NCBI Conserved Domain Search

Conserved domains on [gi|2099547062|gb|UBI50862|]

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polyprotein [rhinovirus A1B]

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: 832.56 E-value: 0e+00

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1707 ECGLPSIHTPSKTKLQPSVFYDVFPGSKEPAVLTDNDPRLEVDFKEALFSKYKGNVECNLNEHMEVAIAHYSAQLATLDI 1786
Cdd:cd23213      3 EVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATLDI 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1787 DPKPIALEDGVFGIEGLEALDLNTSAGFPYVTMGIKKRDLINNKTKDISRLKDALDKYGVDLPMITFLKDELRKKEKISA 1866
Cdd:cd23213     83 DTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKVEK 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1867 GKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPEVFWSKIPVMLDGdCIMAFDYTNYDGSIHPVWFQAL 1946
Cdd:cd23213    163 GKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDG-SLFAFDYTGYDASLSPVWFRAL 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1947 KKVLE--NLSFQSDLIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKNIDLDKLKIIAYGDD 2024
Cdd:cd23213    242 KMVLEkgYSEEAVSLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYGDD 321

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2025 VIFSYKYTLDMEAIANEGKKYGLTITPADKSTEFRKLDYNNVTFLKRGFKQDERHTFLIHPTFPVEEIYESIRWTKKPSQ 2104
Cdd:cd23213    322 VIASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDPRN 401

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2099547062 2105 MQEHVLSLCHLMWHNGRKVYEDFSRKIRSVSAGRALYIPPYDLLKHEWYEKF 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

5.57e-75

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

Pssm-ID: 395757 Cd Length: 127 Bit Score: 244.98 E-value: 5.57e-75

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  872 NLHLFN-SEMHDSILVSYSSDLIIYRTNTIGDDYIPSCNCTEATYYCKHKNRYYPIKVTPHDWYEIQESEYYPKHIQYNL 950
Cdd:pfam00947    1 NRHLAThEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 2099547062  951 LIGEGPCEPGDCGGKLLCRHGVIGIITAGGEGHVAFTDLRQFQCAEE 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

5.58e-64

picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by clustalw. If a representative set is used for a seed, many so-called members are not recognized. The family should probably be split up into sub-families. Capsid proteins of picornaviruses. Picornaviruses are non-enveloped plus-strand ssRNA animal viruses with icosahedral capsids. They include rhinovirus (common cold) and poliovirus. Common structure is an 8-stranded beta sandwich. Variations (one or two extra strands) occur.

Pssm-ID: 395026 Cd Length: 170 Bit Score: 215.25 E-value: 5.58e-64

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062   93 TSQDVANAVVGYGVWPHYLTPQDATAIDKPTQPDTSSNRFYTLESKHWDGNSKGW-WWKLPDALKDMGIFGENMYYHFLG 171
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFfWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  172 RSGYTVHVQCNASKFHQGTLLVAMIPEHQlasakngkvtagynlTHPGDAgrvvgqqrdtnlrqpsddswlnfdgTLLGN 251
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPPGA---------------PPPGSR-------------------------DYLWQ 120

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 2099547062  252 LLIFPHQFINLRSNNSATLIVPYVNAVPMDSMLRHNNWSLVIIPISPLR 300
Cdd:pfam00073  121 ATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGNWTLVVAGWVPLN 169

Peptidase_C3 super family

cl02893

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

1514-1679

8.53e-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: 191.89 E-value: 8.53e-56

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1514 GPEEEFGRSILKNNTCVITTDNGKFTGL--GIYDRILIVPTHADPGKEVQVNGIQTKVLD-SYDLYNRDGIKLEITVIKL 1590
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1591 DRNEKFRDIRKYIPETEDDYPECNLALSANQTEPTIIKVGDVVSYGNI-LLSGNQTARMLKYNYPTKSGYCGGVLYKI-- 1667
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVVIAKve 160

                          170
                   ....*....|....
gi 2099547062 1668 --GQILGIHVGGNG 1679
Cdd:pfam00548  161 gnGKILGMHIAGNG 174

Rhv

pfam00073

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

360-524

8.26e-51

Pssm-ID: 395026 Cd Length: 170 Bit Score: 177.50 E-value: 8.26e-51

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  360 YHPTKEISIPGEVKNLIEMCQVDTLIPVNNVGTNVGNISMYTVQLG-QMEVAQEVFAIKVDItsQPLATTLLGEIASYYT 438
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTdWTSLSKGFFWWKLPL--ALLSMGLLGRLLRYHT 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  439 HWTGSLRFSFMFCGTANTTLKLLLAYTPPGIDKPATR---KDAMLGTHVVWDVGLQSTISLVVPWVSASHFRLTANDK-- 513
Cdd:pfam00073   79 YYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRdylWQATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGnw 158

                          170
                   ....*....|..
gi 2099547062  514 -YSMAGYITCWY 524
Cdd:pfam00073  159 tLVVAGWVPLNY 170

Rhv

pfam00073

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

616-768

2.03e-49

Pssm-ID: 395026 Cd Length: 170 Bit Score: 173.65 E-value: 2.03e-49

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  616 PEDAIETRYVITSQTRDEMSIESFLGRSGCVH-----ISRIKVDYNDYNGQNKNFTQWKITL--QEMAQIRRKFELFTYV 688
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQpdvqgERFYTLDSTDWTSLSKGFFWWKLPLalLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  689 RFDSEVTLVPCiagrGDDIGHVVMQYMYVPPGAPIPKTRdDFSWQSGTNMSIFWQHG-QPFPRFSLPFLSIASAYYMFYD 767
Cdd:pfam00073   81 RGGLEVTVQFN----GSKFHQGKLLVAYVPPGAPPPGSR-DYLWQATLNPHQFWNLGlNSSARLSVPYISIAHYYSTFYD 155


                   .
gi 2099547062  768 G 768
Cdd:pfam00073  156 G 156

Pico_P2B super family

cl03260

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

998-1094

2.21e-45

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

The actual alignment was detected with superfamily member pfam01552:

Pssm-ID: 279840 Cd Length: 101 Bit Score: 159.42 E-value: 2.21e-45

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  998 QGITDYIHMLGEAFGNGFV----DSVKEQINAINPINSISKKVIKWLLRIISAMVIIIRNSSDPQTIIATLTLIGCNGSP 1073
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTqqisDKIKELTNFINPTSKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|.
gi 2099547062 1074 WRFLKEKFCKWTQLTYIHKES 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

2.05e-41

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

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

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2099547062    2 GAQVSRQNVGTHSTQNSVSNGSSLNYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 69
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 68

RNA_helicase

pfam00910

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

1213-1309

7.03e-40

RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in a variety of single stranded RNA viruses.

Pssm-ID: 459992 Cd Length: 102 Bit Score: 143.51 E-value: 7.03e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1213 VMIHGPPGTGKSITTNFLARMI-----TNESDVYSLPPDPKYFDGYDNQSVVIMDDIMQNPDGEDMTLFCQMVSSVTFIP 1287
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALlkklgLPKDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 2099547062 1288 PMADLPDKGKPFDSRFILCSTN 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 ...

1412-1464

6.74e-21

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: 87.87 E-value: 6.74e-21

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2099547062 1412 AIFQG----PISLDAPPPPAIADLLQSVRTPEVIKYCQDNKWIV--PAECQIERDLNIA 1464
Cdd:pfam08727    1 AIFQGidlkIDIKTSPPPEAIADLLQAVDSPEIIDYCEDKGWIVniPAECQIERDIGIA 59

Name

Accession

Description

Interval

E-value

Enterovirus_RdRp

cd23213

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

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: 832.56 E-value: 0e+00

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1707 ECGLPSIHTPSKTKLQPSVFYDVFPGSKEPAVLTDNDPRLEVDFKEALFSKYKGNVECNLNEHMEVAIAHYSAQLATLDI 1786
Cdd:cd23213      3 EVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATLDI 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1787 DPKPIALEDGVFGIEGLEALDLNTSAGFPYVTMGIKKRDLINNKTKDISRLKDALDKYGVDLPMITFLKDELRKKEKISA 1866
Cdd:cd23213     83 DTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKVEK 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1867 GKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPEVFWSKIPVMLDGdCIMAFDYTNYDGSIHPVWFQAL 1946
Cdd:cd23213    163 GKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDG-SLFAFDYTGYDASLSPVWFRAL 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1947 KKVLE--NLSFQSDLIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKNIDLDKLKIIAYGDD 2024
Cdd:cd23213    242 KMVLEkgYSEEAVSLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYGDD 321

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2025 VIFSYKYTLDMEAIANEGKKYGLTITPADKSTEFRKLDYNNVTFLKRGFKQDERHTFLIHPTFPVEEIYESIRWTKKPSQ 2104
Cdd:cd23213    322 VIASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDPRN 401

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2099547062 2105 MQEHVLSLCHLMWHNGRKVYEDFSRKIRSVSAGRALYIPPYDLLKHEWYEKF 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

5.57e-75

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

Pssm-ID: 395757 Cd Length: 127 Bit Score: 244.98 E-value: 5.57e-75

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  872 NLHLFN-SEMHDSILVSYSSDLIIYRTNTIGDDYIPSCNCTEATYYCKHKNRYYPIKVTPHDWYEIQESEYYPKHIQYNL 950
Cdd:pfam00947    1 NRHLAThEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 2099547062  951 LIGEGPCEPGDCGGKLLCRHGVIGIITAGGEGHVAFTDLRQFQCAEE 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

5.58e-64

Pssm-ID: 395026 Cd Length: 170 Bit Score: 215.25 E-value: 5.58e-64

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062   93 TSQDVANAVVGYGVWPHYLTPQDATAIDKPTQPDTSSNRFYTLESKHWDGNSKGW-WWKLPDALKDMGIFGENMYYHFLG 171
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFfWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  172 RSGYTVHVQCNASKFHQGTLLVAMIPEHQlasakngkvtagynlTHPGDAgrvvgqqrdtnlrqpsddswlnfdgTLLGN 251
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPPGA---------------PPPGSR-------------------------DYLWQ 120

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 2099547062  252 LLIFPHQFINLRSNNSATLIVPYVNAVPMDSMLRHNNWSLVIIPISPLR 300
Cdd:pfam00073  121 ATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGNWTLVVAGWVPLN 169

Peptidase_C3

pfam00548

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

1514-1679

8.53e-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: 191.89 E-value: 8.53e-56

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1514 GPEEEFGRSILKNNTCVITTDNGKFTGL--GIYDRILIVPTHADPGKEVQVNGIQTKVLD-SYDLYNRDGIKLEITVIKL 1590
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1591 DRNEKFRDIRKYIPETEDDYPECNLALSANQTEPTIIKVGDVVSYGNI-LLSGNQTARMLKYNYPTKSGYCGGVLYKI-- 1667
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVVIAKve 160

                          170
                   ....*....|....
gi 2099547062 1668 --GQILGIHVGGNG 1679
Cdd:pfam00548  161 gnGKILGMHIAGNG 174

RdRP_1

pfam00680

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

1723-2133

1.49e-52

Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase found in many positive strand RNA eukaryotic viruses. Structural studies indicate that these proteins form the "right hand" structure found in all oligonucleotide polymerases, containing thumb, finger and palm domains, and also the additional bridging finger and thumb domains unique to RNA-directed RNA polymerases.

Pssm-ID: 425815 Cd Length: 450 Bit Score: 192.63 E-value: 1.49e-52

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1723 PSVFYDVFPGSKEPAVLTDNDPR-------LEVDFKEALFSKYK---GNVECNLNEHMEVAIAHYSAQLATLDidPKPIA 1792
Cdd:pfam00680    2 PTERHLVAIPAYVPASLGPEDPRwarsylnTDPYVDDIKKYSRPklpGPADERDKLLNRSAAKMVLSELRGVP--KKANS 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1793 LEDGVFGI---EGLEALDLNTSAGFPYVTMGIKKRDLIN----NKTKDI--SRLKDALDKY--GVDLPMI--TFLKDELR 1859
Cdd:pfam00680   80 TLIVYRAIdgvEQIDPLNWDTSAGYPYVGLGGKKGDLIEhlkdGTEARElaERLAADWEVLqnGTPLKLVyqTCLKDELR 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1860 KKEKISAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTgSAVGCDPevFWSKIPVMLD-----GDCIMAFDYTNY 1934
Cdd:pfam00680  160 PLEKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHP-IQVGINP--FDRGWPRLLRrlarfGDYVYELDYSGF 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1935 DGSIHPVWFQALKKVLENLSFQSD-------LIDRLCYSKH-LFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLD 2006
Cdd:pfam00680  237 DSSVPPWLIRFAFEILRELLGFPSnvkewraILELLIYTPIaLPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYALLK 316

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2007 AYKNIDL------DKLKIIAYGDDVIFSYKYTLD--MEAIANEGKKYGLTITPADKSTEFRKlDYNNVTFLKRGFKQDEr 2078
Cdd:pfam00680  317 SLENDGPrvcnldKYFDFFTYGDDSLVAVSPDFDpvLDRLSPHLKELGLTITPAKKTFPVSR-ELEEVSFLKRTFRKTP- 394

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2099547062 2079 htFLIHPTFPVEEIYESIRWTKKPSQMQEHVLSLCHLMWHNGRKVYEDFSRKIRS 2133
Cdd:pfam00680  395 --GGYRPPLDRKRILAQLEYIRSKPVPSGQLENIRAYASHHGYEFYRDLLYRFVE 447

Rhv

pfam00073

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

360-524

8.26e-51

Pssm-ID: 395026 Cd Length: 170 Bit Score: 177.50 E-value: 8.26e-51

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  360 YHPTKEISIPGEVKNLIEMCQVDTLIPVNNVGTNVGNISMYTVQLG-QMEVAQEVFAIKVDItsQPLATTLLGEIASYYT 438
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTdWTSLSKGFFWWKLPL--ALLSMGLLGRLLRYHT 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  439 HWTGSLRFSFMFCGTANTTLKLLLAYTPPGIDKPATR---KDAMLGTHVVWDVGLQSTISLVVPWVSASHFRLTANDK-- 513
Cdd:pfam00073   79 YYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRdylWQATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGnw 158

                          170
                   ....*....|..
gi 2099547062  514 -YSMAGYITCWY 524
Cdd:pfam00073  159 tLVVAGWVPLNY 170

Rhv

pfam00073

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

616-768

2.03e-49

Pssm-ID: 395026 Cd Length: 170 Bit Score: 173.65 E-value: 2.03e-49

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  616 PEDAIETRYVITSQTRDEMSIESFLGRSGCVH-----ISRIKVDYNDYNGQNKNFTQWKITL--QEMAQIRRKFELFTYV 688
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQpdvqgERFYTLDSTDWTSLSKGFFWWKLPLalLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  689 RFDSEVTLVPCiagrGDDIGHVVMQYMYVPPGAPIPKTRdDFSWQSGTNMSIFWQHG-QPFPRFSLPFLSIASAYYMFYD 767
Cdd:pfam00073   81 RGGLEVTVQFN----GSKFHQGKLLVAYVPPGAPPPGSR-DYLWQATLNPHQFWNLGlNSSARLSVPYISIAHYYSTFYD 155


                   .
gi 2099547062  768 G 768
Cdd:pfam00073  156 G 156

Pico_P2B

pfam01552

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

998-1094

2.21e-45

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

Pssm-ID: 279840 Cd Length: 101 Bit Score: 159.42 E-value: 2.21e-45

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  998 QGITDYIHMLGEAFGNGFV----DSVKEQINAINPINSISKKVIKWLLRIISAMVIIIRNSSDPQTIIATLTLIGCNGSP 1073
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTqqisDKIKELTNFINPTSKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|.
gi 2099547062 1074 WRFLKEKFCKWTQLTYIHKES 1094
Cdd:pfam01552   81 WQFLKEKACAVLEIPYVHKQG 101

rhv_like

cd00205

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

375-558

3.55e-43

Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA animal viruses with icosahedral capsids composed of 60 copies each of 4 virus encoded proteins; alignment includes picornaviridae, like poliovirus, hepatitis A virus, rhinovirus, foot-and-mouth disease virus and encephalomyocarditis virus; common structure is an 8-stranded beta sandwich

Pssm-ID: 119412 Cd Length: 178 Bit Score: 156.02 E-value: 3.55e-43

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  375 LIEMCQVDTLIPVNNVGTNVGNismytvqlgqmevaQEVFAIKVDITSQPL--ATTLLGEIASYYTHWTGSLRFSFMFCG 452
Cdd:cd00205      1 VESFADRPTTVGTNNWNSSASG--------------TQLFQWKLSPALGFLllQNTPLGALLSYFTYWRGDLEVTVQFNG 66

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  453 TANTTLKLLLAYTPPGIDKPA---TRKDAMLGTHVVWDVGLQSTISLVVPWVSASHFRLTANDKY---SMAGYITCWYQT 526
Cdd:cd00205     67 SKFHTGRLLVAYVPPGAPAPTtgdTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDGYgplNSFGTLVVRVLT 146

                          170       180       190
                   ....*....|....*....|....*....|..
gi 2099547062  527 NLVVPPNTPQTADMLCFVSAcKDFCLRMARDT 558
Cdd:cd00205    147 PLTVPSGAPTTVDITVYVRA-GDFELYGPRPP 177

Pico_P1A

pfam02226

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

2-69

2.05e-41

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

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2099547062    2 GAQVSRQNVGTHSTQNSVSNGSSLNYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 69
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 68

RNA_helicase

pfam00910

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

1213-1309

7.03e-40

RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in a variety of single stranded RNA viruses.

Pssm-ID: 459992 Cd Length: 102 Bit Score: 143.51 E-value: 7.03e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1213 VMIHGPPGTGKSITTNFLARMI-----TNESDVYSLPPDPKYFDGYDNQSVVIMDDIMQNPDGEDMTLFCQMVSSVTFIP 1287
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALlkklgLPKDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 2099547062 1288 PMADLPDKGKPFDSRFILCSTN 1309
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

rhv_like

cd00205

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

125-329

4.77e-38

Pssm-ID: 119412 Cd Length: 178 Bit Score: 141.38 E-value: 4.77e-38

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  125 PDTSSNRFYTLESKHW---DGNSKGWWWKLPDA----LKDMGIFGENMYYHFLGRSGYTVHVQCNASKFHQGTLLVAMIP 197
Cdd:cd00205      1 VESFADRPTTVGTNNWnssASGTQLFQWKLSPAlgflLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  198 EHQLASAKNgkvtagynlthpgdagrvvgqqrdtnlrqpsddswlnfdgTLLGNLLIFPHQFINLRSNNSATLIVPYVNA 277
Cdd:cd00205     81 PGAPAPTTG----------------------------------------DTRWQATLNPHVIWDLGTNSSVTFVVPYVSP 120

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2099547062  278 VPMDSMLRH------NNWSLVIIPISPLRSEATSSNIVPITVSISPMCAEFSGARAKN 329
Cdd:cd00205    121 TPYRSTRYDgygplnSFGTLVVRVLTPLTVPSGAPTTVDITVYVRAGDFELYGPRPPR 178

rhv_like

cd00205

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

636-824

1.07e-35

Pssm-ID: 119412 Cd Length: 178 Bit Score: 134.45 E-value: 1.07e-35

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  636 IESFLGRSGCVHISRIkvdynDYNGQNKNFTQWKITLQE------MAQIRRKFELFTYVRFDSEVTLVPCiagrGDDIGH 709
Cdd:cd00205      1 VESFADRPTTVGTNNW-----NSSASGTQLFQWKLSPALgflllqNTPLGALLSYFTYWRGDLEVTVQFN----GSKFHT 71

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  710 VVMQYMYVPPGAPIPKTrDDFSWQSGTNMSIFWQHG-QPFPRFSLPFLSIASAYYMFYDGYDgdnssakygsvVTNDMGT 788
Cdd:cd00205     72 GRLLVAYVPPGAPAPTT-GDTRWQATLNPHVIWDLGtNSSVTFVVPYVSPTPYRSTRYDGYG-----------PLNSFGT 139

                          170       180       190
                   ....*....|....*....|....*....|....*....
gi 2099547062  789 ICSRIVTE---RQEHPVVITTHIYHKAKHTKAWCPRPPR 824
Cdd:cd00205    140 LVVRVLTPltvPSGAPTTVDITVYVRAGDFELYGPRPPR 178

P3A

pfam08727

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

1412-1464

6.74e-21

Pssm-ID: 400873 Cd Length: 59 Bit Score: 87.87 E-value: 6.74e-21

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2099547062 1412 AIFQG----PISLDAPPPPAIADLLQSVRTPEVIKYCQDNKWIV--PAECQIERDLNIA 1464
Cdd:pfam08727    1 AIFQGidlkIDIKTSPPPEAIADLLQAVDSPEIIDYCEDKGWIVniPAECQIERDIGIA 59

DEXXQc_SF1

cd18043

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

1212-1269

4.82e-04

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

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1212 AVMIHGPPGTGKS-----ITTNFLAR----------------------MITNESDVYSLPPDPKYFDgydnqsVVIMDDI 1264
Cdd:cd18043     16 NVVIQGPPGTGKSqtianIIANALARgkrvlfvsekkaaldvvrfpcwIMSPLSVSQYLPLNRNLFD------LVIFDEA 89


                   ....*
gi 2099547062 1265 MQNPD 1269
Cdd:cd18043     90 SQIPI 94

CDC6

COG1474

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

1213-1251

4.86e-03

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

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

                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 2099547062 1213 VMIHGPPGTGKSITTNFLARMITNESDVYSLPPDPKYFD 1251
Cdd:COG1474     54 VLIYGPTGTGKTAVAKYVLEELEEEAEERGVDVRVVYVN 92

Name

Accession

Description

Interval

E-value

Enterovirus_RdRp

cd23213

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

1707-2156

0e+00

Pssm-ID: 438063 Cd Length: 453 Bit Score: 832.56 E-value: 0e+00

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1707 ECGLPSIHTPSKTKLQPSVFYDVFPGSKEPAVLTDNDPRLEVDFKEALFSKYKGNVECNLNEHMEVAIAHYSAQLATLDI 1786
Cdd:cd23213      3 EVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATLDI 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1787 DPKPIALEDGVFGIEGLEALDLNTSAGFPYVTMGIKKRDLINNKTKDISRLKDALDKYGVDLPMITFLKDELRKKEKISA 1866
Cdd:cd23213     83 DTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKVEK 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1867 GKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPEVFWSKIPVMLDGdCIMAFDYTNYDGSIHPVWFQAL 1946
Cdd:cd23213    163 GKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDG-SLFAFDYTGYDASLSPVWFRAL 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1947 KKVLE--NLSFQSDLIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKNIDLDKLKIIAYGDD 2024
Cdd:cd23213    242 KMVLEkgYSEEAVSLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYGDD 321

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2025 VIFSYKYTLDMEAIANEGKKYGLTITPADKSTEFRKLDYNNVTFLKRGFKQDERHTFLIHPTFPVEEIYESIRWTKKPSQ 2104
Cdd:cd23213    322 VIASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDPRN 401

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2099547062 2105 MQEHVLSLCHLMWHNGRKVYEDFSRKIRSVSAGRALYIPPYDLLKHEWYEKF 2156
Cdd:cd23213    402 TQDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453

Sapelovirus_RdRp

cd23218

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

1795-2156

3.00e-165

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Sapelovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Sapelovirus genus within the family Picornaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. Viruses in Sapelovirus are non-enveloped, with icosahedral, spherical, and round geometries, and T=pseudo3 symmetry. Sapelovirus, formerly known as porcine enterovirus (PEV)-8, is known to infect pigs asymptomatically but can cause reproductive failure and severe neurologic, enteric, or respiratory signs. Sapelovirus infections have been reported worldwide in pigs. The genus Sapelovirus contains three species, with a unique genome organization: Sapelovirus A, also known as porcine sapelovirus (PSV); Sapelovirus B as simian sapelovirus; and Avian sapelovirus represented by duck picornavirus. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438068 Cd Length: 366 Bit Score: 511.37 E-value: 3.00e-165

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1795 DGVFGIEGLEALDLNTSAGFPYVTMGIKKRDLINNKTKDISRLKDALDKYGVDLPMITFLKDELRKKEKISAGKTRVIEA 1874
Cdd:cd23218      1 DVVYGIDNLEGLDLNTSAGYPYNTMGIRKKDLIPPRGEPLSPLLKALDLHGYDLPFTTYLKDELRPKEKVKMGKTRLIEC 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1875 SSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPEVFWSKIPVMLDGDCIMAFDYTNYDGSIHPVWFQALKKVLENLS 1954
Cdd:cd23218     81 SSLNDTIRMKRIFGRLFQTFHKNPGTYTGSAVGCNPDVHWSKFAEEGGMDNVCAFDYTNWDASLSPFWFDALKLFLSKLG 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1955 FQS---DLIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKNIDLDKLKIIAYGDDVIFSYKY 2031
Cdd:cd23218    161 YSErdiVLIDHLCYSNHIFKNEGYKVAGGMPSGCSGTSIFNSIINNIVVRTLVLLVYKGINLDELRILCYGDDLLVAYPY 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2032 TLDMEAIANEGKKYGLTITPADKSTEF---RKLdyNNVTFLKRGFKQDERHTFLIHPTFPVEEIYESIRWTKKPSQMQEH 2108
Cdd:cd23218    241 PLDPNVLADLGKSLGLTMTPADKSDTFqgcTKL--TEVTFLKRSFVFDEEFPFLCHPVFPMEEVHESIRWTRNASTTQEH 318

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*...
gi 2099547062 2109 VLSLCHLMWHNGRKVYEDFSRKIRSVSAGRALYIPPYDLLKHEWYEKF 2156
Cdd:cd23218    319 VTSLCLLAWHNGEEVYEEFCEKIRSVPVGRALILPPYSQLRRSWLDMF 366

Rabovirus_RdRp

cd23230

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

1798-2156

3.14e-162

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: 502.88 E-value: 3.14e-162

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1798 FGIEGLEALDLNTSAGFPYVTMGIKKRDLINNKTKDISRLKDALDKYGVDLPMITFLKDELRKKEKISAGKTRVIEASSI 1877
Cdd:cd23230      3 YGIENLEGLDLNTSAGYPYVLNGIKKRDILDPETRDTTKLQECLDKYGVDLPFVTYLKDELRPLEKIKKGKTRLIECSSM 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1878 NDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPEVFWSKIPVMLDGDcIMAFDYTNYDGSIHPVWFQALKKVLENLSFqS 1957
Cdd:cd23230     83 NDTIRMKMMFGRLFATYHRNPGPITGSAVGCNPDIHWTKFRAEMHGE-IIAFDYSNYDASLNKVWFECLKMVLKNFGF-K 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1958 DL--IDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKNIDLDKLKIIAYGDDVIFSYKYTLDM 2035
Cdd:cd23230    161 DLrpIDHIIRSRHIYKGIEYDVEGGMPSGCSGTSIFNSIINNIIIMTLVLDAYKGIDLEQLKIIAYGDDVIVTYPYPLDA 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2036 EAIANEGKKYGLTITPADKSTEFRKLDYNNVTFLKRGFKQDERHTFLIHPTFPVEEIYESIRWTKKPSQMQEHVLSLCHL 2115
Cdd:cd23230    241 ALLADCGKKYGLKMTPPDKSAEFKNVTWEDVTFLKRRFKPAKHYPFLIHPVFDQQEILESLRWTRNPAHTQEHVRSLAEL 320

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|.
gi 2099547062 2116 MWHNGRKVYEDFSRKIRSVSAGRALYIPPYDLLKHEWYEKF 2156
Cdd:cd23230    321 AWHSGRKSYEEFCNLVKSTNVGKACILPPYESFKRMWLDQF 361

ps-ssRNA_Picornaviridae

cd23193

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

1797-2132

1.67e-137

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: 433.13 E-value: 1.67e-137

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1797 VFGIEGLEALDLNTSAGFPYVTMGIKKRDLINNKTKDIS-----RLKDALDKYGVDLPMITFLKDELRKKEKISAGKTRV 1871
Cdd:cd23193      2 INGIDGLDPIDLNTSPGYPYTTQGLRRRDLIDNDKGGVSplleeEEQVLLDLDGPDVVFTTFLKDELRPKEKVKAGKTRV 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1872 IEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPEVFWSKIPVMLDGDCIMAFDYTNYDGSIHPVWFQALKKVLE 1951
Cdd:cd23193     82 IEAAPLDYVIAGRMVFGRLFAQFHSNPGILTGSAVGCNPDTDWTRLFASLKQDNVYDLDYSGFDASLSSQLFEAAVEVLA 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1952 NLS----FQSDLIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKnIDLDKLKIIAYGDDVIF 2027
Cdd:cd23193    162 ECHgdpeLVLRYLEPIINSKHVVGDERYTVEGGMPSGCPCTSILNSICNNLVVRYALLETGK-FDPDEYYILAYGDDVLV 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2028 SYKYTLDMEAIANEGKKY-GLTITPADKSTEFRKLDYNNVTFLKRGFKQDERhTFLIHPTFPVEEIYESIRWTKKPSQMQ 2106
Cdd:cd23193    241 STDEPIDPSDLAEFYKKYfGMTVTPADKSSDFPESSPIEDVFLKRRFFVPDG-TFLIHPVMDLETLEQSLMWCGRGGFFQ 319

                          330       340
                   ....*....|....*....|....*.
gi 2099547062 2107 EHVLSLCHLMWHNGRKVYEDFSRKIR 2132
Cdd:cd23193    320 QLLSSLCELALHHGPEEYERLVSKVR 345

Cosavirus_RdRp

cd23226

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

1711-2156

2.17e-84

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: 285.37 E-value: 2.17e-84

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1711 PSIHTPSKTKLQ-PSVFYDVFPgSKEPAVLTDNDPRLE--VDFKEALFSKYKGNVECNLNEHMEVAIAhYSAQLAT---L 1784
Cdd:cd23226     10 PRVHVPRQSKLKrTNATYPATG-KYGPAVLSKNDPRLDpdVDFDKVIFSKHVANVVIDEDTSFWNALK-MSAQIYAekfK 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1785 DIDPKPIALEDGVFGIEGLEALDLNTSAGFPYVTMgikKRDLINNKTKDI------SRLKDALDKYGVDLPMITFLKDEL 1858
Cdd:cd23226     88 GVDFSPLTVEEAILGIPGLDRMDPNTASGLPYTKT---RRQMIDFQEGKIldpelqERLDTWLSGKQPEMLYQTFLKDEI 164

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1859 RKKEKISAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPEVFWSKIPVMLDG-DCIMAFDYTNYDGS 1937
Cdd:cd23226    165 RPIEKVKAGKTRIIDVTPLDHVLAFRIVLGRFMAHFHNNYGFELGSAVGCDPDVAWANFGFALSSkKYQYDFDYSNFDAS 244

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1938 iHPVwfqALKKVLENLSFQSD---------LIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAY 2008
Cdd:cd23226    245 -HSE---SIFELLKQFVFTKDngfdhrcslMIDSLVTSTHCYEDQRMTIRGGLPSGTSGTSVINTIINNIIFKAALYHTY 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2009 KNIDLDKLKIIAYGDDVIFSYKYTLDMEAIANEGKKYGLTITPADKSTEFRKLDYNNVTFLKRGFKqdeRHTFLIHPTFP 2088
Cdd:cd23226    321 SNFEWDDVQMLAYGDDIVAASDCLLDLDRVKYFMALIGYKITPADKGEKFIPKDMQNIQFLKRSFR---KVAGVWAPIMD 397

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2099547062 2089 VEEIYESIRWTkKPSQMQEHVLSLCHLMWHNGRKVYEdfsrKIRSVSAGRALYIPPYDLLKHEWYEKF 2156
Cdd:cd23226    398 LENLQAMLSWY-KPGTLQEKLDSVARLAHFCGEKVYD----HLFTTFVKDGFQIKPWKQLHFEWLNRF 460

Mischivirus_RdRp

cd23227

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

1711-2156

2.43e-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: 282.60 E-value: 2.43e-83

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1711 PSIHTPSKTKLQPSVFYDVFPGSKEPAVLTDNDPRL--EVDFKEALFSKYKGNvECNLNEHMEVAIAHYSAQLAT-LDID 1787
Cdd:cd23227     10 PRIHVPRKTKLRKSPAYPIFKPDAGPAVLSKNDPRLaeGVDFDKQVFSKHSAN-QKEYPKAFRRMARWYADRVFTyLGKD 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1788 PKPIALEDGVFGIEGLEALDLNTSAGFPYVTMGIKKRDLINNKTKDISR--LKDALDKYG----VDLPMITFLKDELRKK 1861
Cdd:cd23227     89 NGPLSVKDAIKGIDNLDAMDPTTSPGLPYSAAGIKRTDLLDFDTGEIISpaLRAEYNKYVsgdySDHVFQTFLKDEIRSE 168

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1862 EKISAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPEVFWSKIPVML-DGDCIMAFDYTNYDGSIHP 1940
Cdd:cd23227    169 EKIKAGKTRIVDVPSLAHVIIGRVLLGKFCSKFQASPGTELGSAIGCNPDWDWTYFAHQLmERQWCYDIDYSNFDSTHGT 248

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1941 VWFQALKKVL---ENlSFQ---SDLIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKNIDLD 2014
Cdd:cd23227    249 GMFELLIDCFftpEN-GFSpavAPYLRSLAFSKHAWMDKRYKIEGGLPSGCSATSVLNTVMNNIIIRALLSLTYKNFHPE 327

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2015 KLKIIAYGDDVIFSYKYTLD---MEAIANEGKKYGLTItpADKSTEFRKLD-YNNVTFLKRGFKQDERHTFLIHPTFPVE 2090
Cdd:cd23227    328 DVLVLAYGDDLLVASDYQLDfnrVREKAAEHTLYKLTT--ANKAPDFPETStLLDCQFLKRKFVLHSTRNFIWRPVMDVT 405

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2099547062 2091 EIyESIRWTKKPSQMQEHVLSLCHLMWHNGRKVYEDFSRKIRSVSagraLYIPPYDLLKHEWYEKF 2156
Cdd:cd23227    406 NL-KTMLSFYKPNTLSEKLLSVAQLAFHSGYTVYEELFAPFKELQ----MTVPSWWYLEHEWEHNF 466

Dicipivirus_RdRp

cd23222

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

1722-2152

6.42e-82

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: 278.01 E-value: 6.42e-82

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1722 QPSVFYDVFPGSKEPAVLTDNDPRL--EVDFKEALFSKYKGNVEC---NLNEHMEVAIAHYSAQLATldiDPKPIAL-ED 1795
Cdd:cd23222      1 KPSPVYGVYPVTKEPAPLKPTDRRIdeGVDFNEPVFGKYGADMKEpfrNLDVGRDVVIARLKKVLPN---KKFAPCTvSE 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1796 GVFGIEGLEALDLNTSAGFPYVTMGIKKRDLINNKTK-----------DISRLKDALDKYgvdlPMITFLKDELRKKEKI 1864
Cdd:cd23222     78 ALNGKDGLPKLDLKQASGYPYNLSAIKRKHLIESDKDgfltatpkllaDIEESKKHPEKF----PYTSFLKDELRSVKKV 153

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1865 SAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPEVFWSKI-PVMLDGDCIMAFDYTNYDGSIHPVWF 1943
Cdd:cd23222    154 KAGKTRVVEAGSLPVIVEGRMIFGNLFAYFNTHPGFETMAAVGCDPEVCWTDWyYKMREKAHTWDYDYTGFDGSIPSCSF 233

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1944 QALKKVL----ENLSFQSDLIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKNIDLDKLKII 2019
Cdd:cd23222    234 DALADLLcefvENEDDVRRYISNIKNSYHAYDGNLYLIEGAMPSGCAGTSVFNCLINAMLCFSCFMDLEPEMDPFEPLLI 313

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2020 AYGDDVIFSYKYTLDMEAIANEGKK-YGLTITPADKSTEFR-KLDYNNVTFLKRGFKQDERHTfLIHPTFPVEEIYESIR 2097
Cdd:cd23222    314 AYGDDILVSSDHDLFPSRVSEWMKAnTTFKITPADKGEIFNdDSDVSDVRFLKRLFVEDPVCE-LIHPVIETETLEPSLN 392

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2099547062 2098 WTKKpSQMQEHVLSLCHLMWHNGRKVYEDFSRKIRSVSAGRALYIP---PYDLLKHEW 2152
Cdd:cd23222    393 WCHE-GEFETKVDAISMLAFHHGPEYYRDWCKKLTDICEERNISPPglkPYSVHRNRW 449

Cardiovirus_RdRp

cd23211

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

1711-2156

5.31e-81

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: 275.57 E-value: 5.31e-81

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1711 PSIHTPSKTKLQPSVFYDVFPGSKEPAVLTDNDPRLEVDFKEALFSKYKGNVEcNLNEHMEVAIAHYSAQL-ATLDIDPK 1789
Cdd:cd23211     10 PVVHVPRKTKLRRTVAHPVFQPKFEPAVLSKYDPRTDKDVDEVAFSKHTTNQE-SLPPVFRMVAKEYANRVfTLLGKDNG 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1790 PIALEDGVFGIEGLEALDLNTSAGFPYVTMGIKKRDLINNKTKD-ISRLKDALDKYGV----DLPMITFLKDELRKKEKI 1864
Cdd:cd23211     89 RLTVEQAVLGLEGMDPMEKDTSPGLPYTQQGLRRTDVVDFETATmIPFLAEAHRKMVEgdysDVVYQSFLKDEIRPIEKV 168

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1865 SAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPEVFWSKIPVMLDG-DCIMAFDYTNYDGSIHPVWF 1943
Cdd:cd23211    169 QAAKTRIVDVPPFEHCILGRQLLGRFASKFQTNPGLELGSAIGCDPDVDWTAFAVALSGfKYVYDVDYSNFDSTHSTAMF 248

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1944 QALkkvLENLSFQSDLIDR--------LCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKNIDLDK 2015
Cdd:cd23211    249 ELL---IENFFTEENGFDPrigeylrsLAVSRHAYEERRVLIRGGLPSGCAATSMLNTIMNNIIIRAGLYLTYKNFEFDD 325

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2016 LKIIAYGDDVIFSYKYTLDMEAIANEGKKYGLTITPADKSTEFRKLDY-NNVTFLKRGFKQDErhTFLIHPTFPvEEIYE 2094
Cdd:cd23211    326 IKVLSYGDDLLVATNYQIDFNLVKARLAKFGYKITPANKTSTFPLTSTlEDVVFLKRKFVKEN--SYLYRPVMD-RENLK 402

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2099547062 2095 SIRWTKKPSQMQEHVLSLCHLMWHNGRKVYEDFSRKIRSVsagrALYIPPYDLLKHEWYEKF 2156
Cdd:cd23211    403 AMLSYYRPGTLKEKLTSIALLAVHSGKQVYDEIFAPFREV----GIVVPTYESVLYRWLSLF 460

Megrivirus_RdRp

cd23223

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

1727-2131

4.22e-77

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: 263.24 E-value: 4.22e-77

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1727 YDVFPGSKEPAVLTDNDPRLE--VDFKEALFSKYKGNVEC--NLNEHMEVAIAHYSAQLATLDIDPKPI-ALEDGVFGIE 1801
Cdd:cd23223      2 YGAFPVTHGPAALTNKDKRLEegVDLDDVMFSKHVPDHPGwpTLEPAMSYVVEDLMHKLGFSKDEPVPMwTLEQAINGEG 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1802 GLEALDLNTSAGFPYVTMGIKKR---DLINNKTKDISRLKDALD---KYGVDLPMITFLKDELRKKEKISAGKTRVIEAS 1875
Cdd:cd23223     82 VMDGIDMGQSPGYPYNAQGRSRRsffEWNGEKWQPTEELKKEVDhalKDPDDFYFSTFLKDELRPLEKVKAGKTRLVDGD 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1876 SINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPEVFWSKIPVMLDGDC---IMAFDYTNYDGSIHPVWFQALKKVLEN 1952
Cdd:cd23223    162 SLPRILAMRMVFGPLFEAMLRKNGPEIHSAVGCNPDTDWTRYYHEMGPDSfpyCFDLDYSCFDSTEPKIAFRLMAKYLKP 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1953 LsFQSDL---IDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAykNIDLDKLKIIAYGDDVIFSY 2029
Cdd:cd23223    242 Y-FSVDVtpfFEALATSKHVYGDKAYEMEGGMPSGCVGTSMFNCINNSAFIVSALIAL--KISPEDCAWICYGDDVIIST 318

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2030 KYTLDMEAIAN-EGKKYGLTITPADKSTEFRKLD-YNNVTFLKRGFKQDERHTFLIHPTFPVEEIYESIRW-TKKPsqMQ 2106
Cdd:cd23223    319 DEKALSKRIADfYHKNTNLVVTPASKSGDFPETStIYDVTFLKRFFQPDSHYPHLIHPYMPLEHLEQSVMWqTDGP--FQ 396

                          410       420
                   ....*....|....*....|....*
gi 2099547062 2107 EHVLSLCHLMWHNGRKVYEDFSRKI 2131
Cdd:cd23223    397 QKLDSLCLLAFHAGGPDYREFVDAI 421

Pico_P2A

pfam00947

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

872-997

5.57e-75

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

Pssm-ID: 395757 Cd Length: 127 Bit Score: 244.98 E-value: 5.57e-75

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  872 NLHLFN-SEMHDSILVSYSSDLIIYRTNTIGDDYIPSCNCTEATYYCKHKNRYYPIKVTPHDWYEIQESEYYPKHIQYNL 950
Cdd:pfam00947    1 NRHLAThEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 2099547062  951 LIGEGPCEPGDCGGKLLCRHGVIGIITAGGEGHVAFTDLRQFQCAEE 997
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVRDLLWLEE 127

Aphthovirus_RdRp

cd23210

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

1713-2155

6.46e-72

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: 249.09 E-value: 6.46e-72

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1713 IHTPSKTKLQPSVFYDVFPGSKEPAVLTDNDPRLE--VDFKEALFSKYKGNVECNLNEH--MEVAIAHYSAQL-ATLDID 1787
Cdd:cd23210      6 VHVMRKTKLAPTVAHGVFNPEFGPAALSNKDPRLNegVVLDEVIFSKHKGDTKMSAEDKalFRRCAADYASRLhSVLGTA 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1788 PKPIALEDGVFGIEGLEALDLNTSAGFPYVTMGIKKRDLI---NNKTKDISRL-KDALDKYGVDLPMITFLKDELRKKEK 1863
Cdd:cd23210     86 NAPLSIYEAIKGVDGLDAMEPDTAPGLPWALQGKRRGALIdfeNGTVGPEVEAaLKLMEKREYKFACQTFLKDEIRPMEK 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1864 ISAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPEVFWSKIPVMLDG-DCIMAFDYTNYDGSiHPVw 1942
Cdd:cd23210    166 VRAGKTRIVDVLPVEHILYTRMMIGRFCAQMHSNNGPQIGSAVGCNPDVDWQRFGTHFAQyRNVWDVDYSAFDAN-HCS- 243

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1943 fQALKKVLENLsFQSD---------LIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKNIDL 2013
Cdd:cd23210    244 -DAMNIMFEEV-FRTEfgfhpnaewILKTLVNTEHAYENKRITVEGGMPSGCSATSIINTILNNIYVLYALRRHYEGVEL 321

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2014 DKLKIIAYGDDVIFSYKYTLDMEAIANEGKKYGLTITPADKSTEFRKLDY--NNVTFLKRGFKQDERHTFLiHPTFPVEE 2091
Cdd:cd23210    322 DTYTMISYGDDIVVASDYDLDFEALKPHFKSLGQTITPADKSDKGFVLGHsiTDVTFLKRHFHMDYGTGFY-KPVMASKT 400

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2099547062 2092 IyESIRWTKKPSQMQEHVLSLCHLMWHNG----RKVYEDFsrkirsvsAGrALYIPPYDLLKHEWYEK 2155
Cdd:cd23210    401 L-EAILSFARRGTIQEKLISVAGLAVHSGpdeyRRLFEPF--------QG-LFEIPSYRSLYLRWVNA 458

ps-ssRNAv-Picornavirales

cd23169

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

1851-2132

3.73e-70

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This family contains the catalytic core domain of RdRp of Picornavirales, an order of (+)ssRNA viruses. The order Picornavirales comprises viruses that historically are referred to as picorna-like viruses and which are classified into eight virus families: Caliciviridae, Dicistroviridae, Iflaviridae, Marnaviridae, Picornaviridae, Polycipiviridae, Secoviridae, and Solinviviridae. All known genomes of Picornavirales members encode proteins with helicase, 3C-like protease, and RdRp domains, as well as capsid proteins with related structures, although the genome organizations can differ among viruses. The picornavirus genome is replicated via a negative-sense (-) RNA intermediate by the viral RdRp, named 3Dpol, which uses VPg (the product of 3B) as a primer to initiate the replication process. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438019 Cd Length: 309 Bit Score: 238.65 E-value: 3.73e-70

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1851 ITFLKDELRKKEKISAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPGvVTGSAVGCDPE-VFWSKIPVML--DGDCIM 1927
Cdd:cd23169      4 VDCLKDELRPIEKVKAGKTRLFSASPLDYTIAFRKYFGDFIAAFQKNRI-KLEHAVGINPDsVEWTRLYRRLlkKGPNIF 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1928 AFDYTNYDGSIHPVWFQALKKVLENLSFQSD----------LIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINN 1997
Cdd:cd23169     83 AGDYSNFDGSLPPDVMEAAFDIINDWYDEYVddedervrkvLFEELINTIHLVGNLVYQVHGGNPSGNPLTTIINSIVNL 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1998 IIIRTLVLDAYKNIDLDK----LKIIAYGDDVIFS----YKYTLDMEAIANEGKKYGLTITPADKS---TEFRKLDynNV 2066
Cdd:cd23169    163 LYIRYAWLRITGLTSLSDfkknVRLVTYGDDVIISvsdeVKDEFNFVTISEFLKELGITYTDADKSgdiVPYRPLE--EV 240

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2067 TFLKRGFKQDErHTFLIHPTFPVEEIYESIRWTKKPSQMQE---HVLSLCHLMWH-NGRKVYEDFSRKIR 2132
Cdd:cd23169    241 TFLKRGFRPHP-TPGLVLAPLDLESIEEQLNWTRKEDDLLEatiENARAALLLAFgHGPEYYNKFRQKLN 309

Rosavirus_RdRp

cd23221

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

1799-2156

1.10e-69

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: 240.21 E-value: 1.10e-69

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1799 GIEGLEALDLNTSAGFPYVTMGIKKR---DLINNKTKDISRLKDALDKYGVDLPM---ITFLKDELRKKEKISAGKTRVI 1872
Cdd:cd23221      4 GIDNMDGLDMNQSPGVPYVSEGVSRRslfDCVDGQWVPRERLASDIAQVSGDPSLghfATFLKDELRSTEKVAAGKTRVV 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1873 EASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPEVFWSKIPVMLDGDC-IMAFDYTNYDGSIHPVWFQALKKVLE 1951
Cdd:cd23221     84 EAGSLPHIIVGRKIFGNLFALFNSNPGFQTMCAVGCDPDVTWTELYHPLSAKTyVFDYDYSGFDGSVPSCCFDALADLLA 163

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1952 NL-SFQSDL---IDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKNIDLDKLKIIAYGDDVIF 2027
Cdd:cd23221    164 DFvEGEEDVrkyISSLKTSFHHYKGKLWRLDGAMPSGCCGTSVFNSLINAMLLFSAFSQICPDFRASEPLLVAYGDDVLV 243

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2028 SYKYTLDMEAIAN-EGKKYGLTITPADKSTEFR-KLDYNNVTFLKRGFKQDERHTFLIHPTFPVEEIYESIRWtKKPSQM 2105
Cdd:cd23221    244 GTDQPLFPSKVAEwVNSHTTFRITPADKGSVFNdESDIHSVQFLKRHFTPDPDFPALIHPTIDPDTYEQSVMW-QRTGDF 322

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2099547062 2106 QEHVLSLCHLMWHNGRKVYEDFSRKI--RSVSAGRAL-YIPPYDLLKHEWYEKF 2156
Cdd:cd23221    323 QETVNSLALLVFHRGPKSYSRWCESVtrKCVDGGYPPpFFPPFSLLRHQWLKKF 376

Kobuvirus_RdRp

cd23214

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

1711-2152

9.94e-68

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: 237.05 E-value: 9.94e-68

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1711 PSIHTPSKTKLQPSVFYDVFPGSKEPAVLTDNDPRLE--VDFKEALFSKY-KGNVECNLnEHMEVAIAHYSAQLATLdid 1787
Cdd:cd23214      1 PGVNVNRKSRLGPSPAYGAFPVKKQPAPLTQKDDRLEdgIRLDDQLFLKHnKGDMDEPW-PGLEAAADLYFSKFPTM--- 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1788 PKPIALEDGVFGIEGLEALDLNTSAGFPYVTMGIKKRDLINNKTKDI----SRLKDALDKYGVDLPMI--TFLKDELRKK 1861
Cdd:cd23214     77 IRTLTQEEAINGTPNLEGLDMNQAAGYPWNTMGRSRRSLFVEVQPGIyvpkPELQAEIDKTLEDPDYFysTFLKDELRPT 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1862 EKISAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVvTGSAVGCDPEVFWSKIPVML-DGDCIMAFDYTNYDGSIHP 1940
Cdd:cd23214    157 AKVTLGLTRVVEAAPIHAIVAGRMLLGGLIEYMQARPGK-HGSAVGCNPDLHWTKFFYKFcHYPQVFDLDYKCFDATLPS 235

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1941 VWFQALKKVLENLSFQ---SDLIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTlVLDAYKNIDLDKLK 2017
Cdd:cd23214    236 CAFRIVEDHLERLTGDervTRYIESIRHSHHVYGNETYEMIGGNPSGCVGTSIINTIINNICVLS-ALIQHPDFSPESFR 314

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2018 IIAYGDDVIFSYKYTLDMEAIANEGKKYG-LTITPADKSTEFRKLD-YNNVTFLKRGFKQDERHTFLIHPTFPVEEIYES 2095
Cdd:cd23214    315 ILAYGDDVIYGCDPPIHPSFIKEFYDKHTpLVVTPANKGSDFPETStIYDVTFLKRWFVPDDIRPFYIHPVMDPDTYEQS 394

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2096 IRWTKKpSQMQEHVLSLCHLMWHNGRKVYEDFSRKIRSVSAGRALYIP---PYDLLKHEW 2152
Cdd:cd23214    395 VMWLRD-GDFQDLVTSLCYLAFHSGPKTYDRWCTRVRDQVMKTTGFPPtflPYSYLQTRW 453

Mosavirus_RdRp

cd23225

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

1804-2155

1.35e-67

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: 234.04 E-value: 1.35e-67

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1804 EALDLNTSAGFPYVTMGIKKRDLINNKTKD-------ISRLKDALDKY--GVDLP-MITFLKDELRKKEKISAGKTRVIE 1873
Cdd:cd23225     10 DAMDMTKAVGYPYCLDSIKRLDLVEIKETEngkvylpTERLVEETEKFftGEEKPkFVTFLKDEVRSNEKIKQGKTRIVD 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1874 ASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPEVFWSKIPVMLDGDCIMAFDYTNYDgSIHP-VWFQALKK--VL 1950
Cdd:cd23225     90 ASPFPYAIAGRMVMQNFMSNMMRCNGTEVGSAVGCDPDTEWTRYFFELCDRYVFDLDYKAFD-STHPtAMFNLLAErfFT 168

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1951 ENLSFQSD----LIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYK--NIDLDKLKIIAYGDD 2024
Cdd:cd23225    169 ERNGFDQQavriFLNGLSDSDHVYEGKHFRIRGGLPSGCPCTSILNTVINNIIVRAAILGAYQidTVDFQKFRMLAYGDD 248

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2025 VIFSYKYTL---DMEAIANEGKKYglTITPADKSTEF-RKLDYNNVTFLKRGFKQDERHTFLIHPTFPVEEIYESIRWTk 2100
Cdd:cd23225    249 VVYATPQPIkpqDLADWLHANTNY--KVTPASKAGTFpEESTIWDVTFLKRSFKPDEDHGHLIRPVMAVGNLKQMLSFM- 325

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2099547062 2101 KPSQMQEHVLSLCHLMWHNGRKVYEDFSRKIRSVSAGRAlyIPPYDLLKHEWYEK 2155
Cdd:cd23225    326 RPGTFPDKVRSVAGLAVHCGEEDYNQLADAVALYVPGVS--MPAYKYMKACWYAK 378

Teschovirus_RdRp

cd23212

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

1789-2125

2.00e-64

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

Pssm-ID: 438062 Cd Length: 354 Bit Score: 223.73 E-value: 2.00e-64

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1789 KPIALEDGVFGIEGLEALDLNTSAGFPYVTMGIKKRDLINNKTKDISRLKDALDKYgVDLP-----MITFLKDELRKKEK 1863
Cdd:cd23212      9 EPLSVREAVEGIDGLDPMDMDKSPGLPYVKKGLRRTDLWNPKTGPSIELMAEINRY-LDYNydkhvFLTFLKDELRPKEK 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1864 ISAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPEVFWSKIPVMLDGDCIMAFDYTNYDGSIHPVWF 1943
Cdd:cd23212     88 VQAGKTRVIDVAGFGHAIVGRMLFGRLFAFFHKNPGWNTGSAVGVNPDLAWTQIFYTAPSRNVLAMDYSGFDASHTSGMF 167

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1944 QALKKVLENLSF---QSDLIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKnidlDKLKIIA 2020
Cdd:cd23212    168 CILKHFLTTLGYgtlQLSYIDSLCYSKHHWDDETYRLDGGLPSGCSGTTIFNTIMNNIVARAAASYAAE----GPVGILC 243

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2021 YGDDVIFSYKYTLDMEAIANEGKKYGLTITPADKSTEFRKLDYNNVTFLKRGFKQDERhtfLIHPTFPVEEIYESIRWTk 2100
Cdd:cd23212    244 YGDDILVSSPEKFPVSDWLEFYSKTPYKVTAADKSEQIDWRDITQCTFLKRGFVLDGS---LVRPVMEEQHLAELLKWA- 319

                          330       340
                   ....*....|....*....|....*
gi 2099547062 2101 KPSQMQEHVLSLCHLMWHNGRKVYE 2125
Cdd:cd23212    320 RPGTLQAKLLSIAQLAFHLPRQAYD 344

Rhv

pfam00073

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

93-300

5.58e-64

Pssm-ID: 395026 Cd Length: 170 Bit Score: 215.25 E-value: 5.58e-64

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062   93 TSQDVANAVVGYGVWPHYLTPQDATAIDKPTQPDTSSNRFYTLESKHWDGNSKGW-WWKLPDALKDMGIFGENMYYHFLG 171
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFfWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  172 RSGYTVHVQCNASKFHQGTLLVAMIPEHQlasakngkvtagynlTHPGDAgrvvgqqrdtnlrqpsddswlnfdgTLLGN 251
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPPGA---------------PPPGSR-------------------------DYLWQ 120

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 2099547062  252 LLIFPHQFINLRSNNSATLIVPYVNAVPMDSMLRHNNWSLVIIPISPLR 300
Cdd:pfam00073  121 ATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGNWTLVVAGWVPLN 169

RNA_dep_RNAP

cd01699

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

1837-2099

1.02e-60

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: 210.22 E-value: 1.02e-60

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1837 LKDALDKYGV------DLPMITFLKDELRKKEKISAGKTRVIEASSINDTILFRTTFGNLFSKFHLNpGVVTGSAVGCDP 1910
Cdd:cd01699      1 LEKAVESLEDlplirpDLVFTTFLKDELRPLEKVEAGKTRLIQPRPLDYNIALRMYLGPFEAKLMKN-RGGLPIAVGINP 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1911 EVF-WSKIPVMLD--GDCIMAFDYTNYDGSIHPVWFQALKKVLENLS------FQSDLIDRLCYS-KHLFKSTYYEVAGG 1980
Cdd:cd01699     80 YSRdWTILANKLRsfSPVAIALDYSRFDSSLSPQLLEAEHSIYNALYddddelERRNLLRSLTNNsLHIGFNEVYKVRGG 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1981 VPSGCSGTSIFNTMINNIIIRTLVLDAYKNIDLDKLKIIAYGDDVIFSYK---YTLDMEAIANEGKKYGLTITPADKS-T 2056
Cdd:cd01699    160 RPSGDPLTSIGNSIINCILVRYAFRKLGGKSFFKNVRLLNYGDDCLLSVEkadDKFNLETLAEWLKEYGLTMTDEDKVeS 239

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|...
gi 2099547062 2057 EFRKLdyNNVTFLKRGFKQDErhTFLIHPTFPVEEIYESIRWT 2099
Cdd:cd01699    240 PFRPL--EEVEFLKRRFVLDE--GGGWRAPLDPSSILSKLSWS 278

Fipivirus_RdRp

cd23229

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

1797-2152

3.16e-56

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: 201.57 E-value: 3.16e-56

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1797 VFGIEGLEALDLNTSAGFPYVTMGIKKRDLIN---NKTKDISRLKDALDKYGVDLPM-----------ITFLKDELRKKE 1862
Cdd:cd23229      2 VEGIPGMEGLDMKTSAGYPWCEQNQKKKDKIKllaGKNFLVRPLREVVHIVVDWYIMppdmpkpeikyVVYLKDELLSSD 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1863 KISAGKTRVIEASSINDTILFRTTFGNLFSKFHL-NP--GVVTGSAVGCDPEVFWSKIPVMLDGDCIMAFDYTNYDGSIH 1939
Cdd:cd23229     82 KVKMGRTRWICAAPVQLVCAWKKVFGRAIAAIHLeSVtdGKSTGCAVGMDPETAWTDIALARPGWPVIALDYSNFDGSLQ 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1940 PVWFQALKKVLENLSFQSDLI-DRLC----YSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINnIIIRTLVLDAYKNIDL- 2013
Cdd:cd23229    162 SFVITGAVRILGYIAGLPDGQsYRLAefvyDVKQIVGKYLYTTVGPLPSGCPSTSIIGSLCN-VLMLLYTLSHATGQRYs 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2014 ---DKLKIIAYGDDVIF----SYKYTLDMEAIANEgKKYGLTITPA-DKSTEFRKLDYNNVTFLKRGFKQDERHTFLIHP 2085
Cdd:cd23229    241 afrDWMHVVTYGDDVLVfvhpEVVVVLDTLAHEMY-LVFGVTATDAtDKRAPPQLRELSNVTFLKRGFRQCSSVPFLVHP 319

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2099547062 2086 TFPVEEIYESIRWTKKPSQMQEHVLSLCHLMWHNGRKVYEDFSRKIRS------VSAGRALY--IPPYDLLKHEW 2152
Cdd:cd23229    320 TMDKSTIYQMLAWKRKGTTLAENVKCAAEFMMHHGEEEYEDFVGVVKEcstligVDQRSKVYeeLCSYAELHDHW 394

Peptidase_C3

pfam00548

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

1514-1679

8.53e-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: 191.89 E-value: 8.53e-56

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1514 GPEEEFGRSILKNNTCVITTDNGKFTGL--GIYDRILIVPTHADPGKEVQVNGIQTKVLD-SYDLYNRDGIKLEITVIKL 1590
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1591 DRNEKFRDIRKYIPETEDDYPECNLALSANQTEPTIIKVGDVVSYGNI-LLSGNQTARMLKYNYPTKSGYCGGVLYKI-- 1667
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVVIAKve 160

                          170
                   ....*....|....
gi 2099547062 1668 --GQILGIHVGGNG 1679
Cdd:pfam00548  161 gnGKILGMHIAGNG 174

RdRP_1

pfam00680

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

1723-2133

1.49e-52

Pssm-ID: 425815 Cd Length: 450 Bit Score: 192.63 E-value: 1.49e-52

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1723 PSVFYDVFPGSKEPAVLTDNDPR-------LEVDFKEALFSKYK---GNVECNLNEHMEVAIAHYSAQLATLDidPKPIA 1792
Cdd:pfam00680    2 PTERHLVAIPAYVPASLGPEDPRwarsylnTDPYVDDIKKYSRPklpGPADERDKLLNRSAAKMVLSELRGVP--KKANS 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1793 LEDGVFGI---EGLEALDLNTSAGFPYVTMGIKKRDLIN----NKTKDI--SRLKDALDKY--GVDLPMI--TFLKDELR 1859
Cdd:pfam00680   80 TLIVYRAIdgvEQIDPLNWDTSAGYPYVGLGGKKGDLIEhlkdGTEARElaERLAADWEVLqnGTPLKLVyqTCLKDELR 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1860 KKEKISAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTgSAVGCDPevFWSKIPVMLD-----GDCIMAFDYTNY 1934
Cdd:pfam00680  160 PLEKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHP-IQVGINP--FDRGWPRLLRrlarfGDYVYELDYSGF 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1935 DGSIHPVWFQALKKVLENLSFQSD-------LIDRLCYSKH-LFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLD 2006
Cdd:pfam00680  237 DSSVPPWLIRFAFEILRELLGFPSnvkewraILELLIYTPIaLPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYALLK 316

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2007 AYKNIDL------DKLKIIAYGDDVIFSYKYTLD--MEAIANEGKKYGLTITPADKSTEFRKlDYNNVTFLKRGFKQDEr 2078
Cdd:pfam00680  317 SLENDGPrvcnldKYFDFFTYGDDSLVAVSPDFDpvLDRLSPHLKELGLTITPAKKTFPVSR-ELEEVSFLKRTFRKTP- 394

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2099547062 2079 htFLIHPTFPVEEIYESIRWTKKPSQMQEHVLSLCHLMWHNGRKVYEDFSRKIRS 2133
Cdd:pfam00680  395 --GGYRPPLDRKRILAQLEYIRSKPVPSGQLENIRAYASHHGYEFYRDLLYRFVE 447

Rhv

pfam00073

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

360-524

8.26e-51

Pssm-ID: 395026 Cd Length: 170 Bit Score: 177.50 E-value: 8.26e-51

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  360 YHPTKEISIPGEVKNLIEMCQVDTLIPVNNVGTNVGNISMYTVQLG-QMEVAQEVFAIKVDItsQPLATTLLGEIASYYT 438
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTdWTSLSKGFFWWKLPL--ALLSMGLLGRLLRYHT 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  439 HWTGSLRFSFMFCGTANTTLKLLLAYTPPGIDKPATR---KDAMLGTHVVWDVGLQSTISLVVPWVSASHFRLTANDK-- 513
Cdd:pfam00073   79 YYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRdylWQATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGnw 158

                          170
                   ....*....|..
gi 2099547062  514 -YSMAGYITCWY 524
Cdd:pfam00073  159 tLVVAGWVPLNY 170

Rhv

pfam00073

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

616-768

2.03e-49

Pssm-ID: 395026 Cd Length: 170 Bit Score: 173.65 E-value: 2.03e-49

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  616 PEDAIETRYVITSQTRDEMSIESFLGRSGCVH-----ISRIKVDYNDYNGQNKNFTQWKITL--QEMAQIRRKFELFTYV 688
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQpdvqgERFYTLDSTDWTSLSKGFFWWKLPLalLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  689 RFDSEVTLVPCiagrGDDIGHVVMQYMYVPPGAPIPKTRdDFSWQSGTNMSIFWQHG-QPFPRFSLPFLSIASAYYMFYD 767
Cdd:pfam00073   81 RGGLEVTVQFN----GSKFHQGKLLVAYVPPGAPPPGSR-DYLWQATLNPHQFWNLGlNSSARLSVPYISIAHYYSTFYD 155


                   .
gi 2099547062  768 G 768
Cdd:pfam00073  156 G 156

Passerivirus_RdRp

cd23224

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

1795-2154

8.54e-49

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Passerivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Passerivirus genus within the family Picornaviridae, order Picornavirales. The Passerivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. There are two species in this genus: Passerivirus A and a second, novel passerivirus (Passerivirus B) that was discovered in 2018 in a population of Hungarian home-reared finches, where it achieved an over 50 percent mortality rate. Birds serve as natural hosts. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438074 Cd Length: 380 Bit Score: 179.51 E-value: 8.54e-49

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1795 DGVFGIEGLEALDLNTSAGFPYvTMGIKKRDLINN----KTKDISRLKDALDK--YGVDLPMITFLKDELRKKEKISAGK 1868
Cdd:cd23224      1 EAINGTPLLDGLDMKQSPGYPW-SLTTNRRSLFTQdetgKYYPVPELEEAVLAclENPDYFYTTHLKDELRPVEKALAGK 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1869 TRVIEASSINDTILFRTTFGNLFSKFHLNPGVVtGSAVGCDPEVFWSKIPVMLDGDC-IMAFDYTNYDGSIHPVWFQALK 1947
Cdd:cd23224     80 TRLIEAAPIHAIIAGRMLLGGLFEYMHARPGEH-GSAVGCDPDYHWTPFFHSFDEFSqVWALDYSCFDSTLPSCCFDLIA 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1948 KVLENL-----SFQSDLIDR----LCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLdAYKNIDLDKLKI 2018
Cdd:cd23224    159 QKLAKIitpgeGIAPDAIVKyirsISISKHVFGNEAYLMVGGNPSGCVGTSILNSMINNCVLISAFL-TQKDFNPNQMRI 237

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2019 IAYGDDVIFSYKYTLDMEAIAN-EGKKYGLTITPADKSTEFRklDYN---NVTFLKRGFKQDERHTFLIHPTFPVEEIYE 2094
Cdd:cd23224    238 LTYGDDVLYATNPPIHPRVVKKfFDENTTLIVTPATKAGDFP--DEStiwDVTFLKRYFVPDEIRPWYVHPVIEPATYEQ 315

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2099547062 2095 SIRWTKKpSQMQEHVLSLCHLMWHNGRKVYEDFSRKIRSVSAGRALY--IPPYDLLKHEWYE 2154
Cdd:cd23224    316 SVMWTRG-GDFQDVVTSLSFLAHHAGPTNYMIWEEKVRKAAAAKGVSlnILPYSYLQHRWML 376

Hepatovirus_RdRp

cd23215

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

1747-2153

4.41e-48

RNA-dependent RNA polymerase (RdRp) in the genus Hepatovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Hepatovirus genus within the family Picornaviridae, order Picornavirales. Hepatoviruses are 27- to 32-nm, nonenveloped, icosahedral viruses with a (+)ssRNA linear genome of approximately 7.5-kb. The Hepatovirus genus has nine species, Hepatovirus A-I, of which Hepatovirus A is responsible for a self-limiting viral hepatitis in human beings and may be transmitted by the fecal-oral route during acute infection or by the ingestion of uncooked contaminated shellfish. RdRps are multi-domain proteins that play a pivotal role in enterovirus replication. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of hepatoviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438065 Cd Length: 464 Bit Score: 180.04 E-value: 4.41e-48

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1747 EVDFKEALFSKYKGNVECNLNEHMEVAIAHYSAQLATLDIDPKPIALEDGVFGIEGLEALDLNTSAGFPYVTMGIKKRDL 1826
Cdd:cd23215     21 EIDPMAVMLSKYSLPIVEEPVDYKDVVVFYQNKILGKDILYDEFFDLEQAITGVPGMDAINMDSSPGYPYVQEKLTKSDL 100

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1827 I----NNKTKDI-SRLKDALD------KYGVDLPMI--TFLKDELRKKEKISAGKTRVIEASSINDTILFRTTFGNLFSK 1893
Cdd:cd23215    101 IwlddNGELLGMhPRLAQRILfnltmmDNGNDLDVVytTCPKDELRPLEKVLESKTRAIDACPLDFTIICRMFWGPAISY 180

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1894 FHLNPGVVTGSAVGCDPEVFWSKI-PVMLD-GDCIMAFDYTNYDGSIHPVWFQALKKVLENLS-----FQSDLIDRLCYS 1966
Cdd:cd23215    181 FQLNPGFHTGVAVGIDPDRDWDALfKTMIRfGDYGIDLDFSSFDASLSPFMIREACRVLSELSgvpdhQGQALINTIIYS 260

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1967 KHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKNIDL---DKLKIIAYGDDVIFSYKYTLDME------- 2036
Cdd:cd23215    261 KHLLYNLCYHVCGSMPSGSPCTSLLNSIVNNVNLYYVFSKIFKKSPVffyDAVKFLCYGDDVLIVFSRDLEIKnldklgq 340

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2037 AIANEGKKYGLTITPADKStEFRKLDYNNVTFLKRGFKQDERHtflIHPTFPVEEIYESIRWTKKPSQMQEHVLSLCHLM 2116
Cdd:cd23215    341 RIQDEFKLLGMTATSADKG-EPQVVPVSELTFLKRSFNLIEDR---FRPAISEKTIWSLVAWQRSNAEFEQNLDTACWFA 416

                          410       420       430
                   ....*....|....*....|....*....|....*..
gi 2099547062 2117 WHNGRKVYEDFSRKIRSVSAGRALyipPYDLLKHEWY 2153
Cdd:cd23215    417 FMHGYDFYQNFYLQLQSCLEKEMI---DYRLKSYEWW 450

Pico_P2B

pfam01552

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

998-1094

2.21e-45

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

Pssm-ID: 279840 Cd Length: 101 Bit Score: 159.42 E-value: 2.21e-45

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  998 QGITDYIHMLGEAFGNGFV----DSVKEQINAINPINSISKKVIKWLLRIISAMVIIIRNSSDPQTIIATLTLIGCNGSP 1073
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTqqisDKIKELTNFINPTSKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|.
gi 2099547062 1074 WRFLKEKFCKWTQLTYIHKES 1094
Cdd:pfam01552   81 WQFLKEKACAVLEIPYVHKQG 101

Dicistroviridae_RdRp

cd23194

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

1853-2132

3.28e-43

RNA-dependent RNA polymerase (RdRp) in the family Dicistroviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the RdRp of RNA viruses belonging to the family Dicistroviridae, order Picornavirales. Dicistroviridae is a family of small non-enveloped viruses with a (+)ssRNA genome of approximately 8-10 kilobases. The family contains 3 genera: Aparavirus, Cripavirus, and Triatovirus. All members infect arthropod hosts with some having devastating economic consequences, such as acute bee paralysis virus, Kashmir bee virus, and Israeli acute paralysis virus in domesticated honeybees, and taura syndrome virus and mud crab virus in the seafood industry. On the contrary, host specificity and other desirable traits make several members of this group amenable to development as biopesticides for insect control, such as Solenopsis invicta virus 1 against fire ants, and triatoma virus against triatomine bugs that vector Chagas disease. Members in the family Dicistroviridae have similarity to viruses in the Picornavirales members (Iflaviridae, Picornaviridae, Marnaviridae and Secoviridae). The genomes of viruses of these taxa encode proteins with helicase, 3C-like protease, and RdRp domains, as well as capsid proteins with related structures, although the genome organizations can differ among viruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438044 [Multi-domain] Cd Length: 315 Bit Score: 161.13 E-value: 3.28e-43

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1853 FLKDELRKKEKISAGKTRVIEASSINDTILFRTTFGNLFSkfHLNPG-VVTGSAVGCDP---EvfWSKIPVML--DGDCI 1926
Cdd:cd23194     11 TLKDERRPIEKVDAGKTRVFSAGPMDYTIAFRMYFLGFVA--HLMRNrIDNEIAVGTNVyslD--WDKLARKLlsKGDKV 86

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1927 MAFDYTNYDGSIHPvwfQALKKVLE------NLSFQSDLIDR-----LCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMI 1995
Cdd:cd23194     87 IAGDFSNFDGSLNP---QILWAILDiinewyDDGEENALIRRvlwedIVNSVHICGGYVYQWTHSQPSGNPLTAIINSIY 163

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1996 NNIIIRTLVLDAYKNIDLDKLK-------IIAYGDDVIFS----YKYTLDMEAIANEGKKYGLTITPADKSTE---FRKL 2061
Cdd:cd23194    164 NSIIMRYVYLLLTKEAGLMTMSdfnkhvsMVSYGDDNVINvsdeVSEWFNQLTITEAMAEIGMTYTDETKTGEivpYRSL 243

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2062 DynNVTFLKRGFKQDERHTFLIHPtFPVEEIYESIRWTKKPSQMQE----------HVLSLcHlmwhnGRKVYEDFSRKI 2131
Cdd:cd23194    244 E--EVSFLKRGFRYDDDLGRWVAP-LDLDTILEMPNWVRKGKDPEEitkqnvenalRELSL-H-----GEEVFDKWAPKI 314


                   .
gi 2099547062 2132 R 2132
Cdd:cd23194    315 R 315

rhv_like

cd00205

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

375-558

3.55e-43

Pssm-ID: 119412 Cd Length: 178 Bit Score: 156.02 E-value: 3.55e-43

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  375 LIEMCQVDTLIPVNNVGTNVGNismytvqlgqmevaQEVFAIKVDITSQPL--ATTLLGEIASYYTHWTGSLRFSFMFCG 452
Cdd:cd00205      1 VESFADRPTTVGTNNWNSSASG--------------TQLFQWKLSPALGFLllQNTPLGALLSYFTYWRGDLEVTVQFNG 66

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  453 TANTTLKLLLAYTPPGIDKPA---TRKDAMLGTHVVWDVGLQSTISLVVPWVSASHFRLTANDKY---SMAGYITCWYQT 526
Cdd:cd00205     67 SKFHTGRLLVAYVPPGAPAPTtgdTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDGYgplNSFGTLVVRVLT 146

                          170       180       190
                   ....*....|....*....|....*....|..
gi 2099547062  527 NLVVPPNTPQTADMLCFVSAcKDFCLRMARDT 558
Cdd:cd00205    147 PLTVPSGAPTTVDITVYVRA-GDFELYGPRPP 177

Pico_P1A

pfam02226

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

2-69

2.05e-41

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

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2099547062    2 GAQVSRQNVGTHSTQNSVSNGSSLNYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 69
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 68

Parechovirus_RdRp

cd23217

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

1797-2150

4.73e-41

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

Pssm-ID: 438067 Cd Length: 371 Bit Score: 156.57 E-value: 4.73e-41

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1797 VFGIEGLEALDLNTSAGFPYVTMGIKKRDLINNKTKDISR--LKDALDKYGVDLP-------MITFLKDELRKKEKISAG 1867
Cdd:cd23217      2 VLGTSHLNSLDLSTSPGYKYVKSGYKKRDLLSLEPFSVSPqlEKDVKDKLHAVYKgnqpttiFNACLKDELRKLDKIAQG 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1868 KTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPEVFWS-KIPVMLDGDciMAFDYTNYDGSIHPVWFQAL 1946
Cdd:cd23217     82 KTRCIEACSIDYVIAYRVVMSSLYEAIYQTPCQELGLAVGMNPWTDWDfMINALNPYN--YGLDYSSYDGSLSEMLMWEA 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1947 KKVLENLSFQSDLIDRL----CYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLvldAY-KNIDLDKLKIIaY 2021
Cdd:cd23217    160 VEVLAYCHESPDLVMQLhkpvINSDHVVMDERWLVHGGMPSGSPCTTVLNSICNLLVCIYL---AYlQSPGIECLPIV-Y 235

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2022 GDDVIFSYKYTLDMEAIANEGKK-YGLTITPADKSTEFRKLDYNNVTFLKRGFKQDERHTFLIHpTFPVEEIYESIRWTK 2100
Cdd:cd23217    236 GDDVIFSVSSEIDPEYLVSSAADsFGMEVTGSDKDEPPSLLPRMEVEFLKRTTGYFPGSTYKVG-ALDLETMEQHIMWMK 314

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2099547062 2101 K----PSQMQEHVLSLChlmwHNGRKVYEDFSRKIRSVSAGRALYIPPYDLLKH 2150
Cdd:cd23217    315 NlstfPQQLQSFENELC----LHGKDIYDDYKKIFNPYLKEWNITMDDYDVVIH 364

Crohivirus_RdRp

cd23232

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

1793-2146

4.60e-40

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Crohivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Crohivirus genus within the family Picornaviridae, order Picornavirales. The Crohivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. Crohivirus is a new genus containing two species, Crohivirus A and Crohivirus B. Crohivirus A (Crohivirus 1, CroV-1) is a novel picornavirus found the lesser red musk shrew (Crocidura hirta) which is found in southern Africa. The genome sequence is most closely related to the parechoviruses. Crohivirus B consists of a virus which has been found in the straw-colored fruit bat (Eidolon helvum). RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438082 Cd Length: 373 Bit Score: 153.72 E-value: 4.60e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1793 LEDGVFGIEGLEALDLNTSAGFPYVTMGIKKRDLIN-NK-------TKDISRLKDALDKYG-VDLPMITFLKDELRKKEK 1863
Cdd:cd23232      1 IEEACFEEGDEHALDLKTSPGFKYVQMGLKKTDLVNrPNkfihpilRNDVRLIFDEMAKGQmPVVTFTAHLKDELRKLEK 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1864 ISAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPEVFWSKIPVMLDgDCIMAFDYTNYDGSIHPVWF 1943
Cdd:cd23232     81 IRSGKTRCIEACDFDYTVAHKMMFGTLYKAIYDTPGIITGLAVGMNPWKDWELIQQSLF-KYNYDFDYKTFDGSLSRELM 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1944 QALKKVLENLSFQSDLIDRL----CYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKNidldKLKII 2019
Cdd:cd23232    160 LHAVDILSACVENDEMAKLMlsvvVESVHLVLDQKWNVSGGMPSGSPCTTVLNSVCNLIVSSTIADMCTEG----DFKIL 235

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2020 AYGDDVIFSYKYTLDMEAIANEGK-KYGLTITPADKSTEFRKLDYNNVTFLKRGFKQDERHTFLIHpTFPVEEIYESIRW 2098
Cdd:cd23232    236 VYGDDLIISSTAPLDCDRFKTLVElHYGMEVTPGDKGDEFKVKDREQVSFLKRVTRKFPGTNYRVG-ALDLDTVKQHLMW 314

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*...
gi 2099547062 2099 TKKPSQMQEHVLSLCHLMWHNGRKVYEDFSRKIRSVSAGRALYIPPYD 2146
Cdd:cd23232    315 CKSYSSFKQQLDSALMEVAMHGEETYNGFLTEIKTKLDKFKIYPPKFK 362

RNA_helicase

pfam00910

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

1213-1309

7.03e-40

RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in a variety of single stranded RNA viruses.

Pssm-ID: 459992 Cd Length: 102 Bit Score: 143.51 E-value: 7.03e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1213 VMIHGPPGTGKSITTNFLARMI-----TNESDVYSLPPDPKYFDGYDNQSVVIMDDIMQNPDGEDMTLFCQMVSSVTFIP 1287
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALlkklgLPKDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 2099547062 1288 PMADLPDKGKPFDSRFILCSTN 1309
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

rhv_like

cd00205

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

125-329

4.77e-38

Pssm-ID: 119412 Cd Length: 178 Bit Score: 141.38 E-value: 4.77e-38

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  125 PDTSSNRFYTLESKHW---DGNSKGWWWKLPDA----LKDMGIFGENMYYHFLGRSGYTVHVQCNASKFHQGTLLVAMIP 197
Cdd:cd00205      1 VESFADRPTTVGTNNWnssASGTQLFQWKLSPAlgflLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  198 EHQLASAKNgkvtagynlthpgdagrvvgqqrdtnlrqpsddswlnfdgTLLGNLLIFPHQFINLRSNNSATLIVPYVNA 277
Cdd:cd00205     81 PGAPAPTTG----------------------------------------DTRWQATLNPHVIWDLGTNSSVTFVVPYVSP 120

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2099547062  278 VPMDSMLRH------NNWSLVIIPISPLRSEATSSNIVPITVSISPMCAEFSGARAKN 329
Cdd:cd00205    121 TPYRSTRYDgygplnSFGTLVVRVLTPLTVPSGAPTTVDITVYVRAGDFELYGPRPPR 178

Limnipivirus_RdRp

cd23228

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

1802-2147

2.15e-36

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: 143.48 E-value: 2.15e-36

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1802 GLEALDLNTSAGFPYVTMGIKKRDL--INNK---------TKDISRLKDALDKYG-VDLPMITFLKDELRKKEKISAGKT 1869
Cdd:cd23228      6 GTNPIDKNTSPGLKYTRDGLKKSDLytIDEDgnvvvsdmlRADVEAWEELIQSGGyPTTLFTACLKDELRSDEKVALGKT 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1870 RVIEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPEVFWSKIPVMLDG-DCIMAFDYTNYDGSIHPVWFQALKK 1948
Cdd:cd23228     86 RVIEAAELDYVVAYRMYMSSIYSDLYNAYAGDTGIAAGINPPADGHRLREELSQyDSFLALDYSRFDGSLPEMLMRAAVE 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1949 VLENLSFQSDLIDRL----CYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDA----YKNIDLDKLK--- 2017
Cdd:cd23228    166 ILADLHEDPDLVRRLhetvIISKHLVVDEDWTVKGGMPSGSPCTTVLNCICNLLVLEYAFLVHfgvyEDDDGVGLPQcdy 245

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2018 -IIAYGDDVIFSY---KYTLDM-EAIANegkKYGLTITPADKSTEFRKLDYNNVTFLKRGF-KQDERHTFLIHPTFPVEE 2091
Cdd:cd23228    246 lSVVYGDDCIVAYngmEMGLAFaETIED---TFGMEVTPASKVGDHFNVELHEVEFLKRKFfAFETEEYDRIALRLSENT 322

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2099547062 2092 IYESIRWTKKPSQMQEHVLSLCHLMWHNGRKVYEDFSRKIRSVSAGRALYI--PPYDL 2147
Cdd:cd23228    323 IVQSLMWMRNLKTFPDQVQSLMMELSAWGKEKYDKLRDTCKRRLAKQNLQVtvPGYDI 380

rhv_like

cd00205

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

636-824

1.07e-35

Pssm-ID: 119412 Cd Length: 178 Bit Score: 134.45 E-value: 1.07e-35

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  636 IESFLGRSGCVHISRIkvdynDYNGQNKNFTQWKITLQE------MAQIRRKFELFTYVRFDSEVTLVPCiagrGDDIGH 709
Cdd:cd00205      1 VESFADRPTTVGTNNW-----NSSASGTQLFQWKLSPALgflllqNTPLGALLSYFTYWRGDLEVTVQFN----GSKFHT 71

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  710 VVMQYMYVPPGAPIPKTrDDFSWQSGTNMSIFWQHG-QPFPRFSLPFLSIASAYYMFYDGYDgdnssakygsvVTNDMGT 788
Cdd:cd00205     72 GRLLVAYVPPGAPAPTT-GDTRWQATLNPHVIWDLGtNSSVTFVVPYVSPTPYRSTRYDGYG-----------PLNSFGT 139

                          170       180       190
                   ....*....|....*....|....*....|....*....
gi 2099547062  789 ICSRIVTE---RQEHPVVITTHIYHKAKHTKAWCPRPPR 824
Cdd:cd00205    140 LVVRVLTPltvPSGAPTTVDITVYVRAGDFELYGPRPPR 178

Kunsagivirus_RdRp

cd23219

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

1793-2125

2.23e-35

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: 139.23 E-value: 2.23e-35

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1793 LEDGVFgiEGLEALDLNTSAGFPYVtmGIKKRDLINNKTK--------DISRLKDALDKYGVD-LPMITFLKDELRKKEK 1863
Cdd:cd23219      1 IEEAVF--DTVTPMDHTASAGPKYP--GTKRSELIDFQNRiisdrlrnDVLELQFRGTSGGAGeVKFSSFLKDELRPLSK 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1864 ISAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDpeVFWSKIPVMLD-GDCIMAFDYTNYDGSIHPVW 1942
Cdd:cd23219     77 IRSGDTRVVECSSLDYTVAFRMQFLRVLQMCYGSDPTLTGLAPGMN--VYTDMLPLCTSlYDYNLCLDFSKYDSRLPLQV 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1943 FQALKKVLENLS----FQSDLIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDAYKNIDldkLKI 2018
Cdd:cd23219    155 MHRVAQLISNLTpdpqVSMRLFQPIIISTHIVGSYEVVVEGGMPSGCPITTIMNSVCNVVMTSYAMLLLDPDSD---FWP 231

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2019 IAYGDDVIFSYKYTLDMEA---IANEgkKYGLTITPADKSTEFRKLDYNNVTFLKRGFKQDERHTFLIhPTFPVEEIYES 2095
Cdd:cd23219    232 VAYGDDNIVSTRKPIDTELfcsILNE--EFGMILTGADKTTTVQAVPPMSVDFLKRRLRYTPEFPLPV-PVLPLDSMLSR 308

                          330       340       350
                   ....*....|....*....|....*....|
gi 2099547062 2096 IRWTKKPSQMQEHVLSLCHLMWHNGRKVYE 2125
Cdd:cd23219    309 ICWCKGETEFKDQLESFSYELALYGQEVYE 338

Avisivirus_RdRp

cd23231

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

1806-2146

4.15e-35

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: 138.87 E-value: 4.15e-35

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1806 LDLNTSAGFPYvtMGIKKRDLINNKT--KDISRLKDA---LDKYGVDLPMITFLKDELRKKEKISAGKTRVIEASSINDT 1880
Cdd:cd23231     11 IDWGTSPGDKY--KGKTKAQLVDDKKfkADVMNLVRFngdPNREPPDVYFTTYLKDELRPKEKAKAGKTRVISAASFDYT 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1881 ILFRTTFGNLFSKFHLNpGVVTGSAVGCDPEVFWSKIPVMLDGDCImAFDYTNYDGSIHPVWFQALKKVLENLSFQSDLI 1960
Cdd:cd23231     89 IACRMVFGPILRQLFAW-GREFGFGPGLNPYTHFDELYDKILPFVI-CLDYSGFDGSLSSELMFHAAQVIACFSEKPEAI 166

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1961 DRLCY----SKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDayKNIDLDKLKIIAYGDDVIFSYKYTLDME 2036
Cdd:cd23231    167 MASAEltigSTERVSDEVWYVYGGMPSGSPWTTTLNTICNLLMCYTYLLD--MGHCWSETFVVAYGDDVVISANIKHNLE 244

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2037 AIANEGK-KYGLTITPADKSTEFRKLDYNNVTFLKRGFKQDErhtFL--IHPTFPVEEIYESIRWTKkpSQMQEHVLSLC 2113
Cdd:cd23231    245 GIEQWFKtKFGATVTPSDKQGKITWTTKNNMEFLKRRPKQLD---FLpkIVGALDLDNMLDRIQWTK--GHFQDQLNSFY 319

                          330       340       350
                   ....*....|....*....|....*....|....*
gi 2099547062 2114 HLMWHNGRKVYEDFSRKIrsvsAGRA--LYIPPYD 2146
Cdd:cd23231    320 LELALHGRETYNEIRAKL----APRApqLVHPTYA 350

Aalivirus_RdRp

cd23216

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

1806-2133

2.59e-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: 121.31 E-value: 2.59e-29

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1806 LDLNTSAGFPYvtMGIKKRDLINNKT--KDISRLKDALDKYgvdlpMITFLKDELRKKEKISAGKTRVIEASSINDTILF 1883
Cdd:cd23216     12 IDWQTSPGLKY--KGRTKADLVQDPKfkEDVKEILAGKPTF-----FTTYLKDELRSIEKIANGNTRAIEAANFDHVVAW 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1884 RTTFGNLFSKFHLNPGVVTGSAVGCDPEVFWSKIPVMLDGDcIMAFDYTNYDGSIHPVWFQALKKVL----ENLSFQSDL 1959
Cdd:cd23216     85 RQVMGNIVKQLFSDHDRVTGFAPGMNPYTHFDSLMDQVKWN-VLALDFKKFDGSLSPQVMEEAVDILasfhDMPQMVVDI 163

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1960 IDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVLDayKNIDLDKLKIIAYGDDVIFS---YKYTLDME 2036
Cdd:cd23216    164 HKHTIYSTNVVSDETWFVEGGMCSGSPCTTVLNTICNLLVNTTILLS--EGIQPDNFYIAAYGDDTIISvdgLSSSLPDP 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2037 AIANEGKK--YGLTITPADKSTEFRKLDYNNVTFLKR--GFKQDERHTFLIhptFPVEEIYESIRWTKkpSQMQEHVLSL 2112
Cdd:cd23216    242 KIMQQKYKewFGMTVTSADKGSEITWDTRNHVQFLKRrpGFFPGTQKVVGV---LDLESMMEHIAWTK--GSFQDQLNSF 316

                          330       340
                   ....*....|....*....|.
gi 2099547062 2113 CHLMWHNGRKVYEDFSRKIRS 2133
Cdd:cd23216    317 YQELVLHGEQVYMTVRQTLKS 337

Caliciviridae_RdRp

cd23192

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

1854-2078

1.13e-27

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

Pssm-ID: 438042 Cd Length: 310 Bit Score: 115.82 E-value: 1.13e-27

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1854 LKDELRKKEKISAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPGvVTGSAVGCDPEVfwSKIPVM----LDGDCIMAF 1929
Cdd:cd23192      7 LKDELRPVEKIAEGKRRLLWGCDVGVTLVAAAAFGPVADALKAVCP-TGPIAVGINMDS--EDVEVIferlSGFRYHYCL 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1930 DYTNYDGSIHPVWFQALKKVLENLSFQSDLIDRLCYSKH-----LFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLV 2004
Cdd:cd23192     84 DYSKWDSTQSPAVTAAAIDILADLSEETPLRDSVVETLSsppmgIFDDVIFVTKRGLPSGMPFTSVINSLNHWLLFSAAV 163

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2005 LDAYK-------NIdLDKLKIIAYGDDVIFSYK--YTLDMEAIANEGKKYGLTITPADKSTEFRKLDYNNVTFLKRGFKQ 2075
Cdd:cd23192    164 LKAYElvgiytgNV-FDEADFFTYGDDGVYAMPpaTASVMDEIIENLKSYGLKPTAADKTENPDIPPLQGPVFLKRTFVR 242


                   ...
gi 2099547062 2076 DER 2078
Cdd:cd23192    243 TPG 245

Marnaviridae_RdRp

cd23195

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

1854-2132

3.48e-26

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: 111.38 E-value: 3.48e-26

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1854 LKDELRKKEKisaGKTRVIEASSINDTILFRTTFGNLFSKFHLNPgVVTGSAVGCD---PEvfWSKIPVML---DGDCIM 1927
Cdd:cd23195      7 LKDEPTKLTK---DKVRVFQAAPVALQLLVRKYFLPIARFLQMNP-LLSECAVGINaqsPE--WEELYEHLtkfGEDRII 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1928 AFDYTNYDGSIHPVWFQALKKVLENLSFQS------DL-IDR-----LCYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMI 1995
Cdd:cd23195     81 AGDYSKYDKRMSAQLILAAFKILIDIAAKSggyseeDLkIMRgiatdIAYPLVDFNGDLIQFFGSNPSGHPLTVIINSIV 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1996 NNIIIRTLVLDAYKNIDL----DKLKIIAYGDDVIFSYK---YTLDMEAIANEGKKYGLTITPADKSTEFRK-LDYNNVT 2067
Cdd:cd23195    161 NSLYMRYAYYSLYPEKEVppfrDVVALMTYGDDNIMSVSpgyPWFNHTSIAEFLAKIGIKYTMADKEAESVPfIHISEAD 240

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2099547062 2068 FLKRGFKQDERHtFLIHPtfPVEE--IYESIRWTKKPS------QMQEHVLSLCHLMWHNGRKVYEDFSRKIR 2132
Cdd:cd23195    241 FLKRKFVFDPEL-GVYVG--PLDEdsIFKSLHCYLKSKvltpeeQAAQNIDGALREWFFHGREVYEKRREQLK 310

Aquamavirus_RdRp

cd23220

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

1806-2124

1.09e-23

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: 104.79 E-value: 1.09e-23

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1806 LDLNTSAGFPYVtmGIKKRDLIN--NKT--KDISRLKDALDKYGVDLPMITFLKDELRKKEKISAGKTRVIEASSINDTI 1881
Cdd:cd23220     12 LNFNGTAGAKYP--GMNRRQLLLplNPQvrDDVVKLAGDVGNGTATVVFETFMKDELRPKEKIESGKTRIVESCPLDYLL 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1882 LFRTTFGNLFSKFHLNPGVVTGSAVGCDpeVFWSKIPVMLD-GDCIMAFDYTNYDGSIHPVWFQALKKVLENLSFQSDLI 1960
Cdd:cd23220     90 LYRMVMLKSMIWWYNSDCIKTGVAPGMN--VYTDFVPMVKQfKKIKYCLDFSAYDSTLSDEILAAGVEVLACTSAVPSYV 167

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1961 DRL----CYSKHLFKSTYYEVAGGVPSGCSGTSIFNTMINNIIIRTLVldayKNIDLDKLKIIAYGDDVIFSYKYTLDME 2036
Cdd:cd23220    168 RKLhapiICSHHWHNNVVDLVLGGMPSGAPCTSVLNSIVNVLMARYIC----ALMDIDYPVMVAYGDDNVVSFDEEIDIE 243

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2037 AIAN-EGKKYGLTITPADKSTEFRKLdyNNVTFLKRG--FKQDERHTFlihPTFPVEEIYESIRWTKKPSQMQEHVLSLC 2113
Cdd:cd23220    244 RMVSlYKTEFGVTATNHDKTPVPRPM--ANPVFLKRRlrFNPDLNIQF---PVLPLGEMIDRMCWTRGPEHLSDQTFSFA 318

                          330
                   ....*....|.
gi 2099547062 2114 HLMWHNGRKVY 2124
Cdd:cd23220    319 IELAGYGKQVY 329

P3A

pfam08727

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

1412-1464

6.74e-21

Pssm-ID: 400873 Cd Length: 59 Bit Score: 87.87 E-value: 6.74e-21

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2099547062 1412 AIFQG----PISLDAPPPPAIADLLQSVRTPEVIKYCQDNKWIV--PAECQIERDLNIA 1464
Cdd:pfam08727    1 AIFQGidlkIDIKTSPPPEAIADLLQAVDSPEIIDYCEDKGWIVniPAECQIERDIGIA 59

Secoviridae_RdRp

cd23196

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

1844-2077

2.82e-15

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: 78.96 E-value: 2.82e-15

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1844 YGVDLPmitflKDELRKKEK-ISAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTgSAVGCDP-EVFWSKIPVML 1921
Cdd:cd23196      2 NCVECP-----KDERLKKRKvLEKPKTRLFDVLPMEYNLLLRKYFLNFVRFIQANRHRLP-CQVGINPySREWTTLYDRL 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1922 --DGDCIMAFDYTNYDG----SIHPVWFQALKKVL---ENLSFQSDLIDRLCYSKHLFKSTYYEVAGGVPSGCSGTSIFN 1992
Cdd:cd23196     76 aeKSDTALNCDYSRFDGllshQVYVWIADMINRLYgdgDEAKARRNLLMMFCGRRSICGRQVYMVRGGMPSGCALTVIIN 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1993 TMINNIIIR----TLVLDAYKNIDLDKLKIIAYGDDVIFSYKYTL----DMEAIANEGKKYGLTITPA-DKST---EFRK 2060
Cdd:cd23196    156 SIFNEILIRyvyrKVVPRPARNNFNKYVRLVVYGDDNLISVKEEIipyfDGPVIKKEMAKVGVTITDGtDKTSptlERKP 235

                          250
                   ....*....|....*..
gi 2099547062 2061 LDynNVTFLKRGFKQDE 2077
Cdd:cd23196    236 LE--SLDFLKRGFRVQS 250

Nora-virus_RdRp

cd23200

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

1854-2132

6.46e-12

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: 68.79 E-value: 6.46e-12

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1854 LKDELRKKEKISAGKTRVIEASSINDTILFRTTFGNLFSKFHlNPGVVTGSAVGCDPE-VFWSKIPV-MLDGDCIMAFDY 1931
Cdd:cd23200      7 LKDQPIKIAQAKSGRTRVFHCIPVDLILFSGALYGPYKEAYT-KAGLKCYHAVGIDPKsVGWQQLATyMTKHPNYFDADY 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1932 TNYDGSIHPVWFQALKKVLENL--SFQSDLIDRLCYSKHLFK--------STYYEVAGGVPSGCSGTSIFNTMINNII-- 1999
Cdd:cd23200     86 KNYDKYLHRQVFKAVRKIQRSViqQVCPDKWDKARAVEELDAidtyvvdyQTVYKTNRGNKSGSYTTTIDNCLANDIYgl 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2000 ---IRTLVLDAYKNIdLDKLKIIAYGDDVIFS----YKYTLDMEAIANEGKKYGLTITPADKSTEFRKLDY-NNVTFLKR 2071
Cdd:cd23200    166 yawVKTTGLRSLWDY-RQNVSSVAFGDDIIKSvsdeYKDKYNYCTYRDVLNATGHIMTPGSKDGEEKPFTSfENLQFLKR 244

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2099547062 2072 GFKQDERHTF--LIHPTFPVEEIYESIRWTKKPSQ---MQEHVLSLchLMWhnGRKVYEDFSRKIR 2132
Cdd:cd23200    245 GFKLENGMVLapLLQRSIEGPFVWTDIREDQITVWvnlVQEQLIEA--ALW--GEEYYNELCQKLK 306

Polycipiviridae_RdRp

cd23198

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

1853-2131

1.45e-11

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: 67.82 E-value: 1.45e-11

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1853 FLKDELRKKEKI-----SAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPGVVTGSAVGCDPE--------VFWSKIPV 1919
Cdd:cd23198      6 FPKDELRPIYKAlgdpqTPPKTRSVTCMNVYYILAWRRVTLDFWASMHRAADGNFPFCPGINPEgpdwnrlyHYLNRHPN 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1920 MLDgdcimaFDYTNYDGSIHPVWFQALKKVLENL------SFQSDLIDRL------CYSKhlFKSTYYEVAGGVPSGCSG 1987
Cdd:cd23198     86 AVD------FDVSNWDGHLPAELFYAVLDIIKTVlglkpnSPNAKVIYSIltevmnCHIQ--FEDIIYQKLRGLISGFPG 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1988 TSIFNTMINNIIIRTLVLDAYKNIDLDK--------LKIIAYGDDVIFSY----KYTLDMEAIANEGKKYGLTITPADKS 2055
Cdd:cd23198    158 TAEVNTLAHWLLIYYIYLYLAQNTIYDMtitaflrnVSAIFYGDDIIITIsdeiLHWFNGKTIQRMYEEHGYPVTSAAKD 237

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 2056 TE--FRKlDYNNVTFLKRGFKQderhtflIHPTF-----PVEEIYESIRWTKKPS----QMQEHVLSLCHLMWHNGRKVY 2124
Cdd:cd23198    238 TEipESK-PLSDCQFLKSSWNP-------ILPGYyirkmDIEVVYDLVYWVRAKEhprdQFYSNYHDALRILFGHGEQVF 309


                   ....*..
gi 2099547062 2125 EDFSRKI 2131
Cdd:cd23198    310 EAFREQV 316

Iflaviridae_RdRp

cd23197

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

1849-2127

1.45e-11

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: 67.97 E-value: 1.45e-11

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1849 PMITFLKDELRKKEKI-SAGKTRVIEASSINDTILFRTTFGNLFSKFHLNPgVVTGSAVGCDPE-VFWSKI--PVMLDGD 1924
Cdd:cd23197      7 VYWAHLKDELRPSEKLrRFGGTRVFSVPPLELVLNSRRFLLPFMDAFQSFP-IEAHHAIGLNPNsGDWRRLrdTLLEKGP 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1925 CIMAFDYTNYDGSIHPVWFQALKKVLENLSFQ--------SDLIDRLCYSKH----LFKSTYYEVAGGVPSGCSGTSIFN 1992
Cdd:cd23197     86 CLLQMDYKNYSDAIPKECVAKAFHIIVDYYRKwhcltveiENALKTLFLDTAdaelLVYGDVFKVNNGVLAGHPMTSVVN 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1993 TMINniiirtLVLDAYKNIDLDKLK---------IIAYGDDVIFSYKYTL----DMEAIANEGKKYGLTITPADKSTEFR 2059
Cdd:cd23197    166 SVVN------LILMNYMWIKITRRRaseffkltyIIVMGDDVVISLPKQLteefDCRKICAEFAKYDIKVTDSEKNLTGE 239

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2099547062 2060 KLDYNNV---TFLKRGFKQDERHTFLIHPTFPVEEIYESIRWTKKPSQMQEHVLSLCH----LMWHNGRKVYEDF 2127
Cdd:cd23197    240 PKPYDSFdkfEFLSRGFSDCDAYPDITFAPVKTIALFDCPLWISKGQDEEEQTIQAIQagllLAFDHGPEFFGKY 314

ps-ssRNAv_RdRp-like

cd23167

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

1926-2029

1.25e-08

Pssm-ID: 438017 [Multi-domain] Cd Length: 73 Bit Score: 53.50 E-value: 1.25e-08

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1926 IMAFDYTNYDGSIHPVWFQAlkkvlenlsfqsdlidrlcyskhlfkstyyevagGVPSGCSGTSIFNTMINNIIIRTLVL 2005
Cdd:cd23167      2 VVESDYSGFDSSISPDLLKA----------------------------------GQPSGSPNTSADNSLINLLLARLALR 47

                           90       100
                   ....*....|....*....|....*
gi 2099547062 2006 DAYKNIDLDK-LKIIAYGDDVIFSY 2029
Cdd:cd23167     48 KACGRAEFLNsVGILVYGDDSLVSV 72

RdRP_4

pfam02123

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

1861-2073

1.48e-08

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

Pssm-ID: 280316 Cd Length: 465 Bit Score: 59.40 E-value: 1.48e-08

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1861 KEKISAGKTRvieassindTILFRTTFGNLFSKFHLNPG--VVTGSAVGCDPEV-----FWSKIPVMLDGDCIMAFDYTN 1933
Cdd:pfam02123  236 SMKLEHGKSR---------AIYACDTRSYLAFEYLLAPVekAWANKSVILNPGEgdisgFDWSVQDWKRGGVSLMLDYDD 306

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1934 YDgSIHPVWfqALKKVLENL-----SFQSDLIDRLCYSkhlFKSTY---------YEVAGGVPSGCSGTSIFNTMINNII 1999
Cdd:pfam02123  307 FN-SQHSTE--SMRAVFERLrrrlpDEPAEAADWLVCS---MDSMYqlsdgtllaQRVPGTLKSGHRATTFINSVLNCAY 380

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2099547062 2000 IRTLVLDAyknidLDKLKIIAYGDDVIFSYKYTLDMEAIANEGKKYGLTITPADKSTEFRKLDYNNVTFLKRGF 2073
Cdd:pfam02123  381 AELAGAPW-----ADVPTSIHMGDDVLEGLRTPADATSLLDKYARLGFKVNPSKQSVGHTIAEFLRVAFCSHEV 449

ps-ssRNAv_Nodaviridae_RdRp

cd23173

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

1930-2073

7.36e-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: 55.60 E-value: 7.36e-08

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1930 DYTNYDGSIHPvWFQALKKVL------------ENLSFQSDLIDRLCYSKHLFKstyYEVAGGVPSGCSGTSIFNTMINN 1997
Cdd:cd23173     89 DYSRFDGTISE-WLRRNVEFAaylrwfhpeyraELLKLLDAEINCPARTKTGVK---YDPGVSRLSGSPTTTDGNTIINA 164

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1998 II----IRTLVLD---AYKNIDLdklkiiAYGDDVIFSYKYTLDMEAIAnegKKYGLTItpadKSTEFRklDYNNVTFLK 2070
Cdd:cd23173    165 FVsycaLRETGYSpeeAFALLGL------YYGDDGLSDNLPAEALEKVA---KDLGLKL----KIEVVR--PGQPVTFLG 229


                   ...
gi 2099547062 2071 RGF 2073
Cdd:cd23173    230 RVF 232

ps-ssRNAv_Astroviridae_RdRp

cd23172

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

1853-2034

1.99e-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: 51.32 E-value: 1.99e-06

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1853 FLKDELRKKEKISAGKTRVIEASsinDTILFRttFGNLF-----SKFHLNPGVvTGSAVGCDPevFWSKIPVMLD----- 1922
Cdd:cd23172      7 FLKKEILKKEKIEDGDIRQILCP---DPIFAR--IGARFeqdqnNLMKERTLT-NEGQVGWSP--FYGGFDARVRrlgsk 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1923 GDCIMAFDYTNYDGSIhPVW-FQALKKV-LENLS-FQSDLIDRLC--YSKHLF-KST------YYEVAGGVPSGCSGTSI 1990
Cdd:cd23172     79 GNYFVEFDWTRFDGTI-PAElFRHIRKLrWSFLDpEKTEENRKVYdwYVHNLLnRYVllptgeVTRVTKGNPSGQISTTM 157

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2099547062 1991 FNTMInNIIIRTLVLdAY----KNIDLDKL----KIIAYGDDVIFSYKYTLD 2034
Cdd:cd23172    158 DNCMV-NTFLTAFEF-AYvygpKTGTLKELwdnyDTIVYGDDRLSGYPSLPD 207

Calici_coat

pfam00915

Calicivirus coat protein;

424-531

2.23e-04

Calicivirus coat protein;

Pssm-ID: 459994 Cd Length: 291 Bit Score: 45.65 E-value: 2.23e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062  424 PLATTLLGEIASYYTHWTGSLRFSFMFCGTANTTLKLLLAYTPPGIDkPATRKDAMLGTHVVWDVGLQSTISLVVPWVSA 503
Cdd:pfam00915   90 PHLNPFLLHLSQMYNGWSGGMRVRFMVAGSGVFGGKLAASVIPPGVE-PITSASMLQFPHVLFDARQLEPVIFTIPDLRN 168

                           90       100
                   ....*....|....*....|....*...
gi 2099547062  504 SHFRLTANDKYSMAgyITCWYQTNLVVP 531
Cdd:pfam00915  169 TLFHNMDRNTDTTR--LVIMVYNPLINP 194

DEXXQc_SF1

cd18043

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

1212-1269

4.82e-04

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547062 1212 AVMIHGPPGTGKS-----ITTNFLAR----------------------MITNESDVYSLPPDPKYFDgydnqsVVIMDDI 1264
Cdd:cd18043     16 NVVIQGPPGTGKSqtianIIANALARgkrvlfvsekkaaldvvrfpcwIMSPLSVSQYLPLNRNLFD------LVIFDEA 89


                   ....*
gi 2099547062 1265 MQNPD 1269
Cdd:cd18043     90 SQIPI 94

ps-ssRNAv_Potyviridae_RdRp

cd23175

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

1853-1896

5.83e-04

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

Pssm-ID: 438025 Cd Length: 236 Bit Score: 43.59 E-value: 5.83e-04

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 2099547062 1853 FLKDELRKKEKISAGKTRVIEASSInDTIL----FRTTFGNLFSKFHL 1896
Cdd:cd23175      9 SLKAELRPIEKVEANKTRTFTAAPI-DTLLggkvCVDDFNNQFYSLHL 55

CDC6

COG1474

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

1213-1251

4.86e-03

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

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

                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 2099547062 1213 VMIHGPPGTGKSITTNFLARMITNESDVYSLPPDPKYFD 1251
Cdd:COG1474     54 VLIYGPTGTGKTAVAKYVLEELEEEAEERGVDVRVVYVN 92

Blast search parameters

Data Source:	Precalculated data, version = cdd.v.3.21
Preset Options:	Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01