VQAGKTRVIDVAGFGHAIVGRMLFGRLFAFFHKNPGWNTGSAVGVNPDLAWTQIFYTAPSRNVLAMDYSGFDASHTSGMF 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1945 ELLKKILDELGFPG---DMVRKLCNSKHIYKTSYYEVEGGMPSGCAGTSIFNTMINNVIIRTLVldtyKHINLDKLKILA 2021
Cdd:cd23212   168 CILKHFLTTLGYGTlqlSYIDSLCYSKHHWDDETYRLDGGLPSGCSGTTIFNTIMNNIVARAAA----SYAAEGPVGILC 243

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2022 YGDDVLFSYPFELDMAELASEGVKYGLTITPADKSDKFQKLTYENATFLKRGFKPDEKhsfLIHPIYPVSEVQESIRWTK 2101
Cdd:cd23212   244 YGDDILVSSPEKFPVSDWLEFYSKTPYKVTAADKSEQIDWRDITQCTFLKRGFVLDGS---LVRPVMEEQHLAELLKWAR 320

                         330       340
                  ....*....|....*....|....*....
gi 254942204 2102 nPRNMQEHVLSLCHLLWHSGRDKYDQFVA 2130
Cdd:cd23212   321 -PGTLQAKLLSIAQLAFHLPRQAYDRLML 348

Kobuvirus_RdRp

cd23214

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

1720-2153

4.42e-61

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: 217.79 E-value: 4.42e-61

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1720 KTKLQPSVFHDIFPGEKAPVVLSPKDPRLL--VDLDGAIFSKYKGNKNVELTDNMVTAAAHYAAQLATLdinPEPISLEE 1797
Cdd:cd23214     8 KSRLGPSPAYGAFPVKKQPAPLTQKDDRLEdgIRLDDQLFLKHNKGDMDEPWPGLEAAADLYFSKFPTM---IRTLTQEE 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1798 SVYGIEGLEALDLHTSAGYPYTAHGIKKKDLIPKDRN-----LAKLKCAMEKYGLDLPMI--TFLKDELRKPEKICSGKT 1870
Cdd:cd23214    85 AINGTPNLEGLDMNQAAGYPWNTMGRSRRSLFVEVQPgiyvpKPELQAEIDKTLEDPDYFysTFLKDELRPTAKVTLGLT 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1871 RIIEASSLNDTVQFRMVFGNLFSTFHKNPGTiTGSAVGCDPEVFWSKIPLML-DGDCLMAFDYTNYDGSLHPIWFELLKK 1949
Cdd:cd23214   165 RVVEAAPIHAIVAGRMLLGGLIEYMQARPGK-HGSAVGCNPDLHWTKFFYKFcHYPQVFDLDYKCFDATLPSCAFRIVED 243

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1950 ILDELgfPGD-----MVRKLCNSKHIYKTSYYEVEGGMPSGCAGTSIFNTMINNVIIRTlVLDTYKHINLDKLKILAYGD 2024
Cdd:cd23214   244 HLERL--TGDervtrYIESIRHSHHVYGNETYEMIGGNPSGCVGTSIINTIINNICVLS-ALIQHPDFSPESFRILAYGD 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2025 DVLFSYPFELDMAELASEGVKYG-LTITPADKSDKF-QKLTYENATFLKRGFKPDEKHSFLIHPIYPVSEVQESIRWTKN 2102
Cdd:cd23214   321 DVIYGCDPPIHPSFIKEFYDKHTpLVVTPANKGSDFpETSTIYDVTFLKRWFVPDDIRPFYIHPVMDPDTYEQSVMWLRD 400

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....
gi 254942204 2103 PrNMQEHVLSLCHLLWHSGRDKYDQFVAKIRSVSAGRALYIP---PYELLCHEW 2153
Cdd:cd23214   401 G-DFQDLVTSLCYLAFHSGPKTYDRWCTRVRDQVMKTTGFPPtflPYSYLQTRW 453

Rhv

pfam00073

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

93-300

6.36e-60

Pssm-ID: 395026 Cd Length: 170 Bit Score: 203.70 E-value: 6.36e-60

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204    93 TSQDVANAVVGYGVWPQYLPDDDASAIDKPTHPDTSSNRFYTLESKEWKSDSKGW-WWKLPDALKNMGIFGENLFYHFLG 171
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFfWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204   172 RAGYTVHVQCNASKFHQGALVVAAIPEHQlayigsenvsvgykhTHPGESgrtlndrennnsqqptdeswlncdgTLLGN 251
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPPGA---------------PPPGSR-------------------------DYLWQ 120

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 254942204   252 ITIFPHQFINLRSNNSATLILPYVNAVPMDSMVRHNNWSIVIIPVSPLQ 300
Cdd:pfam00073  121 ATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGNWTLVVAGWVPLN 169

Passerivirus_RdRp

cd23224

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

1797-2153

8.66e-56

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: 199.93 E-value: 8.66e-56

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1797 ESVYGIEGLEALDLHTSAGYPYTAHGIKKKDLIPKDRNLAKLKCAMEKYGL------DLPMITFLKDELRKPEKICSGKT 1870
Cdd:cd23224     1 EAINGTPLLDGLDMKQSPGYPWSLTTNRRSLFTQDETGKYYPVPELEEAVLaclenpDYFYTTHLKDELRPVEKALAGKT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1871 RIIEASSLNDTVQFRMVFGNLFSTFHKNPGTItGSAVGCDPEVFWSKIPLMLDGDC-LMAFDYTNYDGSLHPIWFELLKK 1949
Cdd:cd23224    81 RLIEAAPIHAIIAGRMLLGGLFEYMHARPGEH-GSAVGCDPDYHWTPFFHSFDEFSqVWALDYSCFDSTLPSCCFDLIAQ 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1950 ILDEL--GFPG-------DMVRKLCNSKHIYKTSYYEVEGGMPSGCAGTSIFNTMINNVIIRTLVLdTYKHINLDKLKIL 2020
Cdd:cd23224   160 KLAKIitPGEGiapdaivKYIRSISISKHVFGNEAYLMVGGNPSGCVGTSILNSMINNCVLISAFL-TQKDFNPNQMRIL 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2021 AYGDDVLFSYPFELDMAELAS-EGVKYGLTITPADKSDKF-QKLTYENATFLKRGFKPDEKHSFLIHPIYPVSEVQESIR 2098
Cdd:cd23224   239 TYGDDVLYATNPPIHPRVVKKfFDENTTLIVTPATKAGDFpDESTIWDVTFLKRYFVPDEIRPWYVHPVIEPATYEQSVM 318

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 254942204 2099 WTKNPrNMQEHVLSLCHLLWHSGRDKYDQFVAKIRSVSAGRALY--IPPYELLCHEW 2153
Cdd:cd23224   319 WTRGG-DFQDVVTSLSFLAHHAGPTNYMIWEEKVRKAAAAKGVSlnILPYSYLQHRW 374

RNA_dep_RNAP

cd01699

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

1841-2100

2.31e-55

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: 194.81 E-value: 2.31e-55

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1841 AMEKY------GLDLPMITFLKDELRKPEKICSGKTRIIEASSLNDTVQFRMVFGNLFSTFHKNpGTITGSAVGCDPEVF 1914
Cdd:cd01699     4 AVESLedlpliRPDLVFTTFLKDELRPLEKVEAGKTRLIQPRPLDYNIALRMYLGPFEAKLMKN-RGGLPIAVGINPYSR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1915 -WSKIPLMLD--GDCLMAFDYTNYDGSLHPIWFELLKKIL------DELGFPGDMVRKLCNS-KHIYKTSYYEVEGGMPS 1984
Cdd:cd01699    83 dWTILANKLRsfSPVAIALDYSRFDSSLSPQLLEAEHSIYnalyddDDELERRNLLRSLTNNsLHIGFNEVYKVRGGRPS 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1985 GCAGTSIFNTMINNVIIRTLVLDTYKHINLDKLKILAYGDDVLFSYPFELD---MAELASEGVKYGLTITPADKSDKFQK 2061
Cdd:cd01699   163 GDPLTSIGNSIINCILVRYAFRKLGGKSFFKNVRLLNYGDDCLLSVEKADDkfnLETLAEWLKEYGLTMTDEDKVESPFR 242

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 254942204 2062 lTYENATFLKRGFKPDEkhSFLIHPIYPVSEVQESIRWT 2100
Cdd:cd01699   243 -PLEEVEFLKRRFVLDE--GGGWRAPLDPSSILSKLSWS 278

Peptidase_C3

pfam00548

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

1516-1681

6.97e-55

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: 189.58 E-value: 6.97e-55

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  1516 GPQEEFGRSLIKHNSCVVTTCNGKFTGL--GIYDNVMIIPTHADAGTQVEIDGIKTNVVD-SYDLCNSQGVKLEITVLKL 1592
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  1593 KRNEKFRDIRKYIPETEDDYPECCLALVANQVEPTIIEVGDCLSYGNI-LLSGNQTARMIKYNYPTKSGYCGGILYKI-- 1669
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVVIAKve 160

                          170
                   ....*....|....
gi 254942204  1670 --GLVLGIHVGGNG 1681
Cdd:pfam00548  161 gnGKILGMHIAGNG 174

Fipivirus_RdRp

cd23229

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

1799-2153

2.11e-54

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: 196.18 E-value: 2.11e-54

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1799 VYGIEGLEALDLHTSAGYPYTAHGIKKKDLIPKDRNL-----AKLKCAMEKYGL----------DLPMITFLKDELRKPE 1863
Cdd:cd23229     2 VEGIPGMEGLDMKTSAGYPWCEQNQKKKDKIKLLAGKnflvrPLREVVHIVVDWyimppdmpkpEIKYVVYLKDELLSSD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1864 KICSGKTRIIEASSLNDTVQFRMVFGNLFSTFHK-NP--GTITGSAVGCDPEVFWSKIPLMLDGDCLMAFDYTNYDGSLH 1940
Cdd:cd23229    82 KVKMGRTRWICAAPVQLVCAWKKVFGRAIAAIHLeSVtdGKSTGCAVGMDPETAWTDIALARPGWPVIALDYSNFDGSLQ 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1941 PIWFELLKKILDEL-GFPGDMVRKLC----NSKHIYKTSYYEVEGGMPSGCAGTSIFNTMINnVIIRTLVLD-----TYK 2010
Cdd:cd23229   162 SFVITGAVRILGYIaGLPDGQSYRLAefvyDVKQIVGKYLYTTVGPLPSGCPSTSIIGSLCN-VLMLLYTLShatgqRYS 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2011 HINlDKLKILAYGDDVL-FSYP-FELDMAELASEGVK-YGLTITPADKSDK-FQKLTYENATFLKRGFKPDEKHSFLIHP 2086
Cdd:cd23229   241 AFR-DWMHVVTYGDDVLvFVHPeVVVVLDTLAHEMYLvFGVTATDATDKRApPQLRELSNVTFLKRGFRQCSSVPFLVHP 319

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 254942204 2087 IYPVSEVQESIRWTKNPRNMQEHVLSLCHLLWHSGRDKYDQFVAKIRS------VSAGRALY--IPPYELLCHEW 2153
Cdd:cd23229   320 TMDKSTIYQMLAWKRKGTTLAENVKCAAEFMMHHGEEEYEDFVGVVKEcstligVDQRSKVYeeLCSYAELHDHW 394

RdRP_1

pfam00680

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

1725-2134

1.33e-52

Pssm-ID: 425815 Cd Length: 450 Bit Score: 192.63 E-value: 1.33e-52

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  1725 PSVFHDIFPGEKAPVVLSPKDPRL---LVDLDGAI--FSKYKGNKNVELTDNMVTAAAHYAAQLATLDINP-----EPIS 1794
Cdd:pfam00680    2 PTERHLVAIPAYVPASLGPEDPRWarsYLNTDPYVddIKKYSRPKLPGPADERDKLLNRSAAKMVLSELRGvpkkaNSTL 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  1795 LEESVY-GIEGLEALDLHTSAGYPYTAHGIKKKDLI------PKDRNLA-KLKCAMEKYGLDLPM----ITFLKDELRKP 1862
Cdd:pfam00680   82 IVYRAIdGVEQIDPLNWDTSAGYPYVGLGGKKGDLIehlkdgTEARELAeRLAADWEVLQNGTPLklvyQTCLKDELRPL 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  1863 EKICSGKTRIIEASSLNDTVQFRMVFGNLFSTFHKNPGtITGSAVGCDPevFWSKIPLMLD-----GDCLMAFDYTNYDG 1937
Cdd:pfam00680  162 EKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNG-FHPIQVGINP--FDRGWPRLLRrlarfGDYVYELDYSGFDS 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  1938 SLHPIWFELLKKILDEL-GFP------GDMVRKLCNSKH-IYKTSYYEVEGGMPSGCAGTSIFNTMINNVIIRTLVL--- 2006
Cdd:pfam00680  239 SVPPWLIRFAFEILRELlGFPsnvkewRAILELLIYTPIaLPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYALLksl 318

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  2007 --DTYKHINLDKLKILA-YGDDVLF--SYPFELDMAELASEGVKYGLTITPADKSDKFQKlTYENATFLKRGFKPDEkhs 2081
Cdd:pfam00680  319 enDGPRVCNLDKYFDFFtYGDDSLVavSPDFDPVLDRLSPHLKELGLTITPAKKTFPVSR-ELEEVSFLKRTFRKTP--- 394

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|...
gi 254942204  2082 FLIHPIYPVSEVQESIRWTKNPRNMQEHVLSLCHLLWHSGRDKYDQFVAKIRS 2134
Cdd:pfam00680  395 GGYRPPLDRKRILAQLEYIRSKPVPSGQLENIRAYASHHGYEFYRDLLYRFVE 447

Rhv

pfam00073

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

358-523

2.64e-49

Pssm-ID: 395026 Cd Length: 170 Bit Score: 173.27 E-value: 2.64e-49

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204   358 FHPTKEIFIPGRVTNLSEICQVDSMIPINNTVASHKRVSMYAVRVGVQTAPAREVFAIPVDVASqpLATTLIGEIASYYT 437
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFFWWKLPLAL--LSMGLLGRLLRYHT 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204   438 HWTGSIRFSFMFCGTANTSLKLLVAYTPPGVPKPDSRTK---AMLGTHVVWDVGLQSTVSMVVPWVSASHYRLTTPD--- 511
Cdd:pfam00073   79 YYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRDYlwqATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDgnw 158

                          170
                   ....*....|..
gi 254942204   512 TYSKAGYITSWY 523
Cdd:pfam00073  159 TLVVAGWVPLNY 170

Hepatovirus_RdRp

cd23215

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

1791-2154

1.07e-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: 172.72 E-value: 1.07e-45

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1791 EPISLEESVYGIEGLEALDLHTSAGYPYTAHGIKKKDLI------------PKDRNLAKLKCAMEKYG--LDLPMITFLK 1856
Cdd:cd23215    63 EFFDLEQAITGVPGMDAINMDSSPGYPYVQEKLTKSDLIwlddngellgmhPRLAQRILFNLTMMDNGndLDVVYTTCPK 142

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1857 DELRKPEKICSGKTRIIEASSLNDTVQFRMVFGNLFSTFHKNPGTITGSAVGCDPEVFWSKI--PLMLDGDCLMAFDYTN 1934
Cdd:cd23215   143 DELRPLEKVLESKTRAIDACPLDFTIICRMFWGPAISYFQLNPGFHTGVAVGIDPDRDWDALfkTMIRFGDYGIDLDFSS 222

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1935 YDGSLHPIWFELLKKILDEL-GFPGDMVRKLCN----SKHIYKTSYYEVEGGMPSGCAGTSIFNTMINNVIIRTLVLDTY 2009
Cdd:cd23215   223 FDASLSPFMIREACRVLSELsGVPDHQGQALINtiiySKHLLYNLCYHVCGSMPSGSPCTSLLNSIVNNVNLYYVFSKIF 302

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2010 KHINL---DKLKILAYGDDVL--FSYPFELDMAE-----LASEGVKYGLTITPADKSDKFQKLTYEnATFLKRGFKPDEK 2079
Cdd:cd23215   303 KKSPVffyDAVKFLCYGDDVLivFSRDLEIKNLDklgqrIQDEFKLLGMTATSADKGEPQVVPVSE-LTFLKRSFNLIED 381

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 254942204 2080 HsflIHPIYPVSEVQESIRWTKNPRNMQEHVLSLCHLLWHSGRDKYDQFVAKIRSVSAGRALyipPYELLCHEWY 2154
Cdd:cd23215   382 R---FRPAISEKTIWSLVAWQRSNAEFEQNLDTACWFAFMHGYDFYQNFYLQLQSCLEKEMI---DYRLKSYEWW 450

Rhv

pfam00073

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

615-769

1.98e-45

Pssm-ID: 395026 Cd Length: 170 Bit Score: 162.10 E-value: 1.98e-45

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204   615 PEDTVETRYVITDQTRDEMSVESFLGRSGCISEMHTivehGEGVY-------NAVDKNFTKWKITL--KEMAQIRRKCEL 685
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQ----GERFYtldstdwTSLSKGFFWWKLPLalLSMGLLGRLLRY 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204   686 FTYLRFDSEITIVPTiagqGNDIGHVVLQYMFVPPGAPIPTKRdDYTWQSGTNASVFWQQG-QTYPRFTIPFMSIASAYY 764
Cdd:pfam00073   77 HTYYRGGLEVTVQFN----GSKFHQGKLLVAYVPPGAPPPGSR-DYLWQATLNPHQFWNLGlNSSARLSVPYISIAHYYS 151


                   ....*
gi 254942204   765 MFYDG 769
Cdd:pfam00073  152 TFYDG 156

Pico_P2B

pfam01552

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

1000-1096

8.56e-43

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: 152.10 E-value: 8.56e-43

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  1000 QGITDYIHTLGEAFGAGFV----DNIKDQIQAINPINRITSKIVKWIIRIISAVTIIIRNSADPHTIVATLALIGCSGSP 1075
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTqqisDKIKELTNFINPTSKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|.
gi 254942204  1076 WRFIKEKVCNWLQLSYIHKES 1096
Cdd:pfam01552   81 WQFLKEKACAVLEIPYVHKQG 101

Dicistroviridae_RdRp

cd23194

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

1854-2133

1.45e-42

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: 159.20 E-value: 1.45e-42

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1854 FLKDELRKPEKICSGKTRIIEASSLNDTVQFRMVFGNLFSTFHKNpgTIT-GSAVGCDP---EvfWSKIPLML--DGDCL 1927
Cdd:cd23194    11 TLKDERRPIEKVDAGKTRVFSAGPMDYTIAFRMYFLGFVAHLMRN--RIDnEIAVGTNVyslD--WDKLARKLlsKGDKV 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1928 MAFDYTNYDGSLHPiwfELLKKILDEL-GFPGD-----MVRK-----LCNSKHIYKTSYYEVEGGMPSGCAGTSIFNTMI 1996
Cdd:cd23194    87 IAGDFSNFDGSLNP---QILWAILDIInEWYDDgeenaLIRRvlwedIVNSVHICGGYVYQWTHSQPSGNPLTAIINSIY 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1997 NNVIIRTLVLD--------TYKHINlDKLKILAYGDDVLFSYP------F-ELDMAELASEgvkYGLTITPADKSD---K 2058
Cdd:cd23194   164 NSIIMRYVYLLltkeaglmTMSDFN-KHVSMVSYGDDNVINVSdevsewFnQLTITEAMAE---IGMTYTDETKTGeivP 239

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2059 FQKLtyENATFLKRGFKPDEKHSFLIHPIyPVSEVQESIRWTKNPRNMQE----------HVLSLcHllwhsGRDKYDQF 2128
Cdd:cd23194   240 YRSL--EEVSFLKRGFRYDDDLGRWVAPL-DLDTILEMPNWVRKGKDPEEitkqnvenalRELSL-H-----GEEVFDKW 310


                  ....*
gi 254942204 2129 VAKIR 2133
Cdd:cd23194   311 APKIR 315

rhv_like

cd00205

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

373-558

9.88e-41

Pssm-ID: 119412 Cd Length: 178 Bit Score: 149.08 E-value: 9.88e-41

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  373 LSEICQVDSMIPINNTVASHKRVSMYAVRVgvqtaparevfaiPVDVASQPLATTLIGEIASYYTHWTGSIRFSFMFCGT 452
Cdd:cd00205     1 VESFADRPTTVGTNNWNSSASGTQLFQWKL-------------SPALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGS 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  453 ANTSLKLLVAYTPPGVPKP---DSRTKAMLGTHVVWDVGLQSTVSMVVPWVSASHYRLTT---PDTYSKAGYITSWYQTN 526
Cdd:cd00205    68 KFHTGRLLVAYVPPGAPAPttgDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRydgYGPLNSFGTLVVRVLTP 147

                         170       180       190
                  ....*....|....*....|....*....|..
gi 254942204  527 FVVPPCTPKTADIICFVSGcKDFCLRMARDTN 558
Cdd:cd00205   148 LTVPSGAPTTVDITVYVRA-GDFELYGPRPPR 178

Pico_P1A

pfam02226

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

2-69

1.05e-40

Pssm-ID: 308053 Cd Length: 68 Bit Score: 144.82 E-value: 1.05e-40

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 254942204     2 GAQVSRQNVGTHSTQNAVSNGSSLNYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLTKGIPTLQ 69
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 68

Crohivirus_RdRp

cd23232

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

1795-2147

6.35e-40

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: 153.33 E-value: 6.35e-40

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1795 LEESVYGIEGLEALDLHTSAGYPYTAHGIKKKDLIPKD---------RNLAKLKCAM-EKYGLDLPMITFLKDELRKPEK 1864
Cdd:cd23232     1 IEEACFEEGDEHALDLKTSPGFKYVQMGLKKTDLVNRPnkfihpilrNDVRLIFDEMaKGQMPVVTFTAHLKDELRKLEK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1865 ICSGKTRIIEASSLNDTVQFRMVFGNLFSTFHKNPGTITGSAVGCDPEVFWSKIPLMLDgDCLMAFDYTNYDGSLHPIWF 1944
Cdd:cd23232    81 IRSGKTRCIEACDFDYTVAHKMMFGTLYKAIYDTPGIITGLAVGMNPWKDWELIQQSLF-KYNYDFDYKTFDGSLSRELM 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1945 ELLKKILDELGFPGDMVRKL----CNSKHIYKTSYYEVEGGMPSGCAGTSIFNTMINNVIIRTLVLDTYKhinlDKLKIL 2020
Cdd:cd23232   160 LHAVDILSACVENDEMAKLMlsvvVESVHLVLDQKWNVSGGMPSGSPCTTVLNSVCNLIVSSTIADMCTE----GDFKIL 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2021 AYGDDVLFSYPFELDmAELASEGVK--YGLTITPADKSDKFQKLTYENATFLKRGFKPDEKHSFLIHPIyPVSEVQESIR 2098
Cdd:cd23232   236 VYGDDLIISSTAPLD-CDRFKTLVElhYGMEVTPGDKGDEFKVKDREQVSFLKRVTRKFPGTNYRVGAL-DLDTVKQHLM 313

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*....
gi 254942204 2099 WTKNPRNMQEHVLSLCHLLWHSGRDKYDQFVAKIRSVSAGRALYIPPYE 2147
Cdd:cd23232   314 WCKSYSSFKQQLDSALMEVAMHGEETYNGFLTEIKTKLDKFKIYPPKFK 362

RNA_helicase

pfam00910

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

1215-1311

4.71e-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: 141.20 E-value: 4.71e-39

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  1215 VLFHGEPGTGKSIATSILARMI-----TTESDIYSLPPSPKYFDGYDQQSVVIMDDIMQNPSGEDMSLFCQMVSSVPFIP 1289
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALlkklgLPKDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 254942204  1290 PMADLPDKGKPFSSDYVLASTN 1311
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

Parechovirus_RdRp

cd23217

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

1798-2135

1.67e-38

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: 149.25 E-value: 1.67e-38

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1798 SVYGIEGLEALDLHTSAGYPYTAHGIKKKDLI--------PKDRNLAKLKCAmEKYGLDLP---MITFLKDELRKPEKIC 1866
Cdd:cd23217     1 AVLGTSHLNSLDLSTSPGYKYVKSGYKKRDLLslepfsvsPQLEKDVKDKLH-AVYKGNQPttiFNACLKDELRKLDKIA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1867 SGKTRIIEASSLNDTVQFRMVFGNLFSTFHKNPGTITGSAVGCDPevfWSKIPLMLDG--DCLMAFDYTNYDGSLHPiwf 1944
Cdd:cd23217    80 QGKTRCIEACSIDYVIAYRVVMSSLYEAIYQTPCQELGLAVGMNP---WTDWDFMINAlnPYNYGLDYSSYDGSLSE--- 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1945 ELLKKILDELGF---PGDMVRKL----CNSKHIYKTSYYEVEGGMPSGCAGTSIFNTMINNVIIRTLVLDtyKHINLDKL 2017
Cdd:cd23217   154 MLMWEAVEVLAYcheSPDLVMQLhkpvINSDHVVMDERWLVHGGMPSGSPCTTVLNSICNLLVCIYLAYL--QSPGIECL 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2018 KILaYGDDVLFSYPFELDMAELASEGVK-YGLTITPADKSDKFQKLTYENATFLKRGFKPDEKHSFLIHPIyPVSEVQES 2096
Cdd:cd23217   232 PIV-YGDDVIFSVSSEIDPEYLVSSAADsFGMEVTGSDKDEPPSLLPRMEVEFLKRTTGYFPGSTYKVGAL-DLETMEQH 309

                         330       340       350
                  ....*....|....*....|....*....|....*....
gi 254942204 2097 IRWTKNPRNMQEHVLSLCHLLWHSGRDKYDQFVAKIRSV 2135
Cdd:cd23217   310 IMWMKNLSTFPQQLQSFENELCLHGKDIYDDYKKIFNPY 348

rhv_like

cd00205

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

635-825

6.89e-38

Pssm-ID: 119412 Cd Length: 178 Bit Score: 140.99 E-value: 6.89e-38

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  635 VESFLGRSGCISEMHTIVEHGEGVYNAVDKNFTKWKITLKeMAQIRRKCELFTYLRFDSEITIVPTiagqGNDIGHVVLQ 714
Cdd:cd00205     1 VESFADRPTTVGTNNWNSSASGTQLFQWKLSPALGFLLLQ-NTPLGALLSYFTYWRGDLEVTVQFN----GSKFHTGRLL 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  715 YMFVPPGAPIPTKrDDYTWQSGTNASVFWQ-QGQTYPRFTIPFMSIASAYYMFYDGYEddtpnskygavVTNDMGTLCVR 793
Cdd:cd00205    76 VAYVPPGAPAPTT-GDTRWQATLNPHVIWDlGTNSSVTFVVPYVSPTPYRSTRYDGYG-----------PLNSFGTLVVR 143

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 254942204  794 IVTEQQANTVHITS---RVYHKAKHISAWCPRPPR 825
Cdd:cd00205   144 VLTPLTVPSGAPTTvdiTVYVRAGDFELYGPRPPR 178

Limnipivirus_RdRp

cd23228

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

1804-2148

2.56e-37

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: 146.18 E-value: 2.56e-37

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1804 GLEALDLHTSAGYPYTAHGIKKKDL--IPKDRNLA---KLKCAMEKYgLDL------PMITF---LKDELRKPEKICSGK 1869
Cdd:cd23228     6 GTNPIDKNTSPGLKYTRDGLKKSDLytIDEDGNVVvsdMLRADVEAW-EELiqsggyPTTLFtacLKDELRSDEKVALGK 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1870 TRIIEASSLNDTVQFRMVFGNLFSTFHKNPGTITGSAVGCDPEVFWSKIPLMLDG-DCLMAFDYTNYDGSLHPIWFELLK 1948
Cdd:cd23228    85 TRVIEAAELDYVVAYRMYMSSIYSDLYNAYAGDTGIAAGINPPADGHRLREELSQyDSFLALDYSRFDGSLPEMLMRAAV 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1949 KILDELGFPGDMVRKL----CNSKHIYKTSYYEVEGGMPSGCAGTSIFNTMINNVIIRTLVLDT----YKHINLDKLK-- 2018
Cdd:cd23228   165 EILADLHEDPDLVRRLhetvIISKHLVVDEDWTVKGGMPSGSPCTTVLNCICNLLVLEYAFLVHfgvyEDDDGVGLPQcd 244

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2019 --ILAYGDDVLFSYPFE---LDMAELASEGvkYGLTITPADKSDKFQKLTYENATFLKRGF-KPDEKHSFLIHPIYPVSE 2092
Cdd:cd23228   245 ylSVVYGDDCIVAYNGMemgLAFAETIEDT--FGMEVTPASKVGDHFNVELHEVEFLKRKFfAFETEEYDRIALRLSENT 322

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 254942204 2093 VQESIRWTKNPRNMQEHVLSLCHLLWHSGRDKYDQFVAKIRSVSAGRALYI--PPYEL 2148
Cdd:cd23228   323 IVQSLMWMRNLKTFPDQVQSLMMELSAWGKEKYDKLRDTCKRRLAKQNLQVtvPGYDI 380

rhv_like

cd00205

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

125-328

1.01e-33

Pssm-ID: 119412 Cd Length: 178 Bit Score: 129.05 E-value: 1.01e-33

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  125 PDTSSNRFYTLESKEWK---SDSKGWWWKLPDA----LKNMGIFGENLFYHFLGRAGYTVHVQCNASKFHQGALVVAAIP 197
Cdd:cd00205     1 VESFADRPTTVGTNNWNssaSGTQLFQWKLSPAlgflLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  198 EHQLAYIgsenvsvgykhthpgesgrtlndrennnsqqptdeswlncDGTLLGNITIFPHQFINLRSNNSATLILPYVNA 277
Cdd:cd00205    81 PGAPAPT----------------------------------------TGDTRWQATLNPHVIWDLGTNSSVTFVVPYVSP 120

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 254942204  278 VPMDSMVRH------NNWSIVIIPVSPLQTIEGTP-YVPITLSISPMASEFSGARNTS 328
Cdd:cd00205   121 TPYRSTRYDgygplnSFGTLVVRVLTPLTVPSGAPtTVDITVYVRAGDFELYGPRPPR 178

Kunsagivirus_RdRp

cd23219

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

1795-2125

2.29e-33

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: 133.45 E-value: 2.29e-33

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1795 LEESVYgiEGLEALDLHTSAGYPYTahGIKKKDLI--------PKDRN-LAKLKCAMEKYGLD-LPMITFLKDELRKPEK 1864
Cdd:cd23219     1 IEEAVF--DTVTPMDHTASAGPKYP--GTKRSELIdfqnriisDRLRNdVLELQFRGTSGGAGeVKFSSFLKDELRPLSK 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1865 ICSGKTRIIEASSLNDTVQFRMVFGNLFSTFHKNPGTITGSAVGCDpeVFWSKIPLMLD-GDCLMAFDYTNYDGSLHPIW 1943
Cdd:cd23219    77 IRSGDTRVVECSSLDYTVAFRMQFLRVLQMCYGSDPTLTGLAPGMN--VYTDMLPLCTSlYDYNLCLDFSKYDSRLPLQV 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1944 FELLKKILDELGFPGDMVRKL----CNSKHIYKTSYYEVEGGMPSGCAGTSIFNTMINNVIIR--TLVLDTYKHinldkL 2017
Cdd:cd23219   155 MHRVAQLISNLTPDPQVSMRLfqpiIISTHIVGSYEVVVEGGMPSGCPITTIMNSVCNVVMTSyaMLLLDPDSD-----F 229

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2018 KILAYGDDVLFSYPFELDMAE----LASEgvkYGLTITPADKSDKFQKLTYENATFLKRGFKPDEKHSFLIhPIYPVSEV 2093
Cdd:cd23219   230 WPVAYGDDNIVSTRKPIDTELfcsiLNEE---FGMILTGADKTTTVQAVPPMSVDFLKRRLRYTPEFPLPV-PVLPLDSM 305

                         330       340       350
                  ....*....|....*....|....*....|..
gi 254942204 2094 QESIRWTKNPRNMQEHVLSLCHLLWHSGRDKY 2125
Cdd:cd23219   306 LSRICWCKGETEFKDQLESFSYELALYGQEVY 337

Aalivirus_RdRp

cd23216

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

1808-2125

2.72e-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: 124.01 E-value: 2.72e-30

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1808 LDLHTSAGYPYTahGIKKKDLI--PKDRNLAKLKCAmekyGLDLPMITFLKDELRKPEKICSGKTRIIEASSLNDTVQFR 1885
Cdd:cd23216    12 IDWQTSPGLKYK--GRTKADLVqdPKFKEDVKEILA----GKPTFFTTYLKDELRSIEKIANGNTRAIEAANFDHVVAWR 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1886 MVFGNLFSTFHKNPGTITGSAVGCDPEVFWSKIPLMLDGDcLMAFDYTNYDGSLHPIWFELLKKIL----DELGFPGDMV 1961
Cdd:cd23216    86 QVMGNIVKQLFSDHDRVTGFAPGMNPYTHFDSLMDQVKWN-VLALDFKKFDGSLSPQVMEEAVDILasfhDMPQMVVDIH 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1962 RKLCNSKHIYKTSYYEVEGGMPSGCAGTSIFNTMINNVIIRTLVLDtyKHINLDKLKILAYGDDVLFS---YPFELDMAE 2038
Cdd:cd23216   165 KHTIYSTNVVSDETWFVEGGMCSGSPCTTVLNTICNLLVNTTILLS--EGIQPDNFYIAAYGDDTIISvdgLSSSLPDPK 242

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2039 LASEGVK--YGLTITPADKSDKFQKLTYENATFLKR--GFKPDEKHsflIHPIYPVSEVQESIRWTKNprNMQEHVLSLC 2114
Cdd:cd23216   243 IMQQKYKewFGMTVTSADKGSEITWDTRNHVQFLKRrpGFFPGTQK---VVGVLDLESMMEHIAWTKG--SFQDQLNSFY 317

                         330
                  ....*....|.
gi 254942204 2115 HLLWHSGRDKY 2125
Cdd:cd23216   318 QELVLHGEQVY 328

Avisivirus_RdRp

cd23231

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

1808-2132

3.05e-28

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: 118.84 E-value: 3.05e-28

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1808 LDLHTSAGYPYtaHGIKKKDLI--PKDR----NLAKLKCAMEKYGLDLPMITFLKDELRKPEKICSGKTRIIEASSLNDT 1881
Cdd:cd23231    11 IDWGTSPGDKY--KGKTKAQLVddKKFKadvmNLVRFNGDPNREPPDVYFTTYLKDELRPKEKAKAGKTRVISAASFDYT 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1882 VQFRMVFGNLFSTFHKNpGTITGSAVGCDP-----EVFWSKIPLMLdgdCLmafDYTNYDGSLHPiwfELLKKILDELG- 1955
Cdd:cd23231    89 IACRMVFGPILRQLFAW-GREFGFGPGLNPythfdELYDKILPFVI---CL---DYSGFDGSLSS---ELMFHAAQVIAc 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1956 FPGD--MVRKLC----NSKHIYKTSYYEVEGGMPSGCAGTSIFNTMINNVIIRTLVLDTYKHInlDKLKILAYGDDVLFS 2029
Cdd:cd23231   159 FSEKpeAIMASAeltiGSTERVSDEVWYVYGGMPSGSPWTTTLNTICNLLMCYTYLLDMGHCW--SETFVVAYGDDVVIS 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2030 YPFELDMaelasEGV------KYGLTITPADKSDKFQKLTYENATFLKRgfKPDEKhSFL--IHPIYPVSEVQESIRWTK 2101
Cdd:cd23231   237 ANIKHNL-----EGIeqwfktKFGATVTPSDKQGKITWTTKNNMEFLKR--RPKQL-DFLpkIVGALDLDNMLDRIQWTK 308

                         330       340       350
                  ....*....|....*....|....*....|.
gi 254942204 2102 NprNMQEHVLSLCHLLWHSGRDKYDQFVAKI 2132
Cdd:cd23231   309 G--HFQDQLNSFYLELALHGRETYNEIRAKL 337

Caliciviridae_RdRp

cd23192

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

1855-2078

1.98e-24

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: 106.19 E-value: 1.98e-24

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1855 LKDELRKPEKICSGKTRIIEASSLNDTVQFRMVFGNLFSTFHKNPGTiTGSAVGCDPE-VFWSKIPLML-DGDCLMAFDY 1932
Cdd:cd23192     7 LKDELRPVEKIAEGKRRLLWGCDVGVTLVAAAAFGPVADALKAVCPT-GPIAVGINMDsEDVEVIFERLsGFRYHYCLDY 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1933 TNYDGSLHPiwfELLK---KILDELGFPGDMVRKLCNSKH-----IYKTSYYEVEGGMPSGCAGTSIFNTMINNVIIRTL 2004
Cdd:cd23192    86 SKWDSTQSP---AVTAaaiDILADLSEETPLRDSVVETLSsppmgIFDDVIFVTKRGLPSGMPFTSVINSLNHWLLFSAA 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2005 VLDTYKHINL------DKLKILAYGDDVLFSYP--FELDMAELASEGVKYGLTITPADKSDKFQKLTYENATFLKRGFKP 2076
Cdd:cd23192   163 VLKAYELVGIytgnvfDEADFFTYGDDGVYAMPpaTASVMDEIIENLKSYGLKPTAADKTENPDIPPLQGPVFLKRTFVR 242


                  ..
gi 254942204 2077 DE 2078
Cdd:cd23192   243 TP 244

Aquamavirus_RdRp

cd23220

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

1853-2127

1.84e-22

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: 100.94 E-value: 1.84e-22

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1853 TFLKDELRKPEKICSGKTRIIEASSLNDTVQFRMVFGNLFSTFHKNPGTITGSAVGCDpeVFWSKIPLMLDGD----CLm 1928
Cdd:cd23220    60 TFMKDELRPKEKIESGKTRIVESCPLDYLLLYRMVMLKSMIWWYNSDCIKTGVAPGMN--VYTDFVPMVKQFKkikyCL- 136

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1929 afDYTNYDGSLHPIWFELLKKILDELGFPGDMVRKLCN----SKHIYKTSYYEVEGGMPSGCAGTSIFNTMINNVIIRTL 2004
Cdd:cd23220   137 --DFSAYDSTLSDEILAAGVEVLACTSAVPSYVRKLHApiicSHHWHNNVVDLVLGGMPSGAPCTSVLNSIVNVLMARYI 214

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2005 VldtyKHINLDKLKILAYGDDVLFSYPFELDMAELAS-EGVKYGLTITPADKSDKFQKLTyeNATFLKRG--FKPDEKHS 2081
Cdd:cd23220   215 C----ALMDIDYPVMVAYGDDNVVSFDEEIDIERMVSlYKTEFGVTATNHDKTPVPRPMA--NPVFLKRRlrFNPDLNIQ 288

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 254942204 2082 FlihPIYPVSEVQESIRWTKNPRNMQEHVLSLCHLLWHSGRDKYDQ 2127
Cdd:cd23220   289 F---PVLPLGEMIDRMCWTRGPEHLSDQTFSFAIELAGYGKQVYTH 331

Marnaviridae_RdRp

cd23195

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

1855-2133

4.01e-20

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: 93.28 E-value: 4.01e-20

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1855 LKDELRKPEKicsGKTRIIEASSLNDTVQFRMVFGNLFSTFHKNPgTITGSAVGCD---PEvfWSKIPLML---DGDCLM 1928
Cdd:cd23195     7 LKDEPTKLTK---DKVRVFQAAPVALQLLVRKYFLPIARFLQMNP-LLSECAVGINaqsPE--WEELYEHLtkfGEDRII 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1929 AFDYTNYDGSLHPIW----FELLKKILDEL-GFPGD-------MVRKLCNSKHIYKTSYYEVEGGMPSGCAGTSIFNTMI 1996
Cdd:cd23195    81 AGDYSKYDKRMSAQLilaaFKILIDIAAKSgGYSEEdlkimrgIATDIAYPLVDFNGDLIQFFGSNPSGHPLTVIINSIV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1997 NNVIIRTlvldTYKHINLDKLK--------ILAYGDDVLFS----YPFeLDMAELASEGVKYGLTITPADKSDKFQK-LT 2063
Cdd:cd23195   161 NSLYMRY----AYYSLYPEKEVppfrdvvaLMTYGDDNIMSvspgYPW-FNHTSIAEFLAKIGIKYTMADKEAESVPfIH 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2064 YENATFLKRGFKPDEKHSfliHPIYPVSEvqESI-------RWTKNPrNMQEHVLSL----CHLLWHSGRDKYDQFVAKI 2132
Cdd:cd23195   236 ISEADFLKRKFVFDPELG---VYVGPLDE--DSIfkslhcyLKSKVL-TPEEQAAQNidgaLREWFFHGREVYEKRREQL 309


                  .
gi 254942204 2133 R 2133
Cdd:cd23195   310 K 310

P3A

pfam08727

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

1413-1466

5.27e-17

Pssm-ID: 400873 Cd Length: 59 Bit Score: 76.69 E-value: 5.27e-17

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 254942204  1413 AIFQG---PIDVVNKPPPPAILDLLKSVRNPDVIKYCEENKWIV--PADCKLERDLNYA 1466
Cdd:pfam08727    1 AIFQGidlKIDIKTSPPPEAIADLLQAVDSPEIIDYCEDKGWIVniPAECQIERDIGIA 59

Secoviridae_RdRp

cd23196

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

1855-2075

3.83e-16

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

Pssm-ID: 438046 Cd Length: 309 Bit Score: 81.66 E-value: 3.83e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1855 LKDELRKPEKICSG-KTRIIEASSLNDTVQFRMVFGNLFSTFHKNPGTITgSAVGCDP-EVFWSKI--PLMLDGDCLMAF 1930
Cdd:cd23196     7 PKDERLKKRKVLEKpKTRLFDVLPMEYNLLLRKYFLNFVRFIQANRHRLP-CQVGINPySREWTTLydRLAEKSDTALNC 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1931 DYTNYDGSL-HPIWFELLKKI------LDELGFPGDMVRKLCNSKHIYKTSYYEVEGGMPSGCAGTSIFNTMINNVIIRT 2003
Cdd:cd23196    86 DYSRFDGLLsHQVYVWIADMInrlygdGDEAKARRNLLMMFCGRRSICGRQVYMVRGGMPSGCALTVIINSIFNEILIRY 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2004 LvldtYKHI-------NLDKL-KILAYGDDVLFSYPFEL----DMAELASEGVKYGLTITpaDKSDK----FQKLTYENA 2067
Cdd:cd23196   166 V----YRKVvprparnNFNKYvRLVVYGDDNLISVKEEIipyfDGPVIKKEMAKVGVTIT--DGTDKtsptLERKPLESL 239


                  ....*...
gi 254942204 2068 TFLKRGFK 2075
Cdd:cd23196   240 DFLKRGFR 247

Iflaviridae_RdRp

cd23197

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

1850-2089

1.38e-10

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: 64.89 E-value: 1.38e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1850 PMITFLKDELRKPEKICS-GKTRIIEASSLNDTVQFRMVFGNLFSTFHKNPGTITgSAVGCDPE-VFWSKI--PLMLDGD 1925
Cdd:cd23197     7 VYWAHLKDELRPSEKLRRfGGTRVFSVPPLELVLNSRRFLLPFMDAFQSFPIEAH-HAIGLNPNsGDWRRLrdTLLEKGP 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1926 CLMAFDYTNYDGSLHpiW------FELLKKILDELGFP----GDMVRKLC----NSKHIYKTSYYEVEGGMPSGCAGTSI 1991
Cdd:cd23197    86 CLLQMDYKNYSDAIP--KecvakaFHIIVDYYRKWHCLtveiENALKTLFldtaDAELLVYGDVFKVNNGVLAGHPMTSV 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1992 FNTMINnviirtLVLDTYKHINLDKLK---------ILAYGDDVLFSYPFEL----DMAELASEGVKYGLTITPADKSDK 2058
Cdd:cd23197   164 VNSVVN------LILMNYMWIKITRRRaseffkltyIIVMGDDVVISLPKQLteefDCRKICAEFAKYDIKVTDSEKNLT 237

                         250       260       270
                  ....*....|....*....|....*....|....
gi 254942204 2059 FQKLTYENA---TFLKRGFKpdekhsflIHPIYP 2089
Cdd:cd23197   238 GEPKPYDSFdkfEFLSRGFS--------DCDAYP 263

ps-ssRNAv_RdRp-like

cd23167

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

1927-2031

1.19e-09

Pssm-ID: 438017 [Multi-domain] Cd Length: 73 Bit Score: 56.58 E-value: 1.19e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1927 LMAFDYTNYDGSLHPIWFELlkkildelgfpgdmvrklcnskhiyktsyyevegGMPSGCAGTSIFNTMINNVIIRTLVL 2006
Cdd:cd23167     2 VVESDYSGFDSSISPDLLKA----------------------------------GQPSGSPNTSADNSLINLLLARLALR 47

                          90       100
                  ....*....|....*....|....*.
gi 254942204 2007 DTYKHINLDK-LKILAYGDDVLFSYP 2031
Cdd:cd23167    48 KACGRAEFLNsVGILVYGDDSLVSVP 73

RdRP_4

pfam02123

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

1862-2084

4.14e-08

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

Pssm-ID: 280316 Cd Length: 465 Bit Score: 58.24 E-value: 4.14e-08

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  1862 PEKICSGKTRIIEASSLNDTVQFRMVfgnLFSTFHK--------NPGTitGSAVGcdpevFWSKIPLMLDGDCLMAFDYT 1933
Cdd:pfam02123  236 SMKLEHGKSRAIYACDTRSYLAFEYL---LAPVEKAwanksvilNPGE--GDISG-----FDWSVQDWKRGGVSLMLDYD 305

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204  1934 NYD-----GSLHPIWFELLKKILDELGFPGDMVRKLCNSKHIY---KTSYYEVEGGMPSGCAGTSIFNTMINNVIIRTLV 2005
Cdd:pfam02123  306 DFNsqhstESMRAVFERLRRRLPDEPAEAADWLVCSMDSMYQLsdgTLLAQRVPGTLKSGHRATTFINSVLNCAYAELAG 385

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 254942204  2006 LDTykhinLDKLKILAYGDDVLFSYPFELDMAELASEGVKYGLTITPADKSDkfqklTYENATFLKRGFKPDEKHSFLI 2084
Cdd:pfam02123  386 APW-----ADVPTSIHMGDDVLEGLRTPADATSLLDKYARLGFKVNPSKQSV-----GHTIAEFLRVAFCSHEVRGYLA 454

Nora-virus_RdRp

cd23200

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

1855-2133

1.39e-05

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: 49.53 E-value: 1.39e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1855 LKDELRKPEKICSGKTRIIEASSLNDTVQFRMVFGNLFSTFHKnPGTITGSAVGCDPE-VFW-------SKIPLMLDGDc 1926
Cdd:cd23200     7 LKDQPIKIAQAKSGRTRVFHCIPVDLILFSGALYGPYKEAYTK-AGLKCYHAVGIDPKsVGWqqlatymTKHPNYFDAD- 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1927 lmafdYTNYDGSLHPIWFELLKKILDelgfpgDMVRKLC-----NSKHI------------YKTSYYEVEGGmPSGCAGT 1989
Cdd:cd23200    85 -----YKNYDKYLHRQVFKAVRKIQR------SVIQQVCpdkwdKARAVeeldaidtyvvdYQTVYKTNRGN-KSGSYTT 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1990 SIFNTMINNVI-----IRTLVLDTYKHInLDKLKILAYGDDVLFS----YPFELDMAELASEGVKYGLTITPADKSDKFQ 2060
Cdd:cd23200   153 TIDNCLANDIYglyawVKTTGLRSLWDY-RQNVSSVAFGDDIIKSvsdeYKDKYNYCTYRDVLNATGHIMTPGSKDGEEK 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2061 KLTY-ENATFLKRGFKpdEKHSFLIHPIYPVSeVQESIRWTKNPRNMQEHVLSLCH------LLWhsGRDKYDQFVAKIR 2133
Cdd:cd23200   232 PFTSfENLQFLKRGFK--LENGMVLAPLLQRS-IEGPFVWTDIREDQITVWVNLVQeqlieaALW--GEEYYNELCQKLK 306

Calici_coat

pfam00915

Calicivirus coat protein;

418-512

7.30e-05

Calicivirus coat protein;

Pssm-ID: 459994 Cd Length: 291 Bit Score: 47.20 E-value: 7.30e-05

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204   418 DVASQPLATTLIGEIASYYTHWTGSIRFSFMFCGTANTSLKLLVAYTPPGVpKPDSRTKAMLGTHVVWDVGLQSTVSMVV 497
Cdd:pfam00915   85 DQSLGPHLNPFLLHLSQMYNGWSGGMRVRFMVAGSGVFGGKLAASVIPPGV-EPITSASMLQFPHVLFDARQLEPVIFTI 163

                           90
                   ....*....|....*
gi 254942204   498 PWVSASHYRLTTPDT 512
Cdd:pfam00915  164 PDLRNTLFHNMDRNT 178

ps-ssRNAv_EoPV-like_RdRp

cd23171

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

1849-2076

2.04e-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: 45.28 E-value: 2.04e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1849 LPMITFL---KDELRKPEKicsgKTRIIEASSLNDTVQFRMVFGNLFSTFHKNPGTItgsAVGCDpeVFWSKIPLMLDG- 1924
Cdd:cd23171    11 LPPTTFMdfpKDELLKPGK----DTRLINGAPLHHTLDMRRYLMEFFAAITTINNKI---AVGID--VHSGDWALIHGGa 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1925 DCLMAFDYTNYDGSLHPIWFELLKKIL------------DELGFPGDMVRKLCNSKHIYKTSYYEVEGGMPSGCAGTSIF 1992
Cdd:cd23171    82 DDVVDEDYSGFGPGFHSQWLDVIRRIAvawckhhktvdpEYENVVRCLIRELQNAYHVAGDLVYQVLCGSPSGAFATDRI 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1993 NTMINNVIIRTLVLDTYKHI-NLDKLKILAYGDDV-----LFSY-PFELDMAELasegvkyGLTITPADKSdkfqkltye 2065
Cdd:cd23171   162 NSLANLCYHCLCYLRKYGTLtGFWSHYLLVYGDDTrrretAYTGdEFQDCMASI-------GITVNRDKSG--------- 225

                         250
                  ....*....|.
gi 254942204 2066 NATFLKRGFKP 2076
Cdd:cd23171   226 VTSFLKRQFIP 236

SpoVK

COG0464

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...

1191-1236

2.17e-03

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];

Pssm-ID: 440232 [Multi-domain] Cd Length: 397 Bit Score: 42.98 E-value: 2.17e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 254942204 1191 KRIKELLKRSEMILRTAKRTEPVGVLFHGEPGTGKSIATSILARMI 1236
Cdd:COG0464   170 RELVALPLKRPELREEYGLPPPRGLLLYGPPGTGKTLLARALAGEL 215

ps-ssRNAv_Nodaviridae_RdRp

cd23173

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

1931-2077

2.90e-03

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: 41.73 E-value: 2.90e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 1931 DYTNYDGSLHPIWFELLKKIL----------DELGfpgDMVRKLCNSKHIYKTSY-YEVEGGMPSGCAGTSIFNTMINNV 1999
Cdd:cd23173    89 DYSRFDGTISEWLRRNVEFAAylrwfhpeyrAELL---KLLDAEINCPARTKTGVkYDPGVSRLSGSPTTTDGNTIINAF 165

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254942204 2000 I----IRTLVLDTYKHINldklKI-LAYGDDVLFSYPFELDMAELASegvKYGLTItpadKSDKFQKltYENATFLKRGF 2074
Cdd:cd23173   166 VsycaLRETGYSPEEAFA----LLgLYYGDDGLSDNLPAEALEKVAK---DLGLKL----KIEVVRP--GQPVTFLGRVF 232


                  ...
gi 254942204 2075 kPD 2077
Cdd:cd23173   233 -PD 234

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