NCBI Conserved Domain Search

Conserved domains on [gi|2395881893|gb|WAK75500|]

View

polyprotein [rhinovirus B3]

Protein Classification

Graphical summary

Zoom to residue level

show extra options »

Show site features Horizontal zoom: ×

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 ...

1727-2178

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: 788.26 E-value: 0e+00

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1727 VRDVGLNPINTPTKTKLHPSIFYNVFPGSKQPAVLSDNDPRLEVKLTESLFSKYKGNVQMEPTENMLVAVDHYAGQLMSL 1806
Cdd:cd23213      1 NKEVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1807 DISTKELTLKEALYGVDGLEPIDVTTSAGYPYVSLGIKKRDILNKETQDTEKMKFYLDKYGIDLPLVTYIKDELRSADKV 1886
Cdd:cd23213     81 DIDTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKV 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1887 RLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVIPCLMDGHLMAFDYSNF*ASLSPVWFEC 1966
Cdd:cd23213    161 EKGKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDGSLFAFDYTGYDASLSPVWFRA 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1967 LERVLSKLGFKH-PTLIQ*ICNTHHIFRDEIYKVEGGMPSGCSGTSIFNSMINNIIIRTLILDAYKGIDLDSLRILAYGD 2045
Cdd:cd23213    241 LKMVLEKGYSEEaVSLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYGD 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2046 DLIVSYPFELDSNILATIGKNYGLTITPPDKSDTFTKITWENITFLKRYFRPDPQFPFLVHPVMPMQDIYESIRWTKDPR 2125
Cdd:cd23213    321 DVIASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDPR 400

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2395881893 2126 NTQDHVRSLCMLAWHSGEKDYNDFIAKIRTTDIGKCLNLPEYSVLRRRWLDLF 2178
Cdd:cd23213    401 NTQDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453

Pico_P2A super family

cl03031

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

873-999

1.45e-64

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

The actual alignment was detected with superfamily member pfam00947:

Pssm-ID: 395757 Cd Length: 127 Bit Score: 215.32 E-value: 1.45e-64

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  873 NYHLMTPEDHLNLITPYPNRDLAVVATGAHGAETIPHCSCTSGVYYSRYYRKFYPIICERPTNIWIEGGPYYPSRYQAGV 952
Cdd:pfam00947    1 NRHLATHEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 2395881893  953 MKGVGPAEPGDCGGILRCIHGPIGLLTAGGGG*VCFADIRQLDFIAD 999
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVRDLLWLEE 127

Rhv

pfam00073

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

93-298

3.64e-58

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: 198.69 E-value: 3.64e-58

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893   93 TTQEAANAVVCYAEWPEYLSDSDASDVNKTSKPDTSVCRFYTLDSKTWKATSKGW-CWKLPDALKDMGVFGQNMFYHSLG 171
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFfWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  172 RTGYTIHVQCNATKFHSGCLLVVVIPEH*lasheggtvsvkykYTHPGDRgidldtvevaggptsdaiynmdgTLLGNLL 251
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPPG---------------APPPGSR-----------------------DYLWQAT 122

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 2395881893  252 IFPHQFINLRTNNTATIVVPYINSVPIDSMTRHNNVSLMVIPIAPLN 298
Cdd:pfam00073  123 LNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGNWTLVVAGWVPLN 169

RNA_helicase

pfam00910

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

1224-1322

2.44e-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: 145.05 E-value: 2.44e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1224 VLIHGTPGSGKSLTTSIVGRALAEHFN---SSVYSLPPDPKHFDGYQQQEVVIMDDLNQNPDGQDISMFCQMVSSVDFLP 1300
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKKLGlpkDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 2395881893 1301 PMASLDNKGMLFTSNFVLASTN 1322
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

Peptidase_C3 super family

cl02893

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

1537-1701

7.87e-40

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: 146.44 E-value: 7.87e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1537 GPNTEFALSLLRKNILTITTEKGEFTSL--GIHDRICVLPTHAQPSDSVLVNGQRIQIKD-KYKLVDPDNTNLELTIIEL 1613
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1614 DRNEKFRDIRGFISEDL-EGIDATLVVHSNGFTNTMLDVGPITMAGLI-NLSNTPTTRMIRYDYPTKTGQCGGVL----C 1687
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRItKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVViakvE 160

                          170
                   ....*....|....
gi 2395881893 1688 TTGKIFGIHVGGNG 1701
Cdd:pfam00548  161 GNGKILGMHIAGNG 174

Rhv

pfam00073

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

614-770

9.35e-40

Pssm-ID: 395026 Cd Length: 170 Bit Score: 145.92 E-value: 9.35e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  614 PSDNVETRTTYMHFNGSETDVESFLGRAACV--HVTEIKNKDAAGLDNHKREGLFNDWKINLS--SLVQLRKKLELFTYV 689
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVqpDVQGERFYTLDSTDWTSLSKGFFWWKLPLAllSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  690 RFDSEYTILATASQpeassyS*NLTVQAMYVPPGAPNPKEWdDYTWQSASNPSVFFKVGETS--RFSVPFVGLASAYNCF 767
Cdd:pfam00073   81 RGGLEVTVQFNGSK------FHQGKLLVAYVPPGAPPPGSR-DYLWQATLNPHQFWNLGLNSsaRLSVPYISIAHYYSTF 153


                   ...
gi 2395881893  768 YDG 770
Cdd:pfam00073  154 YDG 156

rhv_like

cd00205

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

374-556

5.20e-37

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: 138.30 E-value: 5.20e-37

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  374 LLEIIQVDTLIPMNNTGTNDNvtnyliplhadrqNEQIFGTKL--FIGDGVFKTTLLGEIAQYYTHWSGSLRISLMYTGP 451
Cdd:cd00205      1 VESFADRPTTVGTNNWNSSAS-------------GTQLFQWKLspALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGS 67

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  452 ALSSAKLILAYTPPGTRGP---EDRKEAMLGTHVVWDIGLQSTIVMTIPWTSGVQFRYTD---PDTYTSAGYLSCWYQTS 525
Cdd:cd00205     68 KFHTGRLLVAYVPPGAPAPttgDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRydgYGPLNSFGTLVVRVLTP 147

                          170       180       190
                   ....*....|....*....|....*....|.
gi 2395881893  526 LILPPQTSGQVYLLSFISACpDFKLRLMKDT 556
Cdd:cd00205    148 LTVPSGAPTTVDITVYVRAG-DFELYGPRPP 177

Pico_P2B super family

cl03260

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

1001-1099

8.10e-29

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: 112.04 E-value: 8.10e-29

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1001 QGLGDYITSLGRAFGTGFTDQISAKVCELQDVAKDF--LTTKVLSKVVKMISALVIICRNHDDLVTVTATLALLGCDGSP 1078
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTQQISDKIKELTNFINPTskIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|.
gi 2395881893 1079 WRFLKMYISKHFQVPYIERQA 1099
Cdd:pfam01552   81 WQFLKEKACAVLEIPYVHKQG 101

Pico_P1A super family

cl03490

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

2-69

1.09e-21

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.

The actual alignment was detected with superfamily member pfam02226:

Pssm-ID: 308053 Cd Length: 68 Bit Score: 90.51 E-value: 1.09e-21

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2395881893    2 GAQVSTQKSGSHENQNILTNGSNQTFTVINYYKDAASSSSAGQSFSMDPSKFTEPVKDLMLKGAPALN 69
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 68

P3A super family

cl07374

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

1432-1485

3.97e-16

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: 74.38 E-value: 3.97e-16

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2395881893 1432 YKDLEIDVCNTPPP*CISDLLKSVDSEEVREYCKKKKWIIpQIPT--NIERAVNQA 1485
Cdd:pfam08727    5 GIDLKIDIKTSPPPEAIADLLQAVDSPEIIDYCEDKGWIV-NIPAecQIERDIGIA 59

Name

Accession

Description

Interval

E-value

Enterovirus_RdRp

cd23213

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

1727-2178

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: 788.26 E-value: 0e+00

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1727 VRDVGLNPINTPTKTKLHPSIFYNVFPGSKQPAVLSDNDPRLEVKLTESLFSKYKGNVQMEPTENMLVAVDHYAGQLMSL 1806
Cdd:cd23213      1 NKEVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1807 DISTKELTLKEALYGVDGLEPIDVTTSAGYPYVSLGIKKRDILNKETQDTEKMKFYLDKYGIDLPLVTYIKDELRSADKV 1886
Cdd:cd23213     81 DIDTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKV 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1887 RLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVIPCLMDGHLMAFDYSNF*ASLSPVWFEC 1966
Cdd:cd23213    161 EKGKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDGSLFAFDYTGYDASLSPVWFRA 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1967 LERVLSKLGFKH-PTLIQ*ICNTHHIFRDEIYKVEGGMPSGCSGTSIFNSMINNIIIRTLILDAYKGIDLDSLRILAYGD 2045
Cdd:cd23213    241 LKMVLEKGYSEEaVSLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYGD 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2046 DLIVSYPFELDSNILATIGKNYGLTITPPDKSDTFTKITWENITFLKRYFRPDPQFPFLVHPVMPMQDIYESIRWTKDPR 2125
Cdd:cd23213    321 DVIASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDPR 400

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2395881893 2126 NTQDHVRSLCMLAWHSGEKDYNDFIAKIRTTDIGKCLNLPEYSVLRRRWLDLF 2178
Cdd:cd23213    401 NTQDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453

Pico_P2A

pfam00947

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

873-999

1.45e-64

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

Pssm-ID: 395757 Cd Length: 127 Bit Score: 215.32 E-value: 1.45e-64

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  873 NYHLMTPEDHLNLITPYPNRDLAVVATGAHGAETIPHCSCTSGVYYSRYYRKFYPIICERPTNIWIEGGPYYPSRYQAGV 952
Cdd:pfam00947    1 NRHLATHEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 2395881893  953 MKGVGPAEPGDCGGILRCIHGPIGLLTAGGGG*VCFADIRQLDFIAD 999
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVRDLLWLEE 127

Rhv

pfam00073

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

93-298

3.64e-58

Pssm-ID: 395026 Cd Length: 170 Bit Score: 198.69 E-value: 3.64e-58

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893   93 TTQEAANAVVCYAEWPEYLSDSDASDVNKTSKPDTSVCRFYTLDSKTWKATSKGW-CWKLPDALKDMGVFGQNMFYHSLG 171
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFfWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  172 RTGYTIHVQCNATKFHSGCLLVVVIPEH*lasheggtvsvkykYTHPGDRgidldtvevaggptsdaiynmdgTLLGNLL 251
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPPG---------------APPPGSR-----------------------DYLWQAT 122

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 2395881893  252 IFPHQFINLRTNNTATIVVPYINSVPIDSMTRHNNVSLMVIPIAPLN 298
Cdd:pfam00073  123 LNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGNWTLVVAGWVPLN 169

RdRP_1

pfam00680

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

1744-2153

7.39e-51

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

Pssm-ID: 425815 Cd Length: 450 Bit Score: 187.62 E-value: 7.39e-51

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1744 HPSIFYNVFPGSKQPAVLSDNDPRL--EVKLTESLF---SKYKGNVQMEPTENMLVAVDHYAGQLMSLDISTK------E 1812
Cdd:pfam00680    1 SPTERHLVAIPAYVPASLGPEDPRWarSYLNTDPYVddiKKYSRPKLPGPADERDKLLNRSAAKMVLSELRGVpkkansT 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1813 LTLKEALYGVDGLEPIDVTTSAGYPYVSLGIKKRDiLNKETQDTEKMKFYLDK---------YGIDLPLV--TYIKDELR 1881
Cdd:pfam00680   81 LIVYRAIDGVEQIDPLNWDTSAGYPYVGLGGKKGD-LIEHLKDGTEARELAERlaadwevlqNGTPLKLVyqTCLKDELR 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1882 SADKVRLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITgSAVGCDP-DVFWSV----IPCLMDGHLMaFDYSNF* 1956
Cdd:pfam00680  160 PLEKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHP-IQVGINPfDRGWPRllrrLARFGDYVYE-LDYSGFD 237

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1957 ASLSP----VWFECLErvlSKLGF-----KHPTLIQ*ICNTHH-IFRDEIYKVEGGMPSGCSGTSIFNSMINNIIIRTLI 2026
Cdd:pfam00680  238 SSVPPwlirFAFEILR---ELLGFpsnvkEWRAILELLIYTPIaLPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYAL 314

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2027 LDAYKGIDLDSLRI------LAYGDDLI--VSYPFELDSNILATIGKNYGLTITPPDKSDTFTKITwENITFLKRYFRPD 2098
Cdd:pfam00680  315 LKSLENDGPRVCNLdkyfdfFTYGDDSLvaVSPDFDPVLDRLSPHLKELGLTITPAKKTFPVSREL-EEVSFLKRTFRKT 393

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2395881893 2099 PQFpflVHPVMPMQDIYESIRWTKDPRNTQDHVRSLCMLAWHSGEKDYNDFIAKI 2153
Cdd:pfam00680  394 PGG---YRPPLDRKRILAQLEYIRSKPVPSGQLENIRAYASHHGYEFYRDLLYRF 445

RNA_helicase

pfam00910

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

1224-1322

2.44e-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: 145.05 E-value: 2.44e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1224 VLIHGTPGSGKSLTTSIVGRALAEHFN---SSVYSLPPDPKHFDGYQQQEVVIMDDLNQNPDGQDISMFCQMVSSVDFLP 1300
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKKLGlpkDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 2395881893 1301 PMASLDNKGMLFTSNFVLASTN 1322
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

Peptidase_C3

pfam00548

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

1537-1701

7.87e-40

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: 146.44 E-value: 7.87e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1537 GPNTEFALSLLRKNILTITTEKGEFTSL--GIHDRICVLPTHAQPSDSVLVNGQRIQIKD-KYKLVDPDNTNLELTIIEL 1613
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1614 DRNEKFRDIRGFISEDL-EGIDATLVVHSNGFTNTMLDVGPITMAGLI-NLSNTPTTRMIRYDYPTKTGQCGGVL----C 1687
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRItKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVViakvE 160

                          170
                   ....*....|....
gi 2395881893 1688 TTGKIFGIHVGGNG 1701
Cdd:pfam00548  161 GNGKILGMHIAGNG 174

Rhv

pfam00073

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

614-770

9.35e-40

Pssm-ID: 395026 Cd Length: 170 Bit Score: 145.92 E-value: 9.35e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  614 PSDNVETRTTYMHFNGSETDVESFLGRAACV--HVTEIKNKDAAGLDNHKREGLFNDWKINLS--SLVQLRKKLELFTYV 689
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVqpDVQGERFYTLDSTDWTSLSKGFFWWKLPLAllSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  690 RFDSEYTILATASQpeassyS*NLTVQAMYVPPGAPNPKEWdDYTWQSASNPSVFFKVGETS--RFSVPFVGLASAYNCF 767
Cdd:pfam00073   81 RGGLEVTVQFNGSK------FHQGKLLVAYVPPGAPPPGSR-DYLWQATLNPHQFWNLGLNSsaRLSVPYISIAHYYSTF 153


                   ...
gi 2395881893  768 YDG 770
Cdd:pfam00073  154 YDG 156

rhv_like

cd00205

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

125-324

1.64e-37

Pssm-ID: 119412 Cd Length: 178 Bit Score: 139.84 E-value: 1.64e-37

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  125 PDTSVCRFYTLDSKTWKA---TSKGWCWKLPDA----LKDMGVFGQNMFYHSLGRTGYTIHVQCNATKFHSGCLLVVVIP 197
Cdd:cd00205      1 VESFADRPTTVGTNNWNSsasGTQLFQWKLSPAlgflLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  198 EH*lasheggtvsvkykythpgdrgidldtvevAGGPTSDaiynmdgTLLGNLLIFPHQFINLRTNNTATIVVPYINSVP 277
Cdd:cd00205     81 PG-------------------------------APAPTTG-------DTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTP 122

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2395881893  278 IDSMTRH------NNVSLMVIPIAPLNAPTGSSPTLPVTVTIAPMCTEFTGIR 324
Cdd:cd00205    123 YRSTRYDgygplnSFGTLVVRVLTPLTVPSGAPTTVDITVYVRAGDFELYGPR 175

rhv_like

cd00205

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

374-556

5.20e-37

Pssm-ID: 119412 Cd Length: 178 Bit Score: 138.30 E-value: 5.20e-37

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  374 LLEIIQVDTLIPMNNTGTNDNvtnyliplhadrqNEQIFGTKL--FIGDGVFKTTLLGEIAQYYTHWSGSLRISLMYTGP 451
Cdd:cd00205      1 VESFADRPTTVGTNNWNSSAS-------------GTQLFQWKLspALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGS 67

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  452 ALSSAKLILAYTPPGTRGP---EDRKEAMLGTHVVWDIGLQSTIVMTIPWTSGVQFRYTD---PDTYTSAGYLSCWYQTS 525
Cdd:cd00205     68 KFHTGRLLVAYVPPGAPAPttgDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRydgYGPLNSFGTLVVRVLTP 147

                          170       180       190
                   ....*....|....*....|....*....|.
gi 2395881893  526 LILPPQTSGQVYLLSFISACpDFKLRLMKDT 556
Cdd:cd00205    148 LTVPSGAPTTVDITVYVRAG-DFELYGPRPP 177

Rhv

pfam00073

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

359-522

7.34e-37

Pssm-ID: 395026 Cd Length: 170 Bit Score: 137.44 E-value: 7.34e-37

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  359 YEPTPRIHIPGKVRNLLEIIQVDTLIPMNNTGTN-DNVTNYLIPLHA-DRQNEQIFGTKLfiGDGVFKTTLLGEIAQYYT 436
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDvQGERFYTLDSTDwTSLSKGFFWWKL--PLALLSMGLLGRLLRYHT 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  437 HWSGSLRISLMYTGPALSSAKLILAYTPPGTRGPEDR---KEAMLGTHVVWDIGLQSTIVMTIPWTSGVQFRYT---DPD 510
Cdd:pfam00073   79 YYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRdylWQATLNPHQFWNLGLNSSARLSVPYISIAHYYSTfydGNW 158

                          170
                   ....*....|..
gi 2395881893  511 TYTSAGYLSCWY 522
Cdd:pfam00073  159 TLVVAGWVPLNY 170

rhv_like

cd00205

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

634-826

1.23e-36

Pssm-ID: 119412 Cd Length: 178 Bit Score: 137.14 E-value: 1.23e-36

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  634 VESFLGRAACVHVTEIKNKDAAGLdnhkreglFNDWKINLS------SLVQLRKKLELFTYVRFDSEYTILATASQPeas 707
Cdd:cd00205      1 VESFADRPTTVGTNNWNSSASGTQ--------LFQWKLSPAlgflllQNTPLGALLSYFTYWRGDLEVTVQFNGSKF--- 69

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  708 sys*NLTVQAMYVPPGAPNPKEwDDYTWQSASNPSVFFKVGETS--RFSVPFVGLASAYNCFYDGYShddqdtpygitVL 785
Cdd:cd00205     70 ---HTGRLLVAYVPPGAPAPTT-GDTRWQATLNPHVIWDLGTNSsvTFVVPYVSPTPYRSTRYDGYG-----------PL 134

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....
gi 2395881893  786 NHMGSMAFRVVNEHDV---HTTIVKIRVYHRAKHVEAWIPRAPR 826
Cdd:cd00205    135 NSFGTLVVRVLTPLTVpsgAPTTVDITVYVRAGDFELYGPRPPR 178

Pico_P2B

pfam01552

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

1001-1099

8.10e-29

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: 112.04 E-value: 8.10e-29

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1001 QGLGDYITSLGRAFGTGFTDQISAKVCELQDVAKDF--LTTKVLSKVVKMISALVIICRNHDDLVTVTATLALLGCDGSP 1078
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTQQISDKIKELTNFINPTskIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|.
gi 2395881893 1079 WRFLKMYISKHFQVPYIERQA 1099
Cdd:pfam01552   81 WQFLKEKACAVLEIPYVHKQG 101

Pico_P1A

pfam02226

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

2-69

1.09e-21

Pssm-ID: 308053 Cd Length: 68 Bit Score: 90.51 E-value: 1.09e-21

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2395881893    2 GAQVSTQKSGSHENQNILTNGSNQTFTVINYYKDAASSSSAGQSFSMDPSKFTEPVKDLMLKGAPALN 69
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 68

P3A

pfam08727

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

1432-1485

3.97e-16

Pssm-ID: 400873 Cd Length: 59 Bit Score: 74.38 E-value: 3.97e-16

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2395881893 1432 YKDLEIDVCNTPPP*CISDLLKSVDSEEVREYCKKKKWIIpQIPT--NIERAVNQA 1485
Cdd:pfam08727    5 GIDLKIDIKTSPPPEAIADLLQAVDSPEIIDYCEDKGWIV-NIPAecQIERDIGIA 59

Name

Accession

Description

Interval

E-value

Enterovirus_RdRp

cd23213

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

1727-2178

0e+00

Pssm-ID: 438063 Cd Length: 453 Bit Score: 788.26 E-value: 0e+00

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1727 VRDVGLNPINTPTKTKLHPSIFYNVFPGSKQPAVLSDNDPRLEVKLTESLFSKYKGNVQMEPTENMLVAVDHYAGQLMSL 1806
Cdd:cd23213      1 NKEVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1807 DISTKELTLKEALYGVDGLEPIDVTTSAGYPYVSLGIKKRDILNKETQDTEKMKFYLDKYGIDLPLVTYIKDELRSADKV 1886
Cdd:cd23213     81 DIDTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKV 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1887 RLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVIPCLMDGHLMAFDYSNF*ASLSPVWFEC 1966
Cdd:cd23213    161 EKGKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDGSLFAFDYTGYDASLSPVWFRA 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1967 LERVLSKLGFKH-PTLIQ*ICNTHHIFRDEIYKVEGGMPSGCSGTSIFNSMINNIIIRTLILDAYKGIDLDSLRILAYGD 2045
Cdd:cd23213    241 LKMVLEKGYSEEaVSLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYGD 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2046 DLIVSYPFELDSNILATIGKNYGLTITPPDKSDTFTKITWENITFLKRYFRPDPQFPFLVHPVMPMQDIYESIRWTKDPR 2125
Cdd:cd23213    321 DVIASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDPR 400

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2395881893 2126 NTQDHVRSLCMLAWHSGEKDYNDFIAKIRTTDIGKCLNLPEYSVLRRRWLDLF 2178
Cdd:cd23213    401 NTQDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453

Rabovirus_RdRp

cd23230

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

1818-2178

7.63e-174

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: 534.85 E-value: 7.63e-174

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1818 ALYGVDGLEPIDVTTSAGYPYVSLGIKKRDILNKETQDTEKMKFYLDKYGIDLPLVTYIKDELRSADKVRLGKSRLIEAS 1897
Cdd:cd23230      1 AAYGIENLEGLDLNTSAGYPYVLNGIKKRDILDPETRDTTKLQECLDKYGVDLPFVTYLKDELRPLEKIKKGKTRLIECS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1898 SLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVIPCLMDGHLMAFDYSNF*ASLSPVWFECLERVLSKLGFK 1977
Cdd:cd23230     81 SMNDTIRMKMMFGRLFATYHRNPGPITGSAVGCNPDIHWTKFRAEMHGEIIAFDYSNYDASLNKVWFECLKMVLKNFGFK 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1978 HPTLIQ*ICNTHHIFRDEIYKVEGGMPSGCSGTSIFNSMINNIIIRTLILDAYKGIDLDSLRILAYGDDLIVSYPFELDS 2057
Cdd:cd23230    161 DLRPIDHIIRSRHIYKGIEYDVEGGMPSGCSGTSIFNSIINNIIIMTLVLDAYKGIDLEQLKIIAYGDDVIVTYPYPLDA 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2058 NILATIGKNYGLTITPPDKSDTFTKITWENITFLKRYFRPDPQFPFLVHPVMPMQDIYESIRWTKDPRNTQDHVRSLCML 2137
Cdd:cd23230    241 ALLADCGKKYGLKMTPPDKSAEFKNVTWEDVTFLKRRFKPAKHYPFLIHPVFDQQEILESLRWTRNPAHTQEHVRSLAEL 320

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|.
gi 2395881893 2138 AWHSGEKDYNDFIAKIRTTDIGKCLNLPEYSVLRRRWLDLF 2178
Cdd:cd23230    321 AWHSGRKSYEEFCNLVKSTNVGKACILPPYESFKRMWLDQF 361

Sapelovirus_RdRp

cd23218

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

1817-2178

2.09e-160

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: 498.27 E-value: 2.09e-160

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1817 EALYGVDGLEPIDVTTSAGYPYVSLGIKKRDILNKETQDTEKMKFYLDKYGIDLPLVTYIKDELRSADKVRLGKSRLIEA 1896
Cdd:cd23218      1 DVVYGIDNLEGLDLNTSAGYPYNTMGIRKKDLIPPRGEPLSPLLKALDLHGYDLPFTTYLKDELRPKEKVKMGKTRLIEC 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1897 SSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVIPCLMD-GHLMAFDYSNF*ASLSPVWFECLERVLSKLG 1975
Cdd:cd23218     81 SSLNDTIRMKRIFGRLFQTFHKNPGTYTGSAVGCNPDVHWSKFAEEGGmDNVCAFDYTNWDASLSPFWFDALKLFLSKLG 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1976 F--KHPTLIQ*ICNTHHIFRDEIYKVEGGMPSGCSGTSIFNSMINNIIIRTLILDAYKGIDLDSLRILAYGDDLIVSYPF 2053
Cdd:cd23218    161 YseRDIVLIDHLCYSNHIFKNEGYKVAGGMPSGCSGTSIFNSIINNIVVRTLVLLVYKGINLDELRILCYGDDLLVAYPY 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2054 ELDSNILATIGKNYGLTITPPDKSDTF---TKITweNITFLKRYFRPDPQFPFLVHPVMPMQDIYESIRWTKDPRNTQDH 2130
Cdd:cd23218    241 PLDPNVLADLGKSLGLTMTPADKSDTFqgcTKLT--EVTFLKRSFVFDEEFPFLCHPVFPMEEVHESIRWTRNASTTQEH 318

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*...
gi 2395881893 2131 VRSLCMLAWHSGEKDYNDFIAKIRTTDIGKCLNLPEYSVLRRRWLDLF 2178
Cdd:cd23218    319 VTSLCLLAWHNGEEVYEEFCEKIRSVPVGRALILPPYSQLRRSWLDMF 366

ps-ssRNA_Picornaviridae

cd23193

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

1818-2154

4.51e-141

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: 443.14 E-value: 4.51e-141

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1818 ALYGVDGLEPIDVTTSAGYPYVSLGIKKRDILNKETQDT-----EKMKFYLDKYGIDLPLVTYIKDELRSADKVRLGKSR 1892
Cdd:cd23193      1 AINGIDGLDPIDLNTSPGYPYTTQGLRRRDLIDNDKGGVsplleEEEQVLLDLDGPDVVFTTFLKDELRPKEKVKAGKTR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1893 LIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVIP-CLMDGHLMAFDYSNF*ASLSPVWFECLERVL 1971
Cdd:cd23193     81 VIEAAPLDYVIAGRMVFGRLFAQFHSNPGILTGSAVGCNPDTDWTRLFaSLKQDNVYDLDYSGFDASLSSQLFEAAVEVL 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1972 S-KLGFKHPT--LIQ*ICNTHHIFRDEIYKVEGGMPSGCSGTSIFNSMINNIIIRTLILDAYKgIDLDSLRILAYGDDLI 2048
Cdd:cd23193    161 AeCHGDPELVlrYLEPIINSKHVVGDERYTVEGGMPSGCPCTSILNSICNNLVVRYALLETGK-FDPDEYYILAYGDDVL 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2049 VSYPFELDSNILATIGKNY-GLTITPPDKSDTFTKITWENITFLKRYFRPDPQFpFLVHPVMPMQDIYESIRWTKDPRNT 2127
Cdd:cd23193    240 VSTDEPIDPSDLAEFYKKYfGMTVTPADKSSDFPESSPIEDVFLKRRFFVPDGT-FLIHPVMDLETLEQSLMWCGRGGFF 318

                          330       340
                   ....*....|....*....|....*..
gi 2395881893 2128 QDHVRSLCMLAWHSGEKDYNDFIAKIR 2154
Cdd:cd23193    319 QQLLSSLCELALHHGPEEYERLVSKVR 345

Dicipivirus_RdRp

cd23222

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

1745-2175

1.12e-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: 280.32 E-value: 1.12e-82

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1745 PSIFYNVFPGSKQPAVLSDNDPRL--EVKLTESLFSKYKGNVQmEPTENMLVAVDHYAGQLMSLdISTKEL---TLKEAL 1819
Cdd:cd23222      2 PSPVYGVYPVTKEPAPLKPTDRRIdeGVDFNEPVFGKYGADMK-EPFRNLDVGRDVVIARLKKV-LPNKKFapcTVSEAL 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1820 YGVDGLEPIDVTTSAGYPYVSLGIKKRDIL--NKETQDTEKMKFYLD-----KYGIDLPLVTYIKDELRSADKVRLGKSR 1892
Cdd:cd23222     80 NGKDGLPKLDLKQASGYPYNLSAIKRKHLIesDKDGFLTATPKLLADieeskKHPEKFPYTSFLKDELRSVKKVKAGKTR 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1893 LIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWS--VIPCLMDGHLMAFDYSNF*ASLSPVWFECLERV 1970
Cdd:cd23222    160 VVEAGSLPVIVEGRMIFGNLFAYFNTHPGFETMAAVGCDPEVCWTdwYYKMREKAHTWDYDYTGFDGSIPSCSFDALADL 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1971 LSKLGFKHPTL---IQ*ICNTHHIFRDEIYKVEGGMPSGCSGTSIFNSMINNIIIRTLILDAYKGIDLDSLRILAYGDDL 2047
Cdd:cd23222    240 LCEFVENEDDVrryISNIKNSYHAYDGNLYLIEGAMPSGCAGTSVFNCLINAMLCFSCFMDLEPEMDPFEPLLIAYGDDI 319

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2048 IVSYPFEL-DSNILATIGKNYGLTITPPDKSDTFTKIT-WENITFLKRYFRPDPQFPfLVHPVMPMQDIYESIRWTKdpR 2125
Cdd:cd23222    320 LVSSDHDLfPSRVSEWMKANTTFKITPADKGEIFNDDSdVSDVRFLKRLFVEDPVCE-LIHPVIETETLEPSLNWCH--E 396

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2395881893 2126 NT-QDHVRSLCMLAWHSGEKDYNDFIAKIrtTDigKCLNLPE-------YSVLRRRWL 2175
Cdd:cd23222    397 GEfETKVDAISMLAFHHGPEYYRDWCKKL--TD--ICEERNIsppglkpYSVHRNRWL 450

Megrivirus_RdRp

cd23223

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

1749-2161

4.08e-78

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: 266.32 E-value: 4.08e-78

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1749 YNVFPGSKQPAVLSDNDPRLE--VKLTESLFSKYKGNVQMEPTenMLVAVDHYAGQLM-SLDISTKE----LTLKEALYG 1821
Cdd:cd23223      2 YGAFPVTHGPAALTNKDKRLEegVDLDDVMFSKHVPDHPGWPT--LEPAMSYVVEDLMhKLGFSKDEpvpmWTLEQAING 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1822 VDGLEPIDVTTSAGYPYVSLGIKKR---DILNKETQDTEKMKFYLD---KYGIDLPLVTYIKDELRSADKVRLGKSRLIE 1895
Cdd:cd23223     80 EGVMDGIDMGQSPGYPYNAQGRSRRsffEWNGEKWQPTEELKKEVDhalKDPDDFYFSTFLKDELRPLEKVKAGKTRLVD 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1896 ASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVI-----PCLMDgHLMAFDYSNF*ASLSPVWFECLERV 1970
Cdd:cd23223    160 GDSLPRILAMRMVFGPLFEAMLRKNGPEIHSAVGCNPDTDWTRYyhemgPDSFP-YCFDLDYSCFDSTEPKIAFRLMAKY 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1971 LsKLGFKHPT--LIQ*ICNTHHIFRDEIYKVEGGMPSGCSGTSIFNSMINNIIIRTLILDAykGIDLDSLRILAYGDDLI 2048
Cdd:cd23223    239 L-KPYFSVDVtpFFEALATSKHVYGDKAYEMEGGMPSGCVGTSMFNCINNSAFIVSALIAL--KISPEDCAWICYGDDVI 315

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2049 VSYPFE-LDSNILATIGKNYGLTITPPDKSDTFTKI-TWENITFLKRYFRPDPQFPFLVHPVMPMQDIYESIRWTKD-Pr 2125
Cdd:cd23223    316 ISTDEKaLSKRIADFYHKNTNLVVTPASKSGDFPETsTIYDVTFLKRFFQPDSHYPHLIHPYMPLEHLEQSVMWQTDgP- 394

                          410       420       430
                   ....*....|....*....|....*....|....*.
gi 2395881893 2126 nTQDHVRSLCMLAWHSGEKDYNDFIAKIrttdIGKC 2161
Cdd:cd23223    395 -FQQKLDSLCLLAFHAGGPDYREFVDAI----DKKC 425

Cardiovirus_RdRp

cd23211

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

1735-2178

1.41e-77

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: 265.55 E-value: 1.41e-77

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1735 INTPTKTKLHPSIFYNVFPGSKQPAVLSDNDPRLEVKLTESLFSKYKGNVQMEPTENMLVAVDhYAGQLMS-LDISTKEL 1813
Cdd:cd23211     12 VHVPRKTKLRRTVAHPVFQPKFEPAVLSKYDPRTDKDVDEVAFSKHTTNQESLPPVFRMVAKE-YANRVFTlLGKDNGRL 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1814 TLKEALYGVDGLEPIDVTTSAGYPYVSLGIKKRDILNKET-----QDTEKMKFYLDKYGIDLPLVTYIKDELRSADKVRL 1888
Cdd:cd23211     91 TVEQAVLGLEGMDPMEKDTSPGLPYTQQGLRRTDVVDFETatmipFLAEAHRKMVEGDYSDVVYQSFLKDEIRPIEKVQA 170

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1889 GKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVIPCLMDGHLMAFD--YSNF*ASLSPVWFEC 1966
Cdd:cd23211    171 AKTRIVDVPPFEHCILGRQLLGRFASKFQTNPGLELGSAIGCDPDVDWTAFAVALSGFKYVYDvdYSNFDSTHSTAMFEL 250

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1967 L--ERVLSKLGFKHPT--LIQ*ICNTHHIFRDEIYKVEGGMPSGCSGTSIFNSMINNIIIRTLILDAYKGIDLDSLRILA 2042
Cdd:cd23211    251 LieNFFTEENGFDPRIgeYLRSLAVSRHAYEERRVLIRGGLPSGCAATSMLNTIMNNIIIRAGLYLTYKNFEFDDIKVLS 330

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2043 YGDDLIVSYPFELDSNILATIGKNYGLTITPPDKSDTFTKI-TWENITFLKRYFRPDPqfPFLVHPVMPMQDIYESIRWT 2121
Cdd:cd23211    331 YGDDLLVATNYQIDFNLVKARLAKFGYKITPANKTSTFPLTsTLEDVVFLKRKFVKEN--SYLYRPVMDRENLKAMLSYY 408

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2395881893 2122 KdPRNTQDHVRSLCMLAWHSGEKDYNDFIAKIRTTDIgkclNLPEYSVLRRRWLDLF 2178
Cdd:cd23211    409 R-PGTLKEKLTSIALLAVHSGKQVYDEIFAPFREVGI----VVPTYESVLYRWLSLF 460

Cosavirus_RdRp

cd23226

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

1735-2178

2.99e-77

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: 264.96 E-value: 2.99e-77

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1735 INTPTKTKLHPSifYNVFPGSKQ--PAVLSDNDPRLE--VKLTESLFSKYKGNVQMEPTEN----MLVAVDHYAGQLMSL 1806
Cdd:cd23226     12 VHVPRQSKLKRT--NATYPATGKygPAVLSKNDPRLDpdVDFDKVIFSKHVANVVIDEDTSfwnaLKMSAQIYAEKFKGV 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1807 DISTkeLTLKEALYGVDGLEPIDVTTSAGYPYVS-----LGIKKRDILNKETQdtEKMKFYLDKYGIDLPLVTYIKDELR 1881
Cdd:cd23226     90 DFSP--LTVEEAILGIPGLDRMDPNTASGLPYTKtrrqmIDFQEGKILDPELQ--ERLDTWLSGKQPEMLYQTFLKDEIR 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1882 SADKVRLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVIPCLMDG--HLMAFDYSNF*ASL 1959
Cdd:cd23226    166 PIEKVKAGKTRIIDVTPLDHVLAFRIVLGRFMAHFHNNYGFELGSAVGCDPDVAWANFGFALSSkkYQYDFDYSNFDASH 245

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1960 SPVWFECLERVL--SKLGFKH--PTLIQ*ICNTHHIFRDEIYKVEGGMPSGCSGTSIFNSMINNIIIRTLILDAYKGIDL 2035
Cdd:cd23226    246 SESIFELLKQFVftKDNGFDHrcSLMIDSLVTSTHCYEDQRMTIRGGLPSGTSGTSVINTIINNIIFKAALYHTYSNFEW 325

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2036 DSLRILAYGDDLIVSYPFELDSNILATIGKNYGLTITPPDKSDTFTKITWENITFLKRYFRpdpQFPFLVHPVMPMQDIY 2115
Cdd:cd23226    326 DDVQMLAYGDDIVAASDCLLDLDRVKYFMALIGYKITPADKGEKFIPKDMQNIQFLKRSFR---KVAGVWAPIMDLENLQ 402

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2395881893 2116 ESIRWTKdPRNTQDHVRSLCMLAWHSGEKDYNdfiaKIRTTDIGKCLNLPEYSVLRRRWLDLF 2178
Cdd:cd23226    403 AMLSWYK-PGTLQEKLDSVARLAHFCGEKVYD----HLFTTFVKDGFQIKPWKQLHFEWLNRF 460

Aphthovirus_RdRp

cd23210

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

1735-2175

1.56e-75

RNA-dependent RNA polymerase (RdRp) in the Aphthovirus genus of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the Aphthovirus genus within the family Picornaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. This genus includes species such as bovine rhinitis A virus, bovine rhinitis B virus, equine rhinitis A virus, and food-and-mouth disease virus (FMDV). Aphthoviruses primarily infect via the upper respiratory tract. FMDV infects mainly cloven-hoofed animals, but has been isolated from at least 70 species of mammals. Aphthoviruses are non-enveloped and have an icosahedral capsid with a diameter of around 27 to 30 nm. The assembled viral capsid contains a single copy of the RNA genome and 60 copies of the four viral capsid proteins VP1, VP2, VP3, and VP4. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438060 Cd Length: 458 Bit Score: 259.88 E-value: 1.56e-75

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1735 INTPTKTKLHPSIFYNVFPGSKQPAVLSDNDPRLE--VKLTESLFSKYKGNVQM--EPTENMLVAVDHYAGQLMS-LDIS 1809
Cdd:cd23210      6 VHVMRKTKLAPTVAHGVFNPEFGPAALSNKDPRLNegVVLDEVIFSKHKGDTKMsaEDKALFRRCAADYASRLHSvLGTA 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1810 TKELTLKEALYGVDGLEPIDVTTSAGYPYVSLGIKKRDILNKET----QDTEKMKFYLDKYGIDLPLVTYIKDELRSADK 1885
Cdd:cd23210     86 NAPLSIYEAIKGVDGLDAMEPDTAPGLPWALQGKRRGALIDFENgtvgPEVEAALKLMEKREYKFACQTFLKDEIRPMEK 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1886 VRLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVIPCLMDGH--LMAFDYSNF*AS-LSPV 1962
Cdd:cd23210    166 VRAGKTRIVDVLPVEHILYTRMMIGRFCAQMHSNNGPQIGSAVGCNPDVDWQRFGTHFAQYrnVWDVDYSAFDANhCSDA 245

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1963 WFECLERVLSK-LGFKH--PTLIQ*ICNTHHIFRDEIYKVEGGMPSGCSGTSIFNSMINNIIIRTLILDAYKGIDLDSLR 2039
Cdd:cd23210    246 MNIMFEEVFRTeFGFHPnaEWILKTLVNTEHAYENKRITVEGGMPSGCSATSIINTILNNIYVLYALRRHYEGVELDTYT 325

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2040 ILAYGDDLIVSYPFELDSNILATIGKNYGLTITPPDKSDTF--TKITWENITFLKRYFRPDPQFPFLvHPVMPMQDIyES 2117
Cdd:cd23210    326 MISYGDDIVVASDYDLDFEALKPHFKSLGQTITPADKSDKGfvLGHSITDVTFLKRHFHMDYGTGFY-KPVMASKTL-EA 403

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2395881893 2118 IRWTKDPRNTQDHVRSLCMLAWHSGEKDYNDFIAKIRTTdigkcLNLPEYSVLRRRWL 2175
Cdd:cd23210    404 ILSFARRGTIQEKLISVAGLAVHSGPDEYRRLFEPFQGL-----FEIPSYRSLYLRWV 456

Kobuvirus_RdRp

cd23214

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

1735-2177

9.78e-75

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: 257.47 E-value: 9.78e-75

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1735 INTPTKTKLHPSIFYNVFPGSKQPAVLSDNDPRLE--VKLTESLFSKYKGNVQMEPTENMLVAVDHYAGQLMSldiSTKE 1812
Cdd:cd23214      3 VNVNRKSRLGPSPAYGAFPVKKQPAPLTQKDDRLEdgIRLDDQLFLKHNKGDMDEPWPGLEAAADLYFSKFPT---MIRT 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1813 LTLKEALYGVDGLEPIDVTTSAGYPYVSLGIKKRDILNKET----QDTEKMKFYLDKYGIDLPLV--TYIKDELRSADKV 1886
Cdd:cd23214     80 LTQEEAINGTPNLEGLDMNQAAGYPWNTMGRSRRSLFVEVQpgiyVPKPELQAEIDKTLEDPDYFysTFLKDELRPTAKV 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1887 RLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIiTGSAVGCDPDVFWS-------VIPCLMDghlmaFDYSNF*ASL 1959
Cdd:cd23214    160 TLGLTRVVEAAPIHAIVAGRMLLGGLIEYMQARPGK-HGSAVGCNPDLHWTkffykfcHYPQVFD-----LDYKCFDATL 233

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1960 SPVWFECLERVLSKL--GFKHPTLIQ*ICNTHHIFRDEIYKVEGGMPSGCSGTSIFNSMINNI-IIRTLIldAYKGIDLD 2036
Cdd:cd23214    234 PSCAFRIVEDHLERLtgDERVTRYIESIRHSHHVYGNETYEMIGGNPSGCVGTSIINTIINNIcVLSALI--QHPDFSPE 311

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2037 SLRILAYGDDLIVSY-PFELDSNILATIGKNYGLTITPPDKSDTFTKI-TWENITFLKRYFRPDPQFPFLVHPVMPmQDI 2114
Cdd:cd23214    312 SFRILAYGDDVIYGCdPPIHPSFIKEFYDKHTPLVVTPANKGSDFPETsTIYDVTFLKRWFVPDDIRPFYIHPVMD-PDT 390

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2395881893 2115 YE-SIRWTKDPrNTQDHVRSLCMLAWHSGEKDYNDFIAKIR---TTDIGKCLNLPEYSVLRRRWLDL 2177
Cdd:cd23214    391 YEqSVMWLRDG-DFQDLVTSLCYLAFHSGPKTYDRWCTRVRdqvMKTTGFPPTFLPYSYLQTRWLNL 456

Mischivirus_RdRp

cd23227

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

1735-2174

1.17e-73

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: 254.49 E-value: 1.17e-73

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1735 INTPTKTKLHPSIFYNVFPGSKQPAVLSDNDPRL--EVKLTESLFSKYKGNVQMEPTENMLVAvDHYAGQLMS-LDISTK 1811
Cdd:cd23227     12 IHVPRKTKLRKSPAYPIFKPDAGPAVLSKNDPRLaeGVDFDKQVFSKHSANQKEYPKAFRRMA-RWYADRVFTyLGKDNG 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1812 ELTLKEALYGVDGLEPIDVTTSAGYPYVSLGIKKRDILNKETQD------TEKMKFYLDKYGIDLPLVTYIKDELRSADK 1885
Cdd:cd23227     91 PLSVKDAIKGIDNLDAMDPTTSPGLPYSAAGIKRTDLLDFDTGEiispalRAEYNKYVSGDYSDHVFQTFLKDEIRSEEK 170

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1886 VRLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVIPC-LMDGH-LMAFDYSNF*ASLSPVW 1963
Cdd:cd23227    171 IKAGKTRIVDVPSLAHVIIGRVLLGKFCSKFQASPGTELGSAIGCNPDWDWTYFAHqLMERQwCYDIDYSNFDSTHGTGM 250

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1964 FECL-ERVLSKLGFKHPTL---IQ*ICNTHHIFRDEIYKVEGGMPSGCSGTSIFNSMINNIIIRTLILDAYKGIDLDSLR 2039
Cdd:cd23227    251 FELLiDCFFTPENGFSPAVapyLRSLAFSKHAWMDKRYKIEGGLPSGCSATSVLNTVMNNIIIRALLSLTYKNFHPEDVL 330

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2040 ILAYGDDLIVSYPFELDSNIL-ATIGKNYGLTITPPDKSDTFTKI-TWENITFLKRYFRPDPQFPFLVHPVMPMQDIYES 2117
Cdd:cd23227    331 VLAYGDDLLVASDYQLDFNRVrEKAAEHTLYKLTTANKAPDFPETsTLLDCQFLKRKFVLHSTRNFIWRPVMDVTNLKTM 410

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2395881893 2118 IRWTKdPRNTQDHVRSLCMLAWHSGEKDYNDFIAKIRTTDIgkclNLPEYSVLRRRW 2174
Cdd:cd23227    411 LSFYK-PNTLSEKLLSVAQLAFHSGYTVYEELFAPFKELQM----TVPSWWYLEHEW 462

ps-ssRNAv-Picornavirales

cd23169

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

1873-2154

7.63e-71

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: 240.57 E-value: 7.63e-71

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1873 VTYIKDELRSADKVRLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPgIITGSAVGCDPD-VFWSVIP---CLMDGHLM 1948
Cdd:cd23169      4 VDCLKDELRPIEKVKAGKTRLFSASPLDYTIAFRKYFGDFIAAFQKNR-IKLEHAVGINPDsVEWTRLYrrlLKKGPNIF 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1949 AFDYSNF*ASLSPVWFECLERVLSKLGFKHP---------TLIQ*ICNTHHIFRDEIYKVEGGMPSGCSGTSIFNSMINN 2019
Cdd:cd23169     83 AGDYSNFDGSLPPDVMEAAFDIINDWYDEYVddedervrkVLFEELINTIHLVGNLVYQVHGGNPSGNPLTTIINSIVNL 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2020 IIIRTLILDAYKGIDLDS----LRILAYGDDLIVS----YPFELDSNILATIGKNYGLTITPPDKSDTFTK-ITWENITF 2090
Cdd:cd23169    163 LYIRYAWLRITGLTSLSDfkknVRLVTYGDDVIISvsdeVKDEFNFVTISEFLKELGITYTDADKSGDIVPyRPLEEVTF 242

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2395881893 2091 LKRYFRPDPQfPFLVHPVMPMQDIYESIRWTK---DPRNTQDHVRSLCMLAWHS-GEKDYNDFIAKIR 2154
Cdd:cd23169    243 LKRGFRPHPT-PGLVLAPLDLESIEEQLNWTRkedDLLEATIENARAALLLAFGhGPEYYNKFRQKLN 309

Mosavirus_RdRp

cd23225

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

1823-2177

2.66e-69

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Mosavirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Mosavirus genus within the family Picornaviridae, order Picornavirales. The Mosavirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. This genus includes two species: Mosavirus A, which found in the feces of a canyon mouse (Peromyscus crinitus), and Mosavirus B, which contains marmot mosavirus. Mosavirus stands for mouse stool-associated picornavirus. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438075 Cd Length: 378 Bit Score: 238.66 E-value: 2.66e-69

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1823 DGL-EPIDVTTSAGYPYVSLGIKKRDILnkETQDTEKMKFYL---------DKY--GIDLP-LVTYIKDELRSADKVRLG 1889
Cdd:cd23225      6 DGIsDAMDMTKAVGYPYCLDSIKRLDLV--EIKETENGKVYLpterlveetEKFftGEEKPkFVTFLKDEVRSNEKIKQG 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1890 KSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVIPC-LMDGHLMAFDYSNF*ASLSPVWFECLE 1968
Cdd:cd23225     84 KTRIVDASPFPYAIAGRMVMQNFMSNMMRCNGTEVGSAVGCDPDTEWTRYFFeLCDRYVFDLDYKAFDSTHPTAMFNLLA 163

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1969 R--VLSKLGFKHPT---LIQ*ICNTHHIFRDEIYKVEGGMPSGCSGTSIFNSMINNIIIRTLILDAYKG--IDLDSLRIL 2041
Cdd:cd23225    164 ErfFTERNGFDQQAvriFLNGLSDSDHVYEGKHFRIRGGLPSGCPCTSILNTVINNIIVRAAILGAYQIdtVDFQKFRML 243

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2042 AYGDDLIVSYPFELDSNILAT-IGKNYGLTITPPDKSDTF-TKITWENITFLKRYFRPDPQFPFLVHPVMPMQDIYESIR 2119
Cdd:cd23225    244 AYGDDVVYATPQPIKPQDLADwLHANTNYKVTPASKAGTFpEESTIWDVTFLKRSFKPDEDHGHLIRPVMAVGNLKQMLS 323

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2395881893 2120 WTKdPRNTQDHVRSLCMLAWHSGEKDYNDFIAKIRTTDIGkcLNLPEYSVLRRRWLDL 2177
Cdd:cd23225    324 FMR-PGTFPDKVRSVAGLAVHCGEEDYNQLADAVALYVPG--VSMPAYKYMKACWYAK 378

Rosavirus_RdRp

cd23221

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

1818-2178

2.79e-66

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: 230.19 E-value: 2.79e-66

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1818 ALYGVDGLEPIDVTTSAGYPYVSLGIKKR---DILNKETQDTEKMKFYLDKYGIDLPL---VTYIKDELRSADKVRLGKS 1891
Cdd:cd23221      1 AINGIDNMDGLDMNQSPGVPYVSEGVSRRslfDCVDGQWVPRERLASDIAQVSGDPSLghfATFLKDELRSTEKVAAGKT 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1892 RLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVI--PCLMDGHLMAFDYSNF*ASLSPVWFECLER 1969
Cdd:cd23221     81 RVVEAGSLPHIIVGRKIFGNLFALFNSNPGFQTMCAVGCDPDVTWTELyhPLSAKTYVFDYDYSGFDGSVPSCCFDALAD 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1970 VLSKLGFKHPTL---IQ*ICNTHHIFRDEIYKVEGGMPSGCSGTSIFNSMINNIIIRTLILDAYKGIDLDSLRILAYGDD 2046
Cdd:cd23221    161 LLADFVEGEEDVrkyISSLKTSFHHYKGKLWRLDGAMPSGCCGTSVFNSLINAMLLFSAFSQICPDFRASEPLLVAYGDD 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2047 LIVSYPFEL-DSNILATIGKNYGLTITPPDKSDTFTKIT-WENITFLKRYFRPDPQFPFLVHPVMPMQDIYESIRWTKdP 2124
Cdd:cd23221    241 VLVGTDQPLfPSKVAEWVNSHTTFRITPADKGSVFNDESdIHSVQFLKRHFTPDPDFPALIHPTIDPDTYEQSVMWQR-T 319

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2395881893 2125 RNTQDHVRSLCMLAWHSGEKDYNDFIAKIrttdIGKCLN-------LPEYSVLRRRWLDLF 2178
Cdd:cd23221    320 GDFQETVNSLALLVFHRGPKSYSRWCESV----TRKCVDggypppfFPPFSLLRHQWLKKF 376

Pico_P2A

pfam00947

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

873-999

1.45e-64

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

Pssm-ID: 395757 Cd Length: 127 Bit Score: 215.32 E-value: 1.45e-64

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  873 NYHLMTPEDHLNLITPYPNRDLAVVATGAHGAETIPHCSCTSGVYYSRYYRKFYPIICERPTNIWIEGGPYYPSRYQAGV 952
Cdd:pfam00947    1 NRHLATHEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 2395881893  953 MKGVGPAEPGDCGGILRCIHGPIGLLTAGGGG*VCFADIRQLDFIAD 999
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVRDLLWLEE 127

Teschovirus_RdRp

cd23212

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

1813-2140

5.81e-61

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: 213.71 E-value: 5.81e-61

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1813 LTLKEALYGVDGLEPIDVTTSAGYPYVSLGIKKRDILNKETQDTEKMKFYLDKYgIDLP-----LVTYIKDELRSADKVR 1887
Cdd:cd23212     11 LSVREAVEGIDGLDPMDMDKSPGLPYVKKGLRRTDLWNPKTGPSIELMAEINRY-LDYNydkhvFLTFLKDELRPKEKVQ 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1888 LGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWS-VIPCLMDGHLMAFDYSNF*ASLSPVWFEC 1966
Cdd:cd23212     90 AGKTRVIDVAGFGHAIVGRMLFGRLFAFFHKNPGWNTGSAVGVNPDLAWTqIFYTAPSRNVLAMDYSGFDASHTSGMFCI 169

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1967 LERVLSKLGFK--HPTLIQ*ICNTHHIFRDEIYKVEGGMPSGCSGTSIFNSMINNIIIRTLILDAYKGidldSLRILAYG 2044
Cdd:cd23212    170 LKHFLTTLGYGtlQLSYIDSLCYSKHHWDDETYRLDGGLPSGCSGTTIFNTIMNNIVARAAASYAAEG----PVGILCYG 245

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2045 DDLIVSYPFELDSNILATIGKNYGLTITPPDKSDtftKITWENI---TFLKRYFRPDPQfpfLVHPVMPMQDIYESIRWT 2121
Cdd:cd23212    246 DDILVSSPEKFPVSDWLEFYSKTPYKVTAADKSE---QIDWRDItqcTFLKRGFVLDGS---LVRPVMEEQHLAELLKWA 319

                          330
                   ....*....|....*....
gi 2395881893 2122 KdPRNTQDHVRSLCMLAWH 2140
Cdd:cd23212    320 R-PGTLQAKLLSIAQLAFH 337

RNA_dep_RNAP

cd01699

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

1867-2121

2.65e-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: 209.06 E-value: 2.65e-60

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1867 GIDLPLVTYIKDELRSADKVRLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNpGIITGSAVGCDPDVF-WSVIPCLMDG 1945
Cdd:cd01699     15 RPDLVFTTFLKDELRPLEKVEAGKTRLIQPRPLDYNIALRMYLGPFEAKLMKN-RGGLPIAVGINPYSRdWTILANKLRS 93

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1946 ---HLMAFDYSNF*ASLSPVWFECLERVLSKLGFKH-----PTLIQ*ICNT-HHIFRDEIYKVEGGMPSGCSGTSIFNSM 2016
Cdd:cd01699     94 fspVAIALDYSRFDSSLSPQLLEAEHSIYNALYDDDdelerRNLLRSLTNNsLHIGFNEVYKVRGGRPSGDPLTSIGNSI 173

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2017 INNIIIRTLILDAYKGIDLDSLRILAYGDDLIVSYPFELD---SNILATIGKNYGLTITPPDKSDTFTKiTWENITFLKR 2093
Cdd:cd01699    174 INCILVRYAFRKLGGKSFFKNVRLLNYGDDCLLSVEKADDkfnLETLAEWLKEYGLTMTDEDKVESPFR-PLEEVEFLKR 252

                          250       260
                   ....*....|....*....|....*...
gi 2395881893 2094 YFRPDPQfpFLVHPVMPMQDIYESIRWT 2121
Cdd:cd01699    253 RFVLDEG--GGWRAPLDPSSILSKLSWS 278

Rhv

pfam00073

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

93-298

3.64e-58

Pssm-ID: 395026 Cd Length: 170 Bit Score: 198.69 E-value: 3.64e-58

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893   93 TTQEAANAVVCYAEWPEYLSDSDASDVNKTSKPDTSVCRFYTLDSKTWKATSKGW-CWKLPDALKDMGVFGQNMFYHSLG 171
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFfWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  172 RTGYTIHVQCNATKFHSGCLLVVVIPEH*lasheggtvsvkykYTHPGDRgidldtvevaggptsdaiynmdgTLLGNLL 251
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPPG---------------APPPGSR-----------------------DYLWQAT 122

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 2395881893  252 IFPHQFINLRTNNTATIVVPYINSVPIDSMTRHNNVSLMVIPIAPLN 298
Cdd:pfam00073  123 LNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGNWTLVVAGWVPLN 169

Passerivirus_RdRp

cd23224

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

1817-2177

2.92e-56

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

Pssm-ID: 438074 Cd Length: 380 Bit Score: 201.09 E-value: 2.92e-56

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1817 EALYGVDGLEPIDVTTSAGYPYvSLGIKKRDILNKETQDTEKMKFYLDKYGI------DLPLVTYIKDELRSADKVRLGK 1890
Cdd:cd23224      1 EAINGTPLLDGLDMKQSPGYPW-SLTTNRRSLFTQDETGKYYPVPELEEAVLaclenpDYFYTTHLKDELRPVEKALAGK 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1891 SRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIItGSAVGCDPDVFWSVIPCLMD--GHLMAFDYSNF*ASLSPVWFECLE 1968
Cdd:cd23224     80 TRLIEAAPIHAIIAGRMLLGGLFEYMHARPGEH-GSAVGCDPDYHWTPFFHSFDefSQVWALDYSCFDSTLPSCCFDLIA 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1969 RVLSKLGFKHPTL--------IQ*ICNTHHIFRDEIYKVEGGMPSGCSGTSIFNSMINNIIIRTLILdAYKGIDLDSLRI 2040
Cdd:cd23224    159 QKLAKIITPGEGIapdaivkyIRSISISKHVFGNEAYLMVGGNPSGCVGTSILNSMINNCVLISAFL-TQKDFNPNQMRI 237

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2041 LAYGDD-LIVSYPFELDSNILATIGKNYGLTITPPDKSDTFT--KITWEnITFLKRYFRPDPQFPFLVHPVMPMQDIYES 2117
Cdd:cd23224    238 LTYGDDvLYATNPPIHPRVVKKFFDENTTLIVTPATKAGDFPdeSTIWD-VTFLKRYFVPDEIRPWYVHPVIEPATYEQS 316

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2395881893 2118 IRWTKDPrNTQDHVRSLCMLAWHSGEKDYNDFIAKIRTTDIGKCL--NLPEYSVLRRRWLDL 2177
Cdd:cd23224    317 VMWTRGG-DFQDVVTSLSFLAHHAGPTNYMIWEEKVRKAAAAKGVslNILPYSYLQHRWMLL 377

RdRP_1

pfam00680

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

1744-2153

7.39e-51

Pssm-ID: 425815 Cd Length: 450 Bit Score: 187.62 E-value: 7.39e-51

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1744 HPSIFYNVFPGSKQPAVLSDNDPRL--EVKLTESLF---SKYKGNVQMEPTENMLVAVDHYAGQLMSLDISTK------E 1812
Cdd:pfam00680    1 SPTERHLVAIPAYVPASLGPEDPRWarSYLNTDPYVddiKKYSRPKLPGPADERDKLLNRSAAKMVLSELRGVpkkansT 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1813 LTLKEALYGVDGLEPIDVTTSAGYPYVSLGIKKRDiLNKETQDTEKMKFYLDK---------YGIDLPLV--TYIKDELR 1881
Cdd:pfam00680   81 LIVYRAIDGVEQIDPLNWDTSAGYPYVGLGGKKGD-LIEHLKDGTEARELAERlaadwevlqNGTPLKLVyqTCLKDELR 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1882 SADKVRLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITgSAVGCDP-DVFWSV----IPCLMDGHLMaFDYSNF* 1956
Cdd:pfam00680  160 PLEKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHP-IQVGINPfDRGWPRllrrLARFGDYVYE-LDYSGFD 237

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1957 ASLSP----VWFECLErvlSKLGF-----KHPTLIQ*ICNTHH-IFRDEIYKVEGGMPSGCSGTSIFNSMINNIIIRTLI 2026
Cdd:pfam00680  238 SSVPPwlirFAFEILR---ELLGFpsnvkEWRAILELLIYTPIaLPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYAL 314

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2027 LDAYKGIDLDSLRI------LAYGDDLI--VSYPFELDSNILATIGKNYGLTITPPDKSDTFTKITwENITFLKRYFRPD 2098
Cdd:pfam00680  315 LKSLENDGPRVCNLdkyfdfFTYGDDSLvaVSPDFDPVLDRLSPHLKELGLTITPAKKTFPVSREL-EEVSFLKRTFRKT 393

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2395881893 2099 PQFpflVHPVMPMQDIYESIRWTKDPRNTQDHVRSLCMLAWHSGEKDYNDFIAKI 2153
Cdd:pfam00680  394 PGG---YRPPLDRKRILAQLEYIRSKPVPSGQLENIRAYASHHGYEFYRDLLYRF 445

Fipivirus_RdRp

cd23229

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

1821-2174

2.66e-48

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: 178.46 E-value: 2.66e-48

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1821 GVDGLEPIDVTTSAGYPYVSLGIKKRDILNKE-----------TQDTEKMKFYLDKYGIDLPLVTYI---KDELRSADKV 1886
Cdd:cd23229      4 GIPGMEGLDMKTSAGYPWCEQNQKKKDKIKLLagknflvrplrEVVHIVVDWYIMPPDMPKPEIKYVvylKDELLSSDKV 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1887 RLGKSRLIEASSLNDSVNMRMKLGNLYKAFH-QNP--GIITGSAVGCDPDVFWSVIP-CLMDGHLMAFDYSNF*ASLSPV 1962
Cdd:cd23229     84 KMGRTRWICAAPVQLVCAWKKVFGRAIAAIHlESVtdGKSTGCAVGMDPETAWTDIAlARPGWPVIALDYSNFDGSLQSF 163

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1963 WFECLERVLSKLGFKHPT----LIQ*ICNTHHIFRDEIYKVEGGMPSGCSGTSIFNSMINnIIIRTLILDAYKGIDL--- 2035
Cdd:cd23229    164 VITGAVRILGYIAGLPDGqsyrLAEFVYDVKQIVGKYLYTTVGPLPSGCPSTSIIGSLCN-VLMLLYTLSHATGQRYsaf 242

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2036 -DSLRILAYGDDLIVSYPFELDSNILAT---IGKNYGLTIT-------PPDKSDTftkitwENITFLKRYFRPDPQFPFL 2104
Cdd:cd23229    243 rDWMHVVTYGDDVLVFVHPEVVVVLDTLaheMYLVFGVTATdatdkraPPQLREL------SNVTFLKRGFRQCSSVPFL 316

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2395881893 2105 VHPVMPMQDIYESIRWTKDPRNTQDHVRSLCMLAWHSGEKDYNDFIAKIRTT-------DIGKCLN-LPEYSVLRRRW 2174
Cdd:cd23229    317 VHPTMDKSTIYQMLAWKRKGTTLAENVKCAAEFMMHHGEEEYEDFVGVVKECstligvdQRSKVYEeLCSYAELHDHW 394

RNA_helicase

pfam00910

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

1224-1322

2.44e-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: 145.05 E-value: 2.44e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1224 VLIHGTPGSGKSLTTSIVGRALAEHFN---SSVYSLPPDPKHFDGYQQQEVVIMDDLNQNPDGQDISMFCQMVSSVDFLP 1300
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKKLGlpkDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 2395881893 1301 PMASLDNKGMLFTSNFVLASTN 1322
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

Hepatovirus_RdRp

cd23215

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

1776-2177

2.75e-40

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: 156.93 E-value: 2.75e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1776 LFSKYKGNVQMEPtENMLVAVDHYAGQLMSLDISTKE-LTLKEALYGVDGLEPIDVTTSAGYPYVSLGIKKRDI------ 1848
Cdd:cd23215     28 MLSKYSLPIVEEP-VDYKDVVVFYQNKILGKDILYDEfFDLEQAITGVPGMDAINMDSSPGYPYVQEKLTKSDLiwlddn 106

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1849 ---LNKETQDTEKMKFYL----DKYGIDLPLVTYIKDELRSADKVRLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPG 1921
Cdd:cd23215    107 gelLGMHPRLAQRILFNLtmmdNGNDLDVVYTTCPKDELRPLEKVLESKTRAIDACPLDFTIICRMFWGPAISYFQLNPG 186

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1922 IITGSAVGCDPDVFWSVIPCLM---DGHLMAFDYSNF*ASLSPVWFECLERVLSKLG----FKHPTLIQ*ICNTHHIFRD 1994
Cdd:cd23215    187 FHTGVAVGIDPDRDWDALFKTMirfGDYGIDLDFSSFDASLSPFMIREACRVLSELSgvpdHQGQALINTIIYSKHLLYN 266

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1995 EIYKVEGGMPSGCSGTSIFNSMINNIIIRTLILDAYKGIDL---DSLRILAYGDDLIVSYPFELDSNILATIGKN----- 2066
Cdd:cd23215    267 LCYHVCGSMPSGSPCTSLLNSIVNNVNLYYVFSKIFKKSPVffyDAVKFLCYGDDVLIVFSRDLEIKNLDKLGQRiqdef 346

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2067 --YGLTITPPDKSDTFTKITWEnITFLKRYFRpdpqfpfLV----HPVMPMQDIYESIRWTKDPRNTQDHVRSLCMLAWH 2140
Cdd:cd23215    347 klLGMTATSADKGEPQVVPVSE-LTFLKRSFN-------LIedrfRPAISEKTIWSLVAWQRSNAEFEQNLDTACWFAFM 418

                          410       420       430
                   ....*....|....*....|....*....|....*....
gi 2395881893 2141 SGEKDYNDFIAKIRTTDIGKCLN--LPEYSVLRRRWLDL 2177
Cdd:cd23215    419 HGYDFYQNFYLQLQSCLEKEMIDyrLKSYEWWRMRFEDL 457

Kunsagivirus_RdRp

cd23219

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

1815-2133

2.86e-40

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: 153.48 E-value: 2.86e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1815 LKEALYgvDGLEPIDVTTSAGYPYVslGIKKRDILNKETQ--------DTEKMKFYLDKYGID-LPLVTYIKDELRSADK 1885
Cdd:cd23219      1 IEEAVF--DTVTPMDHTASAGPKYP--GTKRSELIDFQNRiisdrlrnDVLELQFRGTSGGAGeVKFSSFLKDELRPLSK 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1886 VRLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCdpDVFWSVIPC---LMDGHLmAFDYSNF*ASLSPV 1962
Cdd:cd23219     77 IRSGDTRVVECSSLDYTVAFRMQFLRVLQMCYGSDPTLTGLAPGM--NVYTDMLPLctsLYDYNL-CLDFSKYDSRLPLQ 153

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1963 WFECLERVLSKLGfKHPT----LIQ*ICNTHHIFRDEIYKVEGGMPSGCSGTSIFNSMINNIIIRTLILDAYKGIDldsL 2038
Cdd:cd23219    154 VMHRVAQLISNLT-PDPQvsmrLFQPIIISTHIVGSYEVVVEGGMPSGCPITTIMNSVCNVVMTSYAMLLLDPDSD---F 229

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2039 RILAYGDDLIVSYPFELDSNILATI-GKNYGLTITPPDKSDTFTKITWENITFLKRYFRPDPQFPFLVhPVMPMQDIYES 2117
Cdd:cd23219    230 WPVAYGDDNIVSTRKPIDTELFCSIlNEEFGMILTGADKTTTVQAVPPMSVDFLKRRLRYTPEFPLPV-PVLPLDSMLSR 308

                          330
                   ....*....|....*.
gi 2395881893 2118 IRWTKDPRNTQDHVRS 2133
Cdd:cd23219    309 ICWCKGETEFKDQLES 324

Peptidase_C3

pfam00548

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

1537-1701

7.87e-40

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: 146.44 E-value: 7.87e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1537 GPNTEFALSLLRKNILTITTEKGEFTSL--GIHDRICVLPTHAQPSDSVLVNGQRIQIKD-KYKLVDPDNTNLELTIIEL 1613
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1614 DRNEKFRDIRGFISEDL-EGIDATLVVHSNGFTNTMLDVGPITMAGLI-NLSNTPTTRMIRYDYPTKTGQCGGVL----C 1687
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRItKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVViakvE 160

                          170
                   ....*....|....
gi 2395881893 1688 TTGKIFGIHVGGNG 1701
Cdd:pfam00548  161 GNGKILGMHIAGNG 174

Rhv

pfam00073

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

614-770

9.35e-40

Pssm-ID: 395026 Cd Length: 170 Bit Score: 145.92 E-value: 9.35e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  614 PSDNVETRTTYMHFNGSETDVESFLGRAACV--HVTEIKNKDAAGLDNHKREGLFNDWKINLS--SLVQLRKKLELFTYV 689
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVqpDVQGERFYTLDSTDWTSLSKGFFWWKLPLAllSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  690 RFDSEYTILATASQpeassyS*NLTVQAMYVPPGAPNPKEWdDYTWQSASNPSVFFKVGETS--RFSVPFVGLASAYNCF 767
Cdd:pfam00073   81 RGGLEVTVQFNGSK------FHQGKLLVAYVPPGAPPPGSR-DYLWQATLNPHQFWNLGLNSsaRLSVPYISIAHYYSTF 153


                   ...
gi 2395881893  768 YDG 770
Cdd:pfam00073  154 YDG 156

Parechovirus_RdRp

cd23217

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

1818-2153

2.80e-38

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

Pssm-ID: 438067 Cd Length: 371 Bit Score: 148.48 E-value: 2.80e-38

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1818 ALYGVDGLEPIDVTTSAGYPYVSLGIKKRDILNKET-----QDTEKMKFYL-DKYGIDLP---LVTYIKDELRSADKVRL 1888
Cdd:cd23217      1 AVLGTSHLNSLDLSTSPGYKYVKSGYKKRDLLSLEPfsvspQLEKDVKDKLhAVYKGNQPttiFNACLKDELRKLDKIAQ 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1889 GKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVIPCLMDGHLMAFDYSNF*ASLSPvwfECLE 1968
Cdd:cd23217     81 GKTRCIEACSIDYVIAYRVVMSSLYEAIYQTPCQELGLAVGMNPWTDWDFMINALNPYNYGLDYSSYDGSLSE---MLMW 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1969 RVLSKLGFKH--PTLI----Q*ICNTHHIFRDEIYKVEGGMPSGCSGTSIFNSMINNIIIRTLildAY-KGIDLDSLRIL 2041
Cdd:cd23217    158 EAVEVLAYCHesPDLVmqlhKPVINSDHVVMDERWLVHGGMPSGSPCTTVLNSICNLLVCIYL---AYlQSPGIECLPIV 234

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2042 aYGDDLIVSYPFELDSNILA-TIGKNYGLTITPPDKSDTFTKITWENITFLKRYFRPDPQFPFLVHpVMPMQDIYESIRW 2120
Cdd:cd23217    235 -YGDDVIFSVSSEIDPEYLVsSAADSFGMEVTGSDKDEPPSLLPRMEVEFLKRTTGYFPGSTYKVG-ALDLETMEQHIMW 312

                          330       340       350
                   ....*....|....*....|....*....|....
gi 2395881893 2121 TKDPRNTQDHVRSLCM-LAWHsGEKDYNDFIAKI 2153
Cdd:cd23217    313 MKNLSTFPQQLQSFENeLCLH-GKDIYDDYKKIF 345

rhv_like

cd00205

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

125-324

1.64e-37

Pssm-ID: 119412 Cd Length: 178 Bit Score: 139.84 E-value: 1.64e-37

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  125 PDTSVCRFYTLDSKTWKA---TSKGWCWKLPDA----LKDMGVFGQNMFYHSLGRTGYTIHVQCNATKFHSGCLLVVVIP 197
Cdd:cd00205      1 VESFADRPTTVGTNNWNSsasGTQLFQWKLSPAlgflLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  198 EH*lasheggtvsvkykythpgdrgidldtvevAGGPTSDaiynmdgTLLGNLLIFPHQFINLRTNNTATIVVPYINSVP 277
Cdd:cd00205     81 PG-------------------------------APAPTTG-------DTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTP 122

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2395881893  278 IDSMTRH------NNVSLMVIPIAPLNAPTGSSPTLPVTVTIAPMCTEFTGIR 324
Cdd:cd00205    123 YRSTRYDgygplnSFGTLVVRVLTPLTVPSGAPTTVDITVYVRAGDFELYGPR 175

Limnipivirus_RdRp

cd23228

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

1824-2154

1.82e-37

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Limnipivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Limnipivirus genus within the family Picornaviridae, order Picornavirales. The Limnipivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. This genus contains three species, Limnipivirus A (bluegill picornavirus 1), Limnipivirus B (carp picornavirus 1) and Limnipivirus C (fathead minnow picornavirus 1). Limnipiviruses infect freshwater fishes. The virus can be grown in various fish cell lines. Experimental infection of bluegills with bluegill picornavirus induces morbidity (inflammation and redness at the base of fins, exophthalmia, abdomen distension, internal hemorrhaging and ascites) and mortality. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438078 Cd Length: 390 Bit Score: 146.56 E-value: 1.82e-37

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1824 GLEPIDVTTSAGYPYVSLGIKKRD---ILNKET--------QDTEKMKFYLDKYG-IDLPLVTYIKDELRSADKVRLGKS 1891
Cdd:cd23228      6 GTNPIDKNTSPGLKYTRDGLKKSDlytIDEDGNvvvsdmlrADVEAWEELIQSGGyPTTLFTACLKDELRSDEKVALGKT 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1892 RLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPdvfwsvipcLMDGH-----------LMAFDYSNF*ASLS 1960
Cdd:cd23228     86 RVIEAAELDYVVAYRMYMSSIYSDLYNAYAGDTGIAAGINP---------PADGHrlreelsqydsFLALDYSRFDGSLP 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1961 PVWFECLERVLSKLgFKHPTLIQ*ICNT----HHIFRDEIYKVEGGMPSGCSGTSIFNSMINNIIIRTLILDAYkGIDLD 2036
Cdd:cd23228    157 EMLMRAAVEILADL-HEDPDLVRRLHETviisKHLVVDEDWTVKGGMPSGSPCTTVLNCICNLLVLEYAFLVHF-GVYED 234

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2037 SLR---------ILAYGDDLIVSY-PFELDSNILATIGKNYGLTITPPDKSDTFTKITWENITFLKR-YFRPDPQFPFLV 2105
Cdd:cd23228    235 DDGvglpqcdylSVVYGDDCIVAYnGMEMGLAFAETIEDTFGMEVTPASKVGDHFNVELHEVEFLKRkFFAFETEEYDRI 314

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2395881893 2106 HPVMPMQDIYESIRWTKDPRNTQDHVRSLCM--LAWhsGEKDYNDFIAKIR 2154
Cdd:cd23228    315 ALRLSENTIVQSLMWMRNLKTFPDQVQSLMMelSAW--GKEKYDKLRDTCK 363

Crohivirus_RdRp

cd23232

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

1815-2167

2.36e-37

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: 146.01 E-value: 2.36e-37

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1815 LKEALYGVDGLEPIDVTTSAGYPYVSLGIKKR-----------DILNKETQDTEKMKFYLDKygIDLPLVTYIKDELRSA 1883
Cdd:cd23232      1 IEEACFEEGDEHALDLKTSPGFKYVQMGLKKTdlvnrpnkfihPILRNDVRLIFDEMAKGQM--PVVTFTAHLKDELRKL 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1884 DKVRLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFW-SVIPCLmDGHLMAFDYSNF*ASLSPV 1962
Cdd:cd23232     79 EKIRSGKTRCIEACDFDYTVAHKMMFGTLYKAIYDTPGIITGLAVGMNPWKDWeLIQQSL-FKYNYDFDYKTFDGSLSRE 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1963 WF----ECLERVLSKLGFKHPTLIQ*IcNTHHIFRDEIYKVEGGMPSGCSGTSIFNSMINNIIIRTLILDAYKGidldSL 2038
Cdd:cd23232    158 LMlhavDILSACVENDEMAKLMLSVVV-ESVHLVLDQKWNVSGGMPSGSPCTTVLNSVCNLIVSSTIADMCTEG----DF 232

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2039 RILAYGDDLIVSYPFELD-SNILATIGKNYGLTITPPDKSDTFTKITWENITFLKRYFRPDPQFPFLVHpVMPMQDIYES 2117
Cdd:cd23232    233 KILVYGDDLIISSTAPLDcDRFKTLVELHYGMEVTPGDKGDEFKVKDREQVSFLKRVTRKFPGTNYRVG-ALDLDTVKQH 311

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2118 IRWTKDPRNTQDHVRSLCMLAWHSGEKDYNDFIAKIRTTDIGKCLNLPEY 2167
Cdd:cd23232    312 LMWCKSYSSFKQQLDSALMEVAMHGEETYNGFLTEIKTKLDKFKIYPPKF 361

rhv_like

cd00205

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

374-556

5.20e-37

Pssm-ID: 119412 Cd Length: 178 Bit Score: 138.30 E-value: 5.20e-37

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  374 LLEIIQVDTLIPMNNTGTNDNvtnyliplhadrqNEQIFGTKL--FIGDGVFKTTLLGEIAQYYTHWSGSLRISLMYTGP 451
Cdd:cd00205      1 VESFADRPTTVGTNNWNSSAS-------------GTQLFQWKLspALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGS 67

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  452 ALSSAKLILAYTPPGTRGP---EDRKEAMLGTHVVWDIGLQSTIVMTIPWTSGVQFRYTD---PDTYTSAGYLSCWYQTS 525
Cdd:cd00205     68 KFHTGRLLVAYVPPGAPAPttgDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRydgYGPLNSFGTLVVRVLTP 147

                          170       180       190
                   ....*....|....*....|....*....|.
gi 2395881893  526 LILPPQTSGQVYLLSFISACpDFKLRLMKDT 556
Cdd:cd00205    148 LTVPSGAPTTVDITVYVRAG-DFELYGPRPP 177

Rhv

pfam00073

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

359-522

7.34e-37

Pssm-ID: 395026 Cd Length: 170 Bit Score: 137.44 E-value: 7.34e-37

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  359 YEPTPRIHIPGKVRNLLEIIQVDTLIPMNNTGTN-DNVTNYLIPLHA-DRQNEQIFGTKLfiGDGVFKTTLLGEIAQYYT 436
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDvQGERFYTLDSTDwTSLSKGFFWWKL--PLALLSMGLLGRLLRYHT 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  437 HWSGSLRISLMYTGPALSSAKLILAYTPPGTRGPEDR---KEAMLGTHVVWDIGLQSTIVMTIPWTSGVQFRYT---DPD 510
Cdd:pfam00073   79 YYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRdylWQATLNPHQFWNLGLNSSARLSVPYISIAHYYSTfydGNW 158

                          170
                   ....*....|..
gi 2395881893  511 TYTSAGYLSCWY 522
Cdd:pfam00073  159 TLVVAGWVPLNY 170

Dicistroviridae_RdRp

cd23194

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

1877-2154

8.33e-37

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: 142.64 E-value: 8.33e-37

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1877 KDELRSADKVRLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPgIITGSAVGCDP---DvfWSVIPCLM---DGHLMAF 1950
Cdd:cd23194     13 KDERRPIEKVDAGKTRVFSAGPMDYTIAFRMYFLGFVAHLMRNR-IDNEIAVGTNVyslD--WDKLARKLlskGDKVIAG 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1951 DYSNF*ASLSPvwfECLERVL------SKLGFKHP----TLIQ*ICNTHHIFRDEIYKVEGGMPSGCSGTSIFNSMINNI 2020
Cdd:cd23194     90 DFSNFDGSLNP---QILWAILdiinewYDDGEENAlirrVLWEDIVNSVHICGGYVYQWTHSQPSGNPLTAIINSIYNSI 166

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2021 IIRTLILDAYKGIDLDSL-------RILAYGDDLIVSYPFELDS----NILATIGKNYGLTITPPDKSDT---FTKItwE 2086
Cdd:cd23194    167 IMRYVYLLLTKEAGLMTMsdfnkhvSMVSYGDDNVINVSDEVSEwfnqLTITEAMAEIGMTYTDETKTGEivpYRSL--E 244

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2395881893 2087 NITFLKRYFRPDPQFPFLVHPvMPMQDIYESIRWTK---DPR-NTQDHVRSLCM-LAWHsGEKDYNDFIAKIR 2154
Cdd:cd23194    245 EVSFLKRGFRYDDDLGRWVAP-LDLDTILEMPNWVRkgkDPEeITKQNVENALReLSLH-GEEVFDKWAPKIR 315

rhv_like

cd00205

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

634-826

1.23e-36

Pssm-ID: 119412 Cd Length: 178 Bit Score: 137.14 E-value: 1.23e-36

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  634 VESFLGRAACVHVTEIKNKDAAGLdnhkreglFNDWKINLS------SLVQLRKKLELFTYVRFDSEYTILATASQPeas 707
Cdd:cd00205      1 VESFADRPTTVGTNNWNSSASGTQ--------LFQWKLSPAlgflllQNTPLGALLSYFTYWRGDLEVTVQFNGSKF--- 69

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  708 sys*NLTVQAMYVPPGAPNPKEwDDYTWQSASNPSVFFKVGETS--RFSVPFVGLASAYNCFYDGYShddqdtpygitVL 785
Cdd:cd00205     70 ---HTGRLLVAYVPPGAPAPTT-GDTRWQATLNPHVIWDLGTNSsvTFVVPYVSPTPYRSTRYDGYG-----------PL 134

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....
gi 2395881893  786 NHMGSMAFRVVNEHDV---HTTIVKIRVYHRAKHVEAWIPRAPR 826
Cdd:cd00205    135 NSFGTLVVRVLTPLTVpsgAPTTVDITVYVRAGDFELYGPRPPR 178

Avisivirus_RdRp

cd23231

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

1825-2153

1.53e-34

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Avisivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Avisivirus genus within the family Picornaviridae, order Picornavirales. The Avisivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. Avisivirus is a picornavirus genus containing three species Avisivirus A, Avisivirus B and Avisivirus C. The name Avisivirus is derived from Avihepato sister-clade. Turkeys serve as natural hosts. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438081 Cd Length: 362 Bit Score: 137.33 E-value: 1.53e-34

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1825 LEPIDVTTSAGYPYVslGIKKRDILNKETQDTEKMKFY-----LDKYGIDLPLVTYIKDELRSADKVRLGKSRLIEASSL 1899
Cdd:cd23231      8 LLPIDWGTSPGDKYK--GKTKAQLVDDKKFKADVMNLVrfngdPNREPPDVYFTTYLKDELRPKEKAKAGKTRVISAASF 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1900 NDSVNMRMKLGNLYKAFHQNpGIITGSAVGCDP-----DVFWSVIPclmdgHLMAFDYSNF*ASLS-PVWFECLErVLSK 1973
Cdd:cd23231     86 DYTIACRMVFGPILRQLFAW-GREFGFGPGLNPythfdELYDKILP-----FVICLDYSGFDGSLSsELMFHAAQ-VIAC 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1974 LGFKHPTLI---Q*ICNTHHIFRDEIYKVEGGMPSGCSGTSIFNSMINNIIIRTLILDayKGIDLDSLRILAYGDDLIVS 2050
Cdd:cd23231    159 FSEKPEAIMasaELTIGSTERVSDEVWYVYGGMPSGSPWTTTLNTICNLLMCYTYLLD--MGHCWSETFVVAYGDDVVIS 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2051 YPFELD-SNILATIGKNYGLTITPPDKSdtfTKITW---ENITFLKRyfRPDpQFPFLVHPV--MPMQDIYESIRWTKDp 2124
Cdd:cd23231    237 ANIKHNlEGIEQWFKTKFGATVTPSDKQ---GKITWttkNNMEFLKR--RPK-QLDFLPKIVgaLDLDNMLDRIQWTKG- 309

                          330       340       350
                   ....*....|....*....|....*....|
gi 2395881893 2125 rNTQDHVRSLCM-LAWHsGEKDYNDFIAKI 2153
Cdd:cd23231    310 -HFQDQLNSFYLeLALH-GRETYNEIRAKL 337

Aalivirus_RdRp

cd23216

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

1827-2146

3.90e-32

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: 129.79 E-value: 3.90e-32

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1827 PIDVTTSAGYPYVslGIKKRDILNkETQDTEKMKFYLDkyGIDLPLVTYIKDELRSADKVRLGKSRLIEASSLNDSVNMR 1906
Cdd:cd23216     11 PIDWQTSPGLKYK--GRTKADLVQ-DPKFKEDVKEILA--GKPTFFTTYLKDELRSIEKIANGNTRAIEAANFDHVVAWR 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1907 MKLGNLYKAFHQNPGIITGSAVGCDPdvfWSVIPCLMDG---HLMAFDYSNF*ASLSPVWFECLERVLSKLgFKHPTLIQ 1983
Cdd:cd23216     86 QVMGNIVKQLFSDHDRVTGFAPGMNP---YTHFDSLMDQvkwNVLALDFKKFDGSLSPQVMEEAVDILASF-HDMPQMVV 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1984 *I----CNTHHIFRDEIYKVEGGMPSGCSGTSIFNSMINNIIIRTLILDayKGIDLDSLRILAYGDDLIVS---YPFEL- 2055
Cdd:cd23216    162 DIhkhtIYSTNVVSDETWFVEGGMCSGSPCTTVLNTICNLLVNTTILLS--EGIQPDNFYIAAYGDDTIISvdgLSSSLp 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2056 DSNILATIGKN-YGLTITPPDKSDTFTKITWENITFLKRY--FRPDPQfpfLVHPVMPMQDIYESIRWTKDprNTQDHVR 2132
Cdd:cd23216    240 DPKIMQQKYKEwFGMTVTSADKGSEITWDTRNHVQFLKRRpgFFPGTQ---KVVGVLDLESMMEHIAWTKG--SFQDQLN 314

                          330
                   ....*....|....
gi 2395881893 2133 SLCMLAWHSGEKDY 2146
Cdd:cd23216    315 SFYQELVLHGEQVY 328

Caliciviridae_RdRp

cd23192

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

1877-2147

3.12e-29

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: 120.45 E-value: 3.12e-29

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1877 KDELRSADKVRLGKSRLIEASSLNDSVNMRMKLGNLYKAF--HQNPGIItgsAVGCDPD-VFWSVI--PCLMDGHLMAFD 1951
Cdd:cd23192      8 KDELRPVEKIAEGKRRLLWGCDVGVTLVAAAAFGPVADALkaVCPTGPI---AVGINMDsEDVEVIfeRLSGFRYHYCLD 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1952 YSNF*ASLSP-VWFECLErVLSKLGFKHPtLIQ*ICNTHH-----IFRDEIYKVEGGMPSGCSGTSIFNSMINNIIIRTL 2025
Cdd:cd23192     85 YSKWDSTQSPaVTAAAID-ILADLSEETP-LRDSVVETLSsppmgIFDDVIFVTKRGLPSGMPFTSVINSLNHWLLFSAA 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2026 ILDAYK------GIDLDSLRILAYGDDLIVSYPFELDSNILATIG--KNYGLTITPPDKSDTFTKITWENITFLKRYFRP 2097
Cdd:cd23192    163 VLKAYElvgiytGNVFDEADFFTYGDDGVYAMPPATASVMDEIIEnlKSYGLKPTAADKTENPDIPPLQGPVFLKRTFVR 242

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2395881893 2098 DPqfpflvHPVMPMQDIYESIR---WTKDPrNTQDH---------------VRSLCMLAWHSGEKDYN 2147
Cdd:cd23192    243 TP------GGWRALLDRSSILRqlyWVKGP-NTHDWteppteidheartvqLENVLLEAAQHGPEFYE 303

Pico_P2B

pfam01552

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

1001-1099

8.10e-29

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: 112.04 E-value: 8.10e-29

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1001 QGLGDYITSLGRAFGTGFTDQISAKVCELQDVAKDF--LTTKVLSKVVKMISALVIICRNHDDLVTVTATLALLGCDGSP 1078
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTQQISDKIKELTNFINPTskIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|.
gi 2395881893 1079 WRFLKMYISKHFQVPYIERQA 1099
Cdd:pfam01552   81 WQFLKEKACAVLEIPYVHKQG 101

Aquamavirus_RdRp

cd23220

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

1815-2147

2.72e-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: 103.63 E-value: 2.72e-23

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1815 LKEALYGVDGLEPIDVTTSAGYPyvslGIKKRDILN----KETQDTEKMKFYLDKYGIDLPLVTYIKDELRSADKVRLGK 1890
Cdd:cd23220      1 LNEAINSSESPLNFNGTAGAKYP----GMNRRQLLLplnpQVRDDVVKLAGDVGNGTATVVFETFMKDELRPKEKIESGK 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1891 SRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVIPCLMDGHLMAFDYSNF*ASLSPVW------- 1963
Cdd:cd23220     77 TRIVESCPLDYLLLYRMVMLKSMIWWYNSDCIKTGVAPGMNVYTDFVPMVKQFKKIKYCLDFSAYDSTLSDEIlaagvev 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1964 FECLERVLSKLGFKHPTLIQ*icnTHHIFRDEIYKVEGGMPSGCSGTSIFNSMINNIIIRTLIldayKGIDLDSLRILAY 2043
Cdd:cd23220    157 LACTSAVPSYVRKLHAPIIC----SHHWHNNVVDLVLGGMPSGAPCTSVLNSIVNVLMARYIC----ALMDIDYPVMVAY 228

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2044 GDDLIVSYPFELDSNILATIGKN-YGLTITPPDKSDTFTKITweNITFLKRYFR--PDPQFPFlvhPVMPMQDIYESIRW 2120
Cdd:cd23220    229 GDDNVVSFDEEIDIERMVSLYKTeFGVTATNHDKTPVPRPMA--NPVFLKRRLRfnPDLNIQF---PVLPLGEMIDRMCW 303

                          330       340
                   ....*....|....*....|....*..
gi 2395881893 2121 TKDPRNTQDHVRSLCMLAWHSGEKDYN 2147
Cdd:cd23220    304 TRGPEHLSDQTFSFAIELAGYGKQVYT 330

Pico_P1A

pfam02226

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

2-69

1.09e-21

Pssm-ID: 308053 Cd Length: 68 Bit Score: 90.51 E-value: 1.09e-21

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2395881893    2 GAQVSTQKSGSHENQNILTNGSNQTFTVINYYKDAASSSSAGQSFSMDPSKFTEPVKDLMLKGAPALN 69
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 68

Marnaviridae_RdRp

cd23195

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

1877-2099

7.68e-18

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: 86.73 E-value: 7.68e-18

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1877 KDELRSADKvrlGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPgIITGSAVGCD---PDvfWSvipCLMDgHLMAF--- 1950
Cdd:cd23195      8 KDEPTKLTK---DKVRVFQAAPVALQLLVRKYFLPIARFLQMNP-LLSECAVGINaqsPE--WE---ELYE-HLTKFged 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1951 -----DYSNF*ASLSPVW----FECLERVLSKLG---------FKhpTLIQ*ICNTHHIFRDEIYKVEGGMPSGCSGTSI 2012
Cdd:cd23195     78 riiagDYSKYDKRMSAQLilaaFKILIDIAAKSGgyseedlkiMR--GIATDIAYPLVDFNGDLIQFFGSNPSGHPLTVI 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2013 FNSMINNIIIRTLILDAYKGIDLDSLR----ILAYGDDLI--VSYPFELDSNI-LATIGKNYGLTITPPDKSDTFTK-IT 2084
Cdd:cd23195    156 INSIVNSLYMRYAYYSLYPEKEVPPFRdvvaLMTYGDDNImsVSPGYPWFNHTsIAEFLAKIGIKYTMADKEAESVPfIH 235

                          250
                   ....*....|....*
gi 2395881893 2085 WENITFLKRYFRPDP 2099
Cdd:cd23195    236 ISEADFLKRKFVFDP 250

P3A

pfam08727

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

1432-1485

3.97e-16

Pssm-ID: 400873 Cd Length: 59 Bit Score: 74.38 E-value: 3.97e-16

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2395881893 1432 YKDLEIDVCNTPPP*CISDLLKSVDSEEVREYCKKKKWIIpQIPT--NIERAVNQA 1485
Cdd:pfam08727    5 GIDLKIDIKTSPPPEAIADLLQAVDSPEIIDYCEDKGWIV-NIPAecQIERDIGIA 59

Secoviridae_RdRp

cd23196

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

1866-2129

1.29e-11

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: 68.18 E-value: 1.29e-11

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1866 YGIDLPlvtyiKDELRSADKV-RLGKSRLIEASSLNDSVNMRMKLGNLYkAFHQNPGIITGSAVGCDP-DVFWSVIPCLM 1943
Cdd:cd23196      2 NCVECP-----KDERLKKRKVlEKPKTRLFDVLPMEYNLLLRKYFLNFV-RFIQANRHRLPCQVGINPySREWTTLYDRL 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1944 ---DGHLMAFDYSNF*ASLSPVWFECLERVLSKL-GFKHPTLIQ*-----ICNTHHIFRDEIYKVEGGMPSGCSGTSIFN 2014
Cdd:cd23196     76 aekSDTALNCDYSRFDGLLSHQVYVWIADMINRLyGDGDEAKARRnllmmFCGRRSICGRQVYMVRGGMPSGCALTVIIN 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2015 SMINNIIIRTlildAYKGIDLDSLR--------ILAYGDDLIVSYPFEL----DSNILATIGKNYGLTITppDKSD---- 2078
Cdd:cd23196    156 SIFNEILIRY----VYRKVVPRPARnnfnkyvrLVVYGDDNLISVKEEIipyfDGPVIKKEMAKVGVTIT--DGTDktsp 229

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2395881893 2079 TFTKITWENITFLKRYFRPDPQfpFLVHPVMPMQDIYESIRWTKDPRNTQD 2129
Cdd:cd23196    230 TLERKPLESLDFLKRGFRVQSD--GLVVAPLDKTSLYSRLHYVTAGGDGMY 278

Iflaviridae_RdRp

cd23197

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

1871-2120

1.26e-09

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: 62.19 E-value: 1.26e-09

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1871 PLVTYIKDELRSADKVR-LGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPgIITGSAVGCDPD-VFWS--VIPCLMDGH 1946
Cdd:cd23197      7 VYWAHLKDELRPSEKLRrFGGTRVFSVPPLELVLNSRRFLLPFMDAFQSFP-IEAHHAIGLNPNsGDWRrlRDTLLEKGP 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1947 -LMAFDYSNF*ASLSPVWFECLERVLSKLGFKH-----------PTLIQ*ICNTHHIFRDEIYKVEGGMPSGCSGTSIFN 2014
Cdd:cd23197     86 cLLQMDYKNYSDAIPKECVAKAFHIIVDYYRKWhcltveienalKTLFLDTADAELLVYGDVFKVNNGVLAGHPMTSVVN 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2015 SMINniiirtLILDAYKGIDLDSLR---------ILAYGDDLIVSYPFEL----DSNILATIGKNYGLTITPPDKSDTFT 2081
Cdd:cd23197    166 SVVN------LILMNYMWIKITRRRaseffkltyIIVMGDDVVISLPKQLteefDCRKICAEFAKYDIKVTDSEKNLTGE 239

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|..
gi 2395881893 2082 KITWENI---TFLKRYFRPDPQFPFLVHPVMPMQDIYESIRW 2120
Cdd:cd23197    240 PKPYDSFdkfEFLSRGFSDCDAYPDITFAPVKTIALFDCPLW 281

ps-ssRNAv_RdRp-like

cd23167

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

1946-2052

2.66e-09

Pssm-ID: 438017 [Multi-domain] Cd Length: 73 Bit Score: 55.42 E-value: 2.66e-09

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1946 HLMAFDYSNF*ASLSPVWFEClervlsklgfkhptliq*icnthhifrdeiykvegGMPSGCSGTSIFNSMINNIIIRTL 2025
Cdd:cd23167      1 HVVESDYSGFDSSISPDLLKA-----------------------------------GQPSGSPNTSADNSLINLLLARLA 45

                           90       100
                   ....*....|....*....|....*...
gi 2395881893 2026 ILDAYKGID-LDSLRILAYGDDLIVSYP 2052
Cdd:cd23167     46 LRKACGRAEfLNSVGILVYGDDSLVSVP 73

ps-ssRNAv_EoPV-like_RdRp

cd23171

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

1877-2097

3.83e-08

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the positive-sense single-stranded RNA [(+)ssRNA] picorna-like virus Ectropis obliqua, and related viruses; This group contains the catalytic core domain of RdRp of Ectropis obliqua picorna-like virus (EoPV), and related viruses. EoPV is an insect (+)ssRNA virus that causes a lethal granulosis infection of larvae of the tea looper (Ectropis obliqua), and related insect-infecting iflaviruses. Ectropis obliqua, a species of moth, is one of the most destructive pest insects on tea plants throughout growing areas of this crop in southern China. The EoPV genome contains a single large ORF encoding the capsid proteins at the 5' terminus of the genome with the non-structural proteins at the 3' end of the genome. This organization is similar to typical mammalian picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438021 Cd Length: 239 Bit Score: 56.45 E-value: 3.83e-08

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1877 KDELRSADKvrlgKSRLIEASSLNDSVNMRMKLGNLYKAF-HQNPGIitgsAVGCD-PDVFWSVIPCLMDgHLMAFDYSN 1954
Cdd:cd23171     21 KDELLKPGK----DTRLINGAPLHHTLDMRRYLMEFFAAItTINNKI----AVGIDvHSGDWALIHGGAD-DVVDEDYSG 91

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1955 F*ASLSPVWFECLERVLSKLGFKHPT-----------LIQ*ICNTHHIFRDEIYKVEGGMPSGCSGTSIFNSMINNIIIR 2023
Cdd:cd23171     92 FGPGFHSQWLDVIRRIAVAWCKHHKTvdpeyenvvrcLIRELQNAYHVAGDLVYQVLCGSPSGAFATDRINSLANLCYHC 171

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2395881893 2024 TLILDAYKGI-DLDSLRILAYGDDLI---VSYPFELDSNILATIgknyGLTITPPDKSDTftkitweniTFLKRYFRP 2097
Cdd:cd23171    172 LCYLRKYGTLtGFWSHYLLVYGDDTRrreTAYTGDEFQDCMASI----GITVNRDKSGVT---------SFLKRQFIP 236

Calici_coat

pfam00915

Calicivirus coat protein;

428-554

1.40e-06

Calicivirus coat protein;

Pssm-ID: 459994 Cd Length: 291 Bit Score: 52.20 E-value: 1.40e-06

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893  428 LGEIAQYYTHWSGSLRISLMYTGPALSSAKLILAYTPPGTRgPEDRKEAMLGTHVVWDIGLQSTIVMTIPWTSGVQFRYT 507
Cdd:pfam00915   96 LLHLSQMYNGWSGGMRVRFMVAGSGVFGGKLAASVIPPGVE-PITSASMLQFPHVLFDARQLEPVIFTIPDLRNTLFHNM 174

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 2395881893  508 DPDTYTSAgyLSCWYQTSLILPPQTSGQVYLLSFISACP--DFKLRLMK 554
Cdd:pfam00915  175 DRNTDTTR--LVIMVYNPLINPGGTGDSSVCAVTVETRPspDFNFLLLK 221

Solinviviridae_RdRp

cd23199

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

1927-2096

1.32e-05

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

Pssm-ID: 438049 Cd Length: 323 Bit Score: 49.66 E-value: 1.32e-05

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1927 AVGCDP-----DVFwsvIPCLMDGHLMAFDYSNF*AS----LSPVWFECLERVLSKLGFKHPTLIQ*ICNTHHIFRDEIY 1997
Cdd:cd23199     72 AVGCNPyatfhKFA---TKFFKFKNFFSCDYKNFDRTipkcVFEDFRDMLIQANPHMKNEIYACFQTIIDRIQVSGNSIL 148

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1998 KVEGGMPSGCSGTSIFNSMINNI--------IIRTLILDAYKGIDLDSLRI--LAYGDDLIVSY-----PFELDSNILAT 2062
Cdd:cd23199    149 LVHGGMPSGCVPTAPLNSKVNDImiytayvnILRRADRGDITSYRYYRDLVcrLFYGDDVIIAVddsiaDIFNCQTLSEE 228

                          170       180       190
                   ....*....|....*....|....*....|....*
gi 2395881893 2063 IGKNYGLTITPPDKSDTFTKI-TWENITFLKRYFR 2096
Cdd:cd23199    229 MKILFGMNMTDGSKSDIIPKFeTIETLSFISRFFR 263

ps-ssRNAv_Nodaviridae_RdRp

cd23173

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

1951-2099

1.24e-04

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: 45.97 E-value: 1.24e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1951 DYSNF*ASLSPVWFECLERVLSKLGFK---HPTLIQ*I-------CNTHHIFRdeiYKVEGGMPSGCSGTSIFNSMINNI 2020
Cdd:cd23173     89 DYSRFDGTISEWLRRNVEFAAYLRWFHpeyRAELLKLLdaeincpARTKTGVK---YDPGVSRLSGSPTTTDGNTIINAF 165

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2021 I----IRTLILDAYkgidlDSLRI--LAYGDDLIVSYpfeLDSNILATIGKNYGLTI----TPPDKSdtftkitwenITF 2090
Cdd:cd23173    166 VsycaLRETGYSPE-----EAFALlgLYYGDDGLSDN---LPAEALEKVAKDLGLKLkievVRPGQP----------VTF 227


                   ....*....
gi 2395881893 2091 LKRYFrPDP 2099
Cdd:cd23173    228 LGRVF-PDP 235

Polycipiviridae_RdRp

cd23198

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

1877-2153

3.28e-04

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: 45.10 E-value: 3.28e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1877 KDELRSADKVrLG------KSRLIEASSLNDSVNMRMKLGNLYKAFHQ--------NPGIitgSAVGcdPDvfWSVIPCL 1942
Cdd:cd23198      8 KDELRPIYKA-LGdpqtppKTRSVTCMNVYYILAWRRVTLDFWASMHRaadgnfpfCPGI---NPEG--PD--WNRLYHY 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1943 MDGHLMA--FDYSNF*ASLSPVWFECLERVLSKLGFKHPT---------LIQ*ICNTHHIFRDEIYKVEGGMPSGCSGTS 2011
Cdd:cd23198     80 LNRHPNAvdFDVSNWDGHLPAELFYAVLDIIKTVLGLKPNspnakviysILTEVMNCHIQFEDIIYQKLRGLISGFPGTA 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2012 IFNSMINNIIIRTLILDAYKGIDLDS--------LRILAYGDDLIVSYPFEL----DSNILATIGKNYGLTITPPDKSdt 2079
Cdd:cd23198    160 EVNTLAHWLLIYYIYLYLAQNTIYDMtitaflrnVSAIFYGDDIIITISDEIlhwfNGKTIQRMYEEHGYPVTSAAKD-- 237

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2080 fTKITWE----NITFLKRYFRpdPQFPFLVHPVMPMQDIYESIRWTK---DPR-----NTQDHVRslcmLAWHSGEKDYN 2147
Cdd:cd23198    238 -TEIPESkplsDCQFLKSSWN--PILPGYYIRKMDIEVVYDLVYWVRakeHPRdqfysNYHDALR----ILFGHGEQVFE 310


                   ....*.
gi 2395881893 2148 DFIAKI 2153
Cdd:cd23198    311 AFREQV 316

ps-ssRNAv_Astroviridae_RdRp

cd23172

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

1995-2090

3.98e-04

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: 44.38 E-value: 3.98e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1995 EIYKVEGGMPSGCSGTSIFNSMINniiirtLILDAY--------KGIDLDSLR----ILAYGDDLIVSYP--FELDSNIL 2060
Cdd:cd23172    140 EVTRVTKGNPSGQISTTMDNCMVN------TFLTAFefayvygpKTGTLKELWdnydTIVYGDDRLSGYPslPDPYVERV 213

                           90       100       110
                   ....*....|....*....|....*....|
gi 2395881893 2061 ATIGKNYGLTITPPDKSDTFTKItwENITF 2090
Cdd:cd23172    214 VDMYKDVFGMWVKPEKVKVSDTL--EGLSF 241

RdRP_4

pfam02123

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

1935-2096

4.34e-04

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: 45.14 E-value: 4.34e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 1935 FWSVIPCLMDGH-LMAFDYSNF-----*ASLSPVwFECLERVLSKlgFKHPTLIQ*ICNTHHIF-----RDEIYKVEGGM 2003
Cdd:pfam02123  286 FDWSVQDWKRGGvSLMLDYDDFnsqhsTESMRAV-FERLRRRLPD--EPAEAADWLVCSMDSMYqlsdgTLLAQRVPGTL 362

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395881893 2004 PSGCSGTSIFNSMINNIIIRTLIldaykGIDLDSLRILAYGDDLIVSYPFELDSNILATIGKNYGLTITPPDKSDTFTKI 2083
Cdd:pfam02123  363 KSGHRATTFINSVLNCAYAELAG-----APWADVPTSIHMGDDVLEGLRTPADATSLLDKYARLGFKVNPSKQSVGHTIA 437

                          170
                   ....*....|...
gi 2395881893 2084 TWENITFLKRYFR 2096
Cdd:pfam02123  438 EFLRVAFCSHEVR 450

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