NCBI Conserved Domain Search

Conserved domains on [gi|1129875992|gb|APT69811|]

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polyprotein [rhinovirus A105]

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 ...

1707-2156

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: 821.77 E-value: 0e+00

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1707 ECGLPSIHTPSKTKLQPSVFYDAFPGNKEPAVLSSKDPRLEVDFEKALFSKYKGNEHCVMNDHINVAVSHYSAQLATLDI 1786
Cdd:cd23213      3 EVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATLDI 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1787 NPQPISIEESVFGMEGLEALDLNTSAGFPYVTMGIKKRDLINKQTKDITKLKMALDKYGVDLPMVTFLKDELRKKEKISA 1866
Cdd:cd23213     83 DTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKVEK 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1867 GKTRVIEASSVNDTVLFRTTFGNLFSKFHLNPGIVTGSAVGCDPEVFWSKIPVMLDGdCIMAFDYTNYDGSIHPIWFQAL 1946
Cdd:cd23213    163 GKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDG-SLFAFDYTGYDASLSPVWFRAL 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1947 KQVLT--NLSFEASLIDRLCKSKHIFKNIYYEVEGGVPSGCSGTSIFNTMINNVIIRTLVLDAYKNIDLDKLKIIAYGDD 2024
Cdd:cd23213    242 KMVLEkgYSEEAVSLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYGDD 321

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2025 VIFSYKYQLDMEAIASEGTKYGLTITPADKSTCFKQLDYSNVTFLKRGFKQDEKHQFLIHPTFPVEEIHESIRWTKNPSQ 2104
Cdd:cd23213    322 VIASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDPRN 401

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1129875992 2105 MQEHVLSLCHLMWHNGRDVYKQFEKRIRSVGAGRALYIPPYDLLLHEWYEKF 2156
Cdd:cd23213    402 TQDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453

Pico_P2A

pfam00947

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

872-997

1.40e-73

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

Pssm-ID: 395757 Cd Length: 127 Bit Score: 241.13 E-value: 1.40e-73

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  872 NLHLFN-SDMHDSILVSYSSDLVIYRTNTTGDDYIPTCDCTEATYYCRHKNRYYPIKVTSHDWYEIQESEYYPKHIQYNL 950
Cdd:pfam00947    1 NRHLAThEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1129875992  951 LIGEGPCEPGDCGGKLLCKHGVIGIITAGGEGHVAFIDLRHFHCAEE 997
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVRDLLWLEE 127

Rhv

pfam00073

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

93-300

2.98e-63

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: 213.33 E-value: 2.98e-63

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992   93 TSQDVANAVVGYGVWPHYLTPQDATAIDKPSRPDTSSNRFYTLESKMWNGTSKGW-WWKLPDALKNMGIFGENMFYHFLG 171
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFfWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  172 RSGYTVHVQCNASKFHQGTLIVAMIPEHQlasatygnvaagyklTHPGETgrdvslsrtenrdkqpsddnwlnfdgTLLG 251
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPPGA---------------PPPGSR--------------------------DYLW 119

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 1129875992  252 NITIFPHQFINLRSNNSATIIVPYVNAVPMDSMLRHNNWSLVIIPICPL 300
Cdd:pfam00073  120 QATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGNWTLVVAGWVPL 168

Peptidase_C3 super family

cl02893

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

1514-1679

3.34e-56

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: 193.05 E-value: 3.34e-56

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1514 GPEEEFGRSLIKHNSCVVTTQNGKFTGL--GIYDRTLIIPTHADPGKEVQIDGIATKVED-SYDLFNKDGVKLEITVLKL 1590
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1591 KRNEKFKDIRKYIPENEDDYPDCNLALSANQPETTIINVGDVISYGNI-LLSGTQTARMLKYNYPTKSGYCGGILYKI-- 1667
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVVIAKve 160

                          170
                   ....*....|....
gi 1129875992 1668 --GQVLGIHVGGNG 1679
Cdd:pfam00548  161 gnGKILGMHIAGNG 174

Rhv

pfam00073

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

358-523

7.71e-52

Pssm-ID: 395026 Cd Length: 170 Bit Score: 180.59 E-value: 7.71e-52

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  358 FHPTKEISIPGQVRNLIEMCQVDTLIPINNLEQNIRNVNMYSVVLNQETTTAKEIFAIKVDIASqpLATTMIGEIASYFT 437
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFFWWKLPLAL--LSMGLLGRLLRYHT 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  438 HWTGSLRFSFLFCGTANTTLKLLVAYTPPGIEKPQNR---KDAMLGTHVVWDVGLQSTISMVVPWVSASHYRNTTPD--- 511
Cdd:pfam00073   79 YYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRdylWQATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDgnw 158

                          170
                   ....*....|..
gi 1129875992  512 TYSQAGYITCWY 523
Cdd:pfam00073  159 TLVVAGWVPLNY 170

Rhv

pfam00073

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

615-765

4.26e-44

Pssm-ID: 395026 Cd Length: 170 Bit Score: 158.24 E-value: 4.26e-44

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  615 PEDMIETRYVQTSQTRDEMSLESFLGRSGCIH-----ISELKVKYENYNTEN--FTKWKINL--QEMAQIRRKFELFTYV 685
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQpdvqgERFYTLDSTDWTSLSkgFFWWKLPLalLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  686 RFDSEVTLVPSiaaqGEDIGHVVMQYMYVPPGAPIPKTReDYTWQSGTNASIFWQHG-QTYPRFSLPFLSIASAYYMFYD 764
Cdd:pfam00073   81 RGGLEVTVQFN----GSKFHQGKLLVAYVPPGAPPPGSR-DYLWQATLNPHQFWNLGlNSSARLSVPYISIAHYYSTFYD 155


                   .
gi 1129875992  765 G 765
Cdd:pfam00073  156 G 156

Pico_P2B super family

cl03260

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

998-1094

3.80e-41

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: 147.09 E-value: 3.80e-41

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  998 QGITDYIHMLGEAFGSGFV----DSVKEQINAINPINNISKKIIKWLLRIISAMVIIIRNSSDPQTIIATLTLIGCSGSP 1073
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTqqisDKIKELTNFINPTSKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|.
gi 1129875992 1074 WRFLKEKFCKWTQLNYIHKES 1094
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

1.47e-40

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

Pssm-ID: 308053 Cd Length: 68 Bit Score: 144.44 E-value: 1.47e-40

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1129875992    2 GAQVSRQNVGTHSTQNSVSNGSSLNYFNINYFKDAASSGASKLEFSQDPSKFTDPVKDVLEKGIPTLQ 69
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 68

RNA_helicase

pfam00910

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

1213-1309

2.09e-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: 142.36 E-value: 2.09e-39

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1213 VVIHGEPGTGKSMTTNFLARMI-----TNDSDIYSLPPDPKYFDGYDQQSVVIMDDIMQNPSGDDMTLFCQMVSSVTFIP 1287
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALlkklgLPKDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 1129875992 1288 PMADLPDKGKPFDSRFVLCSTN 1309
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

P3A super family

cl07374

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

1412-1463

5.59e-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: 5.59e-17

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1129875992 1412 AIFQGpISLE-----GPPPAAISDLLQSVRTPEVIKYCEQNKWI--IPAECKIERDLNV 1463
Cdd:pfam08727    1 AIFQG-IDLKidiktSPPPEAIADLLQAVDSPEIIDYCEDKGWIvnIPAECQIERDIGI 58

Name

Accession

Description

Interval

E-value

Enterovirus_RdRp

cd23213

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

1707-2156

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: 821.77 E-value: 0e+00

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1707 ECGLPSIHTPSKTKLQPSVFYDAFPGNKEPAVLSSKDPRLEVDFEKALFSKYKGNEHCVMNDHINVAVSHYSAQLATLDI 1786
Cdd:cd23213      3 EVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATLDI 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1787 NPQPISIEESVFGMEGLEALDLNTSAGFPYVTMGIKKRDLINKQTKDITKLKMALDKYGVDLPMVTFLKDELRKKEKISA 1866
Cdd:cd23213     83 DTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKVEK 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1867 GKTRVIEASSVNDTVLFRTTFGNLFSKFHLNPGIVTGSAVGCDPEVFWSKIPVMLDGdCIMAFDYTNYDGSIHPIWFQAL 1946
Cdd:cd23213    163 GKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDG-SLFAFDYTGYDASLSPVWFRAL 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1947 KQVLT--NLSFEASLIDRLCKSKHIFKNIYYEVEGGVPSGCSGTSIFNTMINNVIIRTLVLDAYKNIDLDKLKIIAYGDD 2024
Cdd:cd23213    242 KMVLEkgYSEEAVSLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYGDD 321

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2025 VIFSYKYQLDMEAIASEGTKYGLTITPADKSTCFKQLDYSNVTFLKRGFKQDEKHQFLIHPTFPVEEIHESIRWTKNPSQ 2104
Cdd:cd23213    322 VIASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDPRN 401

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1129875992 2105 MQEHVLSLCHLMWHNGRDVYKQFEKRIRSVGAGRALYIPPYDLLLHEWYEKF 2156
Cdd:cd23213    402 TQDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453

Pico_P2A

pfam00947

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

872-997

1.40e-73

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

Pssm-ID: 395757 Cd Length: 127 Bit Score: 241.13 E-value: 1.40e-73

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  872 NLHLFN-SDMHDSILVSYSSDLVIYRTNTTGDDYIPTCDCTEATYYCRHKNRYYPIKVTSHDWYEIQESEYYPKHIQYNL 950
Cdd:pfam00947    1 NRHLAThEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1129875992  951 LIGEGPCEPGDCGGKLLCKHGVIGIITAGGEGHVAFIDLRHFHCAEE 997
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVRDLLWLEE 127

Rhv

pfam00073

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

93-300

2.98e-63

Pssm-ID: 395026 Cd Length: 170 Bit Score: 213.33 E-value: 2.98e-63

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992   93 TSQDVANAVVGYGVWPHYLTPQDATAIDKPSRPDTSSNRFYTLESKMWNGTSKGW-WWKLPDALKNMGIFGENMFYHFLG 171
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFfWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  172 RSGYTVHVQCNASKFHQGTLIVAMIPEHQlasatygnvaagyklTHPGETgrdvslsrtenrdkqpsddnwlnfdgTLLG 251
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPPGA---------------PPPGSR--------------------------DYLW 119

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 1129875992  252 NITIFPHQFINLRSNNSATIIVPYVNAVPMDSMLRHNNWSLVIIPICPL 300
Cdd:pfam00073  120 QATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGNWTLVVAGWVPL 168

Peptidase_C3

pfam00548

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

1514-1679

3.34e-56

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: 193.05 E-value: 3.34e-56

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1514 GPEEEFGRSLIKHNSCVVTTQNGKFTGL--GIYDRTLIIPTHADPGKEVQIDGIATKVED-SYDLFNKDGVKLEITVLKL 1590
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1591 KRNEKFKDIRKYIPENEDDYPDCNLALSANQPETTIINVGDVISYGNI-LLSGTQTARMLKYNYPTKSGYCGGILYKI-- 1667
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVVIAKve 160

                          170
                   ....*....|....
gi 1129875992 1668 --GQVLGIHVGGNG 1679
Cdd:pfam00548  161 gnGKILGMHIAGNG 174

Rhv

pfam00073

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

358-523

7.71e-52

Pssm-ID: 395026 Cd Length: 170 Bit Score: 180.59 E-value: 7.71e-52

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  358 FHPTKEISIPGQVRNLIEMCQVDTLIPINNLEQNIRNVNMYSVVLNQETTTAKEIFAIKVDIASqpLATTMIGEIASYFT 437
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFFWWKLPLAL--LSMGLLGRLLRYHT 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  438 HWTGSLRFSFLFCGTANTTLKLLVAYTPPGIEKPQNR---KDAMLGTHVVWDVGLQSTISMVVPWVSASHYRNTTPD--- 511
Cdd:pfam00073   79 YYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRdylWQATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDgnw 158

                          170
                   ....*....|..
gi 1129875992  512 TYSQAGYITCWY 523
Cdd:pfam00073  159 TLVVAGWVPLNY 170

RdRP_1

pfam00680

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

1723-2127

3.80e-51

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: 188.39 E-value: 3.80e-51

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1723 PSVFYDAFPGNKEPAVLSSKDPRLEVDFE------KALfSKYK-----GNEHCVMNDHINVAVSHYSAQLATLDINPQPI 1791
Cdd:pfam00680    2 PTERHLVAIPAYVPASLGPEDPRWARSYLntdpyvDDI-KKYSrpklpGPADERDKLLNRSAAKMVLSELRGVPKKANST 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1792 SIEESVF-GMEGLEALDLNTSAGFPYVTMGIKKRDLINkQTKDIT-------KLKMALDKY--GVDLPMV--TFLKDELR 1859
Cdd:pfam00680   81 LIVYRAIdGVEQIDPLNWDTSAGYPYVGLGGKKGDLIE-HLKDGTearelaeRLAADWEVLqnGTPLKLVyqTCLKDELR 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1860 KKEKISAGKTRVIEASSVNDTVLFRTTFGNLFSKFHLNPGIVTgSAVGCDPevFWSKIPVMLD-----GDCIMAFDYTNY 1934
Cdd:pfam00680  160 PLEKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHP-IQVGINP--FDRGWPRLLRrlarfGDYVYELDYSGF 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1935 DGSIHPIWFQALKQVLT-------NLSFEASLIDRLCKSKHIFKNIY-YEVEGGVPSGCSGTSIFNTMINNVIIRTLVLD 2006
Cdd:pfam00680  237 DSSVPPWLIRFAFEILRellgfpsNVKEWRAILELLIYTPIALPNGTvFKKTGGLPSGSPFTSIINSIVNYLLILYALLK 316

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2007 AYKNIDL------DKLKIIAYGDDVIFSYKYQLD--MEAIASEGTKYGLTITPADKS-TCFKQLDysNVTFLKRGFKQDE 2077
Cdd:pfam00680  317 SLENDGPrvcnldKYFDFFTYGDDSLVAVSPDFDpvLDRLSPHLKELGLTITPAKKTfPVSRELE--EVSFLKRTFRKTP 394

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2078 khqFLIHPTFPVEEIHESIRWTKNPSQMQEHVLSLCHLMWHNGRDVYKQF 2127
Cdd:pfam00680  395 ---GGYRPPLDRKRILAQLEYIRSKPVPSGQLENIRAYASHHGYEFYRDL 441

Rhv

pfam00073

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

615-765

4.26e-44

Pssm-ID: 395026 Cd Length: 170 Bit Score: 158.24 E-value: 4.26e-44

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  615 PEDMIETRYVQTSQTRDEMSLESFLGRSGCIH-----ISELKVKYENYNTEN--FTKWKINL--QEMAQIRRKFELFTYV 685
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQpdvqgERFYTLDSTDWTSLSkgFFWWKLPLalLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  686 RFDSEVTLVPSiaaqGEDIGHVVMQYMYVPPGAPIPKTReDYTWQSGTNASIFWQHG-QTYPRFSLPFLSIASAYYMFYD 764
Cdd:pfam00073   81 RGGLEVTVQFN----GSKFHQGKLLVAYVPPGAPPPGSR-DYLWQATLNPHQFWNLGlNSSARLSVPYISIAHYYSTFYD 155


                   .
gi 1129875992  765 G 765
Cdd:pfam00073  156 G 156

rhv_like

cd00205

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

373-558

7.62e-44

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: 157.94 E-value: 7.62e-44

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  373 LIEMCQVDTLIPINNLEQNirnvnmysvvlnqetTTAKEIFAIKVDIASQPL--ATTMIGEIASYFTHWTGSLRFSFLFC 450
Cdd:cd00205      1 VESFADRPTTVGTNNWNSS---------------ASGTQLFQWKLSPALGFLllQNTPLGALLSYFTYWRGDLEVTVQFN 65

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  451 GTANTTLKLLVAYTPPGIEKPQN---RKDAMLGTHVVWDVGLQSTISMVVPWVSASHYRNTTPDTYSQA---GYITCWYQ 524
Cdd:cd00205     66 GSKFHTGRLLVAYVPPGAPAPTTgdtRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDGYGPLnsfGTLVVRVL 145

                          170       180       190
                   ....*....|....*....|....*....|....
gi 1129875992  525 TNLVVPPNTPTTARMLCFVSGcKDFCLRMARDTN 558
Cdd:cd00205    146 TPLTVPSGAPTTVDITVYVRA-GDFELYGPRPPR 178

Pico_P2B

pfam01552

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

998-1094

3.80e-41

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: 147.09 E-value: 3.80e-41

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  998 QGITDYIHMLGEAFGSGFV----DSVKEQINAINPINNISKKIIKWLLRIISAMVIIIRNSSDPQTIIATLTLIGCSGSP 1073
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTqqisDKIKELTNFINPTSKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|.
gi 1129875992 1074 WRFLKEKFCKWTQLNYIHKES 1094
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

1.47e-40

Pssm-ID: 308053 Cd Length: 68 Bit Score: 144.44 E-value: 1.47e-40

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1129875992    2 GAQVSRQNVGTHSTQNSVSNGSSLNYFNINYFKDAASSGASKLEFSQDPSKFTDPVKDVLEKGIPTLQ 69
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 68

RNA_helicase

pfam00910

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

1213-1309

2.09e-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: 142.36 E-value: 2.09e-39

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1213 VVIHGEPGTGKSMTTNFLARMI-----TNDSDIYSLPPDPKYFDGYDQQSVVIMDDIMQNPSGDDMTLFCQMVSSVTFIP 1287
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALlkklgLPKDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 1129875992 1288 PMADLPDKGKPFDSRFVLCSTN 1309
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

rhv_like

cd00205

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

125-327

1.53e-35

Pssm-ID: 119412 Cd Length: 178 Bit Score: 134.06 E-value: 1.53e-35

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  125 PDTSSNRFYTLESKMWNG---TSKGWWWKLPDA----LKNMGIFGENMFYHFLGRSGYTVHVQCNASKFHQGTLIVAMIP 197
Cdd:cd00205      1 VESFADRPTTVGTNNWNSsasGTQLFQWKLSPAlgflLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  198 EHQLASATygnvaagyklthpgetgrdvslsrtenrdkqpsddnwlnfdGTLLGNITIFPHQFINLRSNNSATIIVPYVN 277
Cdd:cd00205     81 PGAPAPTT-----------------------------------------GDTRWQATLNPHVIWDLGTNSSVTFVVPYVS 119

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1129875992  278 AVPMDSMLRH------NNWSLVIIPICPL-EANGAQPVVPITISISPMCAEFSGARA 327
Cdd:cd00205    120 PTPYRSTRYDgygplnSFGTLVVRVLTPLtVPSGAPTTVDITVYVRAGDFELYGPRP 176

rhv_like

cd00205

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

635-821

1.65e-35

Pssm-ID: 119412 Cd Length: 178 Bit Score: 134.06 E-value: 1.65e-35

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  635 LESFLGRSGCIHISELKvkyENYNTENFTKWKINLQE------MAQIRRKFELFTYVRFDSEVTLV--PSIAAQGedigh 706
Cdd:cd00205      1 VESFADRPTTVGTNNWN---SSASGTQLFQWKLSPALgflllqNTPLGALLSYFTYWRGDLEVTVQfnGSKFHTG----- 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  707 vVMQYMYVPPGAPIPKTrEDYTWQSGTNASIFWQHG-QTYPRFSLPFLSIASAYYMFYDGYDgdqtesrygtvVTNDMGT 785
Cdd:cd00205     73 -RLLVAYVPPGAPAPTT-GDTRWQATLNPHVIWDLGtNSSVTFVVPYVSPTPYRSTRYDGYG-----------PLNSFGT 139

                          170       180       190
                   ....*....|....*....|....*....|....*....
gi 1129875992  786 LCSRIVT---DQHTHPIKITTRVYHKAKHVKAWCPRPPR 821
Cdd:cd00205    140 LVVRVLTpltVPSGAPTTVDITVYVRAGDFELYGPRPPR 178

P3A

pfam08727

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

1412-1463

5.59e-17

Pssm-ID: 400873 Cd Length: 59 Bit Score: 76.69 E-value: 5.59e-17

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1129875992 1412 AIFQGpISLE-----GPPPAAISDLLQSVRTPEVIKYCEQNKWI--IPAECKIERDLNV 1463
Cdd:pfam08727    1 AIFQG-IDLKidiktSPPPEAIADLLQAVDSPEIIDYCEDKGWIvnIPAECQIERDIGI 58

DEXXQc_SF1

cd18043

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

1212-1266

1.03e-03

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

Pssm-ID: 350801 [Multi-domain] Cd Length: 127 Bit Score: 41.03 E-value: 1.03e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1212 AVVIHGEPGTGKSMT-----TNFLAR----------------------MITNDSDIYSLPPDPKYFDgydqqsVVIMDDI 1264
Cdd:cd18043     16 NVVIQGPPGTGKSQTianiiANALARgkrvlfvsekkaaldvvrfpcwIMSPLSVSQYLPLNRNLFD------LVIFDEA 89


                   ..
gi 1129875992 1265 MQ 1266
Cdd:cd18043     90 SQ 91

Name

Accession

Description

Interval

E-value

Enterovirus_RdRp

cd23213

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

1707-2156

0e+00

Pssm-ID: 438063 Cd Length: 453 Bit Score: 821.77 E-value: 0e+00

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1707 ECGLPSIHTPSKTKLQPSVFYDAFPGNKEPAVLSSKDPRLEVDFEKALFSKYKGNEHCVMNDHINVAVSHYSAQLATLDI 1786
Cdd:cd23213      3 EVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATLDI 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1787 NPQPISIEESVFGMEGLEALDLNTSAGFPYVTMGIKKRDLINKQTKDITKLKMALDKYGVDLPMVTFLKDELRKKEKISA 1866
Cdd:cd23213     83 DTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKVEK 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1867 GKTRVIEASSVNDTVLFRTTFGNLFSKFHLNPGIVTGSAVGCDPEVFWSKIPVMLDGdCIMAFDYTNYDGSIHPIWFQAL 1946
Cdd:cd23213    163 GKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDG-SLFAFDYTGYDASLSPVWFRAL 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1947 KQVLT--NLSFEASLIDRLCKSKHIFKNIYYEVEGGVPSGCSGTSIFNTMINNVIIRTLVLDAYKNIDLDKLKIIAYGDD 2024
Cdd:cd23213    242 KMVLEkgYSEEAVSLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYGDD 321

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2025 VIFSYKYQLDMEAIASEGTKYGLTITPADKSTCFKQLDYSNVTFLKRGFKQDEKHQFLIHPTFPVEEIHESIRWTKNPSQ 2104
Cdd:cd23213    322 VIASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDPRN 401

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1129875992 2105 MQEHVLSLCHLMWHNGRDVYKQFEKRIRSVGAGRALYIPPYDLLLHEWYEKF 2156
Cdd:cd23213    402 TQDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453

Sapelovirus_RdRp

cd23218

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

1797-2156

8.99e-163

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: 504.44 E-value: 8.99e-163

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1797 VFGMEGLEALDLNTSAGFPYVTMGIKKRDLINKQTKDITKLKMALDKYGVDLPMVTFLKDELRKKEKISAGKTRVIEASS 1876
Cdd:cd23218      3 VYGIDNLEGLDLNTSAGYPYNTMGIRKKDLIPPRGEPLSPLLKALDLHGYDLPFTTYLKDELRPKEKVKMGKTRLIECSS 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1877 VNDTVLFRTTFGNLFSKFHLNPGIVTGSAVGCDPEVFWSKIPVMLDGDCIMAFDYTNYDGSIHPIWFQALKQVLTNLSFE 1956
Cdd:cd23218     83 LNDTIRMKRIFGRLFQTFHKNPGTYTGSAVGCNPDVHWSKFAEEGGMDNVCAFDYTNWDASLSPFWFDALKLFLSKLGYS 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1957 AS---LIDRLCKSKHIFKNIYYEVEGGVPSGCSGTSIFNTMINNVIIRTLVLDAYKNIDLDKLKIIAYGDDVIFSYKYQL 2033
Cdd:cd23218    163 ERdivLIDHLCYSNHIFKNEGYKVAGGMPSGCSGTSIFNSIINNIVVRTLVLLVYKGINLDELRILCYGDDLLVAYPYPL 242

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2034 DMEAIASEGTKYGLTITPADKSTCF---KQLdySNVTFLKRGFKQDEKHQFLIHPTFPVEEIHESIRWTKNPSQMQEHVL 2110
Cdd:cd23218    243 DPNVLADLGKSLGLTMTPADKSDTFqgcTKL--TEVTFLKRSFVFDEEFPFLCHPVFPMEEVHESIRWTRNASTTQEHVT 320

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*.
gi 1129875992 2111 SLCHLMWHNGRDVYKQFEKRIRSVGAGRALYIPPYDLLLHEWYEKF 2156
Cdd:cd23218    321 SLCLLAWHNGEEVYEEFCEKIRSVPVGRALILPPYSQLRRSWLDMF 366

Rabovirus_RdRp

cd23230

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

1796-2156

7.42e-160

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Rabovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Rabovirus genus within the family Picornaviridae, order Picornavirales. The Rabovirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. The genus Rabovirus consists of four species Rabovirus A, Rabovirus B, Rabovirus C, and Rabovirus D. Viral RNA of this genus was detected in feces of Norway rats (Rattus norvegicus) and mice (Mus musculus) in USA and Germany, in intestinal contents of Himalayan marmots (Marmota himalayana), and in tissue samples of Gairdner's shrewmice (Mus pahari). RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438080 Cd Length: 361 Bit Score: 496.33 E-value: 7.42e-160

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1796 SVFGMEGLEALDLNTSAGFPYVTMGIKKRDLINKQTKDITKLKMALDKYGVDLPMVTFLKDELRKKEKISAGKTRVIEAS 1875
Cdd:cd23230      1 AAYGIENLEGLDLNTSAGYPYVLNGIKKRDILDPETRDTTKLQECLDKYGVDLPFVTYLKDELRPLEKIKKGKTRLIECS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1876 SVNDTVLFRTTFGNLFSKFHLNPGIVTGSAVGCDPEVFWSKIPVMLDGDcIMAFDYTNYDGSIHPIWFQALKQVLTNLSF 1955
Cdd:cd23230     81 SMNDTIRMKMMFGRLFATYHRNPGPITGSAVGCNPDIHWTKFRAEMHGE-IIAFDYSNYDASLNKVWFECLKMVLKNFGF 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1956 -EASLIDRLCKSKHIFKNIYYEVEGGVPSGCSGTSIFNTMINNVIIRTLVLDAYKNIDLDKLKIIAYGDDVIFSYKYQLD 2034
Cdd:cd23230    160 kDLRPIDHIIRSRHIYKGIEYDVEGGMPSGCSGTSIFNSIINNIIIMTLVLDAYKGIDLEQLKIIAYGDDVIVTYPYPLD 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2035 MEAIASEGTKYGLTITPADKSTCFKQLDYSNVTFLKRGFKQDEKHQFLIHPTFPVEEIHESIRWTKNPSQMQEHVLSLCH 2114
Cdd:cd23230    240 AALLADCGKKYGLKMTPPDKSAEFKNVTWEDVTFLKRRFKPAKHYPFLIHPVFDQQEILESLRWTRNPAHTQEHVRSLAE 319

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|..
gi 1129875992 2115 LMWHNGRDVYKQFEKRIRSVGAGRALYIPPYDLLLHEWYEKF 2156
Cdd:cd23230    320 LAWHSGRKSYEEFCNLVKSTNVGKACILPPYESFKRMWLDQF 361

ps-ssRNA_Picornaviridae

cd23193

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

1797-2132

3.96e-134

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: 423.50 E-value: 3.96e-134

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1797 VFGMEGLEALDLNTSAGFPYVTMGIKKRDLINKQTKDIT-----KLKMALDKYGVDLPMVTFLKDELRKKEKISAGKTRV 1871
Cdd:cd23193      2 INGIDGLDPIDLNTSPGYPYTTQGLRRRDLIDNDKGGVSplleeEEQVLLDLDGPDVVFTTFLKDELRPKEKVKAGKTRV 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1872 IEASSVNDTVLFRTTFGNLFSKFHLNPGIVTGSAVGCDPEVFWSKIPVMLDGDCIMAFDYTNYDGSIHPIWFQALKQVLT 1951
Cdd:cd23193     82 IEAAPLDYVIAGRMVFGRLFAQFHSNPGILTGSAVGCNPDTDWTRLFASLKQDNVYDLDYSGFDASLSSQLFEAAVEVLA 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1952 N-LSFEAS---LIDRLCKSKHIFKNIYYEVEGGVPSGCSGTSIFNTMINNVIIRTLVLDAYKnIDLDKLKIIAYGDDVIF 2027
Cdd:cd23193    162 EcHGDPELvlrYLEPIINSKHVVGDERYTVEGGMPSGCPCTSILNSICNNLVVRYALLETGK-FDPDEYYILAYGDDVLV 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2028 SYKYQLDMEAIASEGTKY-GLTITPADKSTCFKQLDYSNVTFLKRGFKQDEkHQFLIHPTFPVEEIHESIRWTKNPSQMQ 2106
Cdd:cd23193    241 STDEPIDPSDLAEFYKKYfGMTVTPADKSSDFPESSPIEDVFLKRRFFVPD-GTFLIHPVMDLETLEQSLMWCGRGGFFQ 319

                          330       340
                   ....*....|....*....|....*.
gi 1129875992 2107 EHVLSLCHLMWHNGRDVYKQFEKRIR 2132
Cdd:cd23193    320 QLLSSLCELALHHGPEEYERLVSKVR 345

Mischivirus_RdRp

cd23227

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

1711-2156

3.85e-83

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: 282.22 E-value: 3.85e-83

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1711 PSIHTPSKTKLQPSVFYDAFPGNKEPAVLSSKDPRL--EVDFEKALFSKYKGNEHcVMNDHINVAVSHYSAQLAT-LDIN 1787
Cdd:cd23227     10 PRIHVPRKTKLRKSPAYPIFKPDAGPAVLSKNDPRLaeGVDFDKQVFSKHSANQK-EYPKAFRRMARWYADRVFTyLGKD 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1788 PQPISIEESVFGMEGLEALDLNTSAGFPYVTMGIKKRDLINKQTKDITK--LKMALDKYG----VDLPMVTFLKDELRKK 1861
Cdd:cd23227     89 NGPLSVKDAIKGIDNLDAMDPTTSPGLPYSAAGIKRTDLLDFDTGEIISpaLRAEYNKYVsgdySDHVFQTFLKDEIRSE 168

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1862 EKISAGKTRVIEASSVNDTVLFRTTFGNLFSKFHLNPGIVTGSAVGCDPEVFWSKIPVML-DGDCIMAFDYTNYDGSIHP 1940
Cdd:cd23227    169 EKIKAGKTRIVDVPSLAHVIIGRVLLGKFCSKFQASPGTELGSAIGCNPDWDWTYFAHQLmERQWCYDIDYSNFDSTHGT 248

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1941 IWFQALKQVL--TNLSFEASLID---RLCKSKHIFKNIYYEVEGGVPSGCSGTSIFNTMINNVIIRTLVLDAYKNIDLDK 2015
Cdd:cd23227    249 GMFELLIDCFftPENGFSPAVAPylrSLAFSKHAWMDKRYKIEGGLPSGCSATSVLNTVMNNIIIRALLSLTYKNFHPED 328

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2016 LKIIAYGDDVIFSYKYQLD---MEAIASEGTKYGLTItpADKSTCFKQLD-YSNVTFLKRGFKQDEKHQFLIHPTFPVEE 2091
Cdd:cd23227    329 VLVLAYGDDLLVASDYQLDfnrVREKAAEHTLYKLTT--ANKAPDFPETStLLDCQFLKRKFVLHSTRNFIWRPVMDVTN 406

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1129875992 2092 IHESIRWTKnPSQMQEHVLSLCHLMWHNGRDVYKQFEKRIRSVGagraLYIPPYDLLLHEWYEKF 2156
Cdd:cd23227    407 LKTMLSFYK-PNTLSEKLLSVAQLAFHSGYTVYEELFAPFKELQ----MTVPSWWYLEHEWEHNF 466

Cosavirus_RdRp

cd23226

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

1697-2156

7.66e-83

RNA-dependent RNA polymerase (RdRp) in the genus Cosavirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Cosavirus genus within the family Picornaviridae, order Picornavirales. The Cosavirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. This genus consists of five species Cosavirus A, Cosavirus B, Cosavirus D, Cosavirus E and Cosavirus F. The candidate species, Cosavirus C, remains unclassified due to a lack of full genome sequence data. Cosaviruses (formerly called Dekaviruses) have been identified in the stools of south Asian children. Cosaviruses are most closely related to members of the Cardiovirus and Senecavirus genera, but they lack a leader polypeptide. The name Cosavirus stands for common stool-associated picornavirus. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438076 Cd Length: 461 Bit Score: 281.14 E-value: 7.66e-83

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1697 GQITNSKPTnecglPSIHTPSKTKLQ-PSVFYDAFPgNKEPAVLSSKDPRLE--VDFEKALFSKYKGN----EHCVMNDH 1769
Cdd:cd23226      1 GQIVNTENG-----PRVHVPRQSKLKrTNATYPATG-KYGPAVLSKNDPRLDpdVDFDKVIFSKHVANvvidEDTSFWNA 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1770 INVAVSHYSAQLATLDINPqpISIEESVFGMEGLEALDLNTSAGFPYVTMgikKRDLINKQTKDI--TKLKMALDKY--- 1844
Cdd:cd23226     75 LKMSAQIYAEKFKGVDFSP--LTVEEAILGIPGLDRMDPNTASGLPYTKT---RRQMIDFQEGKIldPELQERLDTWlsg 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1845 -GVDLPMVTFLKDELRKKEKISAGKTRVIEASSVNDTVLFRTTFGNLFSKFHLNPGIVTGSAVGCDPEVFWSKIPVMLDG 1923
Cdd:cd23226    150 kQPEMLYQTFLKDEIRPIEKVKAGKTRIIDVTPLDHVLAFRIVLGRFMAHFHNNYGFELGSAVGCDPDVAWANFGFALSS 229

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1924 -DCIMAFDYTNYDGSIHPIWFQALKQVLTNLS--FE---ASLIDRLCKSKHIFKNIYYEVEGGVPSGCSGTSIFNTMINN 1997
Cdd:cd23226    230 kKYQYDFDYSNFDASHSESIFELLKQFVFTKDngFDhrcSLMIDSLVTSTHCYEDQRMTIRGGLPSGTSGTSVINTIINN 309

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1998 VIIRTLVLDAYKNIDLDKLKIIAYGDDVIFSYKYQLDMEAIASEGTKYGLTITPADKSTCFKQLDYSNVTFLKRGFKqde 2077
Cdd:cd23226    310 IIFKAALYHTYSNFEWDDVQMLAYGDDIVAASDCLLDLDRVKYFMALIGYKITPADKGEKFIPKDMQNIQFLKRSFR--- 386

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2078 KHQFLIHPTFPVEEIHESIRWTKnPSQMQEHVLSLCHLMWHNGRDVY-KQFEKRIRSvgagrALYIPPYDLLLHEWYEKF 2156
Cdd:cd23226    387 KVAGVWAPIMDLENLQAMLSWYK-PGTLQEKLDSVARLAHFCGEKVYdHLFTTFVKD-----GFQIKPWKQLHFEWLNRF 460

Cardiovirus_RdRp

cd23211

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

1711-2156

2.95e-82

RNA-dependent RNA polymerase (RdRp) in the Cardiovirus genus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Cardiovirus genus within the family Picornaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. Vertebrates serve as natural hosts for the cardioviruses. There are currently six species in the genus: Cardiovirus A-F. Diseases associated with cardioviruses include: myocarditis, encephalitis, multiple sclerosis, and type 1 diabetes. Cardiovirus A is composed of only one serotype, encephalomycarditis virus (EMCV) which causes encephalomyocarditis and reproductive disease in pigs. Cardiovirus B comprises 15 genetic types, Theiler's murine encephalomyelitis virus (TMEV), Vilyuisk human encephalomyelitis virus (VHEV), thera virus (formerly named Theiler-like virus of rats), Saffold virus (SAFV) types 1 to 11, and genet fecal theilovirus (from Geneta geneta). Of these types, only VHEV and SAFV are thought to cause infection in humans. Thus far, Cardiovirus C has only been observed in the brown rat. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438061 Cd Length: 460 Bit Score: 279.42 E-value: 2.95e-82

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1711 PSIHTPSKTKLQPSVFYDAFPGNKEPAVLSSKDPRLEVDFEKALFSKYKGNEHCVMNDHINVAVSHYSAQLATLDINPQP 1790
Cdd:cd23211     10 PVVHVPRKTKLRRTVAHPVFQPKFEPAVLSKYDPRTDKDVDEVAFSKHTTNQESLPPVFRMVAKEYANRVFTLLGKDNGR 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1791 ISIEESVFGMEGLEALDLNTSAGFPYVTMGIKKRDLINKQTKDITKL------KMALDKYGvDLPMVTFLKDELRKKEKI 1864
Cdd:cd23211     90 LTVEQAVLGLEGMDPMEKDTSPGLPYTQQGLRRTDVVDFETATMIPFlaeahrKMVEGDYS-DVVYQSFLKDEIRPIEKV 168

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1865 SAGKTRVIEASSVNDTVLFRTTFGNLFSKFHLNPGIVTGSAVGCDPEVFWSKIPVMLDG-DCIMAFDYTNYDGSIHPIWF 1943
Cdd:cd23211    169 QAAKTRIVDVPPFEHCILGRQLLGRFASKFQTNPGLELGSAIGCDPDVDWTAFAVALSGfKYVYDVDYSNFDSTHSTAMF 248

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1944 QALKQVLTNLS--FE---ASLIDRLCKSKHIFKNIYYEVEGGVPSGCSGTSIFNTMINNVIIRTLVLDAYKNIDLDKLKI 2018
Cdd:cd23211    249 ELLIENFFTEEngFDpriGEYLRSLAVSRHAYEERRVLIRGGLPSGCAATSMLNTIMNNIIIRAGLYLTYKNFEFDDIKV 328

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2019 IAYGDDVIFSYKYQLDMEAIASEGTKYGLTITPADKSTCFKQLDY-SNVTFLKRGFKQDEkhQFLIHPTFPVEEIHESIR 2097
Cdd:cd23211    329 LSYGDDLLVATNYQIDFNLVKARLAKFGYKITPANKTSTFPLTSTlEDVVFLKRKFVKEN--SYLYRPVMDRENLKAMLS 406

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1129875992 2098 WTKnPSQMQEHVLSLCHLMWHNGRDVYKQFEKRIRSVGagraLYIPPYDLLLHEWYEKF 2156
Cdd:cd23211    407 YYR-PGTLKEKLTSIALLAVHSGKQVYDEIFAPFREVG----IVVPTYESVLYRWLSLF 460

Dicipivirus_RdRp

cd23222

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

1722-2152

3.75e-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: 261.45 E-value: 3.75e-76

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1722 QPSVFYDAFPGNKEPAVLSSKDPRL--EVDFEKALFSKYKGNEHCVMNDhINVAVSHYSAQLATLDINPQ--PISIEESV 1797
Cdd:cd23222      1 KPSPVYGVYPVTKEPAPLKPTDRRIdeGVDFNEPVFGKYGADMKEPFRN-LDVGRDVVIARLKKVLPNKKfaPCTVSEAL 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1798 FGMEGLEALDLNTSAGFPYVTMGIKKRDLI--NKQTKDITKLKMALD-----KYGVDLPMVTFLKDELRKKEKISAGKTR 1870
Cdd:cd23222     80 NGKDGLPKLDLKQASGYPYNLSAIKRKHLIesDKDGFLTATPKLLADieeskKHPEKFPYTSFLKDELRSVKKVKAGKTR 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1871 VIEASSVNDTVLFRTTFGNLFSKFHLNPGIVTGSAVGCDPEVFWSKI-PVMLDGDCIMAFDYTNYDGSIHPIWFQALKQV 1949
Cdd:cd23222    160 VVEAGSLPVIVEGRMIFGNLFAYFNTHPGFETMAAVGCDPEVCWTDWyYKMREKAHTWDYDYTGFDGSIPSCSFDALADL 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1950 LTN-LSFEASL---IDRLCKSKHIFKNIYYEVEGGVPSGCSGTSIFNTMINNVIIRTLVLDAYKNIDLDKLKIIAYGDDV 2025
Cdd:cd23222    240 LCEfVENEDDVrryISNIKNSYHAYDGNLYLIEGAMPSGCAGTSVFNCLINAMLCFSCFMDLEPEMDPFEPLLIAYGDDI 319

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2026 IFSYKYQLDMEAIA---SEGTKYglTITPADKSTCFK-QLDYSNVTFLKRGFKQDEKHQfLIHPTFPVEEIHESIRWTkN 2101
Cdd:cd23222    320 LVSSDHDLFPSRVSewmKANTTF--KITPADKGEIFNdDSDVSDVRFLKRLFVEDPVCE-LIHPVIETETLEPSLNWC-H 395

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1129875992 2102 PSQMQEHVLSLCHLMWHNGRDVYKQFEKRIRSVGAGRALYIP---PYDLLLHEW 2152
Cdd:cd23222    396 EGEFETKVDAISMLAFHHGPEYYRDWCKKLTDICEERNISPPglkPYSVHRNRW 449

Aphthovirus_RdRp

cd23210

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

1713-2155

1.06e-74

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: 257.18 E-value: 1.06e-74

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1713 IHTPSKTKLQPSVFYDAFPGNKEPAVLSSKDPRLE--VDFEKALFSKYKGNEHCVMNDH--INVAVSHYSAQL-ATLDIN 1787
Cdd:cd23210      6 VHVMRKTKLAPTVAHGVFNPEFGPAALSNKDPRLNegVVLDEVIFSKHKGDTKMSAEDKalFRRCAADYASRLhSVLGTA 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1788 PQPISIEESVFGMEGLEALDLNTSAGFPYVTMGIKKRDLI---NKQTKDITKLKMAL-DKYGVDLPMVTFLKDELRKKEK 1863
Cdd:cd23210     86 NAPLSIYEAIKGVDGLDAMEPDTAPGLPWALQGKRRGALIdfeNGTVGPEVEAALKLmEKREYKFACQTFLKDEIRPMEK 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1864 ISAGKTRVIEASSVNDTVLFRTTFGNLFSKFHLNPGIVTGSAVGCDPEVFWSKIPVMLDG-DCIMAFDYTNYDGSiHPIw 1942
Cdd:cd23210    166 VRAGKTRIVDVLPVEHILYTRMMIGRFCAQMHSNNGPQIGSAVGCNPDVDWQRFGTHFAQyRNVWDVDYSAFDAN-HCS- 243

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1943 fQALKQVL-----TNLSFEAS---LIDRLCKSKHIFKNIYYEVEGGVPSGCSGTSIFNTMINNVIIRTLVLDAYKNIDLD 2014
Cdd:cd23210    244 -DAMNIMFeevfrTEFGFHPNaewILKTLVNTEHAYENKRITVEGGMPSGCSATSIINTILNNIYVLYALRRHYEGVELD 322

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2015 KLKIIAYGDDVIFSYKYQLDMEAIASEGTKYGLTITPADKSTCFKQLDY--SNVTFLKRGFKQDEKHQFLiHPTFPVEEI 2092
Cdd:cd23210    323 TYTMISYGDDIVVASDYDLDFEALKPHFKSLGQTITPADKSDKGFVLGHsiTDVTFLKRHFHMDYGTGFY-KPVMASKTL 401

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1129875992 2093 hESIRWTKNPSQMQEHVLSLCHLMWHNGRDVYkqfeKRIRSVGAGrALYIPPYDLLLHEWYEK 2155
Cdd:cd23210    402 -EAILSFARRGTIQEKLISVAGLAVHSGPDEY----RRLFEPFQG-LFEIPSYRSLYLRWVNA 458

Pico_P2A

pfam00947

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

872-997

1.40e-73

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

Pssm-ID: 395757 Cd Length: 127 Bit Score: 241.13 E-value: 1.40e-73

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  872 NLHLFN-SDMHDSILVSYSSDLVIYRTNTTGDDYIPTCDCTEATYYCRHKNRYYPIKVTSHDWYEIQESEYYPKHIQYNL 950
Cdd:pfam00947    1 NRHLAThEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1129875992  951 LIGEGPCEPGDCGGKLLCKHGVIGIITAGGEGHVAFIDLRHFHCAEE 997
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVRDLLWLEE 127

Megrivirus_RdRp

cd23223

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

1727-2131

4.86e-71

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: 245.91 E-value: 4.86e-71

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1727 YDAFPGNKEPAVLSSKDPRLE--VDFEKALFSKYKGNEHC--VMNDHINVAVSHYSAQLATLDINPQPI-SIEESVFGME 1801
Cdd:cd23223      2 YGAFPVTHGPAALTNKDKRLEegVDLDDVMFSKHVPDHPGwpTLEPAMSYVVEDLMHKLGFSKDEPVPMwTLEQAINGEG 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1802 GLEALDLNTSAGFPYVTMGIKKR---DLINKQTKDITKLKMALD---KYGVDLPMVTFLKDELRKKEKISAGKTRVIEAS 1875
Cdd:cd23223     82 VMDGIDMGQSPGYPYNAQGRSRRsffEWNGEKWQPTEELKKEVDhalKDPDDFYFSTFLKDELRPLEKVKAGKTRLVDGD 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1876 SVNDTVLFRTTFGNLFSKFHLNPGIVTGSAVGCDPEVFWSKIPVMLDGDC---IMAFDYTNYDGSIHPIWFQALKQVLTN 1952
Cdd:cd23223    162 SLPRILAMRMVFGPLFEAMLRKNGPEIHSAVGCNPDTDWTRYYHEMGPDSfpyCFDLDYSCFDSTEPKIAFRLMAKYLKP 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1953 -LSFEAS-LIDRLCKSKHIFKNIYYEVEGGVPSGCSGTSIFNTMINNVIIRTLVLDAykNIDLDKLKIIAYGDDVIFSYK 2030
Cdd:cd23223    242 yFSVDVTpFFEALATSKHVYGDKAYEMEGGMPSGCVGTSMFNCINNSAFIVSALIAL--KISPEDCAWICYGDDVIISTD 319

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2031 YQLDMEAIASEGTK-YGLTITPADKSTCFKQLD-YSNVTFLKRGFKQDEKHQFLIHPTFPVEEIHESIRW-TKNPsqMQE 2107
Cdd:cd23223    320 EKALSKRIADFYHKnTNLVVTPASKSGDFPETStIYDVTFLKRFFQPDSHYPHLIHPYMPLEHLEQSVMWqTDGP--FQQ 397

                          410       420
                   ....*....|....*....|....
gi 1129875992 2108 HVLSLCHLMWHNGRDVYKQFEKRI 2131
Cdd:cd23223    398 KLDSLCLLAFHAGGPDYREFVDAI 421

Rosavirus_RdRp

cd23221

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

1799-2156

8.75e-68

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: 234.43 E-value: 8.75e-68

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1799 GMEGLEALDLNTSAGFPYVTMGIKKR---DLINKQTKDITKLKMALDKYGVDLPM---VTFLKDELRKKEKISAGKTRVI 1872
Cdd:cd23221      4 GIDNMDGLDMNQSPGVPYVSEGVSRRslfDCVDGQWVPRERLASDIAQVSGDPSLghfATFLKDELRSTEKVAAGKTRVV 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1873 EASSVNDTVLFRTTFGNLFSKFHLNPGIVTGSAVGCDPEVFWSKIPVMLDGDC-IMAFDYTNYDGSIHPIWFQALKQVLT 1951
Cdd:cd23221     84 EAGSLPHIIVGRKIFGNLFALFNSNPGFQTMCAVGCDPDVTWTELYHPLSAKTyVFDYDYSGFDGSVPSCCFDALADLLA 163

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1952 NLsFEA-----SLIDRLCKSKHIFKNIYYEVEGGVPSGCSGTSIFNTMINNVIIRTLVLDAYKNIDLDKLKIIAYGDDVI 2026
Cdd:cd23221    164 DF-VEGeedvrKYISSLKTSFHHYKGKLWRLDGAMPSGCCGTSVFNSLINAMLLFSAFSQICPDFRASEPLLVAYGDDVL 242

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2027 FSYKYQLDMEAIAS-EGTKYGLTITPADKSTCFK-QLDYSNVTFLKRGFKQDEKHQFLIHPTFPVEEIHESIRWTKNpSQ 2104
Cdd:cd23221    243 VGTDQPLFPSKVAEwVNSHTTFRITPADKGSVFNdESDIHSVQFLKRHFTPDPDFPALIHPTIDPDTYEQSVMWQRT-GD 321

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1129875992 2105 MQEHVLSLCHLMWHNGRDVYKQFEKRI--RSVGAGRAL-YIPPYDLLLHEWYEKF 2156
Cdd:cd23221    322 FQETVNSLALLVFHRGPKSYSRWCESVtrKCVDGGYPPpFFPPFSLLRHQWLKKF 376

Teschovirus_RdRp

cd23212

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

1789-2127

1.86e-66

RNA-dependent RNA polymerase (RdRp) in the Teschovirus genus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Teschovirus genus within the family Picornaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. Teschoviruses are emerging pathogens and infect the porcine population only. There are two species in this genus, including Teschovirus A (previously Porcine teschovirus), which is responsible for the porcine enteroviral encephalomyelitis disease caused in pigs, and Teschovirus B. Teschovirus is also known by several other names including Teschen disease, Talfan disease, poliomyelitis suum, benign enzootic paresis, Klobauk disease and contagious porcine paralysis. Teschovirus has a single-stranded, linear, non-segmented RNA genome. The RNA genome is positively sensed meaning that it has the same polarity as the mRNA and no reverse transcription is necessary. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438062 Cd Length: 354 Bit Score: 229.89 E-value: 1.86e-66

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1789 QPISIEESVFGMEGLEALDLNTSAGFPYVTMGIKKRDLINKQTKDITKLKMALDKYgVDLP-----MVTFLKDELRKKEK 1863
Cdd:cd23212      9 EPLSVREAVEGIDGLDPMDMDKSPGLPYVKKGLRRTDLWNPKTGPSIELMAEINRY-LDYNydkhvFLTFLKDELRPKEK 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1864 ISAGKTRVIEASSVNDTVLFRTTFGNLFSKFHLNPGIVTGSAVGCDPEVFWSKIPVMLDGDCIMAFDYTNYDGSIHPIWF 1943
Cdd:cd23212     88 VQAGKTRVIDVAGFGHAIVGRMLFGRLFAFFHKNPGWNTGSAVGVNPDLAWTQIFYTAPSRNVLAMDYSGFDASHTSGMF 167

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1944 QALKQVLTNLSFEA---SLIDRLCKSKHIFKNIYYEVEGGVPSGCSGTSIFNTMINNVIIRTLVLDAYKnidlDKLKIIA 2020
Cdd:cd23212    168 CILKHFLTTLGYGTlqlSYIDSLCYSKHHWDDETYRLDGGLPSGCSGTTIFNTIMNNIVARAAASYAAE----GPVGILC 243

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2021 YGDDVIFSYKYQLDMEAIASEGTKYGLTITPADKSTCFKQLDYSNVTFLKRGFKQDEKhqfLIHPTFPVEEIHESIRWTK 2100
Cdd:cd23212    244 YGDDILVSSPEKFPVSDWLEFYSKTPYKVTAADKSEQIDWRDITQCTFLKRGFVLDGS---LVRPVMEEQHLAELLKWAR 320

                          330       340
                   ....*....|....*....|....*..
gi 1129875992 2101 nPSQMQEHVLSLCHLMWHNGRDVYKQF 2127
Cdd:cd23212    321 -PGTLQAKLLSIAQLAFHLPRQAYDRL 346

Mosavirus_RdRp

cd23225

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

1804-2155

7.17e-66

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: 229.03 E-value: 7.17e-66

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1804 EALDLNTSAGFPYVTMGIKKRDLINKQTKDITKLKMALDK---------YGVDLP-MVTFLKDELRKKEKISAGKTRVIE 1873
Cdd:cd23225     10 DAMDMTKAVGYPYCLDSIKRLDLVEIKETENGKVYLPTERlveetekffTGEEKPkFVTFLKDEVRSNEKIKQGKTRIVD 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1874 ASSVNDTVLFRTTFGNLFSKFHLNPGIVTGSAVGCDPEVFWSKIPVMLDGDCIMAFDYTNYDgSIHPiwfQALKQVLTNL 1953
Cdd:cd23225     90 ASPFPYAIAGRMVMQNFMSNMMRCNGTEVGSAVGCDPDTEWTRYFFELCDRYVFDLDYKAFD-STHP---TAMFNLLAER 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1954 SFEAS----------LIDRLCKSKHIFKNIYYEVEGGVPSGCSGTSIFNTMINNVIIRTLVLDAYK--NIDLDKLKIIAY 2021
Cdd:cd23225    166 FFTERngfdqqavriFLNGLSDSDHVYEGKHFRIRGGLPSGCPCTSILNTVINNIIVRAAILGAYQidTVDFQKFRMLAY 245

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2022 GDDVIFSYKYQL---DMEAIASEGTKYglTITPADKSTCF-KQLDYSNVTFLKRGFKQDEKHQFLIHPTFPVEEIHESIR 2097
Cdd:cd23225    246 GDDVVYATPQPIkpqDLADWLHANTNY--KVTPASKAGTFpEESTIWDVTFLKRSFKPDEDHGHLIRPVMAVGNLKQMLS 323

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1129875992 2098 WTKnPSQMQEHVLSLCHLMWHNGRDVYKQFEKRIRSVGAGRAlyIPPYDLLLHEWYEK 2155
Cdd:cd23225    324 FMR-PGTFPDKVRSVAGLAVHCGEEDYNQLADAVALYVPGVS--MPAYKYMKACWYAK 378

ps-ssRNAv-Picornavirales

cd23169

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

1851-2132

1.51e-65

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: 225.17 E-value: 1.51e-65

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1851 VTFLKDELRKKEKISAGKTRVIEASSVNDTVLFRTTFGNLFSKFHLNPgIVTGSAVGCDPE-VFWSKIPVML--DGDCIM 1927
Cdd:cd23169      4 VDCLKDELRPIEKVKAGKTRLFSASPLDYTIAFRKYFGDFIAAFQKNR-IKLEHAVGINPDsVEWTRLYRRLlkKGPNIF 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1928 AFDYTNYDGSIHPIWFQALKQVLTNL-----SFEAS-----LIDRLCKSKHIFKNIYYEVEGGVPSGCSGTSIFNTMINN 1997
Cdd:cd23169     83 AGDYSNFDGSLPPDVMEAAFDIINDWydeyvDDEDErvrkvLFEELINTIHLVGNLVYQVHGGNPSGNPLTTIINSIVNL 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1998 VIIRTLVLDAYKNIDLDK----LKIIAYGDDVIFS----YKYQLDMEAIASEGTKYGLTITPADKSTC---FKQLDysNV 2066
Cdd:cd23169    163 LYIRYAWLRITGLTSLSDfkknVRLVTYGDDVIISvsdeVKDEFNFVTISEFLKELGITYTDADKSGDivpYRPLE--EV 240

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2067 TFLKRGFKQDEKHqFLIHPTFPVEEIHESIRWTKNPSQMQE---HVLSLCHLMWH-NGRDVYKQFEKRIR 2132
Cdd:cd23169    241 TFLKRGFRPHPTP-GLVLAPLDLESIEEQLNWTRKEDDLLEatiENARAALLLAFgHGPEYYNKFRQKLN 309

Kobuvirus_RdRp

cd23214

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

1711-2152

3.04e-64

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: 227.04 E-value: 3.04e-64

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1711 PSIHTPSKTKLQPSVFYDAFPGNKEPAVLSSKDPRLE--VDFEKALFSKYKGNEHCVMNDHINVAVSHYSAQLATLdinP 1788
Cdd:cd23214      1 PGVNVNRKSRLGPSPAYGAFPVKKQPAPLTQKDDRLEdgIRLDDQLFLKHNKGDMDEPWPGLEAAADLYFSKFPTM---I 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1789 QPISIEESVFGMEGLEALDLNTSAGFPYVTMGIKKRDLINKQTKDI----TKLKMALDKYGVDLPMV--TFLKDELRKKE 1862
Cdd:cd23214     78 RTLTQEEAINGTPNLEGLDMNQAAGYPWNTMGRSRRSLFVEVQPGIyvpkPELQAEIDKTLEDPDYFysTFLKDELRPTA 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1863 KISAGKTRVIEASSVNDTVLFRTTFGNLFSKFHLNPGiVTGSAVGCDPEVFWSKIPVML-DGDCIMAFDYTNYDGSIHPI 1941
Cdd:cd23214    158 KVTLGLTRVVEAAPIHAIVAGRMLLGGLIEYMQARPG-KHGSAVGCNPDLHWTKFFYKFcHYPQVFDLDYKCFDATLPSC 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1942 WFQALKQVLTNLSFE---ASLIDRLCKSKHIFKNIYYEVEGGVPSGCSGTSIFNTMINNVIIRTlVLDAYKNIDLDKLKI 2018
Cdd:cd23214    237 AFRIVEDHLERLTGDervTRYIESIRHSHHVYGNETYEMIGGNPSGCVGTSIINTIINNICVLS-ALIQHPDFSPESFRI 315

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2019 IAYGDDVIFSYKYQLDMEAIASEGTKYG-LTITPADKSTCFKQLD-YSNVTFLKRGFKQDEKHQFLIHPTFPVEEIHESI 2096
Cdd:cd23214    316 LAYGDDVIYGCDPPIHPSFIKEFYDKHTpLVVTPANKGSDFPETStIYDVTFLKRWFVPDDIRPFYIHPVMDPDTYEQSV 395

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1129875992 2097 RWTKNpSQMQEHVLSLCHLMWHNGRDVYKQFEKRIRSVGAGRALYIP---PYDLLLHEW 2152
Cdd:cd23214    396 MWLRD-GDFQDLVTSLCYLAFHSGPKTYDRWCTRVRDQVMKTTGFPPtflPYSYLQTRW 453

Rhv

pfam00073

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

93-300

2.98e-63

Pssm-ID: 395026 Cd Length: 170 Bit Score: 213.33 E-value: 2.98e-63

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992   93 TSQDVANAVVGYGVWPHYLTPQDATAIDKPSRPDTSSNRFYTLESKMWNGTSKGW-WWKLPDALKNMGIFGENMFYHFLG 171
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFfWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  172 RSGYTVHVQCNASKFHQGTLIVAMIPEHQlasatygnvaagyklTHPGETgrdvslsrtenrdkqpsddnwlnfdgTLLG 251
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPPGA---------------PPPGSR--------------------------DYLW 119

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 1129875992  252 NITIFPHQFINLRSNNSATIIVPYVNAVPMDSMLRHNNWSLVIIPICPL 300
Cdd:pfam00073  120 QATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGNWTLVVAGWVPL 168

RNA_dep_RNAP

cd01699

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

1847-2099

3.93e-58

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: 202.90 E-value: 3.93e-58

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1847 DLPMVTFLKDELRKKEKISAGKTRVIEASSVNDTVLFRTTFGNLFSKFHLNpGIVTGSAVGCDPEVF-WSKIPVMLD--G 1923
Cdd:cd01699     17 DLVFTTFLKDELRPLEKVEAGKTRLIQPRPLDYNIALRMYLGPFEAKLMKN-RGGLPIAVGINPYSRdWTILANKLRsfS 95

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1924 DCIMAFDYTNYDGSIHPIWFQALKQVLTNLS------FEASLIDRLCKS-KHIFKNIYYEVEGGVPSGCSGTSIFNTMIN 1996
Cdd:cd01699     96 PVAIALDYSRFDSSLSPQLLEAEHSIYNALYddddelERRNLLRSLTNNsLHIGFNEVYKVRGGRPSGDPLTSIGNSIIN 175

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1997 NVIIRTLVLDAYKNIDLDKLKIIAYGDDVIFSYK---YQLDMEAIASEGTKYGLTITPADKS-TCFKQLdySNVTFLKRG 2072
Cdd:cd01699    176 CILVRYAFRKLGGKSFFKNVRLLNYGDDCLLSVEkadDKFNLETLAEWLKEYGLTMTDEDKVeSPFRPL--EEVEFLKRR 253

                          250       260
                   ....*....|....*....|....*..
gi 1129875992 2073 FKQDEkhQFLIHPTFPVEEIHESIRWT 2099
Cdd:cd01699    254 FVLDE--GGGWRAPLDPSSILSKLSWS 278

Peptidase_C3

pfam00548

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

1514-1679

3.34e-56

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: 193.05 E-value: 3.34e-56

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1514 GPEEEFGRSLIKHNSCVVTTQNGKFTGL--GIYDRTLIIPTHADPGKEVQIDGIATKVED-SYDLFNKDGVKLEITVLKL 1590
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1591 KRNEKFKDIRKYIPENEDDYPDCNLALSANQPETTIINVGDVISYGNI-LLSGTQTARMLKYNYPTKSGYCGGILYKI-- 1667
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVVIAKve 160

                          170
                   ....*....|....
gi 1129875992 1668 --GQVLGIHVGGNG 1679
Cdd:pfam00548  161 gnGKILGMHIAGNG 174

Fipivirus_RdRp

cd23229

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

1797-2152

2.60e-55

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: 198.88 E-value: 2.60e-55

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1797 VFGMEGLEALDLNTSAGFPYVTMGIKKRDLI----NKQTKDITKLK----------MALDKYGVDLPMVTFLKDELRKKE 1862
Cdd:cd23229      2 VEGIPGMEGLDMKTSAGYPWCEQNQKKKDKIkllaGKNFLVRPLREvvhivvdwyiMPPDMPKPEIKYVVYLKDELLSSD 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1863 KISAGKTRVIEASSVNDTVLFRTTFGNLFSKFHL-NP--GIVTGSAVGCDPEVFWSKIPVMLDGDCIMAFDYTNYDGSIH 1939
Cdd:cd23229     82 KVKMGRTRWICAAPVQLVCAWKKVFGRAIAAIHLeSVtdGKSTGCAVGMDPETAWTDIALARPGWPVIALDYSNFDGSLQ 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1940 PIWFQALKQVLTNLS-FEASLIDRLCK----SKHIFKNIYYEVEGGVPSGCSGTSIFNTMINnVIIRTLVLDAYKNIDL- 2013
Cdd:cd23229    162 SFVITGAVRILGYIAgLPDGQSYRLAEfvydVKQIVGKYLYTTVGPLPSGCPSTSIIGSLCN-VLMLLYTLSHATGQRYs 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2014 ---DKLKIIAYGDDVIF----SYKYQLDMEAIASEgTKYGLTITPADKSTCFKQL-DYSNVTFLKRGFKQDEKHQFLIHP 2085
Cdd:cd23229    241 afrDWMHVVTYGDDVLVfvhpEVVVVLDTLAHEMY-LVFGVTATDATDKRAPPQLrELSNVTFLKRGFRQCSSVPFLVHP 319

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1129875992 2086 TFPVEEIHESIRWTKNPSQMQEHVLSLCHLMWHNGRDVYKQFEKRIRS------VGAGRALY--IPPYDLLLHEW 2152
Cdd:cd23229    320 TMDKSTIYQMLAWKRKGTTLAENVKCAAEFMMHHGEEEYEDFVGVVKEcstligVDQRSKVYeeLCSYAELHDHW 394

Rhv

pfam00073

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

358-523

7.71e-52

Pssm-ID: 395026 Cd Length: 170 Bit Score: 180.59 E-value: 7.71e-52

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  358 FHPTKEISIPGQVRNLIEMCQVDTLIPINNLEQNIRNVNMYSVVLNQETTTAKEIFAIKVDIASqpLATTMIGEIASYFT 437
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFFWWKLPLAL--LSMGLLGRLLRYHT 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  438 HWTGSLRFSFLFCGTANTTLKLLVAYTPPGIEKPQNR---KDAMLGTHVVWDVGLQSTISMVVPWVSASHYRNTTPD--- 511
Cdd:pfam00073   79 YYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRdylWQATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDgnw 158

                          170
                   ....*....|..
gi 1129875992  512 TYSQAGYITCWY 523
Cdd:pfam00073  159 TLVVAGWVPLNY 170

RdRP_1

pfam00680

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

1723-2127

3.80e-51

Pssm-ID: 425815 Cd Length: 450 Bit Score: 188.39 E-value: 3.80e-51

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1723 PSVFYDAFPGNKEPAVLSSKDPRLEVDFE------KALfSKYK-----GNEHCVMNDHINVAVSHYSAQLATLDINPQPI 1791
Cdd:pfam00680    2 PTERHLVAIPAYVPASLGPEDPRWARSYLntdpyvDDI-KKYSrpklpGPADERDKLLNRSAAKMVLSELRGVPKKANST 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1792 SIEESVF-GMEGLEALDLNTSAGFPYVTMGIKKRDLINkQTKDIT-------KLKMALDKY--GVDLPMV--TFLKDELR 1859
Cdd:pfam00680   81 LIVYRAIdGVEQIDPLNWDTSAGYPYVGLGGKKGDLIE-HLKDGTearelaeRLAADWEVLqnGTPLKLVyqTCLKDELR 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1860 KKEKISAGKTRVIEASSVNDTVLFRTTFGNLFSKFHLNPGIVTgSAVGCDPevFWSKIPVMLD-----GDCIMAFDYTNY 1934
Cdd:pfam00680  160 PLEKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHP-IQVGINP--FDRGWPRLLRrlarfGDYVYELDYSGF 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1935 DGSIHPIWFQALKQVLT-------NLSFEASLIDRLCKSKHIFKNIY-YEVEGGVPSGCSGTSIFNTMINNVIIRTLVLD 2006
Cdd:pfam00680  237 DSSVPPWLIRFAFEILRellgfpsNVKEWRAILELLIYTPIALPNGTvFKKTGGLPSGSPFTSIINSIVNYLLILYALLK 316

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2007 AYKNIDL------DKLKIIAYGDDVIFSYKYQLD--MEAIASEGTKYGLTITPADKS-TCFKQLDysNVTFLKRGFKQDE 2077
Cdd:pfam00680  317 SLENDGPrvcnldKYFDFFTYGDDSLVAVSPDFDpvLDRLSPHLKELGLTITPAKKTfPVSRELE--EVSFLKRTFRKTP 394

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2078 khqFLIHPTFPVEEIHESIRWTKNPSQMQEHVLSLCHLMWHNGRDVYKQF 2127
Cdd:pfam00680  395 ---GGYRPPLDRKRILAQLEYIRSKPVPSGQLENIRAYASHHGYEFYRDL 441

Hepatovirus_RdRp

cd23215

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

1789-2153

5.13e-49

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: 182.74 E-value: 5.13e-49

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1789 QPISIEESVFGMEGLEALDLNTSAGFPYVTMGIKKRDLI-----------NKQTKDITKLKMALDKYGVDLPMV--TFLK 1855
Cdd:cd23215     63 EFFDLEQAITGVPGMDAINMDSSPGYPYVQEKLTKSDLIwlddngellgmHPRLAQRILFNLTMMDNGNDLDVVytTCPK 142

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1856 DELRKKEKISAGKTRVIEASSVNDTVLFRTTFGNLFSKFHLNPGIVTGSAVGCDPEVFWSKI-PVMLD-GDCIMAFDYTN 1933
Cdd:cd23215    143 DELRPLEKVLESKTRAIDACPLDFTIICRMFWGPAISYFQLNPGFHTGVAVGIDPDRDWDALfKTMIRfGDYGIDLDFSS 222

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1934 YDGSIHPIWFQALKQVLTNLS-----FEASLIDRLCKSKHIFKNIYYEVEGGVPSGCSGTSIFNTMINNVIIRTLVLDAY 2008
Cdd:cd23215    223 FDASLSPFMIREACRVLSELSgvpdhQGQALINTIIYSKHLLYNLCYHVCGSMPSGSPCTSLLNSIVNNVNLYYVFSKIF 302

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2009 KNIDL---DKLKIIAYGDDV--IFSYKYQLDM-----EAIASEGTKYGLTITPADKSTCfKQLDYSNVTFLKRGFKQDEK 2078
Cdd:cd23215    303 KKSPVffyDAVKFLCYGDDVliVFSRDLEIKNldklgQRIQDEFKLLGMTATSADKGEP-QVVPVSELTFLKRSFNLIED 381

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1129875992 2079 HqflIHPTFPVEEIHESIRWTKNPSQMQEHVLSLCHLMWHNGRDVYKQFEKRIRSVGAGRALyipPYDLLLHEWY 2153
Cdd:cd23215    382 R---FRPAISEKTIWSLVAWQRSNAEFEQNLDTACWFAFMHGYDFYQNFYLQLQSCLEKEMI---DYRLKSYEWW 450

Passerivirus_RdRp

cd23224

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

1795-2154

2.51e-48

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: 177.97 E-value: 2.51e-48

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1795 ESVFGMEGLEALDLNTSAGFPYvTMGIKKRDLINK----QTKDITKLKMALDK--YGVDLPMVTFLKDELRKKEKISAGK 1868
Cdd:cd23224      1 EAINGTPLLDGLDMKQSPGYPW-SLTTNRRSLFTQdetgKYYPVPELEEAVLAclENPDYFYTTHLKDELRPVEKALAGK 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1869 TRVIEASSVNDTVLFRTTFGNLFSKFHLNPGiVTGSAVGCDPEVFWSKIPVMLDGDC-IMAFDYTNYDGSIHPIWFQ--- 1944
Cdd:cd23224     80 TRLIEAAPIHAIIAGRMLLGGLFEYMHARPG-EHGSAVGCDPDYHWTPFFHSFDEFSqVWALDYSCFDSTLPSCCFDlia 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1945 -ALKQVLTNLSFEAS-----LIDRLCKSKHIFKNIYYEVEGGVPSGCSGTSIFNTMINNVIIRTLVLdAYKNIDLDKLKI 2018
Cdd:cd23224    159 qKLAKIITPGEGIAPdaivkYIRSISISKHVFGNEAYLMVGGNPSGCVGTSILNSMINNCVLISAFL-TQKDFNPNQMRI 237

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2019 IAYGDDVIFSYKYQLDMEAIAS---EGTKygLTITPADKSTCFKqlDYS---NVTFLKRGFKQDEKHQFLIHPTFPVEEI 2092
Cdd:cd23224    238 LTYGDDVLYATNPPIHPRVVKKffdENTT--LIVTPATKAGDFP--DEStiwDVTFLKRYFVPDEIRPWYVHPVIEPATY 313

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1129875992 2093 HESIRWTKNpSQMQEHVLSLCHLMWHNGRDVYKQFEKRIRSVGAGRALY--IPPYDLLLHEWYE 2154
Cdd:cd23224    314 EQSVMWTRG-GDFQDVVTSLSFLAHHAGPTNYMIWEEKVRKAAAAKGVSlnILPYSYLQHRWML 376

Rhv

pfam00073

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

615-765

4.26e-44

Pssm-ID: 395026 Cd Length: 170 Bit Score: 158.24 E-value: 4.26e-44

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  615 PEDMIETRYVQTSQTRDEMSLESFLGRSGCIH-----ISELKVKYENYNTEN--FTKWKINL--QEMAQIRRKFELFTYV 685
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQpdvqgERFYTLDSTDWTSLSkgFFWWKLPLalLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  686 RFDSEVTLVPSiaaqGEDIGHVVMQYMYVPPGAPIPKTReDYTWQSGTNASIFWQHG-QTYPRFSLPFLSIASAYYMFYD 764
Cdd:pfam00073   81 RGGLEVTVQFN----GSKFHQGKLLVAYVPPGAPPPGSR-DYLWQATLNPHQFWNLGlNSSARLSVPYISIAHYYSTFYD 155


                   .
gi 1129875992  765 G 765
Cdd:pfam00073  156 G 156

rhv_like

cd00205

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

373-558

7.62e-44

Pssm-ID: 119412 Cd Length: 178 Bit Score: 157.94 E-value: 7.62e-44

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  373 LIEMCQVDTLIPINNLEQNirnvnmysvvlnqetTTAKEIFAIKVDIASQPL--ATTMIGEIASYFTHWTGSLRFSFLFC 450
Cdd:cd00205      1 VESFADRPTTVGTNNWNSS---------------ASGTQLFQWKLSPALGFLllQNTPLGALLSYFTYWRGDLEVTVQFN 65

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  451 GTANTTLKLLVAYTPPGIEKPQN---RKDAMLGTHVVWDVGLQSTISMVVPWVSASHYRNTTPDTYSQA---GYITCWYQ 524
Cdd:cd00205     66 GSKFHTGRLLVAYVPPGAPAPTTgdtRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDGYGPLnsfGTLVVRVL 145

                          170       180       190
                   ....*....|....*....|....*....|....
gi 1129875992  525 TNLVVPPNTPTTARMLCFVSGcKDFCLRMARDTN 558
Cdd:cd00205    146 TPLTVPSGAPTTVDITVYVRA-GDFELYGPRPPR 178

Parechovirus_RdRp

cd23217

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

1796-2150

1.40e-43

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Parechovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the Parechovirus genus within the family Picornaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. The Parechovirus genus is comprised of six species, Parechovirus A (formerly named Human parechovirus), Parechovirus B (formerly named Ljungan virus), Parechovirus C (Sebokele virus) and Parechovirus D (ferret parechovirus), Parechovirus E (falcon parechovirus) and Parechovirus F (gecko parechovirus). Humans, ferrets, and various rodents serve as natural hosts. Human parechoviruses may cause gastrointestinal or respiratory illness in infants, and have been implicated in cases of myocarditis and encephalitis. Human parechoviruses replicate in the respiratory and gastrointestinal tract. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438067 Cd Length: 371 Bit Score: 163.88 E-value: 1.40e-43

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1796 SVFGMEGLEALDLNTSAGFPYVTMGIKKRDLINKQ--------TKDITKLKMALdkYGVDLP---MVTFLKDELRKKEKI 1864
Cdd:cd23217      1 AVLGTSHLNSLDLSTSPGYKYVKSGYKKRDLLSLEpfsvspqlEKDVKDKLHAV--YKGNQPttiFNACLKDELRKLDKI 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1865 SAGKTRVIEASSVNDTVLFRTTFGNLFSKFHLNPGIVTGSAVGCDPEVFWS-KIPVMLDGDciMAFDYTNYDGSIHPIWF 1943
Cdd:cd23217     79 AQGKTRCIEACSIDYVIAYRVVMSSLYEAIYQTPCQELGLAVGMNPWTDWDfMINALNPYN--YGLDYSSYDGSLSEMLM 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1944 QALKQVLTNLSFEASLIDRLCK----SKHIFKNIYYEVEGGVPSGCSGTSIFNTMINNVIIRTLvldAY-KNIDLDKLKI 2018
Cdd:cd23217    157 WEAVEVLAYCHESPDLVMQLHKpvinSDHVVMDERWLVHGGMPSGSPCTTVLNSICNLLVCIYL---AYlQSPGIECLPI 233

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2019 IaYGDDVIFSYKYQLDMEA-IASEGTKYGLTITPADKSTCFKQLDYSNVTFLKRgfkqdeKHQFLIHPTFPV-----EEI 2092
Cdd:cd23217    234 V-YGDDVIFSVSSEIDPEYlVSSAADSFGMEVTGSDKDEPPSLLPRMEVEFLKR------TTGYFPGSTYKVgaldlETM 306

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1129875992 2093 HESIRWTKN----PSQMQEHVLSLChlmwHNGRDVYKQFEKRIRSVGAGRALYIPPYDLLLH 2150
Cdd:cd23217    307 EQHIMWMKNlstfPQQLQSFENELC----LHGKDIYDDYKKIFNPYLKEWNITMDDYDVVIH 364

Pico_P2B

pfam01552

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

998-1094

3.80e-41

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: 147.09 E-value: 3.80e-41

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  998 QGITDYIHMLGEAFGSGFV----DSVKEQINAINPINNISKKIIKWLLRIISAMVIIIRNSSDPQTIIATLTLIGCSGSP 1073
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTqqisDKIKELTNFINPTSKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|.
gi 1129875992 1074 WRFLKEKFCKWTQLNYIHKES 1094
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

1.47e-40

Pssm-ID: 308053 Cd Length: 68 Bit Score: 144.44 E-value: 1.47e-40

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1129875992    2 GAQVSRQNVGTHSTQNSVSNGSSLNYFNINYFKDAASSGASKLEFSQDPSKFTDPVKDVLEKGIPTLQ 69
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 68

Dicistroviridae_RdRp

cd23194

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

1853-2132

2.12e-40

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: 153.04 E-value: 2.12e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1853 FLKDELRKKEKISAGKTRVIEASSVNDTVLFRTTFGNLFSkfHLNPG-IVTGSAVGCDP---EvfWSKIPVML--DGDCI 1926
Cdd:cd23194     11 TLKDERRPIEKVDAGKTRVFSAGPMDYTIAFRMYFLGFVA--HLMRNrIDNEIAVGTNVyslD--WDKLARKLlsKGDKV 86

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1927 MAFDYTNYDGSIHPiwfQALKQVLT------NLSFEASLIDR-----LCKSKHIFKNIYYEVEGGVPSGCSGTSIFNTMI 1995
Cdd:cd23194     87 IAGDFSNFDGSLNP---QILWAILDiinewyDDGEENALIRRvlwedIVNSVHICGGYVYQWTHSQPSGNPLTAIINSIY 163

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1996 NNVIIRTLVLDAYKNIDLDKLK-------IIAYGDDVIFS----YKYQLDMEAIASEGTKYGLTITPADKSTcfKQLDY- 2063
Cdd:cd23194    164 NSIIMRYVYLLLTKEAGLMTMSdfnkhvsMVSYGDDNVINvsdeVSEWFNQLTITEAMAEIGMTYTDETKTG--EIVPYr 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2064 --SNVTFLKRGFKQDEKHQFLIHPtFPVEEIHESIRWTKNPSQMQE----------HVLSLcHlmwhnGRDVYKQFEKRI 2131
Cdd:cd23194    242 slEEVSFLKRGFRYDDDLGRWVAP-LDLDTILEMPNWVRKGKDPEEitkqnvenalRELSL-H-----GEEVFDKWAPKI 314


                   .
gi 1129875992 2132 R 2132
Cdd:cd23194    315 R 315

RNA_helicase

pfam00910

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

1213-1309

2.09e-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: 142.36 E-value: 2.09e-39

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1213 VVIHGEPGTGKSMTTNFLARMI-----TNDSDIYSLPPDPKYFDGYDQQSVVIMDDIMQNPSGDDMTLFCQMVSSVTFIP 1287
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALlkklgLPKDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 1129875992 1288 PMADLPDKGKPFDSRFVLCSTN 1309
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

Crohivirus_RdRp

cd23232

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

1793-2146

4.69e-39

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: 151.02 E-value: 4.69e-39

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1793 IEESVFGMEGLEALDLNTSAGFPYVTMGIKKRDLINKQT--------KDITKLKMALDKYG-VDLPMVTFLKDELRKKEK 1863
Cdd:cd23232      1 IEEACFEEGDEHALDLKTSPGFKYVQMGLKKTDLVNRPNkfihpilrNDVRLIFDEMAKGQmPVVTFTAHLKDELRKLEK 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1864 ISAGKTRVIEASSVNDTVLFRTTFGNLFSKFHLNPGIVTGSAVGCDPEVFWSKIPVMLDgDCIMAFDYTNYDGSIHPIWF 1943
Cdd:cd23232     81 IRSGKTRCIEACDFDYTVAHKMMFGTLYKAIYDTPGIITGLAVGMNPWKDWELIQQSLF-KYNYDFDYKTFDGSLSRELM 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1944 QALKQVLTNLSFEASLIDRL----CKSKHIFKNIYYEVEGGVPSGCSGTSIFNTMINNVIIRTLVLDAYKNidldKLKII 2019
Cdd:cd23232    160 LHAVDILSACVENDEMAKLMlsvvVESVHLVLDQKWNVSGGMPSGSPCTTVLNSVCNLIVSSTIADMCTEG----DFKIL 235

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2020 AYGDDVIFSYKYQLDMEAIAS-EGTKYGLTITPADKSTCFKQLDYSNVTFLKRGFKQDEKHQFLIHpTFPVEEIHESIRW 2098
Cdd:cd23232    236 VYGDDLIISSTAPLDCDRFKTlVELHYGMEVTPGDKGDEFKVKDREQVSFLKRVTRKFPGTNYRVG-ALDLDTVKQHLMW 314

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*...
gi 1129875992 2099 TKNPSQMQEHVLSLCHLMWHNGRDVYKQFEKRIRSVGAGRALYIPPYD 2146
Cdd:cd23232    315 CKSYSSFKQQLDSALMEVAMHGEETYNGFLTEIKTKLDKFKIYPPKFK 362

Kunsagivirus_RdRp

cd23219

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

1793-2133

1.02e-38

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: 149.25 E-value: 1.02e-38

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1793 IEESVFgmEGLEALDLNTSAGFPYVtmGIKKRDLINKQTK--------DITKLKMALDKYGVD-LPMVTFLKDELRKKEK 1863
Cdd:cd23219      1 IEEAVF--DTVTPMDHTASAGPKYP--GTKRSELIDFQNRiisdrlrnDVLELQFRGTSGGAGeVKFSSFLKDELRPLSK 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1864 ISAGKTRVIEASSVNDTVLFRTTFGNLFSKFHLNPGIVTGSAVGCDpeVFWSKIPVMLD-GDCIMAFDYTNYDGSIHPIW 1942
Cdd:cd23219     77 IRSGDTRVVECSSLDYTVAFRMQFLRVLQMCYGSDPTLTGLAPGMN--VYTDMLPLCTSlYDYNLCLDFSKYDSRLPLQV 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1943 FQALKQVLTNLS----FEASLIDRLCKSKHIFKNIYYEVEGGVPSGCSGTSIFNTMINNVIIRTLVLDAYKNIDldkLKI 2018
Cdd:cd23219    155 MHRVAQLISNLTpdpqVSMRLFQPIIISTHIVGSYEVVVEGGMPSGCPITTIMNSVCNVVMTSYAMLLLDPDSD---FWP 231

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2019 IAYGDDVIFSYKYQLDMEAIAS-EGTKYGLTITPADKSTCFKQLDYSNVTFLKRGFKQDEKHQFLIhPTFPVEEIHESIR 2097
Cdd:cd23219    232 VAYGDDNIVSTRKPIDTELFCSiLNEEFGMILTGADKTTTVQAVPPMSVDFLKRRLRYTPEFPLPV-PVLPLDSMLSRIC 310

                          330       340       350
                   ....*....|....*....|....*....|....*.
gi 1129875992 2098 WTKNPSQMQEHVLSLCHLMWHNGRDVYkqfeKRIRS 2133
Cdd:cd23219    311 WCKGETEFKDQLESFSYELALYGQEVY----ERVRV 342

rhv_like

cd00205

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

125-327

1.53e-35

Pssm-ID: 119412 Cd Length: 178 Bit Score: 134.06 E-value: 1.53e-35

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  125 PDTSSNRFYTLESKMWNG---TSKGWWWKLPDA----LKNMGIFGENMFYHFLGRSGYTVHVQCNASKFHQGTLIVAMIP 197
Cdd:cd00205      1 VESFADRPTTVGTNNWNSsasGTQLFQWKLSPAlgflLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  198 EHQLASATygnvaagyklthpgetgrdvslsrtenrdkqpsddnwlnfdGTLLGNITIFPHQFINLRSNNSATIIVPYVN 277
Cdd:cd00205     81 PGAPAPTT-----------------------------------------GDTRWQATLNPHVIWDLGTNSSVTFVVPYVS 119

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1129875992  278 AVPMDSMLRH------NNWSLVIIPICPL-EANGAQPVVPITISISPMCAEFSGARA 327
Cdd:cd00205    120 PTPYRSTRYDgygplnSFGTLVVRVLTPLtVPSGAPTTVDITVYVRAGDFELYGPRP 176

rhv_like

cd00205

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

635-821

1.65e-35

Pssm-ID: 119412 Cd Length: 178 Bit Score: 134.06 E-value: 1.65e-35

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  635 LESFLGRSGCIHISELKvkyENYNTENFTKWKINLQE------MAQIRRKFELFTYVRFDSEVTLV--PSIAAQGedigh 706
Cdd:cd00205      1 VESFADRPTTVGTNNWN---SSASGTQLFQWKLSPALgflllqNTPLGALLSYFTYWRGDLEVTVQfnGSKFHTG----- 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  707 vVMQYMYVPPGAPIPKTrEDYTWQSGTNASIFWQHG-QTYPRFSLPFLSIASAYYMFYDGYDgdqtesrygtvVTNDMGT 785
Cdd:cd00205     73 -RLLVAYVPPGAPAPTT-GDTRWQATLNPHVIWDLGtNSSVTFVVPYVSPTPYRSTRYDGYG-----------PLNSFGT 139

                          170       180       190
                   ....*....|....*....|....*....|....*....
gi 1129875992  786 LCSRIVT---DQHTHPIKITTRVYHKAKHVKAWCPRPPR 821
Cdd:cd00205    140 LVVRVLTpltVPSGAPTTVDITVYVRAGDFELYGPRPPR 178

Avisivirus_RdRp

cd23231

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

1806-2146

6.68e-34

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: 135.40 E-value: 6.68e-34

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1806 LDLNTSAGFPYvtMGIKKRDLINKQT--KDITKLKMA---LDKYGVDLPMVTFLKDELRKKEKISAGKTRVIEASSVNDT 1880
Cdd:cd23231     11 IDWGTSPGDKY--KGKTKAQLVDDKKfkADVMNLVRFngdPNREPPDVYFTTYLKDELRPKEKAKAGKTRVISAASFDYT 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1881 VLFRTTFGNLFSKFHLNpGIVTGSAVGCDPEVFWSKIPVMLDGDCImAFDYTNYDGSI-HPIWFQALkQVLTNLSFEASL 1959
Cdd:cd23231     89 IACRMVFGPILRQLFAW-GREFGFGPGLNPYTHFDELYDKILPFVI-CLDYSGFDGSLsSELMFHAA-QVIACFSEKPEA 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1960 IDRLCK----SKHIFKNIYYEVEGGVPSGCSGTSIFNTMINNVIIRTLVLDayKNIDLDKLKIIAYGDDVIFSYKYQLDM 2035
Cdd:cd23231    166 IMASAEltigSTERVSDEVWYVYGGMPSGSPWTTTLNTICNLLMCYTYLLD--MGHCWSETFVVAYGDDVVISANIKHNL 243

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2036 EAIASE-GTKYGLTITPADKSTCFKQLDYSNVTFLKRGFKQDEkhqFL--IHPTFPVEEIHESIRWTKNPSQMQEHVLSL 2112
Cdd:cd23231    244 EGIEQWfKTKFGATVTPSDKQGKITWTTKNNMEFLKRRPKQLD---FLpkIVGALDLDNMLDRIQWTKGHFQDQLNSFYL 320

                          330       340       350
                   ....*....|....*....|....*....|....*.
gi 1129875992 2113 cHLMWHnGRDVYKQfekrIRSVGAGRA--LYIPPYD 2146
Cdd:cd23231    321 -ELALH-GRETYNE----IRAKLAPRApqLVHPTYA 350

Limnipivirus_RdRp

cd23228

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

1802-2147

3.21e-33

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: 134.23 E-value: 3.21e-33

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1802 GLEALDLNTSAGFPYVTMGIKKRDL--INKQ---------TKDITKLKMALDKYG-VDLPMVTFLKDELRKKEKISAGKT 1869
Cdd:cd23228      6 GTNPIDKNTSPGLKYTRDGLKKSDLytIDEDgnvvvsdmlRADVEAWEELIQSGGyPTTLFTACLKDELRSDEKVALGKT 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1870 RVIEASSVNDTVLFRTTFGNLFSKFHLNPGIVTGSAVGCDPEVFWSKIPVMLDG-DCIMAFDYTNYDGSIHPIWFQALKQ 1948
Cdd:cd23228     86 RVIEAAELDYVVAYRMYMSSIYSDLYNAYAGDTGIAAGINPPADGHRLREELSQyDSFLALDYSRFDGSLPEMLMRAAVE 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1949 VLTNLSFEASLIDRLCK----SKHIFKNIYYEVEGGVPSGCSGTSIFNTMINNVIIRTLVLDA----YKNIDLDKLK--- 2017
Cdd:cd23228    166 ILADLHEDPDLVRRLHEtviiSKHLVVDEDWTVKGGMPSGSPCTTVLNCICNLLVLEYAFLVHfgvyEDDDGVGLPQcdy 245

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2018 -IIAYGDDVIFSYKyQLDMEAIASEGTK--YGLTITPADKSTCFKQLDYSNVTFLKRGF-KQDEKHQFLIHPTFPVEEIH 2093
Cdd:cd23228    246 lSVVYGDDCIVAYN-GMEMGLAFAETIEdtFGMEVTPASKVGDHFNVELHEVEFLKRKFfAFETEEYDRIALRLSENTIV 324

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1129875992 2094 ESIRWTKNPSQMQEHVLSLCHLMWHNGRDVY-KQFEKRIRSVGAGR-ALYIPPYDL 2147
Cdd:cd23228    325 QSLMWMRNLKTFPDQVQSLMMELSAWGKEKYdKLRDTCKRRLAKQNlQVTVPGYDI 380

Aalivirus_RdRp

cd23216

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

1789-2133

1.20e-29

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: 122.47 E-value: 1.20e-29

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1789 QPISIEESvfgmegleALDLNTSAGFPYvtMGIKKRDLINKQT-KDITKLKMAldkyGVDLPMVTFLKDELRKKEKISAG 1867
Cdd:cd23216      3 EAISVEEL--------PIDWQTSPGLKY--KGRTKADLVQDPKfKEDVKEILA----GKPTFFTTYLKDELRSIEKIANG 68

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1868 KTRVIEASSVNDTVLFRTTFGNLFSKFHLNPGIVTGSAVGCDPEVFWSKIPVMLDGDcIMAFDYTNYDGSIHPIWFQALK 1947
Cdd:cd23216     69 NTRAIEAANFDHVVAWRQVMGNIVKQLFSDHDRVTGFAPGMNPYTHFDSLMDQVKWN-VLALDFKKFDGSLSPQVMEEAV 147

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1948 QVLTNLSFEASLIDRLCK----SKHIFKNIYYEVEGGVPSGCSGTSIFNTMINNVIIRTLVLDayKNIDLDKLKIIAYGD 2023
Cdd:cd23216    148 DILASFHDMPQMVVDIHKhtiySTNVVSDETWFVEGGMCSGSPCTTVLNTICNLLVNTTILLS--EGIQPDNFYIAAYGD 225

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2024 DVIFS---YKYQLDMEAIASEGTK--YGLTITPADKSTCFKQLDYSNVTFLKR--GFKQDEKHqflIHPTFPVEEIHESI 2096
Cdd:cd23216    226 DTIISvdgLSSSLPDPKIMQQKYKewFGMTVTSADKGSEITWDTRNHVQFLKRrpGFFPGTQK---VVGVLDLESMMEHI 302

                          330       340       350
                   ....*....|....*....|....*....|....*..
gi 1129875992 2097 RWTKnpSQMQEHVLSLCHLMWHNGRDVYKQFEKRIRS 2133
Cdd:cd23216    303 AWTK--GSFQDQLNSFYQELVLHGEQVYMTVRQTLKS 337

Aquamavirus_RdRp

cd23220

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

1806-2129

4.57e-27

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: 114.80 E-value: 4.57e-27

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1806 LDLNTSAGFPYVtmGIKKRDLI---NKQTKD-ITKLKMALDKYGVDLPMVTFLKDELRKKEKISAGKTRVIEASSVNDTV 1881
Cdd:cd23220     12 LNFNGTAGAKYP--GMNRRQLLlplNPQVRDdVVKLAGDVGNGTATVVFETFMKDELRPKEKIESGKTRIVESCPLDYLL 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1882 LFRTTFGNLFSKFHLNPGIVTGSAVGCDpeVFWSKIPVMLD-GDCIMAFDYTNYDGSIHPIWFQALKQVLTNLSFEASLI 1960
Cdd:cd23220     90 LYRMVMLKSMIWWYNSDCIKTGVAPGMN--VYTDFVPMVKQfKKIKYCLDFSAYDSTLSDEILAAGVEVLACTSAVPSYV 167

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1961 DRL----CKSKHIFKNIYYEVEGGVPSGCSGTSIFNTMINNVIIRTLVldayKNIDLDKLKIIAYGDDVIFSYKYQLDME 2036
Cdd:cd23220    168 RKLhapiICSHHWHNNVVDLVLGGMPSGAPCTSVLNSIVNVLMARYIC----ALMDIDYPVMVAYGDDNVVSFDEEIDIE 243

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2037 AIAS-EGTKYGLTITPADKSTCFKQLdySNVTFLKRG--FKQDEKHQFlihPTFPVEEIHESIRWTKNPSQMQEHVLSLC 2113
Cdd:cd23220    244 RMVSlYKTEFGVTATNHDKTPVPRPM--ANPVFLKRRlrFNPDLNIQF---PVLPLGEMIDRMCWTRGPEHLSDQTFSFA 318

                          330
                   ....*....|....*.
gi 1129875992 2114 HLMWHNGRDVYKQFEK 2129
Cdd:cd23220    319 IELAGYGKQVYTHIRD 334

Caliciviridae_RdRp

cd23192

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

1854-2132

1.98e-26

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Caliciviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Caliciviridae, order Picornavirales. Member viruses have a viral (+)ssRNA genome, which is not segmented. The family Caliciviridae, includes eleven genera: seven genera of which infect mammals (Lagovirus, Norovirus, Nebovirus, Recovirus, Sapovirus, Valovirus, and Vesivirus), two genera of which infect birds (Bavovirus, Nacovirus), and two genera of which infect fish (Minovirus and Salovirus). Each genus includes 1-2 species. Human noroviruses are a leading cause of acute gastroenteritis in humans. Furthermore, unclassified caliciviruses have been detected in geese, yellowfin seabream, greater green snake, arctic lamprey, frogs and various Australian birds, highlighting the wide host range of viruses in the family Caliciviridae. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438042 Cd Length: 310 Bit Score: 111.97 E-value: 1.98e-26

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1854 LKDELRKKEKISAGKTRVIEASSVNDTVLFRTTFGNLFSKFHLNPGiVTGSAVGCDPEVfwSKIPVM----LDGDCIMAF 1929
Cdd:cd23192      7 LKDELRPVEKIAEGKRRLLWGCDVGVTLVAAAAFGPVADALKAVCP-TGPIAVGINMDS--EDVEVIferlSGFRYHYCL 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1930 DYTNYDGSIHPIWFQALKQVLTNLSFEASLIDRLCKSKH-----IFKNIYYEVEGGVPSGCSGTSIFNTMINNVIIRTLV 2004
Cdd:cd23192     84 DYSKWDSTQSPAVTAAAIDILADLSEETPLRDSVVETLSsppmgIFDDVIFVTKRGLPSGMPFTSVINSLNHWLLFSAAV 163

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2005 LDAYK-------NIdLDKLKIIAYGDDVIFSYK--YQLDMEAIASEGTKYGLTITPADKSTCFKQLDYSNVTFLKRGFKQ 2075
Cdd:cd23192    164 LKAYElvgiytgNV-FDEADFFTYGDDGVYAMPpaTASVMDEIIENLKSYGLKPTAADKTENPDIPPLQGPVFLKRTFVR 242

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1129875992 2076 DE------------KHQFL-IH------PTFPVEEIHESIRwtknPSQMQEhvlSLCHLMWHnGRDVYKQFEKRIR 2132
Cdd:cd23192    243 TPggwralldrssiLRQLYwVKgpnthdWTEPPTEIDHEAR----TVQLEN---VLLEAAQH-GPEFYEKVLKLVI 310

Marnaviridae_RdRp

cd23195

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

1854-2131

5.43e-22

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: 99.06 E-value: 5.43e-22

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1854 LKDELRKKEKisaGKTRVIEASSVNDTVLFRTTFGNLFSKFHLNPgIVTGSAVGCD---PEvfWSKIPVML---DGDCIM 1927
Cdd:cd23195      7 LKDEPTKLTK---DKVRVFQAAPVALQLLVRKYFLPIARFLQMNP-LLSECAVGINaqsPE--WEELYEHLtkfGEDRII 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1928 AFDYTNYDGSIHPIwfqalkqvLTNLSFEAsLIDRLCKS-------KHIFKNIYYEV--------------EGGVPSGCS 1986
Cdd:cd23195     81 AGDYSKYDKRMSAQ--------LILAAFKI-LIDIAAKSggyseedLKIMRGIATDIayplvdfngdliqfFGSNPSGHP 151

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1987 GTSIFNTMINNVIIRTLVLDAYKNIDL----DKLKIIAYGDDVIFSYK---YQLDMEAIASEGTKYGLTITPADK---ST 2056
Cdd:cd23195    152 LTVIINSIVNSLYMRYAYYSLYPEKEVppfrDVVALMTYGDDNIMSVSpgyPWFNHTSIAEFLAKIGIKYTMADKeaeSV 231

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2057 CFkqLDYSNVTFLKRGFKQDEKHQfLIHPtfPVEEihESI-------RWTKNPS---QMQEHVLSLCHLMWHNGRDVYkq 2126
Cdd:cd23195    232 PF--IHISEADFLKRKFVFDPELG-VYVG--PLDE--DSIfkslhcyLKSKVLTpeeQAAQNIDGALREWFFHGREVY-- 302


                   ....*
gi 1129875992 2127 fEKRI 2131
Cdd:cd23195    303 -EKRR 306

P3A

pfam08727

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

1412-1463

5.59e-17

Pssm-ID: 400873 Cd Length: 59 Bit Score: 76.69 E-value: 5.59e-17

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1129875992 1412 AIFQGpISLE-----GPPPAAISDLLQSVRTPEVIKYCEQNKWI--IPAECKIERDLNV 1463
Cdd:pfam08727    1 AIFQG-IDLKidiktSPPPEAIADLLQAVDSPEIIDYCEDKGWIvnIPAECQIERDIGI 58

Secoviridae_RdRp

cd23196

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

1844-2077

4.36e-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: 81.28 E-value: 4.36e-16

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1844 YGVDLPmvtflKDELRKKEK-ISAGKTRVIEASSVNDTVLFRTTFGNlFSKFHLNPGIVTGSAVGCDP-EVFWSKIPVML 1921
Cdd:cd23196      2 NCVECP-----KDERLKKRKvLEKPKTRLFDVLPMEYNLLLRKYFLN-FVRFIQANRHRLPCQVGINPySREWTTLYDRL 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1922 --DGDCIMAFDYTNYDGSIHpiwfqalKQVLTNLsfeASLIDRLCKSKH-----------------IFKNIYYEVEGGVP 1982
Cdd:cd23196     76 aeKSDTALNCDYSRFDGLLS-------HQVYVWI---ADMINRLYGDGDeakarrnllmmfcgrrsICGRQVYMVRGGMP 145

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1983 SGCSGTSIFNTMINNVIIR----TLVLDAYKNIDLDKLKIIAYGDDVIFSYKYQL----DMEAIASEGTKYGLTITPA-D 2053
Cdd:cd23196    146 SGCALTVIINSIFNEILIRyvyrKVVPRPARNNFNKYVRLVVYGDDNLISVKEEIipyfDGPVIKKEMAKVGVTITDGtD 225

                          250       260
                   ....*....|....*....|....*..
gi 1129875992 2054 KSTC---FKQLdySNVTFLKRGFKQDE 2077
Cdd:cd23196    226 KTSPtleRKPL--ESLDFLKRGFRVQS 250

Iflaviridae_RdRp

cd23197

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

1854-2074

1.16e-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: 65.27 E-value: 1.16e-10

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1854 LKDELRKKEKI-SAGKTRVIEASSVNDTVLFRTTFGNLFSKFHLNPgIVTGSAVGCDPE-VFWSKI--PVMLDGDCIMAF 1929
Cdd:cd23197     12 LKDELRPSEKLrRFGGTRVFSVPPLELVLNSRRFLLPFMDAFQSFP-IEAHHAIGLNPNsGDWRRLrdTLLEKGPCLLQM 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1930 DYTNYDGSIHPIWFQALKQVLTN-------LSFEAS-LIDRLC----KSKHIFKNIYYEVEGGVPSGCSGTSIFNTMINn 1997
Cdd:cd23197     91 DYKNYSDAIPKECVAKAFHIIVDyyrkwhcLTVEIEnALKTLFldtaDAELLVYGDVFKVNNGVLAGHPMTSVVNSVVN- 169

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1998 viirtLVLDAYKNIDLDKLK---------IIAYGDDVIFSYKYQL----DMEAIASEGTKYGLTITPADKSTCFKQLDYS 2064
Cdd:cd23197    170 -----LILMNYMWIKITRRRaseffkltyIIVMGDDVVISLPKQLteefDCRKICAEFAKYDIKVTDSEKNLTGEPKPYD 244

                          250
                   ....*....|...
gi 1129875992 2065 NV---TFLKRGFK 2074
Cdd:cd23197    245 SFdkfEFLSRGFS 257

Polycipiviridae_RdRp

cd23198

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

1853-2131

4.12e-10

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Polycipiviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Polycipiviridae (polycistronic picorna-like viruses), order Picornavirales. Polycipiviridae is a family of picorna-like viruses with non-segmented, linear, (+)ssRNA genomes of approximately 10-12 kb. Their genomes are polycistronic, with four (or more) consecutive 5'-proximal open reading frames (ORFs) encoding structural (and possibly other) proteins and a long 3' ORF encoding the replication polyprotein. Members of species within the family are typically found in ants, with Apple picorna-like virus 1 and the unnamed Polycipiviridae virus in fruit bat stool as exceptions. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438048 Cd Length: 317 Bit Score: 63.59 E-value: 4.12e-10

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1853 FLKDELRKKEKI-----SAGKTRVIEASSVNDTVLFRTTFGNLFSKFH--------LNPGIvtgsavgcDPE-------- 1911
Cdd:cd23198      6 FPKDELRPIYKAlgdpqTPPKTRSVTCMNVYYILAWRRVTLDFWASMHraadgnfpFCPGI--------NPEgpdwnrly 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1912 VFWSKIPVMLDgdcimaFDYTNYDGSIHPIWFQALKQVLTNL------SFEASLIDRL------CkskHI-FKNIYYEVE 1978
Cdd:cd23198     78 HYLNRHPNAVD------FDVSNWDGHLPAELFYAVLDIIKTVlglkpnSPNAKVIYSIltevmnC---HIqFEDIIYQKL 148

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1979 GGVPSGCSGTSIFNTMINNVIIRTLVLDAYKNIDLDK--------LKIIAYGDDVIFSY----KYQLDMEAIASEGTKYG 2046
Cdd:cd23198    149 RGLISGFPGTAEVNTLAHWLLIYYIYLYLAQNTIYDMtitaflrnVSAIFYGDDIIITIsdeiLHWFNGKTIQRMYEEHG 228

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 2047 LTITPADKST---CFKQLdySNVTFLKRGFKQdekhqflIHPTFPVEEIHESI--------RWTKNP-SQMQEHVLSLCH 2114
Cdd:cd23198    229 YPVTSAAKDTeipESKPL--SDCQFLKSSWNP-------ILPGYYIRKMDIEVvydlvywvRAKEHPrDQFYSNYHDALR 299

                          330
                   ....*....|....*..
gi 1129875992 2115 LMWHNGRDVYKQFEKRI 2131
Cdd:cd23198    300 ILFGHGEQVFEAFREQV 316

Nora-virus_RdRp

cd23200

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

1854-2132

5.53e-10

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: 63.02 E-value: 5.53e-10

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1854 LKDELRKKEKISAGKTRVIEASSVNDTVLFRTTFGNLFSKFHlNPGIVTGSAVGCDPE-VFWSKIPV-MLDGDCIMAFDY 1931
Cdd:cd23200      7 LKDQPIKIAQAKSGRTRVFHCIPVDLILFSGALYGPYKEAYT-KAGLKCYHAVGIDPKsVGWQQLATyMTKHPNYFDADY 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1932 TNYDGSIHPIWFQALKQVLTNlsfeasLIDRLCKSKHI-------FKNI---------YYEVEGGVPSGCSGTSIFNTMI 1995
Cdd:cd23200     86 KNYDKYLHRQVFKAVRKIQRS------VIQQVCPDKWDkaraveeLDAIdtyvvdyqtVYKTNRGNKSGSYTTTIDNCLA 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1996 NNVI-----IRTLVLDAYKNIdLDKLKIIAYGDDVIFS----YKYQLDMEAIASEGTKYGLTITPADKSTCFKQLDY-SN 2065
Cdd:cd23200    160 NDIYglyawVKTTGLRSLWDY-RQNVSSVAFGDDIIKSvsdeYKDKYNYCTYRDVLNATGHIMTPGSKDGEEKPFTSfEN 238

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1129875992 2066 VTFLKRGFKQdeKHQFLIHPTFPvEEIHESIRWTKNPSQMQEHVLSLCH------LMWhnGRDVYKQFEKRIR 2132
Cdd:cd23200    239 LQFLKRGFKL--ENGMVLAPLLQ-RSIEGPFVWTDIREDQITVWVNLVQeqlieaALW--GEEYYNELCQKLK 306

RdRP_4

pfam02123

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

1861-2073

1.37e-09

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

Pssm-ID: 280316 Cd Length: 465 Bit Score: 62.86 E-value: 1.37e-09

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1861 KEKISAGKTRvieassvndTVLFRTTFGNLFSKFHLNPG--IVTGSAVGCDPEV-----FWSKIPVMLDGDCIMAFDYTN 1933
Cdd:pfam02123  236 SMKLEHGKSR---------AIYACDTRSYLAFEYLLAPVekAWANKSVILNPGEgdisgFDWSVQDWKRGGVSLMLDYDD 306

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1934 YDgSIHPIW-----FQALKQVLTNlsFEASLIDRLCKS-KHIF-----KNIYYEVEGGVPSGCSGTSIFNTMINNVIIRT 2002
Cdd:pfam02123  307 FN-SQHSTEsmravFERLRRRLPD--EPAEAADWLVCSmDSMYqlsdgTLLAQRVPGTLKSGHRATTFINSVLNCAYAEL 383

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1129875992 2003 LVLDAyknidLDKLKIIAYGDDVIFSYKYQLDMEAIASEGTKYGLTITPADKSTCFKQLDYSNVTFLKRGF 2073
Cdd:pfam02123  384 AGAPW-----ADVPTSIHMGDDVLEGLRTPADATSLLDKYARLGFKVNPSKQSVGHTIAEFLRVAFCSHEV 449

ps-ssRNAv_RdRp-like

cd23167

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

1926-2029

9.12e-09

Pssm-ID: 438017 [Multi-domain] Cd Length: 73 Bit Score: 53.88 E-value: 9.12e-09

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1926 IMAFDYTNYDGSIHPIWFQAlkqvltnlsfeaslidrlckskhifkniyyevegGVPSGCSGTSIFNTMINNVIIRTLVL 2005
Cdd:cd23167      2 VVESDYSGFDSSISPDLLKA----------------------------------GQPSGSPNTSADNSLINLLLARLALR 47

                           90       100
                   ....*....|....*....|....*
gi 1129875992 2006 DAYKNIDLDK-LKIIAYGDDVIFSY 2029
Cdd:cd23167     48 KACGRAEFLNsVGILVYGDDSLVSV 72

ps-ssRNAv_Nodaviridae_RdRp

cd23173

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

1930-2073

5.78e-08

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

Pssm-ID: 438023 Cd Length: 236 Bit Score: 55.98 E-value: 5.78e-08

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1930 DYTNYDGSIHPiWFQAL--------------KQVLTNLSfeASLIDRLCKSKHIFKniyYEVEGGVPSGCSGTSIFNTMI 1995
Cdd:cd23173     89 DYSRFDGTISE-WLRRNvefaaylrwfhpeyRAELLKLL--DAEINCPARTKTGVK---YDPGVSRLSGSPTTTDGNTII 162

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1996 NNVI----IRTLVLD---AYKNIDLdklkiiAYGDDVIFSYKYQLDMEAIASegtKYGLTITpADKSTCfkqldYSNVTF 2068
Cdd:cd23173    163 NAFVsycaLRETGYSpeeAFALLGL------YYGDDGLSDNLPAEALEKVAK---DLGLKLK-IEVVRP-----GQPVTF 227


                   ....*
gi 1129875992 2069 LKRGF 2073
Cdd:cd23173    228 LGRVF 232

ps-ssRNAv_Astroviridae_RdRp

cd23172

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

1853-2034

3.57e-06

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

Pssm-ID: 438022 Cd Length: 243 Bit Score: 50.55 E-value: 3.57e-06

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1853 FLKDELRKKEKISAGKTRVIeasSVNDTVLFRttFGNLF-----SKFHLNPGiVTGSAVGCDPevFWSKIPVMLD----- 1922
Cdd:cd23172      7 FLKKEILKKEKIEDGDIRQI---LCPDPIFAR--IGARFeqdqnNLMKERTL-TNEGQVGWSP--FYGGFDARVRrlgsk 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1923 GDCIMAFDYTNYDGSIhPIW-FQALKQvltnlsFEASLIDRLC--KSKHIFKNI-------Y--------YEVEGGVPSG 1984
Cdd:cd23172     79 GNYFVEFDWTRFDGTI-PAElFRHIRK------LRWSFLDPEKteENRKVYDWYvhnllnrYvllptgevTRVTKGNPSG 151

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1129875992 1985 CSGTSIFNTMInNVIIRTLVLdAY----KNIDLDKL----KIIAYGDDVIFSYKYQLD 2034
Cdd:cd23172    152 QISTTMDNCMV-NTFLTAFEF-AYvygpKTGTLKELwdnyDTIVYGDDRLSGYPSLPD 207

Calici_coat

pfam00915

Calicivirus coat protein;

376-530

3.80e-04

Calicivirus coat protein;

Pssm-ID: 459994 Cd Length: 291 Bit Score: 44.88 E-value: 3.80e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992  376 MCQVDTLIPINNLEQNIRNVNMYSVVLNQETTTAKEifAIKVDIASQPLATTMIGEIASYFTHWTGSLRFSFLFCGTANT 455
Cdd:pfam00915   45 SATAATAGQGKSVDQEWITNFSYHTSQNWSTIEPQG--KVLFDQSLGPHLNPFLLHLSQMYNGWSGGMRVRFMVAGSGVF 122

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1129875992  456 TLKLLVAYTPPGIEkPQNRKDAMLGTHVVWDVGLQSTISMVVPWVSASHYRNTTPDTysQAGYITCWYQTNLVVP 530
Cdd:pfam00915  123 GGKLAASVIPPGVE-PITSASMLQFPHVLFDARQLEPVIFTIPDLRNTLFHNMDRNT--DTTRLVIMVYNPLINP 194

DEXXQc_SF1

cd18043

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

1212-1266

1.03e-03

Pssm-ID: 350801 [Multi-domain] Cd Length: 127 Bit Score: 41.03 E-value: 1.03e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1129875992 1212 AVVIHGEPGTGKSMT-----TNFLAR----------------------MITNDSDIYSLPPDPKYFDgydqqsVVIMDDI 1264
Cdd:cd18043     16 NVVIQGPPGTGKSQTianiiANALARgkrvlfvsekkaaldvvrfpcwIMSPLSVSQYLPLNRNLFD------LVIFDEA 89


                   ..
gi 1129875992 1265 MQ 1266
Cdd:cd18043     90 SQ 91

ps-ssRNAv_Potyviridae_RdRp

cd23175

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

1853-1896

1.25e-03

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

Pssm-ID: 438025 Cd Length: 236 Bit Score: 42.82 E-value: 1.25e-03

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1129875992 1853 FLKDELRKKEKISAGKTRVIEASSVnDTVL----FRTTFGNLFSKFHL 1896
Cdd:cd23175      9 SLKAELRPIEKVEANKTRTFTAAPI-DTLLggkvCVDDFNNQFYSLHL 55

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