NCBI Conserved Domain Search

Conserved domains on [gi|2099546858|gb|UBI50760|]

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polyprotein [rhinovirus C36]

Protein Classification

Graphical summary

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List of domain hits

Name

Accession

Description

Interval

E-value

ps-ssRNAv_RdRp-like super family

cl40470

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

1695-2143

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: 741.27 E-value: 0e+00

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1695 ECGLNPINVPTNTKLKPSVFYDVFPGKKEPAVLNPRDPRLEANLDEAVLGKYKGNKHVEFNQYIQIAVDHYAAQLIMLDV 1774
Cdd:cd23213      3 EVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATLDI 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1775 DSAPLTLEQAVYGVKNLEPLDLTTSAGFPYVALGIKKRDLVNKTTRDVSKLASMIDKYGLDLPYVTYLKDELRAPEKIKA 1854
Cdd:cd23213     83 DTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKVEK 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1855 GKTRIIEASSINDTSHFRMVFGNLFSAFHANPGILTGSAVGCNPDVFWSQMYAMLDGHLLAFDYTNYDGSLNPIWFKALG 1934
Cdd:cd23213    163 GKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDGSLFAFDYTGYDASLSPVWFRALK 242

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1935 MVLNKLGFPGA--MMDKLSSTTHIYRDRVYKTEGGMPSGICGTSIFNTMINNIILRTLILETYKNIDLDKLRIIAYGDDV 2012
Cdd:cd23213    243 MVLEKGYSEEAvsLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYGDDV 322

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 2013 VASYPDPLDPKEIAETGAKYGLTITPADKSTEFREVTWDTVTFLKRKFKVDDEFKFLIHPVYSMDDVYESIRWTKDPRNT 2092
Cdd:cd23213    323 IASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDPRNT 402

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2099546858 2093 QDHVRSLCMLAWHNGKDVYEQFLNQIRTTSVGRALNLPPYTYLRHQWLENF 2143
Cdd:cd23213    403 QDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453

Rhv

pfam00073

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

91-299

5.57e-53

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: 183.67 E-value: 5.57e-53

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858   91 TTQDTLNSVVAYGEWPQYLSDLDASSIDKPTHPETSADRFYTLDSVNWTGTSLGW-WWKLPDCLREMGLFGQNMYYHSMG 169
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFfWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  170 RTGYIIHVQCNATKFHSGCLMVAVIPEHQMayigaggtnvrydqtHPGeaghTITASKQWGehnpdenpfynlngtlfgn 249
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPPGAP---------------PPG----SRDYLWQAT------------------- 122

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 2099546858  250 iqIFPHQMINLRTNNSATIVVPYINCLPMDNMLRHNNLTLMIIPIVKLRH 299
Cdd:pfam00073  123 --LNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGNWTLVVAGWVPLNY 170

Pico_P2A super family

cl03031

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

853-970

2.42e-52

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: 180.27 E-value: 2.42e-52

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  853 NAHLTNPNEH--TILLALTADLQVDATTEPGSDVIPDCDCVEGCYYCKSQDRYFPVKTTQHDWYEIQETVYYPKHIQYNI 930
Cdd:pfam00947    1 NRHLATHEDWhnSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 2099546858  931 LIGEGPAEPGDCGGKLLCRHGVIGILTAGGEGHVAFTDLR 970
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVR 120

RNA_helicase

pfam00910

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

1201-1297

2.35e-39

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

Pssm-ID: 459992 Cd Length: 102 Bit Score: 141.97 E-value: 2.35e-39

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1201 LLIHGDPGCGKSLATTIVSRGLAA-----EGDIYSLPPNPKHFDGYNQQKVVIMDDVGQNPDGEDLGIFCQMVSTTDFHV 1275
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKklglpKDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 2099546858 1276 PMAALEDKGRCFTSDYVLASTN 1297
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

Rhv

pfam00073

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

357-521

2.83e-37

Pssm-ID: 395026 Cd Length: 170 Bit Score: 138.60 E-value: 2.83e-37

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  357 YSPTKEIHIPGKITNMLHIAQVESFLPLNNTDQHVGSIDIY---GVTITGASDNKLIVAIPLQmdntLFATTLLGEVLNY 433
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYtldSTDWTSLSKGFFWWKLPLA----LLSMGLLGRLLRY 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  434 YANWSGSVRVTFMCVCDSFSTGKFLLAYTPPGGRLPRDR---KEAMLGTHVVWDLGLQSSCTMVAPWISSTFFRRTKADK 510
Cdd:pfam00073   77 HTYYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRdylWQATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDG 156

                          170
                   ....*....|....
gi 2099546858  511 ---YSSGGIITLWH 521
Cdd:pfam00073  157 nwtLVVAGWVPLNY 170

Peptidase_C3 super family

cl02893

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

1502-1667

1.33e-35

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: 134.11 E-value: 1.33e-35

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1502 GPEHEFMYALVKRNCHIATTERGEFNLL--GIYGNCAVLPTHAECGEILNVDGREVKVIKRQI-LTDMNDIDTEITLIWL 1578
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDPEVeLVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1579 DQNEKFRDIRRFLPETIQEWDHMKLATNVTKFPMHFVDVGHTVPYGEI-NLSGNPTCRLLKYNYPTKPGQCGAVI----G 1653
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVViakvE 160

                          170
                   ....*....|....
gi 2099546858 1654 STGHIIGIHVGGNG 1667
Cdd:pfam00548  161 GNGKILGMHIAGNG 174

Pico_P2B super family

cl03260

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

979-1072

9.02e-35

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: 128.99 E-value: 9.02e-35

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  979 QGpISNYLTQLGNAFGEGFTQNIKDSFSNISTSI--TDKLTSKVIKWLVRIISALTIMVRNSADTPTILATLALLGCSKS 1056
Cdd:pfam01552    1 QG-ISDYIEHLGAAFGSGFTQQISDKIKELTNFInpTSKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDAS 79

                           90
                   ....*....|....*.
gi 2099546858 1057 PWTFLKEKICTWLGIS 1072
Cdd:pfam01552   80 PWQFLKEKACAVLEIP 95

rhv_like

cd00205

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

632-799

4.68e-32

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: 124.05 E-value: 4.68e-32

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  632 IENFLGRSAL-----WAEFRLQGGFKKWDINFQEQ------AHIRRKLEFFTYVRFDMEVTIVTN----NTGLMQIMFIP 696
Cdd:cd00205      1 VESFADRPTTvgtnnWNSSASGTQLFQWKLSPALGflllqnTPLGALLSYFTYWRGDLEVTVQFNgskfHTGRLLVAYVP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  697 PGIEAPGNISDkRWDGASNPSIFYQPKSGFP-RFTIPFTGLGSAYYMFYDGYDetertgtaygisATNDMGTLCFRAL-- 773
Cdd:cd00205     81 PGAPAPTTGDT-RWQATLNPHVIWDLGTNSSvTFVVPYVSPTPYRSTRYDGYG------------PLNSFGTLVVRVLtp 147

                          170       180       190
                   ....*....|....*....|....*....|.
gi 2099546858  774 -----EDTTNDDVKVFIKPKHTSAWCPRPPR 799
Cdd:cd00205    148 ltvpsGAPTTVDITVYVRAGDFELYGPRPPR 178

Pico_P1A super family

cl03490

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

2-67

1.74e-26

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: 103.99 E-value: 1.74e-26

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2099546858    2 GAQVSKQSVGAHENSITANKGSIVKYFNINYYKDAASSGLTKQDFSQDPSKFTQPLADALTNPALM 67
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPT 66

AAA_16

pfam13191

AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...

1168-1212

3.91e-03

AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily.

Pssm-ID: 433025 [Multi-domain] Cd Length: 167 Bit Score: 40.18 E-value: 3.91e-03

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 2099546858 1168 PLYARENklvtdmqkQLNQLK-AYQRTHRTEPVCLLIHGDPGCGKS 1212
Cdd:pfam13191    1 RLVGREE--------ELEQLLdALDRVRSGRPPSVLLTGEAGTGKT 38

Name

Accession

Description

Interval

E-value

Enterovirus_RdRp

cd23213

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

1695-2143

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: 741.27 E-value: 0e+00

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1695 ECGLNPINVPTNTKLKPSVFYDVFPGKKEPAVLNPRDPRLEANLDEAVLGKYKGNKHVEFNQYIQIAVDHYAAQLIMLDV 1774
Cdd:cd23213      3 EVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATLDI 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1775 DSAPLTLEQAVYGVKNLEPLDLTTSAGFPYVALGIKKRDLVNKTTRDVSKLASMIDKYGLDLPYVTYLKDELRAPEKIKA 1854
Cdd:cd23213     83 DTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKVEK 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1855 GKTRIIEASSINDTSHFRMVFGNLFSAFHANPGILTGSAVGCNPDVFWSQMYAMLDGHLLAFDYTNYDGSLNPIWFKALG 1934
Cdd:cd23213    163 GKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDGSLFAFDYTGYDASLSPVWFRALK 242

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1935 MVLNKLGFPGA--MMDKLSSTTHIYRDRVYKTEGGMPSGICGTSIFNTMINNIILRTLILETYKNIDLDKLRIIAYGDDV 2012
Cdd:cd23213    243 MVLEKGYSEEAvsLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYGDDV 322

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 2013 VASYPDPLDPKEIAETGAKYGLTITPADKSTEFREVTWDTVTFLKRKFKVDDEFKFLIHPVYSMDDVYESIRWTKDPRNT 2092
Cdd:cd23213    323 IASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDPRNT 402

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2099546858 2093 QDHVRSLCMLAWHNGKDVYEQFLNQIRTTSVGRALNLPPYTYLRHQWLENF 2143
Cdd:cd23213    403 QDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453

Rhv

pfam00073

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

91-299

5.57e-53

Pssm-ID: 395026 Cd Length: 170 Bit Score: 183.67 E-value: 5.57e-53

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858   91 TTQDTLNSVVAYGEWPQYLSDLDASSIDKPTHPETSADRFYTLDSVNWTGTSLGW-WWKLPDCLREMGLFGQNMYYHSMG 169
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFfWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  170 RTGYIIHVQCNATKFHSGCLMVAVIPEHQMayigaggtnvrydqtHPGeaghTITASKQWGehnpdenpfynlngtlfgn 249
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPPGAP---------------PPG----SRDYLWQAT------------------- 122

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 2099546858  250 iqIFPHQMINLRTNNSATIVVPYINCLPMDNMLRHNNLTLMIIPIVKLRH 299
Cdd:pfam00073  123 --LNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGNWTLVVAGWVPLNY 170

RdRP_1

pfam00680

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

1711-2118

7.62e-53

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: 193.40 E-value: 7.62e-53

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1711 PSVFYDVFPGKKEPAVLNPRDPRLE---ANLDEAVLGKYKGN---KHVEFNQYIQIAVD----HYAAQLIMLD-VDSAPL 1779
Cdd:pfam00680    2 PTERHLVAIPAYVPASLGPEDPRWArsyLNTDPYVDDIKKYSrpkLPGPADERDKLLNRsaakMVLSELRGVPkKANSTL 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1780 TLEQAVYGVKNLEPLDLTTSAGFPYVALGIKKRDLVNK----TTRDV--SKLASMIDKYG----LDLPYVTYLKDELRAP 1849
Cdd:pfam00680   82 IVYRAIDGVEQIDPLNWDTSAGYPYVGLGGKKGDLIEHlkdgTEARElaERLAADWEVLQngtpLKLVYQTCLKDELRPL 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1850 EKIKAGKTRIIEASSINDTSHFRMVFGNLFSAFHANPGILTgSAVGCNP-DVFWSQMYAMLDGH---LLAFDYTNYDGSL 1925
Cdd:pfam00680  162 EKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHP-IQVGINPfDRGWPRLLRRLARFgdyVYELDYSGFDSSV 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1926 NPIWFKALGMVLN-KLGFP------GAMMDKLSSTTH-IYRDRVYKTEGGMPSGICGTSIFNTMINNIILRTLILETYKN 1997
Cdd:pfam00680  241 PPWLIRFAFEILReLLGFPsnvkewRAILELLIYTPIaLPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYALLKSLEN 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1998 IDL------DKLRIIAYGDDVVASYPDPLDP--KEIAETGAKYGLTITPADKSTE-FREVTwdTVTFLKRKFKVDdefKF 2068
Cdd:pfam00680  321 DGPrvcnldKYFDFFTYGDDSLVAVSPDFDPvlDRLSPHLKELGLTITPAKKTFPvSRELE--EVSFLKRTFRKT---PG 395

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|
gi 2099546858 2069 LIHPVYSMDDVYESIRWTKDPRNTQDHVRSLCMLAWHNGKDVYEQFLNQI 2118
Cdd:pfam00680  396 GYRPPLDRKRILAQLEYIRSKPVPSGQLENIRAYASHHGYEFYRDLLYRF 445

Pico_P2A

pfam00947

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

853-970

2.42e-52

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

Pssm-ID: 395757 Cd Length: 127 Bit Score: 180.27 E-value: 2.42e-52

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  853 NAHLTNPNEH--TILLALTADLQVDATTEPGSDVIPDCDCVEGCYYCKSQDRYFPVKTTQHDWYEIQETVYYPKHIQYNI 930
Cdd:pfam00947    1 NRHLATHEDWhnSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 2099546858  931 LIGEGPAEPGDCGGKLLCRHGVIGILTAGGEGHVAFTDLR 970
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVR 120

RNA_helicase

pfam00910

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

1201-1297

2.35e-39

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

Pssm-ID: 459992 Cd Length: 102 Bit Score: 141.97 E-value: 2.35e-39

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1201 LLIHGDPGCGKSLATTIVSRGLAA-----EGDIYSLPPNPKHFDGYNQQKVVIMDDVGQNPDGEDLGIFCQMVSTTDFHV 1275
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKklglpKDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 2099546858 1276 PMAALEDKGRCFTSDYVLASTN 1297
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

Rhv

pfam00073

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

357-521

2.83e-37

Pssm-ID: 395026 Cd Length: 170 Bit Score: 138.60 E-value: 2.83e-37

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  357 YSPTKEIHIPGKITNMLHIAQVESFLPLNNTDQHVGSIDIY---GVTITGASDNKLIVAIPLQmdntLFATTLLGEVLNY 433
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYtldSTDWTSLSKGFFWWKLPLA----LLSMGLLGRLLRY 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  434 YANWSGSVRVTFMCVCDSFSTGKFLLAYTPPGGRLPRDR---KEAMLGTHVVWDLGLQSSCTMVAPWISSTFFRRTKADK 510
Cdd:pfam00073   77 HTYYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRdylWQATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDG 156

                          170
                   ....*....|....
gi 2099546858  511 ---YSSGGIITLWH 521
Cdd:pfam00073  157 nwtLVVAGWVPLNY 170

rhv_like

cd00205

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

393-555

3.78e-36

Pssm-ID: 119412 Cd Length: 178 Bit Score: 135.99 E-value: 3.78e-36

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  393 SIDIYGVTITGASDNKLIVAIPL--QMDNTLFATTLLGEVLNYYANWSGSVRVTFMCVCDSFSTGKFLLAYTPPGGRLP- 469
Cdd:cd00205      8 PTTVGTNNWNSSASGTQLFQWKLspALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPPGAPAPt 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  470 --RDRKEAMLGTHVVWDLGLQSSCTMVAPWISSTFFRRTKADKY---SSGGIITLWHQTAFVSG-DTANVGTILATCSGC 543
Cdd:cd00205     88 tgDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDGYgplNSFGTLVVRVLTPLTVPsGAPTTVDITVYVRAG 167

                          170
                   ....*....|..
gi 2099546858  544 pDISVRMLRDTP 555
Cdd:cd00205    168 -DFELYGPRPPR 178

Peptidase_C3

pfam00548

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

1502-1667

1.33e-35

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: 134.11 E-value: 1.33e-35

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1502 GPEHEFMYALVKRNCHIATTERGEFNLL--GIYGNCAVLPTHAECGEILNVDGREVKVIKRQI-LTDMNDIDTEITLIWL 1578
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDPEVeLVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1579 DQNEKFRDIRRFLPETIQEWDHMKLATNVTKFPMHFVDVGHTVPYGEI-NLSGNPTCRLLKYNYPTKPGQCGAVI----G 1653
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVViakvE 160

                          170
                   ....*....|....
gi 2099546858 1654 STGHIIGIHVGGNG 1667
Cdd:pfam00548  161 GNGKILGMHIAGNG 174

Pico_P2B

pfam01552

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

979-1072

9.02e-35

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: 128.99 E-value: 9.02e-35

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  979 QGpISNYLTQLGNAFGEGFTQNIKDSFSNISTSI--TDKLTSKVIKWLVRIISALTIMVRNSADTPTILATLALLGCSKS 1056
Cdd:pfam01552    1 QG-ISDYIEHLGAAFGSGFTQQISDKIKELTNFInpTSKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDAS 79

                           90
                   ....*....|....*.
gi 2099546858 1057 PWTFLKEKICTWLGIS 1072
Cdd:pfam01552   80 PWQFLKEKACAVLEIP 95

rhv_like

cd00205

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

123-326

2.14e-32

Pssm-ID: 119412 Cd Length: 178 Bit Score: 125.20 E-value: 2.14e-32

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  123 PETSADRFYTLDSVNWTG---TSLGWWWKLPD----CLREMGLFGQNMYYHSMGRTGYIIHVQCNATKFHSGCLMVAVIP 195
Cdd:cd00205      1 VESFADRPTTVGTNNWNSsasGTQLFQWKLSPalgfLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  196 EHQMAyigaggtnvrydqthpgeaghtitaskqwgehnpdenpfyNLNGTLFGNIQIFPHQMINLRTNNSATIVVPYINC 275
Cdd:cd00205     81 PGAPA----------------------------------------PTTGDTRWQATLNPHVIWDLGTNSSVTFVVPYVSP 120

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2099546858  276 LPMDNMLRHNNL------TLMIIPIVKLRHGTTGTTTLPITVTIAPDKSEFSGPMQT 326
Cdd:cd00205    121 TPYRSTRYDGYGplnsfgTLVVRVLTPLTVPSGAPTTVDITVYVRAGDFELYGPRPP 177

rhv_like

cd00205

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

632-799

4.68e-32

Pssm-ID: 119412 Cd Length: 178 Bit Score: 124.05 E-value: 4.68e-32

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  632 IENFLGRSAL-----WAEFRLQGGFKKWDINFQEQ------AHIRRKLEFFTYVRFDMEVTIVTN----NTGLMQIMFIP 696
Cdd:cd00205      1 VESFADRPTTvgtnnWNSSASGTQLFQWKLSPALGflllqnTPLGALLSYFTYWRGDLEVTVQFNgskfHTGRLLVAYVP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  697 PGIEAPGNISDkRWDGASNPSIFYQPKSGFP-RFTIPFTGLGSAYYMFYDGYDetertgtaygisATNDMGTLCFRAL-- 773
Cdd:cd00205     81 PGAPAPTTGDT-RWQATLNPHVIWDLGTNSSvTFVVPYVSPTPYRSTRYDGYG------------PLNSFGTLVVRVLtp 147

                          170       180       190
                   ....*....|....*....|....*....|.
gi 2099546858  774 -----EDTTNDDVKVFIKPKHTSAWCPRPPR 799
Cdd:cd00205    148 ltvpsGAPTTVDITVYVRAGDFELYGPRPPR 178

Rhv

pfam00073

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

612-746

1.37e-26

Pssm-ID: 395026 Cd Length: 170 Bit Score: 108.17 E-value: 1.37e-26

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  612 PDDVIETRYVINNHVNNEALIENFLGRSAL-----------------WAefRLQGGFKKWDINFQEQAH--IRRKLEFFT 672
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPvqpdvqgerfytldstdWT--SLSKGFFWWKLPLALLSMglLGRLLRYHT 78

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2099546858  673 YVRFDMEVTIVTN----NTGLMQIMFIPPGIEAPGNIsDKRWDGASNPSIFYQPKSG-FPRFTIPFTGLGSAYYMFYDG 746
Cdd:pfam00073   79 YYRGGLEVTVQFNgskfHQGKLLVAYVPPGAPPPGSR-DYLWQATLNPHQFWNLGLNsSARLSVPYISIAHYYSTFYDG 156

Pico_P1A

pfam02226

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

2-67

1.74e-26

Pssm-ID: 308053 Cd Length: 68 Bit Score: 103.99 E-value: 1.74e-26

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2099546858    2 GAQVSKQSVGAHENSITANKGSIVKYFNINYYKDAASSGLTKQDFSQDPSKFTQPLADALTNPALM 67
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPT 66

AAA_16

pfam13191

AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...

1168-1212

3.91e-03

AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily.

Pssm-ID: 433025 [Multi-domain] Cd Length: 167 Bit Score: 40.18 E-value: 3.91e-03

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 2099546858 1168 PLYARENklvtdmqkQLNQLK-AYQRTHRTEPVCLLIHGDPGCGKS 1212
Cdd:pfam13191    1 RLVGREE--------ELEQLLdALDRVRSGRPPSVLLTGEAGTGKT 38

Name

Accession

Description

Interval

E-value

Enterovirus_RdRp

cd23213

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

1695-2143

0e+00

Pssm-ID: 438063 Cd Length: 453 Bit Score: 741.27 E-value: 0e+00

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1695 ECGLNPINVPTNTKLKPSVFYDVFPGKKEPAVLNPRDPRLEANLDEAVLGKYKGNKHVEFNQYIQIAVDHYAAQLIMLDV 1774
Cdd:cd23213      3 EVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATLDI 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1775 DSAPLTLEQAVYGVKNLEPLDLTTSAGFPYVALGIKKRDLVNKTTRDVSKLASMIDKYGLDLPYVTYLKDELRAPEKIKA 1854
Cdd:cd23213     83 DTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKVEK 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1855 GKTRIIEASSINDTSHFRMVFGNLFSAFHANPGILTGSAVGCNPDVFWSQMYAMLDGHLLAFDYTNYDGSLNPIWFKALG 1934
Cdd:cd23213    163 GKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDGSLFAFDYTGYDASLSPVWFRALK 242

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1935 MVLNKLGFPGA--MMDKLSSTTHIYRDRVYKTEGGMPSGICGTSIFNTMINNIILRTLILETYKNIDLDKLRIIAYGDDV 2012
Cdd:cd23213    243 MVLEKGYSEEAvsLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYGDDV 322

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 2013 VASYPDPLDPKEIAETGAKYGLTITPADKSTEFREVTWDTVTFLKRKFKVDDEFKFLIHPVYSMDDVYESIRWTKDPRNT 2092
Cdd:cd23213    323 IASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDPRNT 402

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2099546858 2093 QDHVRSLCMLAWHNGKDVYEQFLNQIRTTSVGRALNLPPYTYLRHQWLENF 2143
Cdd:cd23213    403 QDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453

Rabovirus_RdRp

cd23230

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

1784-2143

2.49e-164

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: 508.65 E-value: 2.49e-164

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1784 AVYGVKNLEPLDLTTSAGFPYVALGIKKRDLVNKTTRDVSKLASMIDKYGLDLPYVTYLKDELRAPEKIKAGKTRIIEAS 1863
Cdd:cd23230      1 AAYGIENLEGLDLNTSAGYPYVLNGIKKRDILDPETRDTTKLQECLDKYGVDLPFVTYLKDELRPLEKIKKGKTRLIECS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1864 SINDTSHFRMVFGNLFSAFHANPGILTGSAVGCNPDVFWSQMYAMLDGHLLAFDYTNYDGSLNPIWFKALGMVLNKLGFP 1943
Cdd:cd23230     81 SMNDTIRMKMMFGRLFATYHRNPGPITGSAVGCNPDIHWTKFRAEMHGEIIAFDYSNYDASLNKVWFECLKMVLKNFGFK 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1944 GAM-MDKLSSTTHIYRDRVYKTEGGMPSGICGTSIFNTMINNIILRTLILETYKNIDLDKLRIIAYGDDVVASYPDPLDP 2022
Cdd:cd23230    161 DLRpIDHIIRSRHIYKGIEYDVEGGMPSGCSGTSIFNSIINNIIIMTLVLDAYKGIDLEQLKIIAYGDDVIVTYPYPLDA 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 2023 KEIAETGAKYGLTITPADKSTEFREVTWDTVTFLKRKFKVDDEFKFLIHPVYSMDDVYESIRWTKDPRNTQDHVRSLCML 2102
Cdd:cd23230    241 ALLADCGKKYGLKMTPPDKSAEFKNVTWEDVTFLKRRFKPAKHYPFLIHPVFDQQEILESLRWTRNPAHTQEHVRSLAEL 320

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|.
gi 2099546858 2103 AWHNGKDVYEQFLNQIRTTSVGRALNLPPYTYLRHQWLENF 2143
Cdd:cd23230    321 AWHSGRKSYEEFCNLVKSTNVGKACILPPYESFKRMWLDQF 361

Sapelovirus_RdRp

cd23218

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

1785-2143

9.66e-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: 495.96 E-value: 9.66e-160

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1785 VYGVKNLEPLDLTTSAGFPYVALGIKKRDLVNKTTRDVSKLASMIDKYGLDLPYVTYLKDELRAPEKIKAGKTRIIEASS 1864
Cdd:cd23218      3 VYGIDNLEGLDLNTSAGYPYNTMGIRKKDLIPPRGEPLSPLLKALDLHGYDLPFTTYLKDELRPKEKVKMGKTRLIECSS 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1865 INDTSHFRMVFGNLFSAFHANPGILTGSAVGCNPDVFWSQMYAMLD-GHLLAFDYTNYDGSLNPIWFKALGMVLNKLGFP 1943
Cdd:cd23218     83 LNDTIRMKRIFGRLFQTFHKNPGTYTGSAVGCNPDVHWSKFAEEGGmDNVCAFDYTNWDASLSPFWFDALKLFLSKLGYS 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1944 G---AMMDKLSSTTHIYRDRVYKTEGGMPSGICGTSIFNTMINNIILRTLILETYKNIDLDKLRIIAYGDDVVASYPDPL 2020
Cdd:cd23218    163 ErdiVLIDHLCYSNHIFKNEGYKVAGGMPSGCSGTSIFNSIINNIVVRTLVLLVYKGINLDELRILCYGDDLLVAYPYPL 242

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 2021 DPKEIAETGAKYGLTITPADKSTEFREVTWDT-VTFLKRKFKVDDEFKFLIHPVYSMDDVYESIRWTKDPRNTQDHVRSL 2099
Cdd:cd23218    243 DPNVLADLGKSLGLTMTPADKSDTFQGCTKLTeVTFLKRSFVFDEEFPFLCHPVFPMEEVHESIRWTRNASTTQEHVTSL 322

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....
gi 2099546858 2100 CMLAWHNGKDVYEQFLNQIRTTSVGRALNLPPYTYLRHQWLENF 2143
Cdd:cd23218    323 CLLAWHNGEEVYEEFCEKIRSVPVGRALILPPYSQLRRSWLDMF 366

ps-ssRNA_Picornaviridae

cd23193

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

1784-2119

1.62e-145

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: 455.47 E-value: 1.62e-145

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1784 AVYGVKNLEPLDLTTSAGFPYVALGIKKRDLVNKTTRDVS-----KLASMIDKYGLDLPYVTYLKDELRAPEKIKAGKTR 1858
Cdd:cd23193      1 AINGIDGLDPIDLNTSPGYPYTTQGLRRRDLIDNDKGGVSplleeEEQVLLDLDGPDVVFTTFLKDELRPKEKVKAGKTR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1859 IIEASSINDTSHFRMVFGNLFSAFHANPGILTGSAVGCNPDVFWSQMYA-MLDGHLLAFDYTNYDGSLNPIWFKALGMVL 1937
Cdd:cd23193     81 VIEAAPLDYVIAGRMVFGRLFAQFHSNPGILTGSAVGCNPDTDWTRLFAsLKQDNVYDLDYSGFDASLSSQLFEAAVEVL 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1938 -NKLGFPGAMMDKLSST---THIYRDRVYKTEGGMPSGICGTSIFNTMINNIILRTLILETYKnIDLDKLRIIAYGDDVV 2013
Cdd:cd23193    161 aECHGDPELVLRYLEPIinsKHVVGDERYTVEGGMPSGCPCTSILNSICNNLVVRYALLETGK-FDPDEYYILAYGDDVL 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 2014 ASYPDPLDPKEIAETGAKY-GLTITPADKSTEFREVTWDTVTFLKRKFKVDDEFkFLIHPVYSMDDVYESIRWTKDPRNT 2092
Cdd:cd23193    240 VSTDEPIDPSDLAEFYKKYfGMTVTPADKSSDFPESSPIEDVFLKRRFFVPDGT-FLIHPVMDLETLEQSLMWCGRGGFF 318

                          330       340
                   ....*....|....*....|....*..
gi 2099546858 2093 QDHVRSLCMLAWHNGKDVYEQFLNQIR 2119
Cdd:cd23193    319 QQLLSSLCELALHHGPEEYERLVSKVR 345

Dicipivirus_RdRp

cd23222

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

1710-2140

7.87e-85

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: 286.48 E-value: 7.87e-85

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1710 KPSVFYDVFPGKKEPAVLNPRDPRL--EANLDEAVLGKYKGNKHVEFNQyIQIAVDHYAAQL--IMLDVDSAPLTLEQAV 1785
Cdd:cd23222      1 KPSPVYGVYPVTKEPAPLKPTDRRIdeGVDFNEPVFGKYGADMKEPFRN-LDVGRDVVIARLkkVLPNKKFAPCTVSEAL 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1786 YGVKNLEPLDLTTSAGFPYVALGIKKRDL--VNKTTRDVS--KLASMID---KYGLDLPYVTYLKDELRAPEKIKAGKTR 1858
Cdd:cd23222     80 NGKDGLPKLDLKQASGYPYNLSAIKRKHLieSDKDGFLTAtpKLLADIEeskKHPEKFPYTSFLKDELRSVKKVKAGKTR 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1859 IIEASSINDTSHFRMVFGNLFSAFHANPGILTGSAVGCNPDVFWSQMYAML--DGHLLAFDYTNYDGSLNPIWFKALGMV 1936
Cdd:cd23222    160 VVEAGSLPVIVEGRMIFGNLFAYFNTHPGFETMAAVGCDPEVCWTDWYYKMreKAHTWDYDYTGFDGSIPSCSFDALADL 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1937 LNKLGFPGA----MMDKLSSTTHIYRDRVYKTEGGMPSGICGTSIFNTMINNIILRTLILETYKNIDLDKLRIIAYGDDV 2012
Cdd:cd23222    240 LCEFVENEDdvrrYISNIKNSYHAYDGNLYLIEGAMPSGCAGTSVFNCLINAMLCFSCFMDLEPEMDPFEPLLIAYGDDI 319

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 2013 VASYPDPLDPKEIAE-TGAKYGLTITPADKSTEFR-EVTWDTVTFLKRKFkVDDEFKFLIHPVYSMDDVYESIRWTKdpR 2090
Cdd:cd23222    320 LVSSDHDLFPSRVSEwMKANTTFKITPADKGEIFNdDSDVSDVRFLKRLF-VEDPVCELIHPVIETETLEPSLNWCH--E 396

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2099546858 2091 NT-QDHVRSLCMLAWHNGKDVYEQFLNQIRTTSVGRALNLP---PYTYLRHQWL 2140
Cdd:cd23222    397 GEfETKVDAISMLAFHHGPEYYRDWCKKLTDICEERNISPPglkPYSVHRNRWL 450

Cosavirus_RdRp

cd23226

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

1685-2143

2.26e-84

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

Pssm-ID: 438076 Cd Length: 461 Bit Score: 285.37 E-value: 2.26e-84

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1685 GAIVSTTHTSEcglnpINVPTNTKLK-PSVFYDVFPgKKEPAVLNPRDPRLE--ANLDEAVLGKYKGNKHVE----FNQY 1757
Cdd:cd23226      1 GQIVNTENGPR-----VHVPRQSKLKrTNATYPATG-KYGPAVLSKNDPRLDpdVDFDKVIFSKHVANVVIDedtsFWNA 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1758 IQIAVDHYAAQLimLDVDSAPLTLEQAVYGVKNLEPLDLTTSAGFPYVAlgiKKRDLVNKTTRDV--SKLASMIDKY--- 1832
Cdd:cd23226     75 LKMSAQIYAEKF--KGVDFSPLTVEEAILGIPGLDRMDPNTASGLPYTK---TRRQMIDFQEGKIldPELQERLDTWlsg 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1833 -GLDLPYVTYLKDELRAPEKIKAGKTRIIEASSINDTSHFRMVFGNLFSAFHANPGILTGSAVGCNPDVFWSQMYAMLDG 1911
Cdd:cd23226    150 kQPEMLYQTFLKDEIRPIEKVKAGKTRIIDVTPLDHVLAFRIVLGRFMAHFHNNYGFELGSAVGCDPDVAWANFGFALSS 229

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1912 --HLLAFDYTNYDGSLNPIWFKALG-MVLNKL-GFP---GAMMDKLSSTTHIYRDRVYKTEGGMPSGICGTSIFNTMINN 1984
Cdd:cd23226    230 kkYQYDFDYSNFDASHSESIFELLKqFVFTKDnGFDhrcSLMIDSLVTSTHCYEDQRMTIRGGLPSGTSGTSVINTIINN 309

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1985 IILRTLILETYKNIDLDKLRIIAYGDDVVASYPDPLDPKEIAETGAKYGLTITPADKSTEFREVTWDTVTFLKRKFKvdd 2064
Cdd:cd23226    310 IIFKAALYHTYSNFEWDDVQMLAYGDDIVAASDCLLDLDRVKYFMALIGYKITPADKGEKFIPKDMQNIQFLKRSFR--- 386

                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2099546858 2065 EFKFLIHPVYSMDDVYESIRWTKdPRNTQDHVRSLCMLAWHNGKDVYeqflNQIRTTSVGRALNLPPYTYLRHQWLENF 2143
Cdd:cd23226    387 KVAGVWAPIMDLENLQAMLSWYK-PGTLQEKLDSVARLAHFCGEKVY----DHLFTTFVKDGFQIKPWKQLHFEWLNRF 460

Mischivirus_RdRp

cd23227

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

1701-2143

1.65e-78

RNA-dependent RNA polymerase (RdRp) in the genus Mischivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Mischivirus genus within the family Picornaviridae, order Picornavirales. The Mischivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. Mischivirus is a picornavirus genus containing five species Mischivirus A, Mischivirus B, Mischivirus C, Mischivirus D and the proposed Mischivirus E. The name is derived from the name originally given to the virus, Miniopterus schreibersii picornavirus, which was found in the common bent-wing bat (aka Schreiber's long-fingered bat or Schreiber's bat) in China and is most closely related to the cardioviruses. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438077 Cd Length: 466 Bit Score: 268.74 E-value: 1.65e-78

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1701 INVPTNTKLKPSVFYDVFPGKKEPAVLNPRDPRL--EANLDEAVLGKYKGNKHVEFNQYIQIAvDHYAAQLIM-LDVDSA 1777
Cdd:cd23227     12 IHVPRKTKLRKSPAYPIFKPDAGPAVLSKNDPRLaeGVDFDKQVFSKHSANQKEYPKAFRRMA-RWYADRVFTyLGKDNG 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1778 PLTLEQAVYGVKNLEPLDLTTSAGFPYVALGIKKRDLVNKTTRDVSKLA------SMIDKYGLDLPYVTYLKDELRAPEK 1851
Cdd:cd23227     91 PLSVKDAIKGIDNLDAMDPTTSPGLPYSAAGIKRTDLLDFDTGEIISPAlraeynKYVSGDYSDHVFQTFLKDEIRSEEK 170

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1852 IKAGKTRIIEASSINDTSHFRMVFGNLFSAFHANPGILTGSAVGCNPDVFWSQMYAML--DGHLLAFDYTNYDGSLNPIW 1929
Cdd:cd23227    171 IKAGKTRIVDVPSLAHVIIGRVLLGKFCSKFQASPGTELGSAIGCNPDWDWTYFAHQLmeRQWCYDIDYSNFDSTHGTGM 250

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1930 FKALG--MVLNKLGFPGAMMDKLSS---TTHIYRDRVYKTEGGMPSGICGTSIFNTMINNIILRTLILETYKNIDLDKLR 2004
Cdd:cd23227    251 FELLIdcFFTPENGFSPAVAPYLRSlafSKHAWMDKRYKIEGGLPSGCSATSVLNTVMNNIIIRALLSLTYKNFHPEDVL 330

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 2005 IIAYGDDVVASYPDPLDPKEIAETGAKYGL-TITPADKSTEFREV-TWDTVTFLKRKFKVDDEFKFLIHPVYSMDDVYES 2082
Cdd:cd23227    331 VLAYGDDLLVASDYQLDFNRVREKAAEHTLyKLTTANKAPDFPETsTLLDCQFLKRKFVLHSTRNFIWRPVMDVTNLKTM 410

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2099546858 2083 IRWTKdPRNTQDHVRSLCMLAWHNGKDVYEQFLNQIRTTSvgraLNLPPYTYLRHQWLENF 2143
Cdd:cd23227    411 LSFYK-PNTLSEKLLSVAQLAFHSGYTVYEELFAPFKELQ----MTVPSWWYLEHEWEHNF 466

Cardiovirus_RdRp

cd23211

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

1701-2143

2.70e-78

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: 267.86 E-value: 2.70e-78

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1701 INVPTNTKLKPSVFYDVFPGKKEPAVLNPRDPRLEANLDEAVLGKYKGNKHvEFNQYIQIAVDHYAAQLI-MLDVDSAPL 1779
Cdd:cd23211     12 VHVPRKTKLRRTVAHPVFQPKFEPAVLSKYDPRTDKDVDEVAFSKHTTNQE-SLPPVFRMVAKEYANRVFtLLGKDNGRL 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1780 TLEQAVYGVKNLEPLDLTTSAGFPYVALGIKKRDLVNKTTR-----DVSKLASMIDKYGLDLPYVTYLKDELRAPEKIKA 1854
Cdd:cd23211     91 TVEQAVLGLEGMDPMEKDTSPGLPYTQQGLRRTDVVDFETAtmipfLAEAHRKMVEGDYSDVVYQSFLKDEIRPIEKVQA 170

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1855 GKTRIIEASSINDTSHFRMVFGNLFSAFHANPGILTGSAVGCNPDVFWSQMYAMLDGHLLAFD--YTNYDGSLNPIWFKA 1932
Cdd:cd23211    171 AKTRIVDVPPFEHCILGRQLLGRFASKFQTNPGLELGSAIGCDPDVDWTAFAVALSGFKYVYDvdYSNFDSTHSTAMFEL 250

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1933 L--GMVLNKLGFP---GAMMDKLSSTTHIYRDRVYKTEGGMPSGICGTSIFNTMINNIILRTLILETYKNIDLDKLRIIA 2007
Cdd:cd23211    251 LieNFFTEENGFDpriGEYLRSLAVSRHAYEERRVLIRGGLPSGCAATSMLNTIMNNIIIRAGLYLTYKNFEFDDIKVLS 330

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 2008 YGDDVVASYPDPLDPKEIAETGAKYGLTITPADKSTEF-REVTWDTVTFLKRKFKVDDefKFLIHPVYSMDDVYESIRWT 2086
Cdd:cd23211    331 YGDDLLVATNYQIDFNLVKARLAKFGYKITPANKTSTFpLTSTLEDVVFLKRKFVKEN--SYLYRPVMDRENLKAMLSYY 408

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2099546858 2087 KdPRNTQDHVRSLCMLAWHNGKDVYEQFLNQIRTTSVgralNLPPYTYLRHQWLENF 2143
Cdd:cd23211    409 R-PGTLKEKLTSIALLAVHSGKQVYDEIFAPFREVGI----VVPTYESVLYRWLSLF 460

Kobuvirus_RdRp

cd23214

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

1701-2140

4.12e-77

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: 264.40 E-value: 4.12e-77

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1701 INVPTNTKLKPSVFYDVFPGKKEPAVLNPRDPRLE--ANLDEAVLGKYKGNKHVEFNQYIQIAVDHYAAQL-IMLDVdsa 1777
Cdd:cd23214      3 VNVNRKSRLGPSPAYGAFPVKKQPAPLTQKDDRLEdgIRLDDQLFLKHNKGDMDEPWPGLEAAADLYFSKFpTMIRT--- 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1778 pLTLEQAVYGVKNLEPLDLTTSAGFPYVALGIKKRDLVNKTTRDV----SKLASMIDKYGLDLPYV--TYLKDELRAPEK 1851
Cdd:cd23214     80 -LTQEEAINGTPNLEGLDMNQAAGYPWNTMGRSRRSLFVEVQPGIyvpkPELQAEIDKTLEDPDYFysTFLKDELRPTAK 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1852 IKAGKTRIIEASSINDTSHFRMVFGNLFSAFHANPGiLTGSAVGCNPDVFWSQ-MYAMLD-GHLLAFDYTNYDGSLNPIW 1929
Cdd:cd23214    159 VTLGLTRVVEAAPIHAIVAGRMLLGGLIEYMQARPG-KHGSAVGCNPDLHWTKfFYKFCHyPQVFDLDYKCFDATLPSCA 237

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1930 FKALGMVLNKL-GFP--GAMMDKLSSTTHIYRDRVYKTEGGMPSGICGTSIFNTMINNI-ILRTLIleTYKNIDLDKLRI 2005
Cdd:cd23214    238 FRIVEDHLERLtGDErvTRYIESIRHSHHVYGNETYEMIGGNPSGCVGTSIINTIINNIcVLSALI--QHPDFSPESFRI 315

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 2006 IAYGDDVVASYPDPLDPKEIAETGAKYG-LTITPADKSTEFREV-TWDTVTFLKRKFKVDDEFKFLIHPVYSMDDVYESI 2083
Cdd:cd23214    316 LAYGDDVIYGCDPPIHPSFIKEFYDKHTpLVVTPANKGSDFPETsTIYDVTFLKRWFVPDDIRPFYIHPVMDPDTYEQSV 395

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 2084 RWTKDPrNTQDHVRSLCMLAWHNGKDVYEQFLNQIR---TTSVGRALNLPPYTYLRHQWL 2140
Cdd:cd23214    396 MWLRDG-DFQDLVTSLCYLAFHSGPKTYDRWCTRVRdqvMKTTGFPPTFLPYSYLQTRWL 454

Megrivirus_RdRp

cd23223

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

1715-2118

6.36e-76

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: 259.77 E-value: 6.36e-76

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1715 YDVFPGKKEPAVLNPRDPRLE--ANLDEAVLGKYKGNKhvEFNQYIQIAVDhYAAQLIMLDVDSAP------LTLEQAVY 1786
Cdd:cd23223      2 YGAFPVTHGPAALTNKDKRLEegVDLDDVMFSKHVPDH--PGWPTLEPAMS-YVVEDLMHKLGFSKdepvpmWTLEQAIN 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1787 GVKNLEPLDLTTSAGFPYVALGIKKRDLVN------KTTRDVSKLASMIDKYGLDLPYVTYLKDELRAPEKIKAGKTRII 1860
Cdd:cd23223     79 GEGVMDGIDMGQSPGYPYNAQGRSRRSFFEwngekwQPTEELKKEVDHALKDPDDFYFSTFLKDELRPLEKVKAGKTRLV 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1861 EASSINDTSHFRMVFGNLFSAFHANPGILTGSAVGCNPDVFWSQMYAML--DGHLLAF--DYTNYDGSLNPIWFKALGMV 1936
Cdd:cd23223    159 DGDSLPRILAMRMVFGPLFEAMLRKNGPEIHSAVGCNPDTDWTRYYHEMgpDSFPYCFdlDYSCFDSTEPKIAFRLMAKY 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1937 LnKLGF---PGAMMDKLSSTTHIYRDRVYKTEGGMPSGICGTSIFNTMINNIILRTLILETykNIDLDKLRIIAYGDDVV 2013
Cdd:cd23223    239 L-KPYFsvdVTPFFEALATSKHVYGDKAYEMEGGMPSGCVGTSMFNCINNSAFIVSALIAL--KISPEDCAWICYGDDVI 315

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 2014 ASYPDPLDPKEIAE-TGAKYGLTITPADKSTEFREV-TWDTVTFLKRKFKVDDEFKFLIHPVYSMDDVYESIRWTKD-Pr 2090
Cdd:cd23223    316 ISTDEKALSKRIADfYHKNTNLVVTPASKSGDFPETsTIYDVTFLKRFFQPDSHYPHLIHPYMPLEHLEQSVMWQTDgP- 394

                          410       420
                   ....*....|....*....|....*...
gi 2099546858 2091 nTQDHVRSLCMLAWHNGKDVYEQFLNQI 2118
Cdd:cd23223    395 -FQQKLDSLCLLAFHAGGPDYREFVDAI 421

Rosavirus_RdRp

cd23221

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

1784-2143

5.31e-75

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: 255.23 E-value: 5.31e-75

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1784 AVYGVKNLEPLDLTTSAGFPYVALGIKKR---DLVNKTTRDVSKLASMIDKYGLDlP----YVTYLKDELRAPEKIKAGK 1856
Cdd:cd23221      1 AINGIDNMDGLDMNQSPGVPYVSEGVSRRslfDCVDGQWVPRERLASDIAQVSGD-PslghFATFLKDELRSTEKVAAGK 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1857 TRIIEASSINDTSHFRMVFGNLFSAFHANPGILTGSAVGCNPDVFWSQMYAMLDGHLLAF--DYTNYDGSLNPIWFKALG 1934
Cdd:cd23221     80 TRVVEAGSLPHIIVGRKIFGNLFALFNSNPGFQTMCAVGCDPDVTWTELYHPLSAKTYVFdyDYSGFDGSVPSCCFDALA 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1935 MVLNKLgFPG-----AMMDKLSSTTHIYRDRVYKTEGGMPSGICGTSIFNTMINNIILRTLILETYKNIDLDKLRIIAYG 2009
Cdd:cd23221    160 DLLADF-VEGeedvrKYISSLKTSFHHYKGKLWRLDGAMPSGCCGTSVFNSLINAMLLFSAFSQICPDFRASEPLLVAYG 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 2010 DDVVASYPDPLDPKEIAE-TGAKYGLTITPADKSTEFR-EVTWDTVTFLKRKFKVDDEFKFLIHPVYSMDDVYESIRWTK 2087
Cdd:cd23221    239 DDVLVGTDQPLFPSKVAEwVNSHTTFRITPADKGSVFNdESDIHSVQFLKRHFTPDPDFPALIHPTIDPDTYEQSVMWQR 318

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2099546858 2088 dPRNTQDHVRSLCMLAWHNGKDVYEQFLNQIRTTSVGRALN---LPPYTYLRHQWLENF 2143
Cdd:cd23221    319 -TGDFQETVNSLALLVFHRGPKSYSRWCESVTRKCVDGGYPppfFPPFSLLRHQWLKKF 376

ps-ssRNAv-Picornavirales

cd23169

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

1837-2119

9.73e-75

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: 251.75 E-value: 9.73e-75

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1837 PYVTYLKDELRAPEKIKAGKTRIIEASSINDTSHFRMVFGNLFSAFHANPgILTGSAVGCNPD-VFWSQMYAML---DGH 1912
Cdd:cd23169      2 IFVDCLKDELRPIEKVKAGKTRLFSASPLDYTIAFRKYFGDFIAAFQKNR-IKLEHAVGINPDsVEWTRLYRRLlkkGPN 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1913 LLAFDYTNYDGSLNPIWFKALGMVLNK--LGFPG--------AMMDKLSSTTHIYRDRVYKTEGGMPSGICGTSIFNTMI 1982
Cdd:cd23169     81 IFAGDYSNFDGSLPPDVMEAAFDIINDwyDEYVDdedervrkVLFEELINTIHLVGNLVYQVHGGNPSGNPLTTIINSIV 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1983 NNIILRTLILETYKNIDLDK----LRIIAYGDDVVAS----YPDPLDPKEIAETGAKYGLTITPADKS-TEFREVTWDTV 2053
Cdd:cd23169    161 NLLYIRYAWLRITGLTSLSDfkknVRLVTYGDDVIISvsdeVKDEFNFVTISEFLKELGITYTDADKSgDIVPYRPLEEV 240

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 2054 TFLKRKFKVDDEfKFLIHPVYSMDDVYESIRWTK---DPRNTQDH-VRSLCMLAWHNGKDVYEQFLNQIR 2119
Cdd:cd23169    241 TFLKRGFRPHPT-PGLVLAPLDLESIEEQLNWTRkedDLLEATIEnARAALLLAFGHGPEYYNKFRQKLN 309

Mosavirus_RdRp

cd23225

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

1792-2140

4.15e-74

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: 252.53 E-value: 4.15e-74

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1792 EPLDLTTSAGFPYVALGIKKRDLVN-------KTTRDVSKLASMIDKY--GLDLP-YVTYLKDELRAPEKIKAGKTRIIE 1861
Cdd:cd23225     10 DAMDMTKAVGYPYCLDSIKRLDLVEiketengKVYLPTERLVEETEKFftGEEKPkFVTFLKDEVRSNEKIKQGKTRIVD 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1862 ASSINDTSHFRMVFGNLFSAFHANPGILTGSAVGCNPDVFWSQ-MYAMLDGHLLAFDYTNYDGSLNPIWFKALG--MVLN 1938
Cdd:cd23225     90 ASPFPYAIAGRMVMQNFMSNMMRCNGTEVGSAVGCDPDTEWTRyFFELCDRYVFDLDYKAFDSTHPTAMFNLLAerFFTE 169

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1939 KLGFPGA----MMDKLSSTTHIYRDRVYKTEGGMPSGICGTSIFNTMINNIILRTLILETYK--NIDLDKLRIIAYGDDV 2012
Cdd:cd23225    170 RNGFDQQavriFLNGLSDSDHVYEGKHFRIRGGLPSGCPCTSILNTVINNIIVRAAILGAYQidTVDFQKFRMLAYGDDV 249

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 2013 VASYPDPLDPKEIAE-TGAKYGLTITPADKSTEFREVT--WDtVTFLKRKFKVDDEFKFLIHPVYSMDDVYESIRWTKdP 2089
Cdd:cd23225    250 VYATPQPIKPQDLADwLHANTNYKVTPASKAGTFPEEStiWD-VTFLKRSFKPDEDHGHLIRPVMAVGNLKQMLSFMR-P 327

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2099546858 2090 RNTQDHVRSLCMLAWHNGKDVYEQFLNQIRTTSVGraLNLPPYTYLRHQWL 2140
Cdd:cd23225    328 GTFPDKVRSVAGLAVHCGEEDYNQLADAVALYVPG--VSMPAYKYMKACWY 376

Aphthovirus_RdRp

cd23210

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

1701-2140

3.81e-69

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: 241.39 E-value: 3.81e-69

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1701 INVPTNTKLKPSVFYDVFPGKKEPAVLNPRDPRLE--ANLDEAVLGKYKGNKHV--EFNQYIQIAVDHYAAQLI-MLDVD 1775
Cdd:cd23210      6 VHVMRKTKLAPTVAHGVFNPEFGPAALSNKDPRLNegVVLDEVIFSKHKGDTKMsaEDKALFRRCAADYASRLHsVLGTA 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1776 SAPLTLEQAVYGVKNLEPLDLTTSAGFPYVALGIKKRDLV---NKTTRDVSKLA-SMIDKYGLDLPYVTYLKDELRAPEK 1851
Cdd:cd23210     86 NAPLSIYEAIKGVDGLDAMEPDTAPGLPWALQGKRRGALIdfeNGTVGPEVEAAlKLMEKREYKFACQTFLKDEIRPMEK 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1852 IKAGKTRIIEASSINDTSHFRMVFGNLFSAFHANPGILTGSAVGCNPDVFWSQMYAMLDGH--LLAFDYTNYDGSLNPiw 1929
Cdd:cd23210    166 VRAGKTRIVDVLPVEHILYTRMMIGRFCAQMHSNNGPQIGSAVGCNPDVDWQRFGTHFAQYrnVWDVDYSAFDANHCS-- 243

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1930 fKALGMVLNKL-----GF-PGA--MMDKLSSTTHIYRDRVYKTEGGMPSGICGTSIFNTMINNIILRTLILETYKNIDLD 2001
Cdd:cd23210    244 -DAMNIMFEEVfrtefGFhPNAewILKTLVNTEHAYENKRITVEGGMPSGCSATSIINTILNNIYVLYALRRHYEGVELD 322

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 2002 KLRIIAYGDDVVASYPDPLDPKEIAETGAKYGLTITPADKSTEFR--EVTWDTVTFLKRKFKVDDEFKFLiHPVYSMDDV 2079
Cdd:cd23210    323 TYTMISYGDDIVVASDYDLDFEALKPHFKSLGQTITPADKSDKGFvlGHSITDVTFLKRHFHMDYGTGFY-KPVMASKTL 401

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2099546858 2080 yESIRWTKDPRNTQDHVRSLCMLAWHNGKDVYEQFLNQIRTTsvgraLNLPPYTYLRHQWL 2140
Cdd:cd23210    402 -EAILSFARRGTIQEKLISVAGLAVHSGPDEYRRLFEPFQGL-----FEIPSYRSLYLRWV 456

Teschovirus_RdRp

cd23212

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

1778-2115

1.58e-63

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

Pssm-ID: 438062 Cd Length: 354 Bit Score: 221.42 E-value: 1.58e-63

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1778 PLTLEQAVYGVKNLEPLDLTTSAGFPYVALGIKKRDLVNKTTRDVSKLASMIDKYgLDLPY-----VTYLKDELRAPEKI 1852
Cdd:cd23212     10 PLSVREAVEGIDGLDPMDMDKSPGLPYVKKGLRRTDLWNPKTGPSIELMAEINRY-LDYNYdkhvfLTFLKDELRPKEKV 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1853 KAGKTRIIEASSINDTSHFRMVFGNLFSAFHANPGILTGSAVGCNPDVFWSQM-YAMLDGHLLAFDYTNYDGSLNPIWFK 1931
Cdd:cd23212     89 QAGKTRVIDVAGFGHAIVGRMLFGRLFAFFHKNPGWNTGSAVGVNPDLAWTQIfYTAPSRNVLAMDYSGFDASHTSGMFC 168

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1932 ALGMVLNKLGFpGAM----MDKLSSTTHIYRDRVYKTEGGMPSGICGTSIFNTMINNIILRTliLETYKNIdlDKLRIIA 2007
Cdd:cd23212    169 ILKHFLTTLGY-GTLqlsyIDSLCYSKHHWDDETYRLDGGLPSGCSGTTIFNTIMNNIVARA--AASYAAE--GPVGILC 243

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 2008 YGDDVVASYPDPLDPKEIAETGAKYGLTITPADKS--TEFREVTwdTVTFLKRKFKVDDEfkfLIHPVYSMDDVYESIRW 2085
Cdd:cd23212    244 YGDDILVSSPEKFPVSDWLEFYSKTPYKVTAADKSeqIDWRDIT--QCTFLKRGFVLDGS---LVRPVMEEQHLAELLKW 318

                          330       340       350
                   ....*....|....*....|....*....|
gi 2099546858 2086 TKdPRNTQDHVRSLCMLAWHNGKDVYEQFL 2115
Cdd:cd23212    319 AR-PGTLQAKLLSIAQLAFHLPRQAYDRLM 347

RNA_dep_RNAP

cd01699

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

1820-2086

3.19e-62

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: 214.45 E-value: 3.19e-62

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1820 RDVSKLASMIdKYGLDLPYVTYLKDELRAPEKIKAGKTRIIEASSINDTSHFRMVFGNLFSAFHANpGILTGSAVGCNPD 1899
Cdd:cd01699      3 KAVESLEDLP-LIRPDLVFTTFLKDELRPLEKVEAGKTRLIQPRPLDYNIALRMYLGPFEAKLMKN-RGGLPIAVGINPY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1900 VF-WSQMYAMLDG---HLLAFDYTNYDGSLNPIWFKALGMVLNKL--GFPGAMMDKLS-----STTHIYRDRVYKTEGGM 1968
Cdd:cd01699     81 SRdWTILANKLRSfspVAIALDYSRFDSSLSPQLLEAEHSIYNALydDDDELERRNLLrsltnNSLHIGFNEVYKVRGGR 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1969 PSGICGTSIFNTMINNIILRTLILETYKNIDLDKLRIIAYGDDVVASYP---DPLDPKEIAETGAKYGLTITPADKsTEF 2045
Cdd:cd01699    161 PSGDPLTSIGNSIINCILVRYAFRKLGGKSFFKNVRLLNYGDDCLLSVEkadDKFNLETLAEWLKEYGLTMTDEDK-VES 239

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|.
gi 2099546858 2046 REVTWDTVTFLKRKFKVDDEfkFLIHPVYSMDDVYESIRWT 2086
Cdd:cd01699    240 PFRPLEEVEFLKRRFVLDEG--GGWRAPLDPSSILSKLSWS 278

Passerivirus_RdRp

cd23224

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

1783-2141

2.08e-59

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: 210.33 E-value: 2.08e-59

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1783 QAVYGVKNLEPLDLTTSAGFPYvALGIKKRDLVNKTTRDVSKLASMIDKYGL------DLPYVTYLKDELRAPEKIKAGK 1856
Cdd:cd23224      1 EAINGTPLLDGLDMKQSPGYPW-SLTTNRRSLFTQDETGKYYPVPELEEAVLaclenpDYFYTTHLKDELRPVEKALAGK 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1857 TRIIEASSINDTSHFRMVFGNLFSAFHANPGiLTGSAVGCNPDVFWSQMYAMLD--GHLLAFDYTNYDGSLNPIWFKALG 1934
Cdd:cd23224     80 TRLIEAAPIHAIIAGRMLLGGLFEYMHARPG-EHGSAVGCDPDYHWTPFFHSFDefSQVWALDYSCFDSTLPSCCFDLIA 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1935 MVLNKL--GFPGAMMD-------KLSSTTHIYRDRVYKTEGGMPSGICGTSIFNTMINNIILRTLILeTYKNIDLDKLRI 2005
Cdd:cd23224    159 QKLAKIitPGEGIAPDaivkyirSISISKHVFGNEAYLMVGGNPSGCVGTSILNSMINNCVLISAFL-TQKDFNPNQMRI 237

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 2006 IAYGDDVVASYPDPLDPKEIAE-TGAKYGLTITPADKSTEF--REVTWDtVTFLKRKFKVDDEFKFLIHPVYSMDDVYES 2082
Cdd:cd23224    238 LTYGDDVLYATNPPIHPRVVKKfFDENTTLIVTPATKAGDFpdESTIWD-VTFLKRYFVPDEIRPWYVHPVIEPATYEQS 316

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2099546858 2083 IRWTKDPrNTQDHVRSLCMLAWHNGKDVYEQFLNQIRTTSVGRAL--NLPPYTYLRHQWLE 2141
Cdd:cd23224    317 VMWTRGG-DFQDVVTSLSFLAHHAGPTNYMIWEEKVRKAAAAKGVslNILPYSYLQHRWML 376

Rhv

pfam00073

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

91-299

5.57e-53

Pssm-ID: 395026 Cd Length: 170 Bit Score: 183.67 E-value: 5.57e-53

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858   91 TTQDTLNSVVAYGEWPQYLSDLDASSIDKPTHPETSADRFYTLDSVNWTGTSLGW-WWKLPDCLREMGLFGQNMYYHSMG 169
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFfWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  170 RTGYIIHVQCNATKFHSGCLMVAVIPEHQMayigaggtnvrydqtHPGeaghTITASKQWGehnpdenpfynlngtlfgn 249
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPPGAP---------------PPG----SRDYLWQAT------------------- 122

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 2099546858  250 iqIFPHQMINLRTNNSATIVVPYINCLPMDNMLRHNNLTLMIIPIVKLRH 299
Cdd:pfam00073  123 --LNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGNWTLVVAGWVPLNY 170

RdRP_1

pfam00680

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

1711-2118

7.62e-53

Pssm-ID: 425815 Cd Length: 450 Bit Score: 193.40 E-value: 7.62e-53

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1711 PSVFYDVFPGKKEPAVLNPRDPRLE---ANLDEAVLGKYKGN---KHVEFNQYIQIAVD----HYAAQLIMLD-VDSAPL 1779
Cdd:pfam00680    2 PTERHLVAIPAYVPASLGPEDPRWArsyLNTDPYVDDIKKYSrpkLPGPADERDKLLNRsaakMVLSELRGVPkKANSTL 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1780 TLEQAVYGVKNLEPLDLTTSAGFPYVALGIKKRDLVNK----TTRDV--SKLASMIDKYG----LDLPYVTYLKDELRAP 1849
Cdd:pfam00680   82 IVYRAIDGVEQIDPLNWDTSAGYPYVGLGGKKGDLIEHlkdgTEARElaERLAADWEVLQngtpLKLVYQTCLKDELRPL 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1850 EKIKAGKTRIIEASSINDTSHFRMVFGNLFSAFHANPGILTgSAVGCNP-DVFWSQMYAMLDGH---LLAFDYTNYDGSL 1925
Cdd:pfam00680  162 EKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHP-IQVGINPfDRGWPRLLRRLARFgdyVYELDYSGFDSSV 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1926 NPIWFKALGMVLN-KLGFP------GAMMDKLSSTTH-IYRDRVYKTEGGMPSGICGTSIFNTMINNIILRTLILETYKN 1997
Cdd:pfam00680  241 PPWLIRFAFEILReLLGFPsnvkewRAILELLIYTPIaLPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYALLKSLEN 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1998 IDL------DKLRIIAYGDDVVASYPDPLDP--KEIAETGAKYGLTITPADKSTE-FREVTwdTVTFLKRKFKVDdefKF 2068
Cdd:pfam00680  321 DGPrvcnldKYFDFFTYGDDSLVAVSPDFDPvlDRLSPHLKELGLTITPAKKTFPvSRELE--EVSFLKRTFRKT---PG 395

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|
gi 2099546858 2069 LIHPVYSMDDVYESIRWTKDPRNTQDHVRSLCMLAWHNGKDVYEQFLNQI 2118
Cdd:pfam00680  396 GYRPPLDRKRILAQLEYIRSKPVPSGQLENIRAYASHHGYEFYRDLLYRF 445

Pico_P2A

pfam00947

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

853-970

2.42e-52

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

Pssm-ID: 395757 Cd Length: 127 Bit Score: 180.27 E-value: 2.42e-52

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  853 NAHLTNPNEH--TILLALTADLQVDATTEPGSDVIPDCDCVEGCYYCKSQDRYFPVKTTQHDWYEIQETVYYPKHIQYNI 930
Cdd:pfam00947    1 NRHLATHEDWhnSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 2099546858  931 LIGEGPAEPGDCGGKLLCRHGVIGILTAGGEGHVAFTDLR 970
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVR 120

Fipivirus_RdRp

cd23229

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

1785-2139

8.50e-51

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: 185.78 E-value: 8.50e-51

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1785 VYGVKNLEPLDLTTSAGFPYVALGIKKRDLVNK-----TTRDVSKLASMIDKYGL---------DLPYVTYLKDELRAPE 1850
Cdd:cd23229      2 VEGIPGMEGLDMKTSAGYPWCEQNQKKKDKIKLlagknFLVRPLREVVHIVVDWYimppdmpkpEIKYVVYLKDELLSSD 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1851 KIKAGKTRIIEASSINDTSHFRMVFGNLFSAFH-ANP--GILTGSAVGCNPDVFWSQMYAMLDG-HLLAFDYTNYDGSLN 1926
Cdd:cd23229     82 KVKMGRTRWICAAPVQLVCAWKKVFGRAIAAIHlESVtdGKSTGCAVGMDPETAWTDIALARPGwPVIALDYSNFDGSLQ 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1927 PIWFKALGMVLNKL-GFPGAMMDKLSS----TTHIYRDRVYKTEGGMPSGICGTSIFNTMINNIILR-------TLILET 1994
Cdd:cd23229    162 SFVITGAVRILGYIaGLPDGQSYRLAEfvydVKQIVGKYLYTTVGPLPSGCPSTSIIGSLCNVLMLLytlshatGQRYSA 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1995 YKnidlDKLRIIAYGDDVVASYPDplDPKEIAETGA-----KYGLTITPA-DKSTEFREVTWDTVTFLKRKFKVDDEFKF 2068
Cdd:cd23229    242 FR----DWMHVVTYGDDVLVFVHP--EVVVVLDTLAhemylVFGVTATDAtDKRAPPQLRELSNVTFLKRGFRQCSSVPF 315

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2099546858 2069 LIHPVYSMDDVYESIRWTKDPRNTQDHVRSLCMLAWHNGKDVYEQFLNQIRTTSV-------GRALN-LPPYTYLRHQW 2139
Cdd:cd23229    316 LVHPTMDKSTIYQMLAWKRKGTTLAENVKCAAEFMMHHGEEEYEDFVGVVKECSTligvdqrSKVYEeLCSYAELHDHW 394

Hepatovirus_RdRp

cd23215

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

1778-2120

6.73e-47

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: 176.58 E-value: 6.73e-47

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1778 PLTLEQAVYGVKNLEPLDLTTSAGFPYVALGIKKRDLV-------------NKTTRDVSKLASMIDKYGLDLPYVTYLKD 1844
Cdd:cd23215     64 FFDLEQAITGVPGMDAINMDSSPGYPYVQEKLTKSDLIwlddngellgmhpRLAQRILFNLTMMDNGNDLDVVYTTCPKD 143

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1845 ELRAPEKIKAGKTRIIEASSINDTSHFRMVFGNLFSAFHANPGILTGSAVGCNPDVFWSQMYAML---DGHLLAFDYTNY 1921
Cdd:cd23215    144 ELRPLEKVLESKTRAIDACPLDFTIICRMFWGPAISYFQLNPGFHTGVAVGIDPDRDWDALFKTMirfGDYGIDLDFSSF 223

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1922 DGSLNPIWFKALGMVLNKLG-----FPGAMMDKLSSTTHIYRDRVYKTEGGMPSGICGTSIFNTMINNIILRTLILETYK 1996
Cdd:cd23215    224 DASLSPFMIREACRVLSELSgvpdhQGQALINTIIYSKHLLYNLCYHVCGSMPSGSPCTSLLNSIVNNVNLYYVFSKIFK 303

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1997 NIDL---DKLRIIAYGDDVVASYPDPLDPKEIAETG-------AKYGLTITPADKStEFREVTWDTVTFLKRKFK-VDDE 2065
Cdd:cd23215    304 KSPVffyDAVKFLCYGDDVLIVFSRDLEIKNLDKLGqriqdefKLLGMTATSADKG-EPQVVPVSELTFLKRSFNlIEDR 382

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2099546858 2066 FKflihPVYSMDDVYESIRWTKDPRNTQDHVRSLCMLAWHNGKDVYEQFLNQIRT 2120
Cdd:cd23215    383 FR----PAISEKTIWSLVAWQRSNAEFEQNLDTACWFAFMHGYDFYQNFYLQLQS 433

Crohivirus_RdRp

cd23232

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

1781-2132

6.58e-45

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: 167.97 E-value: 6.58e-45

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1781 LEQAVYGVKNLEPLDLTTSAGFPYVALGIKKRDLVNKTT--------RDVSKLASMIDKYG-LDLPYVTYLKDELRAPEK 1851
Cdd:cd23232      1 IEEACFEEGDEHALDLKTSPGFKYVQMGLKKTDLVNRPNkfihpilrNDVRLIFDEMAKGQmPVVTFTAHLKDELRKLEK 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1852 IKAGKTRIIEASSINDTSHFRMVFGNLFSAFHANPGILTGSAVGCNPDVFWSQMYAMLDGHLLAFDYTNYDGSL-NPIWF 1930
Cdd:cd23232     81 IRSGKTRCIEACDFDYTVAHKMMFGTLYKAIYDTPGIITGLAVGMNPWKDWELIQQSLFKYNYDFDYKTFDGSLsRELML 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1931 KA---LGMVLNKLGFPGAMMDKLSSTTHIYRDRVYKTEGGMPSGICGTSIFNTMINNIILRTLILETYKNidldKLRIIA 2007
Cdd:cd23232    161 HAvdiLSACVENDEMAKLMLSVVVESVHLVLDQKWNVSGGMPSGSPCTTVLNSVCNLIVSSTIADMCTEG----DFKILV 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 2008 YGDDVVASYPDPLDPKEIAE-TGAKYGLTITPADKSTEFREVTWDTVTFLKRKFKVDDEFKFLIHpVYSMDDVYESIRWT 2086
Cdd:cd23232    237 YGDDLIISSTAPLDCDRFKTlVELHYGMEVTPGDKGDEFKVKDREQVSFLKRVTRKFPGTNYRVG-ALDLDTVKQHLMWC 315

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*.
gi 2099546858 2087 KDPRNTQDHVRSLCMLAWHNGKDVYEQFLNQIRTTSVGRALNLPPY 2132
Cdd:cd23232    316 KSYSSFKQQLDSALMEVAMHGEETYNGFLTEIKTKLDKFKIYPPKF 361

Parechovirus_RdRp

cd23217

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

1784-2116

2.14e-44

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: 166.20 E-value: 2.14e-44

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1784 AVYGVKNLEPLDLTTSAGFPYVALGIKKRDLVNKTTRDVSKLASMIDK------YGLDLP---YVTYLKDELRAPEKIKA 1854
Cdd:cd23217      1 AVLGTSHLNSLDLSTSPGYKYVKSGYKKRDLLSLEPFSVSPQLEKDVKdklhavYKGNQPttiFNACLKDELRKLDKIAQ 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1855 GKTRIIEASSINDTSHFRMVFGNLFSAFHANPGILTGSAVGCNPDVFWSQMYAMLDGHLLAFDYTNYDGSLNPiwfKALG 1934
Cdd:cd23217     81 GKTRCIEACSIDYVIAYRVVMSSLYEAIYQTPCQELGLAVGMNPWTDWDFMINALNPYNYGLDYSSYDGSLSE---MLMW 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1935 MVLNKLGF----PGAMM---DKLSSTTHIYRDRVYKTEGGMPSGICGTSIFNTMINNIILRTLILETYKNIDldkLRIIA 2007
Cdd:cd23217    158 EAVEVLAYchesPDLVMqlhKPVINSDHVVMDERWLVHGGMPSGSPCTTVLNSICNLLVCIYLAYLQSPGIE---CLPIV 234

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 2008 YGDDVVASYPDPLDPKEIAETGAK-YGLTITPADKSTEFREVTWDTVTFLKRKFKVDDEFKFLIHPVySMDDVYESIRWT 2086
Cdd:cd23217    235 YGDDVIFSVSSEIDPEYLVSSAADsFGMEVTGSDKDEPPSLLPRMEVEFLKRTTGYFPGSTYKVGAL-DLETMEQHIMWM 313

                          330       340       350
                   ....*....|....*....|....*....|....
gi 2099546858 2087 KD----PRNTQDHVRSLCMlawhNGKDVYEQFLN 2116
Cdd:cd23217    314 KNlstfPQQLQSFENELCL----HGKDIYDDYKK 343

Dicistroviridae_RdRp

cd23194

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

1838-2119

1.28e-42

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

Pssm-ID: 438044 [Multi-domain] Cd Length: 315 Bit Score: 159.20 E-value: 1.28e-42

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1838 YVTYLKDELRAPEKIKAGKTRIIEASSINDTSHFRMVFGNLFSAFHANPgILTGSAVGCNP---DvfWSQMYAML---DG 1911
Cdd:cd23194      8 FVDTLKDERRPIEKVDAGKTRVFSAGPMDYTIAFRMYFLGFVAHLMRNR-IDNEIAVGTNVyslD--WDKLARKLlskGD 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1912 HLLAFDYTNYDGSLNP-IWFKALGMVLN--KLGFPGAMMDK-----LSSTTHIYRDRVYKTEGGMPSGICGTSIFNTMIN 1983
Cdd:cd23194     85 KVIAGDFSNFDGSLNPqILWAILDIINEwyDDGEENALIRRvlwedIVNSVHICGGYVYQWTHSQPSGNPLTAIINSIYN 164

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1984 NIILR---TLILETYKNIDL----DKLRIIAYGDDVVASYPDPLDPK----EIAETGAKYGLTITPADKSTEfrEVTWDT 2052
Cdd:cd23194    165 SIIMRyvyLLLTKEAGLMTMsdfnKHVSMVSYGDDNVINVSDEVSEWfnqlTITEAMAEIGMTYTDETKTGE--IVPYRS 242

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2099546858 2053 ---VTFLKRKFKVDDEFKFLIHPVySMDDVYESIRWTK---DPR-NTQDHVRSLCM-LAWHnGKDVYEQFLNQIR 2119
Cdd:cd23194    243 leeVSFLKRGFRYDDDLGRWVAPL-DLDTILEMPNWVRkgkDPEeITKQNVENALReLSLH-GEEVFDKWAPKIR 315

Avisivirus_RdRp

cd23231

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

1791-2134

2.24e-41

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: 157.36 E-value: 2.24e-41

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1791 LEPLDLTTSAGFPYValGIKKRDLVN--KTTRDVSKLA---SMIDKYGLDLPYVTYLKDELRAPEKIKAGKTRIIEASSI 1865
Cdd:cd23231      8 LLPIDWGTSPGDKYK--GKTKAQLVDdkKFKADVMNLVrfnGDPNREPPDVYFTTYLKDELRPKEKAKAGKTRVISAASF 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1866 NDTSHFRMVFGNLFSAFHANpGILTGSAVGCNPDVFWSQMYAMLDGHLLAFDYTNYDGSLN-PIWFKALGMVLNKLGFPG 1944
Cdd:cd23231     86 DYTIACRMVFGPILRQLFAW-GREFGFGPGLNPYTHFDELYDKILPFVICLDYSGFDGSLSsELMFHAAQVIACFSEKPE 164

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1945 AMMdKLSSTTHIYRDRV----YKTEGGMPSGICGTSIFNTMINNIILRTLILetYKNIDLDKLRIIAYGDDVVASYPDPL 2020
Cdd:cd23231    165 AIM-ASAELTIGSTERVsdevWYVYGGMPSGSPWTTTLNTICNLLMCYTYLL--DMGHCWSETFVVAYGDDVVISANIKH 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 2021 DPKEIAET-GAKYGLTITPADKSTEFREVTWDTVTFLKRKFKvddEFKFL--IHPVYSMDDVYESIRWTKDprNTQDHVR 2097
Cdd:cd23231    242 NLEGIEQWfKTKFGATVTPSDKQGKITWTTKNNMEFLKRRPK---QLDFLpkIVGALDLDNMLDRIQWTKG--HFQDQLN 316

                          330       340       350
                   ....*....|....*....|....*....|....*...
gi 2099546858 2098 SLCM-LAWHnGKDVYeqflNQIRTTSVGRALNLPPYTY 2134
Cdd:cd23231    317 SFYLeLALH-GRETY----NEIRAKLAPRAPQLVHPTY 349

Limnipivirus_RdRp

cd23228

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

1793-2132

7.86e-41

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: 156.58 E-value: 7.86e-41

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1793 PLDLTTSAGFPYVALGIKKRDL----------VNKTTR-DVSKLASMIDKYG-LDLPYVTYLKDELRAPEKIKAGKTRII 1860
Cdd:cd23228      9 PIDKNTSPGLKYTRDGLKKSDLytidedgnvvVSDMLRaDVEAWEELIQSGGyPTTLFTACLKDELRSDEKVALGKTRVI 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1861 EASSINDTSHFRMVFGNLFSAFHANPGILTGSAVGCNPDVFWSQMYAMLDGH--LLAFDYTNYDGSLNPIWFKALGMVLN 1938
Cdd:cd23228     89 EAAELDYVVAYRMYMSSIYSDLYNAYAGDTGIAAGINPPADGHRLREELSQYdsFLALDYSRFDGSLPEMLMRAAVEILA 168

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1939 KLGFPGAMMDKLSSTT----HIYRDRVYKTEGGMPSGICGTSIFNTMINNIILRTLILET----YKNIDLDKLR----II 2006
Cdd:cd23228    169 DLHEDPDLVRRLHETViiskHLVVDEDWTVKGGMPSGSPCTTVLNCICNLLVLEYAFLVHfgvyEDDDGVGLPQcdylSV 248

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 2007 AYGDDVVASYPDP---LDPKEIAETGakYGLTITPADKSTEFREVTWDTVTFLKRKF-KVDDEFKFLIHPVYSMDDVYES 2082
Cdd:cd23228    249 VYGDDCIVAYNGMemgLAFAETIEDT--FGMEVTPASKVGDHFNVELHEVEFLKRKFfAFETEEYDRIALRLSENTIVQS 326

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2099546858 2083 IRWTKDPRNTQDHVRSLCM--LAWhnGKDVYEQFLNQIRTTSVGRAL--NLPPY 2132
Cdd:cd23228    327 LMWMRNLKTFPDQVQSLMMelSAW--GKEKYDKLRDTCKRRLAKQNLqvTVPGY 378

Kunsagivirus_RdRp

cd23219

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

1781-2118

3.43e-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: 3.43e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1781 LEQAVYgvKNLEPLDLTTSAGFPYValGIKKRDLVNKTTR--------DVSKLASMIDKYGLD-LPYVTYLKDELRAPEK 1851
Cdd:cd23219      1 IEEAVF--DTVTPMDHTASAGPKYP--GTKRSELIDFQNRiisdrlrnDVLELQFRGTSGGAGeVKFSSFLKDELRPLSK 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1852 IKAGKTRIIEASSINDTSHFRMVFGNLFSAFHANPGILTGSAVGCNPDVFWSQMYAMLDGHLLAFDYTNYDGSL-NPIWF 1930
Cdd:cd23219     77 IRSGDTRVVECSSLDYTVAFRMQFLRVLQMCYGSDPTLTGLAPGMNVYTDMLPLCTSLYDYNLCLDFSKYDSRLpLQVMH 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1931 KALGMVLNKLGFPGAMM---DKLSSTTHIYRDRVYKTEGGMPSGICGTSIFNTMINNIILRTLILETYKNIDldkLRIIA 2007
Cdd:cd23219    157 RVAQLISNLTPDPQVSMrlfQPIIISTHIVGSYEVVVEGGMPSGCPITTIMNSVCNVVMTSYAMLLLDPDSD---FWPVA 233

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 2008 YGDDVVASYPDPLD-PKEIAETGAKYGLTITPADKSTEFREVTWDTVTFLKRKFKVDDEFKFLIhPVYSMDDVYESIRWT 2086
Cdd:cd23219    234 YGDDNIVSTRKPIDtELFCSILNEEFGMILTGADKTTTVQAVPPMSVDFLKRRLRYTPEFPLPV-PVLPLDSMLSRICWC 312

                          330       340       350
                   ....*....|....*....|....*....|..
gi 2099546858 2087 KDPRNTQDHVRSLCMLAWHNGKDVYEQFLNQI 2118
Cdd:cd23219    313 KGETEFKDQLESFSYELALYGQEVYERVRVAL 344

RNA_helicase

pfam00910

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

1201-1297

2.35e-39

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

Pssm-ID: 459992 Cd Length: 102 Bit Score: 141.97 E-value: 2.35e-39

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1201 LLIHGDPGCGKSLATTIVSRGLAA-----EGDIYSLPPNPKHFDGYNQQKVVIMDDVGQNPDGEDLGIFCQMVSTTDFHV 1275
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKklglpKDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 2099546858 1276 PMAALEDKGRCFTSDYVLASTN 1297
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

Rhv

pfam00073

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

357-521

2.83e-37

Pssm-ID: 395026 Cd Length: 170 Bit Score: 138.60 E-value: 2.83e-37

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  357 YSPTKEIHIPGKITNMLHIAQVESFLPLNNTDQHVGSIDIY---GVTITGASDNKLIVAIPLQmdntLFATTLLGEVLNY 433
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYtldSTDWTSLSKGFFWWKLPLA----LLSMGLLGRLLRY 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  434 YANWSGSVRVTFMCVCDSFSTGKFLLAYTPPGGRLPRDR---KEAMLGTHVVWDLGLQSSCTMVAPWISSTFFRRTKADK 510
Cdd:pfam00073   77 HTYYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRdylWQATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDG 156

                          170
                   ....*....|....
gi 2099546858  511 ---YSSGGIITLWH 521
Cdd:pfam00073  157 nwtLVVAGWVPLNY 170

rhv_like

cd00205

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

393-555

3.78e-36

Pssm-ID: 119412 Cd Length: 178 Bit Score: 135.99 E-value: 3.78e-36

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  393 SIDIYGVTITGASDNKLIVAIPL--QMDNTLFATTLLGEVLNYYANWSGSVRVTFMCVCDSFSTGKFLLAYTPPGGRLP- 469
Cdd:cd00205      8 PTTVGTNNWNSSASGTQLFQWKLspALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPPGAPAPt 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  470 --RDRKEAMLGTHVVWDLGLQSSCTMVAPWISSTFFRRTKADKY---SSGGIITLWHQTAFVSG-DTANVGTILATCSGC 543
Cdd:cd00205     88 tgDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDGYgplNSFGTLVVRVLTPLTVPsGAPTTVDITVYVRAG 167

                          170
                   ....*....|..
gi 2099546858  544 pDISVRMLRDTP 555
Cdd:cd00205    168 -DFELYGPRPPR 178

Peptidase_C3

pfam00548

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

1502-1667

1.33e-35

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: 134.11 E-value: 1.33e-35

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1502 GPEHEFMYALVKRNCHIATTERGEFNLL--GIYGNCAVLPTHAECGEILNVDGREVKVIKRQI-LTDMNDIDTEITLIWL 1578
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDPEVeLVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1579 DQNEKFRDIRRFLPETIQEWDHMKLATNVTKFPMHFVDVGHTVPYGEI-NLSGNPTCRLLKYNYPTKPGQCGAVI----G 1653
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVViakvE 160

                          170
                   ....*....|....
gi 2099546858 1654 STGHIIGIHVGGNG 1667
Cdd:pfam00548  161 GNGKILGMHIAGNG 174

Pico_P2B

pfam01552

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

979-1072

9.02e-35

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: 128.99 E-value: 9.02e-35

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  979 QGpISNYLTQLGNAFGEGFTQNIKDSFSNISTSI--TDKLTSKVIKWLVRIISALTIMVRNSADTPTILATLALLGCSKS 1056
Cdd:pfam01552    1 QG-ISDYIEHLGAAFGSGFTQQISDKIKELTNFInpTSKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDAS 79

                           90
                   ....*....|....*.
gi 2099546858 1057 PWTFLKEKICTWLGIS 1072
Cdd:pfam01552   80 PWQFLKEKACAVLEIP 95

Aalivirus_RdRp

cd23216

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

1793-2111

2.21e-34

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: 136.34 E-value: 2.21e-34

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1793 PLDLTTSAGFPYValGIKKRDLVN--KTTRDVSKLASmidkyGLDLPYVTYLKDELRAPEKIKAGKTRIIEASSINDTSH 1870
Cdd:cd23216     11 PIDWQTSPGLKYK--GRTKADLVQdpKFKEDVKEILA-----GKPTFFTTYLKDELRSIEKIANGNTRAIEAANFDHVVA 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1871 FRMVFGNLFSAFHANPGILTGSAVGCNPDVFWSQMYAMLDGHLLAFDYTNYDGSLNPIWFKALGMVLNKL-GFPGAMMDK 1949
Cdd:cd23216     84 WRQVMGNIVKQLFSDHDRVTGFAPGMNPYTHFDSLMDQVKWNVLALDFKKFDGSLSPQVMEEAVDILASFhDMPQMVVDI 163

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1950 LSSTTH---IYRDRVYKTEGGMPSGICGTSIFNTMINNIILRTLILEtyKNIDLDKLRIIAYGDDVVAS---YPDPLDPK 2023
Cdd:cd23216    164 HKHTIYstnVVSDETWFVEGGMCSGSPCTTVLNTICNLLVNTTILLS--EGIQPDNFYIAAYGDDTIISvdgLSSSLPDP 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 2024 EIAETGAK--YGLTITPADKSTefrEVTWDT---VTFLKRKFKVDDEFKFLIHpVYSMDDVYESIRWTKDprNTQDHVRS 2098
Cdd:cd23216    242 KIMQQKYKewFGMTVTSADKGS---EITWDTrnhVQFLKRRPGFFPGTQKVVG-VLDLESMMEHIAWTKG--SFQDQLNS 315

                          330
                   ....*....|...
gi 2099546858 2099 LCMLAWHNGKDVY 2111
Cdd:cd23216    316 FYQELVLHGEQVY 328

Caliciviridae_RdRp

cd23192

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

1842-2113

3.73e-33

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: 131.62 E-value: 3.73e-33

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1842 LKDELRAPEKIKAGKTRIIEASSINDTSHFRMVFGNLFSAFHANPGiLTGSAVGCNPD-VFWSQMYAML--DGHLLAFDY 1918
Cdd:cd23192      7 LKDELRPVEKIAEGKRRLLWGCDVGVTLVAAAAFGPVADALKAVCP-TGPIAVGINMDsEDVEVIFERLsgFRYHYCLDY 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1919 TNYDGSLNPIWFKALGMVLNKLGFPG----AMMDKLSST-THIYRDRVYKTEGGMPSGICGTSIFNTMINNIILRTLILE 1993
Cdd:cd23192     86 SKWDSTQSPAVTAAAIDILADLSEETplrdSVVETLSSPpMGIFDDVIFVTKRGLPSGMPFTSVINSLNHWLLFSAAVLK 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1994 TYK-------NIdLDKLRIIAYGDDVVASYPDPL--DPKEIAETGAKYGLTITPADKSTEFREVTWDTVTFLKRKFKVDD 2064
Cdd:cd23192    166 AYElvgiytgNV-FDEADFFTYGDDGVYAMPPATasVMDEIIENLKSYGLKPTAADKTENPDIPPLQGPVFLKRTFVRTP 244

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2099546858 2065 efkfliHPVYSMDDVYESIR---WTKDPrNTQDH---------------VRSLCMLAWHNGKDVYEQ 2113
Cdd:cd23192    245 ------GGWRALLDRSSILRqlyWVKGP-NTHDWteppteidheartvqLENVLLEAAQHGPEFYEK 304

rhv_like

cd00205

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

123-326

2.14e-32

Pssm-ID: 119412 Cd Length: 178 Bit Score: 125.20 E-value: 2.14e-32

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  123 PETSADRFYTLDSVNWTG---TSLGWWWKLPD----CLREMGLFGQNMYYHSMGRTGYIIHVQCNATKFHSGCLMVAVIP 195
Cdd:cd00205      1 VESFADRPTTVGTNNWNSsasGTQLFQWKLSPalgfLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  196 EHQMAyigaggtnvrydqthpgeaghtitaskqwgehnpdenpfyNLNGTLFGNIQIFPHQMINLRTNNSATIVVPYINC 275
Cdd:cd00205     81 PGAPA----------------------------------------PTTGDTRWQATLNPHVIWDLGTNSSVTFVVPYVSP 120

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2099546858  276 LPMDNMLRHNNL------TLMIIPIVKLRHGTTGTTTLPITVTIAPDKSEFSGPMQT 326
Cdd:cd00205    121 TPYRSTRYDGYGplnsfgTLVVRVLTPLTVPSGAPTTVDITVYVRAGDFELYGPRPP 177

rhv_like

cd00205

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

632-799

4.68e-32

Pssm-ID: 119412 Cd Length: 178 Bit Score: 124.05 E-value: 4.68e-32

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  632 IENFLGRSAL-----WAEFRLQGGFKKWDINFQEQ------AHIRRKLEFFTYVRFDMEVTIVTN----NTGLMQIMFIP 696
Cdd:cd00205      1 VESFADRPTTvgtnnWNSSASGTQLFQWKLSPALGflllqnTPLGALLSYFTYWRGDLEVTVQFNgskfHTGRLLVAYVP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  697 PGIEAPGNISDkRWDGASNPSIFYQPKSGFP-RFTIPFTGLGSAYYMFYDGYDetertgtaygisATNDMGTLCFRAL-- 773
Cdd:cd00205     81 PGAPAPTTGDT-RWQATLNPHVIWDLGTNSSvTFVVPYVSPTPYRSTRYDGYG------------PLNSFGTLVVRVLtp 147

                          170       180       190
                   ....*....|....*....|....*....|.
gi 2099546858  774 -----EDTTNDDVKVFIKPKHTSAWCPRPPR 799
Cdd:cd00205    148 ltvpsGAPTTVDITVYVRAGDFELYGPRPPR 178

Rhv

pfam00073

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

612-746

1.37e-26

Pssm-ID: 395026 Cd Length: 170 Bit Score: 108.17 E-value: 1.37e-26

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  612 PDDVIETRYVINNHVNNEALIENFLGRSAL-----------------WAefRLQGGFKKWDINFQEQAH--IRRKLEFFT 672
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPvqpdvqgerfytldstdWT--SLSKGFFWWKLPLALLSMglLGRLLRYHT 78

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2099546858  673 YVRFDMEVTIVTN----NTGLMQIMFIPPGIEAPGNIsDKRWDGASNPSIFYQPKSG-FPRFTIPFTGLGSAYYMFYDG 746
Cdd:pfam00073   79 YYRGGLEVTVQFNgskfHQGKLLVAYVPPGAPPPGSR-DYLWQATLNPHQFWNLGLNsSARLSVPYISIAHYYSTFYDG 156

Pico_P1A

pfam02226

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

2-67

1.74e-26

Pssm-ID: 308053 Cd Length: 68 Bit Score: 103.99 E-value: 1.74e-26

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2099546858    2 GAQVSKQSVGAHENSITANKGSIVKYFNINYYKDAASSGLTKQDFSQDPSKFTQPLADALTNPALM 67
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPT 66

Marnaviridae_RdRp

cd23195

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

1842-2119

6.22e-26

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Marnaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Marnaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. They are mono- or dicistronic, have a polyadenylate tail and have conserved motifs for RNA helicase, RdRp, and structural protein domains. The first RNA virus isolated and characterized that infects a marine protist was Heterosigma akashiwo RNA virus (HaRNAV) in the genus Marnavirus, that infects the toxic bloom-forming Raphidophyte alga, Heterosigma akashiwo. Recently, it has undergone a major taxonomic revision and now includes 20 species within 7 genera, which include Bacillarnavirus, Kusarnavirus, Labyrnavirus, Locarnavirus, Marnavirus, Salisharnavirus, and Sogarnavirus. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438045 Cd Length: 310 Bit Score: 110.61 E-value: 6.22e-26

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1842 LKDElraPEKIKAGKTRIIEASSINDTSHFRMVFGNLFSAFHANPgILTGSAVGCN---PDvfWSQMYAML----DGHLL 1914
Cdd:cd23195      7 LKDE---PTKLTKDKVRVFQAAPVALQLLVRKYFLPIARFLQMNP-LLSECAVGINaqsPE--WEELYEHLtkfgEDRII 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1915 AFDYTNYDGSLNPIWFKALGMVLNKLgfpgamMDKLS--STTHIYRDRVYKTE----------------GGMPSGICGTS 1976
Cdd:cd23195     81 AGDYSKYDKRMSAQLILAAFKILIDI------AAKSGgySEEDLKIMRGIATDiayplvdfngdliqffGSNPSGHPLTV 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1977 IFNTMINNIILRTLILETYKNIDLDKLR----IIAYGDDVVAS----YPDpLDPKEIAETGAKYGLTITPADKSTEFRE- 2047
Cdd:cd23195    155 IINSIVNSLYMRYAYYSLYPEKEVPPFRdvvaLMTYGDDNIMSvspgYPW-FNHTSIAEFLAKIGIKYTMADKEAESVPf 233

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2099546858 2048 VTWDTVTFLKRKFKVDDEFKFLIHPVySMDDVYESIRW-TKDPRNTQDHVRSLCM------LAWHnGKDVYEQFLNQIR 2119
Cdd:cd23195    234 IHISEADFLKRKFVFDPELGVYVGPL-DEDSIFKSLHCyLKSKVLTPEEQAAQNIdgalreWFFH-GREVYEKRREQLK 310

Aquamavirus_RdRp

cd23220

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

1793-2113

6.37e-26

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Aquamavirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Aquamavirus genus within the family Picornaviridae, order Picornavirales. The Aquamavirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. Aquamavirus is a genus containing a single species, Aquamavirus A. This species consists of the previously named seal picornavirus 1, now to be called seal aquamavirus A1. Recently other aquamaviruses have been discovered in bears and seals (unassigned aquamaviruses). RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438070 Cd Length: 338 Bit Score: 111.34 E-value: 6.37e-26

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1793 PLDLTTSAGFPYValGIKKRDLV---NKTTRD-VSKLASMIDKYGLDLPYVTYLKDELRAPEKIKAGKTRIIEASSINDT 1868
Cdd:cd23220     11 PLNFNGTAGAKYP--GMNRRQLLlplNPQVRDdVVKLAGDVGNGTATVVFETFMKDELRPKEKIESGKTRIVESCPLDYL 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1869 SHFRMVFGNLFSAFHANPGILTGSAVGCNPDVFWSQMYAMLDGHLLAFDYTNYDGSLNPIWFKALGMVLNKLGFPGAMMD 1948
Cdd:cd23220     89 LLYRMVMLKSMIWWYNSDCIKTGVAPGMNVYTDFVPMVKQFKKIKYCLDFSAYDSTLSDEILAAGVEVLACTSAVPSYVR 168

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1949 KLSS----TTHIYRDRVYKTEGGMPSGICGTSIFNTMINNIILRTLIletyKNIDLDKLRIIAYGDDVVASYPDPLDPKE 2024
Cdd:cd23220    169 KLHApiicSHHWHNNVVDLVLGGMPSGAPCTSVLNSIVNVLMARYIC----ALMDIDYPVMVAYGDDNVVSFDEEIDIER 244

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 2025 IAET-GAKYGLTITPADKSTEFREVTwdTVTFLKRKFKVDDEFKfLIHPVYSMDDVYESIRWTKDPRNTQDHVRSLCMLA 2103
Cdd:cd23220    245 MVSLyKTEFGVTATNHDKTPVPRPMA--NPVFLKRRLRFNPDLN-IQFPVLPLGEMIDRMCWTRGPEHLSDQTFSFAIEL 321

                          330
                   ....*....|
gi 2099546858 2104 WHNGKDVYEQ 2113
Cdd:cd23220    322 AGYGKQVYTH 331

Iflaviridae_RdRp

cd23197

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

1837-2114

3.85e-15

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: 78.75 E-value: 3.85e-15

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1837 PYVTYLKDELRAPEKIKA-GKTRIIEASSINDTSHFRMVFGNLFSAFHANPgILTGSAVGCNPD-VFWSQMYAML--DGH 1912
Cdd:cd23197      7 VYWAHLKDELRPSEKLRRfGGTRVFSVPPLELVLNSRRFLLPFMDAFQSFP-IEAHHAIGLNPNsGDWRRLRDTLleKGP 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1913 -LLAFDYTNYDGSLnPIWF--KALGMVLNKLGFPGAMM----DKLSSTTHIYRDR-------VYKTEGGMPSGICGTSIF 1978
Cdd:cd23197     86 cLLQMDYKNYSDAI-PKECvaKAFHIIVDYYRKWHCLTveieNALKTLFLDTADAellvygdVFKVNNGVLAGHPMTSVV 164

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1979 NTMINniilrtLILETYKNIDLDKLR---------IIAYGDDVVASYPDPLDP----KEIAETGAKYGLTITPADKSTEF 2045
Cdd:cd23197    165 NSVVN------LILMNYMWIKITRRRaseffkltyIIVMGDDVVISLPKQLTEefdcRKICAEFAKYDIKVTDSEKNLTG 238

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2099546858 2046 REVTWDTV---TFLKRKFKVDDEFKFLIHPVYSMDDVYESIRW-TKDPRN---TQDHVRSLCMLAWHNGKDVYEQF 2114
Cdd:cd23197    239 EPKPYDSFdkfEFLSRGFSDCDAYPDITFAPVKTIALFDCPLWiSKGQDEeeqTIQAIQAGLLLAFDHGPEFFGKY 314

Polycipiviridae_RdRp

cd23198

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

1843-2118

1.20e-14

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: 77.45 E-value: 1.20e-14

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1843 KDELRAPEKI-----KAGKTRIIEASSINDTSHFRMVFGNLFSAFH-ANPGILTgSAVGCNPD-VFWSQMYAMLDGH--L 1913
Cdd:cd23198      8 KDELRPIYKAlgdpqTPPKTRSVTCMNVYYILAWRRVTLDFWASMHrAADGNFP-FCPGINPEgPDWNRLYHYLNRHpnA 86

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1914 LAFDYTNYDGSLNP-IWFKALGMVLNKLGF-PGAMMDKL--SSTT-----HI-YRDRVYKTEGGMPSGICGTSIFNTMIN 1983
Cdd:cd23198     87 VDFDVSNWDGHLPAeLFYAVLDIIKTVLGLkPNSPNAKViySILTevmncHIqFEDIIYQKLRGLISGFPGTAEVNTLAH 166

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1984 NIILRTLILETYKNIDLDK--------LRIIAYGDDVVASYPDPLDP----KEIAETGAKYGLTITPADKSTE--FREVT 2049
Cdd:cd23198    167 WLLIYYIYLYLAQNTIYDMtitaflrnVSAIFYGDDIIITISDEILHwfngKTIQRMYEEHGYPVTSAAKDTEipESKPL 246

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 2050 WDTvTFLKRKFKvddefkfLIHPVY---SMDD--VYESIRWTK---DPR-----NTQDHVRslcmLAWHNGKDVYEQFLN 2116
Cdd:cd23198    247 SDC-QFLKSSWN-------PILPGYyirKMDIevVYDLVYWVRakeHPRdqfysNYHDALR----ILFGHGEQVFEAFRE 314


                   ..
gi 2099546858 2117 QI 2118
Cdd:cd23198    315 QV 316

Secoviridae_RdRp

cd23196

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

1842-2064

5.38e-13

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: 72.03 E-value: 5.38e-13

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1842 LKDELRAPEK-IKAGKTRIIEASSINDTSHFRMVFGNLFSAFHANPGILTgSAVGCNP-DVFWSQMYAML---DGHLLAF 1916
Cdd:cd23196      7 PKDERLKKRKvLEKPKTRLFDVLPMEYNLLLRKYFLNFVRFIQANRHRLP-CQVGINPySREWTTLYDRLaekSDTALNC 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1917 DYTNYDGSLNpiwfkalGMVLNKLGfpgAMMDKLSSTTH-----------------IYRDRVYKTEGGMPSGICGTSIFN 1979
Cdd:cd23196     86 DYSRFDGLLS-------HQVYVWIA---DMINRLYGDGDeakarrnllmmfcgrrsICGRQVYMVRGGMPSGCALTVIIN 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1980 TMINNIILR----TLILETYKNIDLDKLRIIAYGDD-------VVASYpdpLDPKEIAETGAKYGLTITP-ADK-STEFR 2046
Cdd:cd23196    156 SIFNEILIRyvyrKVVPRPARNNFNKYVRLVVYGDDnlisvkeEIIPY---FDGPVIKKEMAKVGVTITDgTDKtSPTLE 232

                          250
                   ....*....|....*...
gi 2099546858 2047 EVTWDTVTFLKRKFKVDD 2064
Cdd:cd23196    233 RKPLESLDFLKRGFRVQS 250

Nora-virus_RdRp

cd23200

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

1842-2064

1.71e-11

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in a novel picorna-like Drosophila virus, Nora virus; This group contains the catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the unclassified Nora virus, a new picorna-like virus family. Nora virus has a (+)ssRNA genome followed by a poly(A) tail. Unlike other picorna-like viruses, the genome has four open reading frames (ORFs). One ORF encodes a picornavirus-like cassette of proteins for virus replication, including an iflavirus-like RdRp and a helicase that is related to those of mammalian picornaviruses. The three other ORFs are not closely related to any previously described viruses. Nora virus is present as a persistent infection in several tested laboratory stocks and wild-caught flies. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438050 Cd Length: 306 Bit Score: 67.64 E-value: 1.71e-11

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1842 LKDELRAPEKIKAGKTRIIEASSINDTSHFRMVFGNLFSAFHaNPGILTGSAVGCNP-DVFWSQMYAMLDGHLLAF--DY 1918
Cdd:cd23200      7 LKDQPIKIAQAKSGRTRVFHCIPVDLILFSGALYGPYKEAYT-KAGLKCYHAVGIDPkSVGWQQLATYMTKHPNYFdaDY 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1919 TNYDGSLNPIWFKALGMVL---------NKLGFPGAMMDKLSSTTHIYRDR-VYKTEGGMPSGICGTSIFNTMINNII-- 1986
Cdd:cd23200     86 KNYDKYLHRQVFKAVRKIQrsviqqvcpDKWDKARAVEELDAIDTYVVDYQtVYKTNRGNKSGSYTTTIDNCLANDIYgl 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1987 ---LRTLILETYKNIdLDKLRIIAYGDDVVAS----YPDPLDPKEIAETGAKYGLTITPADKSTEFREVTWDT-VTFLKR 2058
Cdd:cd23200    166 yawVKTTGLRSLWDY-RQNVSSVAFGDDIIKSvsdeYKDKYNYCTYRDVLNATGHIMTPGSKDGEEKPFTSFEnLQFLKR 244


                   ....*.
gi 2099546858 2059 KFKVDD 2064
Cdd:cd23200    245 GFKLEN 250

ps-ssRNAv_RdRp-like

cd23167

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

1912-2017

1.33e-08

Pssm-ID: 438017 [Multi-domain] Cd Length: 73 Bit Score: 53.50 E-value: 1.33e-08

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1912 HLLAFDYTNYDGSLNPIWFKAlgmvlnklgfpgammdklsstthiyrdrvyktegGMPSGICGTSIFNTMINNIILRTLI 1991
Cdd:cd23167      1 HVVESDYSGFDSSISPDLLKA----------------------------------GQPSGSPNTSADNSLINLLLARLAL 46

                           90       100
                   ....*....|....*....|....*..
gi 2099546858 1992 LETYKNIDLDK-LRIIAYGDDVVASYP 2017
Cdd:cd23167     47 RKACGRAEFLNsVGILVYGDDSLVSVP 73

RdRP_4

pfam02123

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

1847-2049

4.50e-06

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: 51.69 E-value: 4.50e-06

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1847 RAPEKIKAGKTRIIEASsinDT-SHFRMVFGnLFSAFHAnpgiLTGSAVGCNPDV-----FWSQMYAMLDGH-LLAFDYT 1919
Cdd:pfam02123  234 KPSMKLEHGKSRAIYAC---DTrSYLAFEYL-LAPVEKA----WANKSVILNPGEgdisgFDWSVQDWKRGGvSLMLDYD 305

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1920 NYD-----GSLNPIWfkalgmvlnklgfpGAMMDKLSSTTHIYRDRV-----------------YKTEGGMPSGICGTSI 1977
Cdd:pfam02123  306 DFNsqhstESMRAVF--------------ERLRRRLPDEPAEAADWLvcsmdsmyqlsdgtllaQRVPGTLKSGHRATTF 371

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2099546858 1978 FNTMINNIILRTLILEtykniDLDKLRIIAYGDDVVASYPDPLDPKEIAETGAKYGLTITPA-----DKSTEFREVT 2049
Cdd:pfam02123  372 INSVLNCAYAELAGAP-----WADVPTSIHMGDDVLEGLRTPADATSLLDKYARLGFKVNPSkqsvgHTIAEFLRVA 443

Solinviviridae_RdRp

cd23199

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

1893-2061

2.66e-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: 48.50 E-value: 2.66e-05

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1893 AVGCNPDVFWSQMYAMLD--GHLLAFDYTNYDGSLnPIWFkaLGMVLNKL-GFPGAMMDKLSSTTHIYRDRV-------Y 1962
Cdd:cd23199     72 AVGCNPYATFHKFATKFFkfKNFFSCDYKNFDRTI-PKCV--FEDFRDMLiQANPHMKNEIYACFQTIIDRIqvsgnsiL 148

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1963 KTEGGMPSGICGTSIFNTMINNII----------LRTLILETYKNIDLDKLRIIAYGDDVVASYPDPLDPKEIAETGAK- 2031
Cdd:cd23199    149 LVHGGMPSGCVPTAPLNSKVNDIMiytayvnilrRADRGDITSYRYYRDLVCRLFYGDDVIIAVDDSIADIFNCQTLSEe 228

                          170       180       190
                   ....*....|....*....|....*....|....*
gi 2099546858 2032 ----YGLTITPADKSTEFREV-TWDTVTFLKRKFK 2061
Cdd:cd23199    229 mkilFGMNMTDGSKSDIIPKFeTIETLSFISRFFR 263

ps-ssRNAv_Potyviridae_RdRp

cd23175

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

1842-2011

2.70e-05

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

Pssm-ID: 438025 Cd Length: 236 Bit Score: 47.83 E-value: 2.70e-05

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1842 LKDELRAPEKIKAGKTRIIEASSInDT----SHFRMVFGNLFSAFHanpgiLTG-SAVGCNPdvF---WSQMYAMLDGHL 1913
Cdd:cd23175     10 LKAELRPIEKVEANKTRTFTAAPI-DTllggKVCVDDFNNQFYSLH-----LKApWTVGITK--FyggWDKLLRKLPDGW 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1914 LafdYTNYDG-----SLNPIWFKAlgmVLN-KLGF-----PGAMMDKlssttHIYRDRVY-----------KTEGGMPSG 1971
Cdd:cd23175     82 V---YCDADGsqfdsSLTPYLINA---VLRiRLHFmedwdIGEQMLR-----NLYTEIVYtpiltpdgtivKKFKGNNSG 150

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 2099546858 1972 ICGTSIFNTMINNI-----ILRTLIleTYKNIDlDKLRIIAYGDD 2011
Cdd:cd23175    151 QPSTVVDNTLMVMIamyyaLLKLGI--DFEEID-ERCVFFCNGDD 192

ps-ssRNAv_Nodaviridae_RdRp

cd23173

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

1904-2060

2.14e-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: 45.19 E-value: 2.14e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1904 QMYAMLDGHLLAFDYTNYDGS---------LNPI---WFKA---------LGMVLNKLGFpgammdklssTTHIYRdrvY 1962
Cdd:cd23173     76 QEIASSSDGVIETDYSRFDGTisewlrrnvEFAAylrWFHPeyraellklLDAEINCPAR----------TKTGVK---Y 142

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858 1963 KTEGGMPSGICGTSIFNTMINNII----LRtlilETYKNIDLDKLRI-IAYGDDVVAsypDPLDPKEIAETGAKYGLTIt 2037
Cdd:cd23173    143 DPGVSRLSGSPTTTDGNTIINAFVsycaLR----ETGYSPEEAFALLgLYYGDDGLS---DNLPAEALEKVAKDLGLKL- 214

                          170       180
                   ....*....|....*....|....
gi 2099546858 2038 padkstEFREVTWDT-VTFLKRKF 2060
Cdd:cd23173    215 ------KIEVVRPGQpVTFLGRVF 232

Calici_coat

pfam00915

Calicivirus coat protein;

434-564

1.58e-03

Calicivirus coat protein;

Pssm-ID: 459994 Cd Length: 291 Bit Score: 42.96 E-value: 1.58e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546858  434 YANWSGSVRVTFMCVCDSFSTGKFLLAYTPPGGRlPRDRKEAMLGTHVVWDLGLQSSCTMVAPWISSTFFRRTKADKYSS 513
Cdd:pfam00915  103 YNGWSGGMRVRFMVAGSGVFGGKLAASVIPPGVE-PITSASMLQFPHVLFDARQLEPVIFTIPDLRNTLFHNMDRNTDTT 181

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2099546858  514 GGIITLWHQ--TAFVSGDTANVGTILATCSGcPDISVRMLRdTPMAKQPQNIR 564
Cdd:pfam00915  182 RLVIMVYNPliNPGGTGDSSVCAVTVETRPS-PDFNFLLLK-PPGSTVEHGSR 232

AAA_16

pfam13191

AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...

1168-1212

3.91e-03

AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily.

Pssm-ID: 433025 [Multi-domain] Cd Length: 167 Bit Score: 40.18 E-value: 3.91e-03

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 2099546858 1168 PLYARENklvtdmqkQLNQLK-AYQRTHRTEPVCLLIHGDPGCGKS 1212
Cdd:pfam13191    1 RLVGREE--------ELEQLLdALDRVRSGRPPSVLLTGEAGTGKT 38

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