NCBI Conserved Domain Search

Conserved domains on [gi|2099546876|gb|UBI50769|]

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polyprotein [rhinovirus B6]

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 ...

1729-2180

0e+00

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

The actual alignment was detected with superfamily member cd23213:

Pssm-ID: 477363 Cd Length: 453 Bit Score: 788.26 E-value: 0e+00

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1729 VRELNMASINTPTKSKLHPSVFYNVFPGSKEPAVLSDNDPRLEVKLSDSLFSKYKGNIEMKPTENMLIAVDHYAGQLMSL 1808
Cdd:cd23213      1 NKEVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1809 DIPTEELTLKEALYGVDGLEPIDITTSAGYPYVSLGIKKRDILNRETQDVEKMKLYLDKYGIDLPLVTYIKDELRSTDKV 1888
Cdd:cd23213     81 DIDTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKV 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1889 RLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVIPCLMDGHLMAFDYSNFDASLSPVWFEC 1968
Cdd:cd23213    161 EKGKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDGSLFAFDYTGYDASLSPVWFRA 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1969 LEKVLTKLGFKHS-SLIQTICHTHHIFKDEIYVVEGGMPSGCSGTSIFNSMINNIIIRTLVLDAYKGIDLDKLKILAYGD 2047
Cdd:cd23213    241 LKMVLEKGYSEEAvSLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYGD 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2048 DLIVSYPYELDPEVLATLGKKYGLTITPPDKTEKFSKITWDNLTFLKRYFRSDEQFPFLVHPVMPMQDIYESIRWTKDPK 2127
Cdd:cd23213    321 DVIASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDPR 400

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2099546876 2128 NTQDHVRSLCMLAWHSGEKEYNDFTQKIRTTDIGKCLNLPEYSVLRRRWLDLF 2180
Cdd:cd23213    401 NTQDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453

Pico_P2A

pfam00947

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

875-1001

5.83e-70

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

Pssm-ID: 395757 Cd Length: 127 Bit Score: 230.73 E-value: 5.83e-70

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  875 NYHLMTPEDHLNLITPYVSRDLAVVFTGAHGAETIPHCSCTSGVYYSRYYRKFYPVICEKPTTIWIEGSSYYPSRYQTGV 954
Cdd:pfam00947    1 NRHLATHEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 2099546876  955 MKGVGPAEPGDCGGILRCVHGPIGLLTAGGSGYVCFADIRQLDCIAE 1001
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVRDLLWLEE 127

Rhv

pfam00073

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

93-297

1.82e-54

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: 187.90 E-value: 1.82e-54

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876   93 TTQEAANAVVCYAEWPEYLPDNDASDVNKTSKPDTSVCRFYTLESKVWQNSSKGW-CWKLPDALKDMGVFGQNMFFHSLG 171
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFfWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  172 RSGYTIHVQCNATKFHSGCLLVVVIPEHQlashkggnvsvkykyTHPGEggidlstqldedgpvkdpvysmnGTLLGNLL 251
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPPGA---------------PPPGS-----------------------RDYLWQAT 122

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 2099546876  252 IFPHQFINLRTNNTATIVVPYINSVPIDSMTRHNNVSLLVIPIAPL 297
Cdd:pfam00073  123 LNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGNWTLVVAGWVPL 168

Peptidase_C3 super family

cl02893

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

1539-1703

1.99e-41

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: 151.06 E-value: 1.99e-41

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1539 GPNTEFALSLLRKNIVTVTTEKGEFTGL--GIYDRVCVIPTHAQPDNKVLINGQAVQLKD-KYKLVDPDNTNLELTVLTL 1615
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1616 DRNEKFRDIRSFISEDL-EGMEASLVIHSNNFTNTILDVGPITMAGLI-NLSSTPTGRMIRYDYPTKTGQCGGVL----C 1689
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRItKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVViakvE 160

                          170
                   ....*....|....
gi 2099546876 1690 TTGKIFGIHVGGNG 1703
Cdd:pfam00548  161 GNGKILGMHIAGNG 174

Rhv

pfam00073

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

614-770

1.02e-40

Pssm-ID: 395026 Cd Length: 170 Bit Score: 148.61 E-value: 1.02e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  614 PSDNVETRTTYMHFNGSETDVESFLGRAACVHIVEIENKNP--AGIENQKEQKLFNDWKINLS--SLVQLRKKLELFTYV 689
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYtlDSTDWTSLSKGFFWWKLPLAllSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  690 RFDSEYTILATASQptessyASNLVVQAMYVPPGAPNPEKWdDFTWQSASNPSVFFKVG--DTSRFSVPFVGIASAYNCF 767
Cdd:pfam00073   81 RGGLEVTVQFNGSK------FHQGKLLVAYVPPGAPPPGSR-DYLWQATLNPHQFWNLGlnSSARLSVPYISIAHYYSTF 153


                   ...
gi 2099546876  768 YDG 770
Cdd:pfam00073  154 YDG 156

RNA_helicase

pfam00910

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

1226-1324

3.90e-40

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

Pssm-ID: 459992 Cd Length: 102 Bit Score: 144.28 E-value: 3.90e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1226 VLIHGTPGSGKSLTTSIVGRALAEYFN---SSVYSLPPDPKHFDGYQQQEVVIMDDLNQNPDGQDISMFCQMVSSVDFIP 1302
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKKLGlpkDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 2099546876 1303 PMANLDNKGMLFTSNFVLASTN 1324
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

Rhv

pfam00073

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

359-522

3.46e-38

Pssm-ID: 395026 Cd Length: 170 Bit Score: 141.29 E-value: 3.46e-38

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  359 YEPTPRIHIPGKVRNLLEIIQVDTLIPMNNVH-NSDEVNSYLIPLTA-NRQNDQIFGTRLfiGDGVFKTTLLGEIAQYYT 436
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQpDVQGERFYTLDSTDwTSLSKGFFWWKL--PLALLSMGLLGRLLRYHT 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  437 HWSGSLRISLMYTGPALSSAKLILAYTPPGAQGPTNR---KDAMLGTHVVWDIGLQSTIIMTIPWTSGVQFRYT---DPD 510
Cdd:pfam00073   79 YYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRdylWQATLNPHQFWNLGLNSSARLSVPYISIAHYYSTfydGNW 158

                          170
                   ....*....|..
gi 2099546876  511 TYTSAGYLSCWY 522
Cdd:pfam00073  159 TLVVAGWVPLNY 170

Pico_P2B super family

cl03260

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

1003-1101

4.44e-30

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: 115.51 E-value: 4.44e-30

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1003 QGLNDYITSLGRAFGVGFTDQISAKVTELQDVAKDF--LTTKVLSKVVKMISALVIICRNHDDLVTVTATLALLGCDGSP 1080
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTQQISDKIKELTNFINPTskIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|.
gi 2099546876 1081 WRFLKMYISKHFQVPYIERQA 1101
Cdd:pfam01552   81 WQFLKEKACAVLEIPYVHKQG 101

Pico_P1A super family

cl03490

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

2-69

1.08e-21

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

The actual alignment was detected with superfamily member pfam02226:

Pssm-ID: 308053 Cd Length: 68 Bit Score: 90.51 E-value: 1.08e-21

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2099546876    2 GAQVSTQKSGSHENQNILTNGSNQTFTVINYYKDAASSSSAGQSFSMDPSKFTEPVKDLMLKGAPALN 69
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 68

P3A super family

cl07374

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

1434-1483

2.97e-17

Poliovirus 3A protein like; This domain is found in positive-strand RNA viruses. The 3A protein is a critical component of the poliovirus replication complex, and is also an inhibitor of host cell ER to Golgi transport.

The actual alignment was detected with superfamily member pfam08727:

Pssm-ID: 400873 Cd Length: 59 Bit Score: 77.47 E-value: 2.97e-17

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2099546876 1434 YKDLEIDICNTPPPECINDLLKSVDSEEVREYCKKKKWIIP-----QIPTNIDRA 1483
Cdd:pfam08727    5 GIDLKIDIKTSPPPEAIADLLQAVDSPEIIDYCEDKGWIVNipaecQIERDIGIA 59

Name

Accession

Description

Interval

E-value

Enterovirus_RdRp

cd23213

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

1729-2180

0e+00

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

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1729 VRELNMASINTPTKSKLHPSVFYNVFPGSKEPAVLSDNDPRLEVKLSDSLFSKYKGNIEMKPTENMLIAVDHYAGQLMSL 1808
Cdd:cd23213      1 NKEVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1809 DIPTEELTLKEALYGVDGLEPIDITTSAGYPYVSLGIKKRDILNRETQDVEKMKLYLDKYGIDLPLVTYIKDELRSTDKV 1888
Cdd:cd23213     81 DIDTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKV 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1889 RLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVIPCLMDGHLMAFDYSNFDASLSPVWFEC 1968
Cdd:cd23213    161 EKGKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDGSLFAFDYTGYDASLSPVWFRA 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1969 LEKVLTKLGFKHS-SLIQTICHTHHIFKDEIYVVEGGMPSGCSGTSIFNSMINNIIIRTLVLDAYKGIDLDKLKILAYGD 2047
Cdd:cd23213    241 LKMVLEKGYSEEAvSLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYGD 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2048 DLIVSYPYELDPEVLATLGKKYGLTITPPDKTEKFSKITWDNLTFLKRYFRSDEQFPFLVHPVMPMQDIYESIRWTKDPK 2127
Cdd:cd23213    321 DVIASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDPR 400

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2099546876 2128 NTQDHVRSLCMLAWHSGEKEYNDFTQKIRTTDIGKCLNLPEYSVLRRRWLDLF 2180
Cdd:cd23213    401 NTQDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453

Pico_P2A

pfam00947

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

875-1001

5.83e-70

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

Pssm-ID: 395757 Cd Length: 127 Bit Score: 230.73 E-value: 5.83e-70

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  875 NYHLMTPEDHLNLITPYVSRDLAVVFTGAHGAETIPHCSCTSGVYYSRYYRKFYPVICEKPTTIWIEGSSYYPSRYQTGV 954
Cdd:pfam00947    1 NRHLATHEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 2099546876  955 MKGVGPAEPGDCGGILRCVHGPIGLLTAGGSGYVCFADIRQLDCIAE 1001
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVRDLLWLEE 127

Rhv

pfam00073

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

93-297

1.82e-54

Pssm-ID: 395026 Cd Length: 170 Bit Score: 187.90 E-value: 1.82e-54

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876   93 TTQEAANAVVCYAEWPEYLPDNDASDVNKTSKPDTSVCRFYTLESKVWQNSSKGW-CWKLPDALKDMGVFGQNMFFHSLG 171
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFfWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  172 RSGYTIHVQCNATKFHSGCLLVVVIPEHQlashkggnvsvkykyTHPGEggidlstqldedgpvkdpvysmnGTLLGNLL 251
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPPGA---------------PPPGS-----------------------RDYLWQAT 122

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 2099546876  252 IFPHQFINLRTNNTATIVVPYINSVPIDSMTRHNNVSLLVIPIAPL 297
Cdd:pfam00073  123 LNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGNWTLVVAGWVPL 168

RdRP_1

pfam00680

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

1746-2151

3.18e-51

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

Pssm-ID: 425815 Cd Length: 450 Bit Score: 188.77 E-value: 3.18e-51

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1746 HPSVFYNVFPGSKEPAVLSDNDPRLEV------KLSDSLfSKYKGNIEMKPTENMLIAVDHYAGQLMSLDI------PTE 1813
Cdd:pfam00680    1 SPTERHLVAIPAYVPASLGPEDPRWARsylntdPYVDDI-KKYSRPKLPGPADERDKLLNRSAAKMVLSELrgvpkkANS 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1814 ELTLKEALYGVDGLEPIDITTSAGYPYVSLGIKKRDiLNRETQDV-------EKMKLYLDKY--GIDLPLV--TYIKDEL 1882
Cdd:pfam00680   80 TLIVYRAIDGVEQIDPLNWDTSAGYPYVGLGGKKGD-LIEHLKDGtearelaERLAADWEVLqnGTPLKLVyqTCLKDEL 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1883 RSTDKVRLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITgSAVGCDP-DVFWSV----IPCLMDGHLMaFDYSNF 1957
Cdd:pfam00680  159 RPLEKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHP-IQVGINPfDRGWPRllrrLARFGDYVYE-LDYSGF 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1958 DASLSP----VWFECLEkvlTKLGFKHS-----SLIQT-ICHTHHIFKDEIYVVEGGMPSGCSGTSIFNSMINNIIIRTL 2027
Cdd:pfam00680  237 DSSVPPwlirFAFEILR---ELLGFPSNvkewrAILELlIYTPIALPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYA 313

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2028 VL-----DAYKGIDLDKLKILA-YGDDLIVSYPYELDPeVLATLG---KKYGLTITPPDKTEKFSKITwDNLTFLKRYFR 2098
Cdd:pfam00680  314 LLkslenDGPRVCNLDKYFDFFtYGDDSLVAVSPDFDP-VLDRLSphlKELGLTITPAKKTFPVSREL-EEVSFLKRTFR 391

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2099546876 2099 SDeqfPFLVHPVMPMQDIYESIRWTKDPKNTQDHVRSLCMLAWHSGEKEYNDF 2151
Cdd:pfam00680  392 KT---PGGYRPPLDRKRILAQLEYIRSKPVPSGQLENIRAYASHHGYEFYRDL 441

Peptidase_C3

pfam00548

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

1539-1703

1.99e-41

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: 151.06 E-value: 1.99e-41

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1539 GPNTEFALSLLRKNIVTVTTEKGEFTGL--GIYDRVCVIPTHAQPDNKVLINGQAVQLKD-KYKLVDPDNTNLELTVLTL 1615
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1616 DRNEKFRDIRSFISEDL-EGMEASLVIHSNNFTNTILDVGPITMAGLI-NLSSTPTGRMIRYDYPTKTGQCGGVL----C 1689
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRItKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVViakvE 160

                          170
                   ....*....|....
gi 2099546876 1690 TTGKIFGIHVGGNG 1703
Cdd:pfam00548  161 GNGKILGMHIAGNG 174

Rhv

pfam00073

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

614-770

1.02e-40

Pssm-ID: 395026 Cd Length: 170 Bit Score: 148.61 E-value: 1.02e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  614 PSDNVETRTTYMHFNGSETDVESFLGRAACVHIVEIENKNP--AGIENQKEQKLFNDWKINLS--SLVQLRKKLELFTYV 689
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYtlDSTDWTSLSKGFFWWKLPLAllSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  690 RFDSEYTILATASQptessyASNLVVQAMYVPPGAPNPEKWdDFTWQSASNPSVFFKVG--DTSRFSVPFVGIASAYNCF 767
Cdd:pfam00073   81 RGGLEVTVQFNGSK------FHQGKLLVAYVPPGAPPPGSR-DYLWQATLNPHQFWNLGlnSSARLSVPYISIAHYYSTF 153


                   ...
gi 2099546876  768 YDG 770
Cdd:pfam00073  154 YDG 156

RNA_helicase

pfam00910

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

1226-1324

3.90e-40

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

Pssm-ID: 459992 Cd Length: 102 Bit Score: 144.28 E-value: 3.90e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1226 VLIHGTPGSGKSLTTSIVGRALAEYFN---SSVYSLPPDPKHFDGYQQQEVVIMDDLNQNPDGQDISMFCQMVSSVDFIP 1302
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKKLGlpkDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 2099546876 1303 PMANLDNKGMLFTSNFVLASTN 1324
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

Rhv

pfam00073

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

359-522

3.46e-38

Pssm-ID: 395026 Cd Length: 170 Bit Score: 141.29 E-value: 3.46e-38

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  359 YEPTPRIHIPGKVRNLLEIIQVDTLIPMNNVH-NSDEVNSYLIPLTA-NRQNDQIFGTRLfiGDGVFKTTLLGEIAQYYT 436
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQpDVQGERFYTLDSTDwTSLSKGFFWWKL--PLALLSMGLLGRLLRYHT 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  437 HWSGSLRISLMYTGPALSSAKLILAYTPPGAQGPTNR---KDAMLGTHVVWDIGLQSTIIMTIPWTSGVQFRYT---DPD 510
Cdd:pfam00073   79 YYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRdylWQATLNPHQFWNLGLNSSARLSVPYISIAHYYSTfydGNW 158

                          170
                   ....*....|..
gi 2099546876  511 TYTSAGYLSCWY 522
Cdd:pfam00073  159 TLVVAGWVPLNY 170

rhv_like

cd00205

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

634-826

8.70e-38

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: 140.61 E-value: 8.70e-38

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  634 VESFLGRAACVHIVEIENKNPagienqkeQKLFNDWKINLS------SLVQLRKKLELFTYVRFDSEYTILATASQPTes 707
Cdd:cd00205      1 VESFADRPTTVGTNNWNSSAS--------GTQLFQWKLSPAlgflllQNTPLGALLSYFTYWRGDLEVTVQFNGSKFH-- 70

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  708 syasNLVVQAMYVPPGAPNPEKwDDFTWQSASNPSVFFKVGDTS--RFSVPFVGIASAYNCFYDGYShddkdtpygisVL 785
Cdd:cd00205     71 ----TGRLLVAYVPPGAPAPTT-GDTRWQATLNPHVIWDLGTNSsvTFVVPYVSPTPYRSTRYDGYG-----------PL 134

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....
gi 2099546876  786 NHMGSIAFRVVNEHDA---HKTLVKIRVYHRAKHVEAWIPRAPR 826
Cdd:cd00205    135 NSFGTLVVRVLTPLTVpsgAPTTVDITVYVRAGDFELYGPRPPR 178

rhv_like

cd00205

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

125-324

2.38e-37

Pssm-ID: 119412 Cd Length: 178 Bit Score: 139.45 E-value: 2.38e-37

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  125 PDTSVCRFYTLESKVWQNS---SKGWCWKLPDA----LKDMGVFGQNMFFHSLGRSGYTIHVQCNATKFHSGCLLVVVIP 197
Cdd:cd00205      1 VESFADRPTTVGTNNWNSSasgTQLFQWKLSPAlgflLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  198 EHQLAShkggnvsvkykythpgeggidlstqldedgpvkdpvysMNGTLLGNLLIFPHQFINLRTNNTATIVVPYINSVP 277
Cdd:cd00205     81 PGAPAP--------------------------------------TTGDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTP 122

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2099546876  278 IDSMTRH------NNVSLLVIPIAPLVAPTGSPQTLPVTVTIAPMCTEFTGIR 324
Cdd:cd00205    123 YRSTRYDgygplnSFGTLVVRVLTPLTVPSGAPTTVDITVYVRAGDFELYGPR 175

rhv_like

cd00205

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

374-556

4.86e-37

Pssm-ID: 119412 Cd Length: 178 Bit Score: 138.30 E-value: 4.86e-37

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  374 LLEIIQVDTLIPMNNVHNSDEVNSYL-IPLTanrqndqifgtrLFIGDGVFKTTLLGEIAQYYTHWSGSLRISLMYTGPA 452
Cdd:cd00205      1 VESFADRPTTVGTNNWNSSASGTQLFqWKLS------------PALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSK 68

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  453 LSSAKLILAYTPPGAQGPTN---RKDAMLGTHVVWDIGLQSTIIMTIPWTSGVQFRYTD---PDTYTSAGYLSCWYQTSL 526
Cdd:cd00205     69 FHTGRLLVAYVPPGAPAPTTgdtRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRydgYGPLNSFGTLVVRVLTPL 148

                          170       180       190
                   ....*....|....*....|....*....|
gi 2099546876  527 ILPPNTTGQVHLLSFISACpDFKLRLMKDT 556
Cdd:cd00205    149 TVPSGAPTTVDITVYVRAG-DFELYGPRPP 177

Pico_P2B

pfam01552

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

1003-1101

4.44e-30

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: 115.51 E-value: 4.44e-30

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1003 QGLNDYITSLGRAFGVGFTDQISAKVTELQDVAKDF--LTTKVLSKVVKMISALVIICRNHDDLVTVTATLALLGCDGSP 1080
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTQQISDKIKELTNFINPTskIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|.
gi 2099546876 1081 WRFLKMYISKHFQVPYIERQA 1101
Cdd:pfam01552   81 WQFLKEKACAVLEIPYVHKQG 101

Pico_P1A

pfam02226

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

2-69

1.08e-21

Pssm-ID: 308053 Cd Length: 68 Bit Score: 90.51 E-value: 1.08e-21

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2099546876    2 GAQVSTQKSGSHENQNILTNGSNQTFTVINYYKDAASSSSAGQSFSMDPSKFTEPVKDLMLKGAPALN 69
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 68

P3A

pfam08727

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

1434-1483

2.97e-17

Pssm-ID: 400873 Cd Length: 59 Bit Score: 77.47 E-value: 2.97e-17

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2099546876 1434 YKDLEIDICNTPPPECINDLLKSVDSEEVREYCKKKKWIIP-----QIPTNIDRA 1483
Cdd:pfam08727    5 GIDLKIDIKTSPPPEAIADLLQAVDSPEIIDYCEDKGWIVNipaecQIERDIGIA 59

AAA

cd00009

The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...

1219-1349

6.76e-03

The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.

Pssm-ID: 99707 [Multi-domain] Cd Length: 151 Bit Score: 39.44 E-value: 6.76e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1219 QRTEPVCVLIHGTPGSGKSLTTSIVGRALAE------YFNSS----VYSLPPDPKHFDGYQQQE--------VVIMDDLN 1280
Cdd:cd00009     15 ELPPPKNLLLYGPPGTGKTTLARAIANELFRpgapflYLNASdlleGLVVAELFGHFLVRLLFElaekakpgVLFIDEID 94

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2099546876 1281 qnpdgqdiSMFCQMVSSVDFIppMANLDNKGMLFTSNFVLASTNSNTLSPPtilnPEALARRFGFDLDI 1349
Cdd:cd00009     95 --------SLSRGAQNALLRV--LETLNDLRIDRENVRVIGATNRPLLGDL----DRALYDRLDIRIVI 149

Name

Accession

Description

Interval

E-value

Enterovirus_RdRp

cd23213

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

1729-2180

0e+00

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1729 VRELNMASINTPTKSKLHPSVFYNVFPGSKEPAVLSDNDPRLEVKLSDSLFSKYKGNIEMKPTENMLIAVDHYAGQLMSL 1808
Cdd:cd23213      1 NKEVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1809 DIPTEELTLKEALYGVDGLEPIDITTSAGYPYVSLGIKKRDILNRETQDVEKMKLYLDKYGIDLPLVTYIKDELRSTDKV 1888
Cdd:cd23213     81 DIDTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKV 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1889 RLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVIPCLMDGHLMAFDYSNFDASLSPVWFEC 1968
Cdd:cd23213    161 EKGKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDGSLFAFDYTGYDASLSPVWFRA 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1969 LEKVLTKLGFKHS-SLIQTICHTHHIFKDEIYVVEGGMPSGCSGTSIFNSMINNIIIRTLVLDAYKGIDLDKLKILAYGD 2047
Cdd:cd23213    241 LKMVLEKGYSEEAvSLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYGD 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2048 DLIVSYPYELDPEVLATLGKKYGLTITPPDKTEKFSKITWDNLTFLKRYFRSDEQFPFLVHPVMPMQDIYESIRWTKDPK 2127
Cdd:cd23213    321 DVIASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDPR 400

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2099546876 2128 NTQDHVRSLCMLAWHSGEKEYNDFTQKIRTTDIGKCLNLPEYSVLRRRWLDLF 2180
Cdd:cd23213    401 NTQDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453

Rabovirus_RdRp

cd23230

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

1820-2180

3.92e-176

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: 541.40 E-value: 3.92e-176

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1820 ALYGVDGLEPIDITTSAGYPYVSLGIKKRDILNRETQDVEKMKLYLDKYGIDLPLVTYIKDELRSTDKVRLGKSRLIEAS 1899
Cdd:cd23230      1 AAYGIENLEGLDLNTSAGYPYVLNGIKKRDILDPETRDTTKLQECLDKYGVDLPFVTYLKDELRPLEKIKKGKTRLIECS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1900 SLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVIPCLMDGHLMAFDYSNFDASLSPVWFECLEKVLTKLGFK 1979
Cdd:cd23230     81 SMNDTIRMKMMFGRLFATYHRNPGPITGSAVGCNPDIHWTKFRAEMHGEIIAFDYSNYDASLNKVWFECLKMVLKNFGFK 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1980 HSSLIQTICHTHHIFKDEIYVVEGGMPSGCSGTSIFNSMINNIIIRTLVLDAYKGIDLDKLKILAYGDDLIVSYPYELDP 2059
Cdd:cd23230    161 DLRPIDHIIRSRHIYKGIEYDVEGGMPSGCSGTSIFNSIINNIIIMTLVLDAYKGIDLEQLKIIAYGDDVIVTYPYPLDA 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2060 EVLATLGKKYGLTITPPDKTEKFSKITWDNLTFLKRYFRSDEQFPFLVHPVMPMQDIYESIRWTKDPKNTQDHVRSLCML 2139
Cdd:cd23230    241 ALLADCGKKYGLKMTPPDKSAEFKNVTWEDVTFLKRRFKPAKHYPFLIHPVFDQQEILESLRWTRNPAHTQEHVRSLAEL 320

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|.
gi 2099546876 2140 AWHSGEKEYNDFTQKIRTTDIGKCLNLPEYSVLRRRWLDLF 2180
Cdd:cd23230    321 AWHSGRKSYEEFCNLVKSTNVGKACILPPYESFKRMWLDQF 361

Sapelovirus_RdRp

cd23218

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

1819-2180

2.20e-162

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

Pssm-ID: 438068 Cd Length: 366 Bit Score: 503.67 E-value: 2.20e-162

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1819 EALYGVDGLEPIDITTSAGYPYVSLGIKKRDILNRETQDVEKMKLYLDKYGIDLPLVTYIKDELRSTDKVRLGKSRLIEA 1898
Cdd:cd23218      1 DVVYGIDNLEGLDLNTSAGYPYNTMGIRKKDLIPPRGEPLSPLLKALDLHGYDLPFTTYLKDELRPKEKVKMGKTRLIEC 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1899 SSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVIPCLMD-GHLMAFDYSNFDASLSPVWFECLEKVLTKLG 1977
Cdd:cd23218     81 SSLNDTIRMKRIFGRLFQTFHKNPGTYTGSAVGCNPDVHWSKFAEEGGmDNVCAFDYTNWDASLSPFWFDALKLFLSKLG 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1978 FKHSSL--IQTICHTHHIFKDEIYVVEGGMPSGCSGTSIFNSMINNIIIRTLVLDAYKGIDLDKLKILAYGDDLIVSYPY 2055
Cdd:cd23218    161 YSERDIvlIDHLCYSNHIFKNEGYKVAGGMPSGCSGTSIFNSIINNIVVRTLVLLVYKGINLDELRILCYGDDLLVAYPY 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2056 ELDPEVLATLGKKYGLTITPPDKTEKF---SKITwdNLTFLKRYFRSDEQFPFLVHPVMPMQDIYESIRWTKDPKNTQDH 2132
Cdd:cd23218    241 PLDPNVLADLGKSLGLTMTPADKSDTFqgcTKLT--EVTFLKRSFVFDEEFPFLCHPVFPMEEVHESIRWTRNASTTQEH 318

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*...
gi 2099546876 2133 VRSLCMLAWHSGEKEYNDFTQKIRTTDIGKCLNLPEYSVLRRRWLDLF 2180
Cdd:cd23218    319 VTSLCLLAWHNGEEVYEEFCEKIRSVPVGRALILPPYSQLRRSWLDMF 366

ps-ssRNA_Picornaviridae

cd23193

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

1820-2156

2.86e-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: 455.08 E-value: 2.86e-145

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1820 ALYGVDGLEPIDITTSAGYPYVSLGIKKRDILNRETQD-----VEKMKLYLDKYGIDLPLVTYIKDELRSTDKVRLGKSR 1894
Cdd:cd23193      1 AINGIDGLDPIDLNTSPGYPYTTQGLRRRDLIDNDKGGvspllEEEEQVLLDLDGPDVVFTTFLKDELRPKEKVKAGKTR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1895 LIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVIP-CLMDGHLMAFDYSNFDASLSPVWFECLEKVL 1973
Cdd:cd23193     81 VIEAAPLDYVIAGRMVFGRLFAQFHSNPGILTGSAVGCNPDTDWTRLFaSLKQDNVYDLDYSGFDASLSSQLFEAAVEVL 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1974 T-KLGFKHS--SLIQTICHTHHIFKDEIYVVEGGMPSGCSGTSIFNSMINNIIIRTLVLDAYKgIDLDKLKILAYGDDLI 2050
Cdd:cd23193    161 AeCHGDPELvlRYLEPIINSKHVVGDERYTVEGGMPSGCPCTSILNSICNNLVVRYALLETGK-FDPDEYYILAYGDDVL 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2051 VSYPYELDPEVLATLGKKY-GLTITPPDKTEKFSKITWDNLTFLKRYFRSDEQFpFLVHPVMPMQDIYESIRWTKDPKNT 2129
Cdd:cd23193    240 VSTDEPIDPSDLAEFYKKYfGMTVTPADKSSDFPESSPIEDVFLKRRFFVPDGT-FLIHPVMDLETLEQSLMWCGRGGFF 318

                          330       340
                   ....*....|....*....|....*..
gi 2099546876 2130 QDHVRSLCMLAWHSGEKEYNDFTQKIR 2156
Cdd:cd23193    319 QQLLSSLCELALHHGPEEYERLVSKVR 345

Dicipivirus_RdRp

cd23222

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

1747-2177

1.78e-84

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: 285.33 E-value: 1.78e-84

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1747 PSVFYNVFPGSKEPAVLSDNDPRL--EVKLSDSLFSKYKGNIEmKPTENMLIAVDHYAGQLMSLdIPTEEL---TLKEAL 1821
Cdd:cd23222      2 PSPVYGVYPVTKEPAPLKPTDRRIdeGVDFNEPVFGKYGADMK-EPFRNLDVGRDVVIARLKKV-LPNKKFapcTVSEAL 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1822 YGVDGLEPIDITTSAGYPYVSLGIKKRDILN-----------RETQDVEKMKLYLDKYgidlPLVTYIKDELRSTDKVRL 1890
Cdd:cd23222     80 NGKDGLPKLDLKQASGYPYNLSAIKRKHLIEsdkdgfltatpKLLADIEESKKHPEKF----PYTSFLKDELRSVKKVKA 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1891 GKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWS--VIPCLMDGHLMAFDYSNFDASLSPVWFEC 1968
Cdd:cd23222    156 GKTRVVEAGSLPVIVEGRMIFGNLFAYFNTHPGFETMAAVGCDPEVCWTdwYYKMREKAHTWDYDYTGFDGSIPSCSFDA 235

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1969 LEKVLTKLGFKHSSL---IQTICHTHHIFKDEIYVVEGGMPSGCSGTSIFNSMINNIIIRTLVLDAYKGIDLDKLKILAY 2045
Cdd:cd23222    236 LADLLCEFVENEDDVrryISNIKNSYHAYDGNLYLIEGAMPSGCAGTSVFNCLINAMLCFSCFMDLEPEMDPFEPLLIAY 315

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2046 GDDLIVSYPYELDP-EVLATLGKKYGLTITPPDKTEKF---SKITwdNLTFLKRYFRSDEQFPfLVHPVMPMQDIYESIR 2121
Cdd:cd23222    316 GDDILVSSDHDLFPsRVSEWMKANTTFKITPADKGEIFnddSDVS--DVRFLKRLFVEDPVCE-LIHPVIETETLEPSLN 392

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2099546876 2122 WTkDPKNTQDHVRSLCMLAWHSGEKEYNDFTQKIrtTDigKCLNLPE-------YSVLRRRWL 2177
Cdd:cd23222    393 WC-HEGEFETKVDAISMLAFHHGPEYYRDWCKKL--TD--ICEERNIsppglkpYSVHRNRWL 450

Cosavirus_RdRp

cd23226

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

1721-2180

1.63e-79

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: 271.51 E-value: 1.63e-79

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1721 GQIISRQkvrelNMASINTPTKSKLHPSvfYNVFPGSKE--PAVLSDNDPRLE--VKLSDSLFSKYKGNIEMKPTEN--- 1793
Cdd:cd23226      1 GQIVNTE-----NGPRVHVPRQSKLKRT--NATYPATGKygPAVLSKNDPRLDpdVDFDKVIFSKHVANVVIDEDTSfwn 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1794 -MLIAVDHYAGQLMSLDIptEELTLKEALYGVDGLEPIDITTSAGYPYVS-----LGIKKRDILNRETQdvEKMKLYLDK 1867
Cdd:cd23226     74 aLKMSAQIYAEKFKGVDF--SPLTVEEAILGIPGLDRMDPNTASGLPYTKtrrqmIDFQEGKILDPELQ--ERLDTWLSG 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1868 YGIDLPLVTYIKDELRSTDKVRLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVIPCLMDG 1947
Cdd:cd23226    150 KQPEMLYQTFLKDEIRPIEKVKAGKTRIIDVTPLDHVLAFRIVLGRFMAHFHNNYGFELGSAVGCDPDVAWANFGFALSS 229

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1948 --HLMAFDYSNFDASLSPVWFECLEK-VLTKL-GFKH--SSLIQTICHTHHIFKDEIYVVEGGMPSGCSGTSIFNSMINN 2021
Cdd:cd23226    230 kkYQYDFDYSNFDASHSESIFELLKQfVFTKDnGFDHrcSLMIDSLVTSTHCYEDQRMTIRGGLPSGTSGTSVINTIINN 309

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2022 IIIRTLVLDAYKGIDLDKLKILAYGDDLIVSYPYELDPEVLATLGKKYGLTITPPDKTEKFSKITWDNLTFLKRYFRsde 2101
Cdd:cd23226    310 IIFKAALYHTYSNFEWDDVQMLAYGDDIVAASDCLLDLDRVKYFMALIGYKITPADKGEKFIPKDMQNIQFLKRSFR--- 386

                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2099546876 2102 QFPFLVHPVMPMQDIYESIRWTKdPKNTQDHVRSLCMLAWHSGEKEYNdftqKIRTTDIGKCLNLPEYSVLRRRWLDLF 2180
Cdd:cd23226    387 KVAGVWAPIMDLENLQAMLSWYK-PGTLQEKLDSVARLAHFCGEKVYD----HLFTTFVKDGFQIKPWKQLHFEWLNRF 460

Kobuvirus_RdRp

cd23214

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

1737-2179

2.57e-79

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: 270.56 E-value: 2.57e-79

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1737 INTPTKSKLHPSVFYNVFPGSKEPAVLSDNDPRLE--VKLSDSLFSKYKGNIEMKPTENMLIAVDHYAGQLMSLdIPTee 1814
Cdd:cd23214      3 VNVNRKSRLGPSPAYGAFPVKKQPAPLTQKDDRLEdgIRLDDQLFLKHNKGDMDEPWPGLEAAADLYFSKFPTM-IRT-- 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1815 LTLKEALYGVDGLEPIDITTSAGYPYVSLGIKKRDILNRETQDV----EKMKLYLDKYGIDLPLV--TYIKDELRSTDKV 1888
Cdd:cd23214     80 LTQEEAINGTPNLEGLDMNQAAGYPWNTMGRSRRSLFVEVQPGIyvpkPELQAEIDKTLEDPDYFysTFLKDELRPTAKV 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1889 RLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIiTGSAVGCDPDVFWS-------VIPCLMDghlmaFDYSNFDASL 1961
Cdd:cd23214    160 TLGLTRVVEAAPIHAIVAGRMLLGGLIEYMQARPGK-HGSAVGCNPDLHWTkffykfcHYPQVFD-----LDYKCFDATL 233

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1962 SPVWFECLEKVLTKL--GFKHSSLIQTICHTHHIFKDEIYVVEGGMPSGCSGTSIFNSMINNIIIRTlVLDAYKGIDLDK 2039
Cdd:cd23214    234 PSCAFRIVEDHLERLtgDERVTRYIESIRHSHHVYGNETYEMIGGNPSGCVGTSIINTIINNICVLS-ALIQHPDFSPES 312

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2040 LKILAYGDDLIVSYPYELDPEVLATLGKKYG-LTITPPDKTEKFSKI-TWDNLTFLKRYFRSDEQFPFLVHPVMPmQDIY 2117
Cdd:cd23214    313 FRILAYGDDVIYGCDPPIHPSFIKEFYDKHTpLVVTPANKGSDFPETsTIYDVTFLKRWFVPDDIRPFYIHPVMD-PDTY 391

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2099546876 2118 E-SIRWTKDpKNTQDHVRSLCMLAWHSGEKEYNDFTQKIR---TTDIGKCLNLPEYSVLRRRWLDL 2179
Cdd:cd23214    392 EqSVMWLRD-GDFQDLVTSLCYLAFHSGPKTYDRWCTRVRdqvMKTTGFPPTFLPYSYLQTRWLNL 456

Cardiovirus_RdRp

cd23211

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

1737-2180

3.73e-79

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

Pssm-ID: 438061 Cd Length: 460 Bit Score: 270.17 E-value: 3.73e-79

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1737 INTPTKSKLHPSVFYNVFPGSKEPAVLSDNDPRLEVKLSDSLFSKYKGNIEMKPTENMLIAVDhYAGQLMS-LDIPTEEL 1815
Cdd:cd23211     12 VHVPRKTKLRRTVAHPVFQPKFEPAVLSKYDPRTDKDVDEVAFSKHTTNQESLPPVFRMVAKE-YANRVFTlLGKDNGRL 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1816 TLKEALYGVDGLEPIDITTSAGYPYVSLGIKKRDILNRET-----QDVEKMKLYLDKYGIDLPLVTYIKDELRSTDKVRL 1890
Cdd:cd23211     91 TVEQAVLGLEGMDPMEKDTSPGLPYTQQGLRRTDVVDFETatmipFLAEAHRKMVEGDYSDVVYQSFLKDEIRPIEKVQA 170

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1891 GKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVIPCLMDGHLMAFD--YSNFDASLSPVWFEC 1968
Cdd:cd23211    171 AKTRIVDVPPFEHCILGRQLLGRFASKFQTNPGLELGSAIGCDPDVDWTAFAVALSGFKYVYDvdYSNFDSTHSTAMFEL 250

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1969 L-EKVLT-KLGF--KHSSLIQTICHTHHIFKDEIYVVEGGMPSGCSGTSIFNSMINNIIIRTLVLDAYKGIDLDKLKILA 2044
Cdd:cd23211    251 LiENFFTeENGFdpRIGEYLRSLAVSRHAYEERRVLIRGGLPSGCAATSMLNTIMNNIIIRAGLYLTYKNFEFDDIKVLS 330

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2045 YGDDLIVSYPYELDPEVLATLGKKYGLTITPPDKTEKFSKI-TWDNLTFLKRYFRSDEqfPFLVHPVMPMQDIYESIRWT 2123
Cdd:cd23211    331 YGDDLLVATNYQIDFNLVKARLAKFGYKITPANKTSTFPLTsTLEDVVFLKRKFVKEN--SYLYRPVMDRENLKAMLSYY 408

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2099546876 2124 KdPKNTQDHVRSLCMLAWHSGEKEYNDFTQKIRTTDIgkclNLPEYSVLRRRWLDLF 2180
Cdd:cd23211    409 R-PGTLKEKLTSIALLAVHSGKQVYDEIFAPFREVGI----VVPTYESVLYRWLSLF 460

Megrivirus_RdRp

cd23223

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

1751-2163

5.28e-77

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

Pssm-ID: 438073 Cd Length: 432 Bit Score: 263.24 E-value: 5.28e-77

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1751 YNVFPGSKEPAVLSDNDPRLE--VKLSDSLFSKYKGNIEMKPTenMLIAVDHYAGQLM-----SLDIPTEELTLKEALYG 1823
Cdd:cd23223      2 YGAFPVTHGPAALTNKDKRLEegVDLDDVMFSKHVPDHPGWPT--LEPAMSYVVEDLMhklgfSKDEPVPMWTLEQAING 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1824 VDGLEPIDITTSAGYPYVSLGIKKRDILN------RETQDVEKMKLYLDKYGIDLPLVTYIKDELRSTDKVRLGKSRLIE 1897
Cdd:cd23223     80 EGVMDGIDMGQSPGYPYNAQGRSRRSFFEwngekwQPTEELKKEVDHALKDPDDFYFSTFLKDELRPLEKVKAGKTRLVD 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1898 ASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVI-----PCLMDgHLMAFDYSNFDASLSPVWFECLEKV 1972
Cdd:cd23223    160 GDSLPRILAMRMVFGPLFEAMLRKNGPEIHSAVGCNPDTDWTRYyhemgPDSFP-YCFDLDYSCFDSTEPKIAFRLMAKY 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1973 LtKLGFKH--SSLIQTICHTHHIFKDEIYVVEGGMPSGCSGTSIFNSMINNIIIRTLVLDAykGIDLDKLKILAYGDDLI 2050
Cdd:cd23223    239 L-KPYFSVdvTPFFEALATSKHVYGDKAYEMEGGMPSGCVGTSMFNCINNSAFIVSALIAL--KISPEDCAWICYGDDVI 315

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2051 VSYPYELDPEVLATL-GKKYGLTITPPDKTEKFSKI-TWDNLTFLKRYFRSDEQFPFLVHPVMPMQDIYESIRWTKDPKn 2128
Cdd:cd23223    316 ISTDEKALSKRIADFyHKNTNLVVTPASKSGDFPETsTIYDVTFLKRFFQPDSHYPHLIHPYMPLEHLEQSVMWQTDGP- 394

                          410       420       430
                   ....*....|....*....|....*....|....*
gi 2099546876 2129 TQDHVRSLCMLAWHSGEKEYNDFTQKIrttdIGKC 2163
Cdd:cd23223    395 FQQKLDSLCLLAFHAGGPDYREFVDAI----DKKC 425

Aphthovirus_RdRp

cd23210

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

1737-2177

4.29e-75

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

Pssm-ID: 438060 Cd Length: 458 Bit Score: 258.34 E-value: 4.29e-75

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1737 INTPTKSKLHPSVFYNVFPGSKEPAVLSDNDPRLE--VKLSDSLFSKYKGNIEMKPTENMLI--AVDHYAGQLMS-LDIP 1811
Cdd:cd23210      6 VHVMRKTKLAPTVAHGVFNPEFGPAALSNKDPRLNegVVLDEVIFSKHKGDTKMSAEDKALFrrCAADYASRLHSvLGTA 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1812 TEELTLKEALYGVDGLEPIDITTSAGYPYVSLGIKKRDILNRET----QDVEKMKLYLDKYGIDLPLVTYIKDELRSTDK 1887
Cdd:cd23210     86 NAPLSIYEAIKGVDGLDAMEPDTAPGLPWALQGKRRGALIDFENgtvgPEVEAALKLMEKREYKFACQTFLKDEIRPMEK 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1888 VRLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVIPCLMDGH--LMAFDYSNFDAS-LSPV 1964
Cdd:cd23210    166 VRAGKTRIVDVLPVEHILYTRMMIGRFCAQMHSNNGPQIGSAVGCNPDVDWQRFGTHFAQYrnVWDVDYSAFDANhCSDA 245

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1965 WFECLEKVL-TKLGFKHSS--LIQTICHTHHIFKDEIYVVEGGMPSGCSGTSIFNSMINNIIIRTLVLDAYKGIDLDKLK 2041
Cdd:cd23210    246 MNIMFEEVFrTEFGFHPNAewILKTLVNTEHAYENKRITVEGGMPSGCSATSIINTILNNIYVLYALRRHYEGVELDTYT 325

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2042 ILAYGDDLIVSYPYELDPEVLATLGKKYGLTITPPDKTEKF--SKITWDNLTFLKRYFRSDEQFPFLvHPVMPMQDIyES 2119
Cdd:cd23210    326 MISYGDDIVVASDYDLDFEALKPHFKSLGQTITPADKSDKGfvLGHSITDVTFLKRHFHMDYGTGFY-KPVMASKTL-EA 403

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2099546876 2120 IRWTKDPKNTQDHVRSLCMLAWHSGEKEYNDFTQKIRTTdigkcLNLPEYSVLRRRWL 2177
Cdd:cd23210    404 ILSFARRGTIQEKLISVAGLAVHSGPDEYRRLFEPFQGL-----FEIPSYRSLYLRWV 456

Mischivirus_RdRp

cd23227

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

1737-2176

2.28e-71

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: 247.94 E-value: 2.28e-71

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1737 INTPTKSKLHPSVFYNVFPGSKEPAVLSDNDPRL--EVKLSDSLFSKYKGNIEMKPTENMLIAvDHYAGQLMS-LDIPTE 1813
Cdd:cd23227     12 IHVPRKTKLRKSPAYPIFKPDAGPAVLSKNDPRLaeGVDFDKQVFSKHSANQKEYPKAFRRMA-RWYADRVFTyLGKDNG 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1814 ELTLKEALYGVDGLEPIDITTSAGYPYVSLGIKKRDILNRETQDVEKMKL------YLDKYGIDLPLVTYIKDELRSTDK 1887
Cdd:cd23227     91 PLSVKDAIKGIDNLDAMDPTTSPGLPYSAAGIKRTDLLDFDTGEIISPALraeynkYVSGDYSDHVFQTFLKDEIRSEEK 170

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1888 VRLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVIPC-LMDGH-LMAFDYSNFDASLSPVW 1965
Cdd:cd23227    171 IKAGKTRIVDVPSLAHVIIGRVLLGKFCSKFQASPGTELGSAIGCNPDWDWTYFAHqLMERQwCYDIDYSNFDSTHGTGM 250

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1966 FECL-EKVLTKL-GF--KHSSLIQTICHTHHIFKDEIYVVEGGMPSGCSGTSIFNSMINNIIIRTLVLDAYKGIDLDKLK 2041
Cdd:cd23227    251 FELLiDCFFTPEnGFspAVAPYLRSLAFSKHAWMDKRYKIEGGLPSGCSATSVLNTVMNNIIIRALLSLTYKNFHPEDVL 330

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2042 ILAYGDDLIVSYPYELD-PEVLATLGKKYGLTITPPDKTEKFSKI-TWDNLTFLKRYFRSDEQFPFLVHPVMPMQDIYES 2119
Cdd:cd23227    331 VLAYGDDLLVASDYQLDfNRVREKAAEHTLYKLTTANKAPDFPETsTLLDCQFLKRKFVLHSTRNFIWRPVMDVTNLKTM 410

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2099546876 2120 IRWTKdPKNTQDHVRSLCMLAWHSGEKEYNDFTQKIRTTDIgkclNLPEYSVLRRRW 2176
Cdd:cd23227    411 LSFYK-PNTLSEKLLSVAQLAFHSGYTVYEELFAPFKELQM----TVPSWWYLEHEW 462

ps-ssRNAv-Picornavirales

cd23169

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

1875-2156

1.87e-70

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

Pssm-ID: 438019 Cd Length: 309 Bit Score: 239.42 E-value: 1.87e-70

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1875 VTYIKDELRSTDKVRLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPgIITGSAVGCDPD-VFWSVIP---CLMDGHLM 1950
Cdd:cd23169      4 VDCLKDELRPIEKVKAGKTRLFSASPLDYTIAFRKYFGDFIAAFQKNR-IKLEHAVGINPDsVEWTRLYrrlLKKGPNIF 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1951 AFDYSNFDASLSPVWFECLEKVLTKLGFKHSS---------LIQTICHTHHIFKDEIYVVEGGMPSGCSGTSIFNSMINN 2021
Cdd:cd23169     83 AGDYSNFDGSLPPDVMEAAFDIINDWYDEYVDdedervrkvLFEELINTIHLVGNLVYQVHGGNPSGNPLTTIINSIVNL 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2022 IIIRTLVLDAYKGIDLDK----LKILAYGDDLIVS----YPYELDPEVLATLGKKYGLTITPPDKTEKFSK-ITWDNLTF 2092
Cdd:cd23169    163 LYIRYAWLRITGLTSLSDfkknVRLVTYGDDVIISvsdeVKDEFNFVTISEFLKELGITYTDADKSGDIVPyRPLEEVTF 242

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2099546876 2093 LKRYFRSDEQfPFLVHPVMPMQDIYESIRWTK---DPKNTQDHVRSLCMLAWHS-GEKEYNDFTQKIR 2156
Cdd:cd23169    243 LKRGFRPHPT-PGLVLAPLDLESIEEQLNWTRkedDLLEATIENARAALLLAFGhGPEYYNKFRQKLN 309

Mosavirus_RdRp

cd23225

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

1825-2179

4.34e-70

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: 240.97 E-value: 4.34e-70

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1825 DGL-EPIDITTSAGYPYVSLGIKKRDILnrETQDVEKMKLYL---------DKY--GIDLP-LVTYIKDELRSTDKVRLG 1891
Cdd:cd23225      6 DGIsDAMDMTKAVGYPYCLDSIKRLDLV--EIKETENGKVYLpterlveetEKFftGEEKPkFVTFLKDEVRSNEKIKQG 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1892 KSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVIPC-LMDGHLMAFDYSNFDASLSPVWFECLE 1970
Cdd:cd23225     84 KTRIVDASPFPYAIAGRMVMQNFMSNMMRCNGTEVGSAVGCDPDTEWTRYFFeLCDRYVFDLDYKAFDSTHPTAMFNLLA 163

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1971 K--VLTKLGFKHSS---LIQTICHTHHIFKDEIYVVEGGMPSGCSGTSIFNSMINNIIIRTLVLDAYKG--IDLDKLKIL 2043
Cdd:cd23225    164 ErfFTERNGFDQQAvriFLNGLSDSDHVYEGKHFRIRGGLPSGCPCTSILNTVINNIIVRAAILGAYQIdtVDFQKFRML 243

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2044 AYGDDLIVSYPYELDPEVLAT-LGKKYGLTITPPDKTEKF---SKItWDnLTFLKRYFRSDEQFPFLVHPVMPMQDIYES 2119
Cdd:cd23225    244 AYGDDVVYATPQPIKPQDLADwLHANTNYKVTPASKAGTFpeeSTI-WD-VTFLKRSFKPDEDHGHLIRPVMAVGNLKQM 321

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2120 IRWTKdPKNTQDHVRSLCMLAWHSGEKEYNDFTQKIRTTDIGkcLNLPEYSVLRRRWLDL 2179
Cdd:cd23225    322 LSFMR-PGTFPDKVRSVAGLAVHCGEEDYNQLADAVALYVPG--VSMPAYKYMKACWYAK 378

Pico_P2A

pfam00947

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

875-1001

5.83e-70

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

Pssm-ID: 395757 Cd Length: 127 Bit Score: 230.73 E-value: 5.83e-70

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  875 NYHLMTPEDHLNLITPYVSRDLAVVFTGAHGAETIPHCSCTSGVYYSRYYRKFYPVICEKPTTIWIEGSSYYPSRYQTGV 954
Cdd:pfam00947    1 NRHLATHEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 2099546876  955 MKGVGPAEPGDCGGILRCVHGPIGLLTAGGSGYVCFADIRQLDCIAE 1001
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVRDLLWLEE 127

Teschovirus_RdRp

cd23212

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

1813-2149

1.29e-64

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

Pssm-ID: 438062 Cd Length: 354 Bit Score: 224.50 E-value: 1.29e-64

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1813 EELTLKEALYGVDGLEPIDITTSAGYPYVSLGIKKRDILNRETQDVEKMKLYLDKYgIDLP-----LVTYIKDELRSTDK 1887
Cdd:cd23212      9 EPLSVREAVEGIDGLDPMDMDKSPGLPYVKKGLRRTDLWNPKTGPSIELMAEINRY-LDYNydkhvFLTFLKDELRPKEK 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1888 VRLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWS-VIPCLMDGHLMAFDYSNFDASLSPVWF 1966
Cdd:cd23212     88 VQAGKTRVIDVAGFGHAIVGRMLFGRLFAFFHKNPGWNTGSAVGVNPDLAWTqIFYTAPSRNVLAMDYSGFDASHTSGMF 167

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1967 ECLEKVLTKLGFK--HSSLIQTICHTHHIFKDEIYVVEGGMPSGCSGTSIFNSMINNIIIRTLVLDAYKGidldKLKILA 2044
Cdd:cd23212    168 CILKHFLTTLGYGtlQLSYIDSLCYSKHHWDDETYRLDGGLPSGCSGTTIFNTIMNNIVARAAASYAAEG----PVGILC 243

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2045 YGDDLIVSYPYELDPEVLATLGKKYGLTITPPDKTEkfsKITWDNL---TFLKRYFRSDEQfpfLVHPVMPMQDIYESIR 2121
Cdd:cd23212    244 YGDDILVSSPEKFPVSDWLEFYSKTPYKVTAADKSE---QIDWRDItqcTFLKRGFVLDGS---LVRPVMEEQHLAELLK 317

                          330       340
                   ....*....|....*....|....*...
gi 2099546876 2122 WTKdPKNTQDHVRSLCMLAWHSGEKEYN 2149
Cdd:cd23212    318 WAR-PGTLQAKLLSIAQLAFHLPRQAYD 344

Rosavirus_RdRp

cd23221

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

1820-2180

3.57e-64

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: 224.03 E-value: 3.57e-64

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1820 ALYGVDGLEPIDITTSAGYPYVSLGIKKRDILN-RETQDVEKMKLYLD--KYGIDLPL---VTYIKDELRSTDKVRLGKS 1893
Cdd:cd23221      1 AINGIDNMDGLDMNQSPGVPYVSEGVSRRSLFDcVDGQWVPRERLASDiaQVSGDPSLghfATFLKDELRSTEKVAAGKT 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1894 RLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVI--PCLMDGHLMAFDYSNFDASLSPVWFECLEK 1971
Cdd:cd23221     81 RVVEAGSLPHIIVGRKIFGNLFALFNSNPGFQTMCAVGCDPDVTWTELyhPLSAKTYVFDYDYSGFDGSVPSCCFDALAD 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1972 VLTKLGFKHSSL---IQTICHTHHIFKDEIYVVEGGMPSGCSGTSIFNSMINNIIIRTLVLDAYKGIDLDKLKILAYGDD 2048
Cdd:cd23221    161 LLADFVEGEEDVrkyISSLKTSFHHYKGKLWRLDGAMPSGCCGTSVFNSLINAMLLFSAFSQICPDFRASEPLLVAYGDD 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2049 LIVSYPYELDP-EVLATLGKKYGLTITPPDKTEKFSKIT-WDNLTFLKRYFRSDEQFPFLVHPVMPMQDIYESIRWTKdP 2126
Cdd:cd23221    241 VLVGTDQPLFPsKVAEWVNSHTTFRITPADKGSVFNDESdIHSVQFLKRHFTPDPDFPALIHPTIDPDTYEQSVMWQR-T 319

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2099546876 2127 KNTQDHVRSLCMLAWHSGEKEYNDFTQKIrttdIGKCLN-------LPEYSVLRRRWLDLF 2180
Cdd:cd23221    320 GDFQETVNSLALLVFHRGPKSYSRWCESV----TRKCVDggypppfFPPFSLLRHQWLKKF 376

RNA_dep_RNAP

cd01699

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

1856-2123

5.67e-63

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: 216.77 E-value: 5.67e-63

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1856 QDVEKMkLYLDKYGIDLPLVTYIKDELRSTDKVRLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNpGIITGSAVGCDPD 1935
Cdd:cd01699      3 KAVESL-EDLPLIRPDLVFTTFLKDELRPLEKVEAGKTRLIQPRPLDYNIALRMYLGPFEAKLMKN-RGGLPIAVGINPY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1936 VF-WSVIPCLMDG---HLMAFDYSNFDASLSPVWFECLEKVLTKLGFKHSS-----LIQTICHT-HHIFKDEIYVVEGGM 2005
Cdd:cd01699     81 SRdWTILANKLRSfspVAIALDYSRFDSSLSPQLLEAEHSIYNALYDDDDElerrnLLRSLTNNsLHIGFNEVYKVRGGR 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2006 PSGCSGTSIFNSMINNIIIRTLVLDAYKGIDLDKLKILAYGDDLIVSYP---YELDPEVLATLGKKYGLTITPPDKTEKF 2082
Cdd:cd01699    161 PSGDPLTSIGNSIINCILVRYAFRKLGGKSFFKNVRLLNYGDDCLLSVEkadDKFNLETLAEWLKEYGLTMTDEDKVESP 240

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|.
gi 2099546876 2083 SKiTWDNLTFLKRYFRSDEQfpFLVHPVMPMQDIYESIRWT 2123
Cdd:cd01699    241 FR-PLEEVEFLKRRFVLDEG--GGWRAPLDPSSILSKLSWS 278

Passerivirus_RdRp

cd23224

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

1819-2179

8.66e-58

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: 205.71 E-value: 8.66e-58

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1819 EALYGVDGLEPIDITTSAGYPYvSLGIKKRDILNRETQDVEKMKLYLDKYGI------DLPLVTYIKDELRSTDKVRLGK 1892
Cdd:cd23224      1 EAINGTPLLDGLDMKQSPGYPW-SLTTNRRSLFTQDETGKYYPVPELEEAVLaclenpDYFYTTHLKDELRPVEKALAGK 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1893 SRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIItGSAVGCDPDVFWSVIPCLMD--GHLMAFDYSNFDASLSPVWFEC-- 1968
Cdd:cd23224     80 TRLIEAAPIHAIIAGRMLLGGLFEYMHARPGEH-GSAVGCDPDYHWTPFFHSFDefSQVWALDYSCFDSTLPSCCFDLia 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1969 --LEKVLTKL-GFKHSSL---IQTICHTHHIFKDEIYVVEGGMPSGCSGTSIFNSMINNIIIRTLVLdAYKGIDLDKLKI 2042
Cdd:cd23224    159 qkLAKIITPGeGIAPDAIvkyIRSISISKHVFGNEAYLMVGGNPSGCVGTSILNSMINNCVLISAFL-TQKDFNPNQMRI 237

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2043 LAYGDDLIVSYPYELDPEVLAT-LGKKYGLTITPPDKTEKFS--KITWDnLTFLKRYFRSDEQFPFLVHPVMPMQDIYES 2119
Cdd:cd23224    238 LTYGDDVLYATNPPIHPRVVKKfFDENTTLIVTPATKAGDFPdeSTIWD-VTFLKRYFVPDEIRPWYVHPVIEPATYEQS 316

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2099546876 2120 IRWTKDpKNTQDHVRSLCMLAWHSGEKEYNDFTQKIRTTDIGKCL--NLPEYSVLRRRWLDL 2179
Cdd:cd23224    317 VMWTRG-GDFQDVVTSLSFLAHHAGPTNYMIWEEKVRKAAAAKGVslNILPYSYLQHRWMLL 377

Rhv

pfam00073

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

93-297

1.82e-54

Pssm-ID: 395026 Cd Length: 170 Bit Score: 187.90 E-value: 1.82e-54

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876   93 TTQEAANAVVCYAEWPEYLPDNDASDVNKTSKPDTSVCRFYTLESKVWQNSSKGW-CWKLPDALKDMGVFGQNMFFHSLG 171
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFfWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  172 RSGYTIHVQCNATKFHSGCLLVVVIPEHQlashkggnvsvkykyTHPGEggidlstqldedgpvkdpvysmnGTLLGNLL 251
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPPGA---------------PPPGS-----------------------RDYLWQAT 122

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 2099546876  252 IFPHQFINLRTNNTATIVVPYINSVPIDSMTRHNNVSLLVIPIAPL 297
Cdd:pfam00073  123 LNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGNWTLVVAGWVPL 168

RdRP_1

pfam00680

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

1746-2151

3.18e-51

Pssm-ID: 425815 Cd Length: 450 Bit Score: 188.77 E-value: 3.18e-51

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1746 HPSVFYNVFPGSKEPAVLSDNDPRLEV------KLSDSLfSKYKGNIEMKPTENMLIAVDHYAGQLMSLDI------PTE 1813
Cdd:pfam00680    1 SPTERHLVAIPAYVPASLGPEDPRWARsylntdPYVDDI-KKYSRPKLPGPADERDKLLNRSAAKMVLSELrgvpkkANS 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1814 ELTLKEALYGVDGLEPIDITTSAGYPYVSLGIKKRDiLNRETQDV-------EKMKLYLDKY--GIDLPLV--TYIKDEL 1882
Cdd:pfam00680   80 TLIVYRAIDGVEQIDPLNWDTSAGYPYVGLGGKKGD-LIEHLKDGtearelaERLAADWEVLqnGTPLKLVyqTCLKDEL 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1883 RSTDKVRLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITgSAVGCDP-DVFWSV----IPCLMDGHLMaFDYSNF 1957
Cdd:pfam00680  159 RPLEKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHP-IQVGINPfDRGWPRllrrLARFGDYVYE-LDYSGF 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1958 DASLSP----VWFECLEkvlTKLGFKHS-----SLIQT-ICHTHHIFKDEIYVVEGGMPSGCSGTSIFNSMINNIIIRTL 2027
Cdd:pfam00680  237 DSSVPPwlirFAFEILR---ELLGFPSNvkewrAILELlIYTPIALPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYA 313

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2028 VL-----DAYKGIDLDKLKILA-YGDDLIVSYPYELDPeVLATLG---KKYGLTITPPDKTEKFSKITwDNLTFLKRYFR 2098
Cdd:pfam00680  314 LLkslenDGPRVCNLDKYFDFFtYGDDSLVAVSPDFDP-VLDRLSphlKELGLTITPAKKTFPVSREL-EEVSFLKRTFR 391

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2099546876 2099 SDeqfPFLVHPVMPMQDIYESIRWTKDPKNTQDHVRSLCMLAWHSGEKEYNDF 2151
Cdd:pfam00680  392 KT---PGGYRPPLDRKRILAQLEYIRSKPVPSGQLENIRAYASHHGYEFYRDL 441

Fipivirus_RdRp

cd23229

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

1823-2176

5.28e-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: 186.17 E-value: 5.28e-51

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1823 GVDGLEPIDITTSAGYPYVSLGIKKRDI--------------LNRETQDVEKMKLYLDKYGIDLPLVTYIKDELRSTDKV 1888
Cdd:cd23229      4 GIPGMEGLDMKTSAGYPWCEQNQKKKDKikllagknflvrplREVVHIVVDWYIMPPDMPKPEIKYVVYLKDELLSSDKV 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1889 RLGKSRLIEASSLNDSVNMRMKLGNLYKAFH-QNP--GIITGSAVGCDPDVFWSVIP-CLMDGHLMAFDYSNFDASLSPV 1964
Cdd:cd23229     84 KMGRTRWICAAPVQLVCAWKKVFGRAIAAIHlESVtdGKSTGCAVGMDPETAWTDIAlARPGWPVIALDYSNFDGSLQSF 163

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1965 WFECLEKVL---TKLGFKHSS-LIQTICHTHHIFKDEIYVVEGGMPSGCSGTSIFNSMINnIIIRTLVLDAYKGIDL--- 2037
Cdd:cd23229    164 VITGAVRILgyiAGLPDGQSYrLAEFVYDVKQIVGKYLYTTVGPLPSGCPSTSIIGSLCN-VLMLLYTLSHATGQRYsaf 242

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2038 -DKLKILAYGDDLIV----SYPYELDPEVLATLgKKYGLTIT-PPDKTEKFSKITWDNLTFLKRYFRSDEQFPFLVHPVM 2111
Cdd:cd23229    243 rDWMHVVTYGDDVLVfvhpEVVVVLDTLAHEMY-LVFGVTATdATDKRAPPQLRELSNVTFLKRGFRQCSSVPFLVHPTM 321

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2099546876 2112 PMQDIYESIRWTKDPKNTQDHVRSLCMLAWHSGEKEYNDFTQKIRTT-------DIGKCLN-LPEYSVLRRRW 2176
Cdd:cd23229    322 DKSTIYQMLAWKRKGTTLAENVKCAAEFMMHHGEEEYEDFVGVVKECstligvdQRSKVYEeLCSYAELHDHW 394

Hepatovirus_RdRp

cd23215

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

1812-2179

3.75e-45

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

Pssm-ID: 438065 Cd Length: 464 Bit Score: 171.18 E-value: 3.75e-45

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1812 TEELTLKEALYGVDGLEPIDITTSAGYPYVSLGIKKRDIL------------NRETQDVEKMKLYLDKYG-IDLPLVTYI 1878
Cdd:cd23215     62 DEFFDLEQAITGVPGMDAINMDSSPGYPYVQEKLTKSDLIwlddngellgmhPRLAQRILFNLTMMDNGNdLDVVYTTCP 141

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1879 KDELRSTDKVRLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVIPCLM---DGHLMAFDYS 1955
Cdd:cd23215    142 KDELRPLEKVLESKTRAIDACPLDFTIICRMFWGPAISYFQLNPGFHTGVAVGIDPDRDWDALFKTMirfGDYGIDLDFS 221

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1956 NFDASLSPVWFECLEKVLTKLG----FKHSSLIQTICHTHHIFKDEIYVVEGGMPSGCSGTSIFNSMINNIIIRTLVLDA 2031
Cdd:cd23215    222 SFDASLSPFMIREACRVLSELSgvpdHQGQALINTIIYSKHLLYNLCYHVCGSMPSGSPCTSLLNSIVNNVNLYYVFSKI 301

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2032 YKGIDL---DKLKILAYGDDLIVSYPYELDPEVLATLG-------KKYGLTITPPDKTEKFSKITWDnLTFLKRYFRSDE 2101
Cdd:cd23215    302 FKKSPVffyDAVKFLCYGDDVLIVFSRDLEIKNLDKLGqriqdefKLLGMTATSADKGEPQVVPVSE-LTFLKRSFNLIE 380

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2102 QfpfLVHPVMPMQDIYESIRWTKDPKNTQDHVRSLCMLAWHSGEKEYNDFTQKIRTTDIGKCLN--LPEYSVLRRRWLDL 2179
Cdd:cd23215    381 D---RFRPAISEKTIWSLVAWQRSNAEFEQNLDTACWFAFMHGYDFYQNFYLQLQSCLEKEMIDyrLKSYEWWRMRFEDL 457

Peptidase_C3

pfam00548

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

1539-1703

1.99e-41

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: 151.06 E-value: 1.99e-41

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1539 GPNTEFALSLLRKNIVTVTTEKGEFTGL--GIYDRVCVIPTHAQPDNKVLINGQAVQLKD-KYKLVDPDNTNLELTVLTL 1615
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1616 DRNEKFRDIRSFISEDL-EGMEASLVIHSNNFTNTILDVGPITMAGLI-NLSSTPTGRMIRYDYPTKTGQCGGVL----C 1689
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRItKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVViakvE 160

                          170
                   ....*....|....
gi 2099546876 1690 TTGKIFGIHVGGNG 1703
Cdd:pfam00548  161 GNGKILGMHIAGNG 174

Limnipivirus_RdRp

cd23228

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

1826-2156

2.97e-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: 157.73 E-value: 2.97e-41

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1826 GLEPIDITTSAGYPYVSLGIKKRD-----------ILNRETQDVEKMKLYLDKYG-IDLPLVTYIKDELRSTDKVRLGKS 1893
Cdd:cd23228      6 GTNPIDKNTSPGLKYTRDGLKKSDlytidedgnvvVSDMLRADVEAWEELIQSGGyPTTLFTACLKDELRSDEKVALGKT 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1894 RLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPdvfwsvipcLMDGH-----------LMAFDYSNFDASLS 1962
Cdd:cd23228     86 RVIEAAELDYVVAYRMYMSSIYSDLYNAYAGDTGIAAGINP---------PADGHrlreelsqydsFLALDYSRFDGSLP 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1963 PVWFECLEKVLTKLgfkHSS------LIQTICHTHHIFKDEIYVVEGGMPSGCSGTSIFNSMINNIIIRTLVLDAYkGID 2036
Cdd:cd23228    157 EMLMRAAVEILADL---HEDpdlvrrLHETVIISKHLVVDEDWTVKGGMPSGSPCTTVLNCICNLLVLEYAFLVHF-GVY 232

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2037 LDKLK---------ILAYGDDLIVSY-PYELDPEVLATLGKKYGLTITPPDKTEKFSKITWDNLTFLKR-YFRSDEQFPF 2105
Cdd:cd23228    233 EDDDGvglpqcdylSVVYGDDCIVAYnGMEMGLAFAETIEDTFGMEVTPASKVGDHFNVELHEVEFLKRkFFAFETEEYD 312

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2099546876 2106 LVHPVMPMQDIYESIRWTKDPKNTQDHVRSLCM--LAWhsGEKEYNDFTQKIR 2156
Cdd:cd23228    313 RIALRLSENTIVQSLMWMRNLKTFPDQVQSLMMelSAW--GKEKYDKLRDTCK 363

Rhv

pfam00073

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

614-770

1.02e-40

Pssm-ID: 395026 Cd Length: 170 Bit Score: 148.61 E-value: 1.02e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  614 PSDNVETRTTYMHFNGSETDVESFLGRAACVHIVEIENKNP--AGIENQKEQKLFNDWKINLS--SLVQLRKKLELFTYV 689
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYtlDSTDWTSLSKGFFWWKLPLAllSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  690 RFDSEYTILATASQptessyASNLVVQAMYVPPGAPNPEKWdDFTWQSASNPSVFFKVG--DTSRFSVPFVGIASAYNCF 767
Cdd:pfam00073   81 RGGLEVTVQFNGSK------FHQGKLLVAYVPPGAPPPGSR-DYLWQATLNPHQFWNLGlnSSARLSVPYISIAHYYSTF 153


                   ...
gi 2099546876  768 YDG 770
Cdd:pfam00073  154 YDG 156

Kunsagivirus_RdRp

cd23219

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

1817-2135

2.65e-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: 153.87 E-value: 2.65e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1817 LKEALYgvDGLEPIDITTSAGYPYVslGIKKRDILN--------RETQDVEKMKLYLDKYGID-LPLVTYIKDELRSTDK 1887
Cdd:cd23219      1 IEEAVF--DTVTPMDHTASAGPKYP--GTKRSELIDfqnriisdRLRNDVLELQFRGTSGGAGeVKFSSFLKDELRPLSK 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1888 VRLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCdpDVFWSVIPC---LMDGHLmAFDYSNFDASLSPV 1964
Cdd:cd23219     77 IRSGDTRVVECSSLDYTVAFRMQFLRVLQMCYGSDPTLTGLAPGM--NVYTDMLPLctsLYDYNL-CLDFSKYDSRLPLQ 153

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1965 WFECLEKVLTKLGFKHS---SLIQTICHTHHIFKDEIYVVEGGMPSGCSGTSIFNSMINNIIIRTLVLDAYKGIDldkLK 2041
Cdd:cd23219    154 VMHRVAQLISNLTPDPQvsmRLFQPIIISTHIVGSYEVVVEGGMPSGCPITTIMNSVCNVVMTSYAMLLLDPDSD---FW 230

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2042 ILAYGDDLIVSYPYELDPEVLAT-LGKKYGLTITPPDKTEKFSKITWDNLTFLKRYFRSDEQFPFLVhPVMPMQDIYESI 2120
Cdd:cd23219    231 PVAYGDDNIVSTRKPIDTELFCSiLNEEFGMILTGADKTTTVQAVPPMSVDFLKRRLRYTPEFPLPV-PVLPLDSMLSRI 309

                          330
                   ....*....|....*
gi 2099546876 2121 RWTKDPKNTQDHVRS 2135
Cdd:cd23219    310 CWCKGETEFKDQLES 324

Parechovirus_RdRp

cd23217

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

1820-2155

3.75e-40

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: 153.87 E-value: 3.75e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1820 ALYGVDGLEPIDITTSAGYPYVSLGIKKRDILNRETQDVEKM------KLYLDKYGIDLP---LVTYIKDELRSTDKVRL 1890
Cdd:cd23217      1 AVLGTSHLNSLDLSTSPGYKYVKSGYKKRDLLSLEPFSVSPQlekdvkDKLHAVYKGNQPttiFNACLKDELRKLDKIAQ 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1891 GKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVIPCLMDGHLMAFDYSNFDASLSPvwfECLE 1970
Cdd:cd23217     81 GKTRCIEACSIDYVIAYRVVMSSLYEAIYQTPCQELGLAVGMNPWTDWDFMINALNPYNYGLDYSSYDGSLSE---MLMW 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1971 KVLTKLGFKHSS------LIQTICHTHHIFKDEIYVVEGGMPSGCSGTSIFNSMINNIIIRTLvldAY-KGIDLDKLKIL 2043
Cdd:cd23217    158 EAVEVLAYCHESpdlvmqLHKPVINSDHVVMDERWLVHGGMPSGSPCTTVLNSICNLLVCIYL---AYlQSPGIECLPIV 234

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2044 aYGDDLIVSYPYELDPEVLA-TLGKKYGLTITPPDKTEKFSKITWDNLTFLKryfRSDEQFPFLVHPV--MPMQDIYESI 2120
Cdd:cd23217    235 -YGDDVIFSVSSEIDPEYLVsSAADSFGMEVTGSDKDEPPSLLPRMEVEFLK---RTTGYFPGSTYKVgaLDLETMEQHI 310

                          330       340       350
                   ....*....|....*....|....*....|....*.
gi 2099546876 2121 RWTKDPKNTQDHVRSLCM-LAWHsGEKEYNDFTQKI 2155
Cdd:cd23217    311 MWMKNLSTFPQQLQSFENeLCLH-GKDIYDDYKKIF 345

RNA_helicase

pfam00910

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

1226-1324

3.90e-40

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

Pssm-ID: 459992 Cd Length: 102 Bit Score: 144.28 E-value: 3.90e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1226 VLIHGTPGSGKSLTTSIVGRALAEYFN---SSVYSLPPDPKHFDGYQQQEVVIMDDLNQNPDGQDISMFCQMVSSVDFIP 1302
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKKLGlpkDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 2099546876 1303 PMANLDNKGMLFTSNFVLASTN 1324
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

Crohivirus_RdRp

cd23232

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

1817-2169

8.96e-40

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

Pssm-ID: 438082 Cd Length: 373 Bit Score: 152.95 E-value: 8.96e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1817 LKEALYGVDGLEPIDITTSAGYPYVSLGIKKRDILNRET--------QDVEKMKLYLDKYG-IDLPLVTYIKDELRSTDK 1887
Cdd:cd23232      1 IEEACFEEGDEHALDLKTSPGFKYVQMGLKKTDLVNRPNkfihpilrNDVRLIFDEMAKGQmPVVTFTAHLKDELRKLEK 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1888 VRLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFW-SVIPCLmDGHLMAFDYSNFDASLSPVWF 1966
Cdd:cd23232     81 IRSGKTRCIEACDFDYTVAHKMMFGTLYKAIYDTPGIITGLAVGMNPWKDWeLIQQSL-FKYNYDFDYKTFDGSLSRELM 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1967 ----ECLEKVLTKLGFKHSSLIQTIcHTHHIFKDEIYVVEGGMPSGCSGTSIFNSMINNIIIRTLVLDAYKGidldKLKI 2042
Cdd:cd23232    160 lhavDILSACVENDEMAKLMLSVVV-ESVHLVLDQKWNVSGGMPSGSPCTTVLNSVCNLIVSSTIADMCTEG----DFKI 234

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2043 LAYGDDLIVSYPYELDPEVLATLGK-KYGLTITPPDKTEKFSKITWDNLTFLKRYFRSDEQFPFLVHpVMPMQDIYESIR 2121
Cdd:cd23232    235 LVYGDDLIISSTAPLDCDRFKTLVElHYGMEVTPGDKGDEFKVKDREQVSFLKRVTRKFPGTNYRVG-ALDLDTVKQHLM 313

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*...
gi 2099546876 2122 WTKDPKNTQDHVRSLCMLAWHSGEKEYNDFTQKIRTTDIGKCLNLPEY 2169
Cdd:cd23232    314 WCKSYSSFKQQLDSALMEVAMHGEETYNGFLTEIKTKLDKFKIYPPKF 361

Dicistroviridae_RdRp

cd23194

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

1879-2156

1.28e-38

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: 147.65 E-value: 1.28e-38

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1879 KDELRSTDKVRLGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPgIITGSAVGCDP---DvfWSVIPCLM---DGHLMAF 1952
Cdd:cd23194     13 KDERRPIEKVDAGKTRVFSAGPMDYTIAFRMYFLGFVAHLMRNR-IDNEIAVGTNVyslD--WDKLARKLlskGDKVIAG 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1953 DYSNFDASLSPvwfECLEKVLTKL------GFKH----SSLIQTICHTHHIFKDEIYVVEGGMPSGCSGTSIFNSMINNI 2022
Cdd:cd23194     90 DFSNFDGSLNP---QILWAILDIInewyddGEENalirRVLWEDIVNSVHICGGYVYQWTHSQPSGNPLTAIINSIYNSI 166

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2023 IIRTLVLDAYKGIDLDKLK-------ILAYGDDLIVSYPYELDP----EVLATLGKKYGLTITPPDKT---EKFSKItwD 2088
Cdd:cd23194    167 IMRYVYLLLTKEAGLMTMSdfnkhvsMVSYGDDNVINVSDEVSEwfnqLTITEAMAEIGMTYTDETKTgeiVPYRSL--E 244

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2099546876 2089 NLTFLKRYFRSDEQFPFLVHPvMPMQDIYESIRWTK---DPK-NTQDHVRSLCM-LAWHsGEKEYNDFTQKIR 2156
Cdd:cd23194    245 EVSFLKRGFRYDDDLGRWVAP-LDLDTILEMPNWVRkgkDPEeITKQNVENALReLSLH-GEEVFDKWAPKIR 315

Rhv

pfam00073

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

359-522

3.46e-38

Pssm-ID: 395026 Cd Length: 170 Bit Score: 141.29 E-value: 3.46e-38

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  359 YEPTPRIHIPGKVRNLLEIIQVDTLIPMNNVH-NSDEVNSYLIPLTA-NRQNDQIFGTRLfiGDGVFKTTLLGEIAQYYT 436
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQpDVQGERFYTLDSTDwTSLSKGFFWWKL--PLALLSMGLLGRLLRYHT 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  437 HWSGSLRISLMYTGPALSSAKLILAYTPPGAQGPTNR---KDAMLGTHVVWDIGLQSTIIMTIPWTSGVQFRYT---DPD 510
Cdd:pfam00073   79 YYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRdylWQATLNPHQFWNLGLNSSARLSVPYISIAHYYSTfydGNW 158

                          170
                   ....*....|..
gi 2099546876  511 TYTSAGYLSCWY 522
Cdd:pfam00073  159 TLVVAGWVPLNY 170

rhv_like

cd00205

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

634-826

8.70e-38

Pssm-ID: 119412 Cd Length: 178 Bit Score: 140.61 E-value: 8.70e-38

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  634 VESFLGRAACVHIVEIENKNPagienqkeQKLFNDWKINLS------SLVQLRKKLELFTYVRFDSEYTILATASQPTes 707
Cdd:cd00205      1 VESFADRPTTVGTNNWNSSAS--------GTQLFQWKLSPAlgflllQNTPLGALLSYFTYWRGDLEVTVQFNGSKFH-- 70

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  708 syasNLVVQAMYVPPGAPNPEKwDDFTWQSASNPSVFFKVGDTS--RFSVPFVGIASAYNCFYDGYShddkdtpygisVL 785
Cdd:cd00205     71 ----TGRLLVAYVPPGAPAPTT-GDTRWQATLNPHVIWDLGTNSsvTFVVPYVSPTPYRSTRYDGYG-----------PL 134

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....
gi 2099546876  786 NHMGSIAFRVVNEHDA---HKTLVKIRVYHRAKHVEAWIPRAPR 826
Cdd:cd00205    135 NSFGTLVVRVLTPLTVpsgAPTTVDITVYVRAGDFELYGPRPPR 178

Avisivirus_RdRp

cd23231

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

1827-2155

1.10e-37

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: 146.57 E-value: 1.10e-37

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1827 LEPIDITTSAGYPYVslGIKKRDILNRETQDVEKMKLY-----LDKYGIDLPLVTYIKDELRSTDKVRLGKSRLIEASSL 1901
Cdd:cd23231      8 LLPIDWGTSPGDKYK--GKTKAQLVDDKKFKADVMNLVrfngdPNREPPDVYFTTYLKDELRPKEKAKAGKTRVISAASF 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1902 NDSVNMRMKLGNLYKAFHQNpGIITGSAVGCDP-----DVFWSVIPclmdgHLMAFDYSNFDASLS-PVWFECLEkVLTK 1975
Cdd:cd23231     86 DYTIACRMVFGPILRQLFAW-GREFGFGPGLNPythfdELYDKILP-----FVICLDYSGFDGSLSsELMFHAAQ-VIAC 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1976 LGFKHSSLIQ----TICHTHHIfKDEIYVVEGGMPSGCSGTSIFNSMINNIIIRTLVLDayKGIDLDKLKILAYGDDLIV 2051
Cdd:cd23231    159 FSEKPEAIMAsaelTIGSTERV-SDEVWYVYGGMPSGSPWTTTLNTICNLLMCYTYLLD--MGHCWSETFVVAYGDDVVI 235

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2052 SYPYELDPEVLATLGK-KYGLTITPPDKTekfSKITW---DNLTFLKRYFRSDEQFPFLVHpVMPMQDIYESIRWTKDpk 2127
Cdd:cd23231    236 SANIKHNLEGIEQWFKtKFGATVTPSDKQ---GKITWttkNNMEFLKRRPKQLDFLPKIVG-ALDLDNMLDRIQWTKG-- 309

                          330       340
                   ....*....|....*....|....*....
gi 2099546876 2128 NTQDHVRSLCM-LAWHsGEKEYNDFTQKI 2155
Cdd:cd23231    310 HFQDQLNSFYLeLALH-GRETYNEIRAKL 337

rhv_like

cd00205

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

125-324

2.38e-37

Pssm-ID: 119412 Cd Length: 178 Bit Score: 139.45 E-value: 2.38e-37

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  125 PDTSVCRFYTLESKVWQNS---SKGWCWKLPDA----LKDMGVFGQNMFFHSLGRSGYTIHVQCNATKFHSGCLLVVVIP 197
Cdd:cd00205      1 VESFADRPTTVGTNNWNSSasgTQLFQWKLSPAlgflLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  198 EHQLAShkggnvsvkykythpgeggidlstqldedgpvkdpvysMNGTLLGNLLIFPHQFINLRTNNTATIVVPYINSVP 277
Cdd:cd00205     81 PGAPAP--------------------------------------TTGDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTP 122

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2099546876  278 IDSMTRH------NNVSLLVIPIAPLVAPTGSPQTLPVTVTIAPMCTEFTGIR 324
Cdd:cd00205    123 YRSTRYDgygplnSFGTLVVRVLTPLTVPSGAPTTVDITVYVRAGDFELYGPR 175

rhv_like

cd00205

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

374-556

4.86e-37

Pssm-ID: 119412 Cd Length: 178 Bit Score: 138.30 E-value: 4.86e-37

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  374 LLEIIQVDTLIPMNNVHNSDEVNSYL-IPLTanrqndqifgtrLFIGDGVFKTTLLGEIAQYYTHWSGSLRISLMYTGPA 452
Cdd:cd00205      1 VESFADRPTTVGTNNWNSSASGTQLFqWKLS------------PALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSK 68

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  453 LSSAKLILAYTPPGAQGPTN---RKDAMLGTHVVWDIGLQSTIIMTIPWTSGVQFRYTD---PDTYTSAGYLSCWYQTSL 526
Cdd:cd00205     69 FHTGRLLVAYVPPGAPAPTTgdtRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRydgYGPLNSFGTLVVRVLTPL 148

                          170       180       190
                   ....*....|....*....|....*....|
gi 2099546876  527 ILPPNTTGQVHLLSFISACpDFKLRLMKDT 556
Cdd:cd00205    149 TVPSGAPTTVDITVYVRAG-DFELYGPRPP 177

Aalivirus_RdRp

cd23216

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

1829-2157

3.80e-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: 135.57 E-value: 3.80e-34

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1829 PIDITTSAGYPYVslGIKKRDILNrETQDVEKMKLYLDkyGIDLPLVTYIKDELRSTDKVRLGKSRLIEASSLNDSVNMR 1908
Cdd:cd23216     11 PIDWQTSPGLKYK--GRTKADLVQ-DPKFKEDVKEILA--GKPTFFTTYLKDELRSIEKIANGNTRAIEAANFDHVVAWR 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1909 MKLGNLYKAFHQNPGIITGSAVGCDPdvfWSVIPCLMDG---HLMAFDYSNFDASLSPVWFECLEKVLTKLGFKHSSLIQ 1985
Cdd:cd23216     86 QVMGNIVKQLFSDHDRVTGFAPGMNP---YTHFDSLMDQvkwNVLALDFKKFDGSLSPQVMEEAVDILASFHDMPQMVVD 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1986 TICHTHH---IFKDEIYVVEGGMPSGCSGTSIFNSMINNIIIRTLVLDayKGIDLDKLKILAYGDDLIVS---YPYEL-D 2058
Cdd:cd23216    163 IHKHTIYstnVVSDETWFVEGGMCSGSPCTTVLNTICNLLVNTTILLS--EGIQPDNFYIAAYGDDTIISvdgLSSSLpD 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2059 PEVLATLGKK-YGLTITPPDKTekfSKITWD---NLTFLKR---YFRSDEQfpflVHPVMPMQDIYESIRWTKDpkNTQD 2131
Cdd:cd23216    241 PKIMQQKYKEwFGMTVTSADKG---SEITWDtrnHVQFLKRrpgFFPGTQK----VVGVLDLESMMEHIAWTKG--SFQD 311

                          330       340
                   ....*....|....*....|....*.
gi 2099546876 2132 HVRSLCMLAWHSGEKEYNDFTQKIRT 2157
Cdd:cd23216    312 QLNSFYQELVLHGEQVYMTVRQTLKS 337

Pico_P2B

pfam01552

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

1003-1101

4.44e-30

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: 115.51 E-value: 4.44e-30

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1003 QGLNDYITSLGRAFGVGFTDQISAKVTELQDVAKDF--LTTKVLSKVVKMISALVIICRNHDDLVTVTATLALLGCDGSP 1080
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTQQISDKIKELTNFINPTskIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|.
gi 2099546876 1081 WRFLKMYISKHFQVPYIERQA 1101
Cdd:pfam01552   81 WQFLKEKACAVLEIPYVHKQG 101

Caliciviridae_RdRp

cd23192

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

1879-2135

3.66e-29

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

Pssm-ID: 438042 Cd Length: 310 Bit Score: 120.06 E-value: 3.66e-29

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1879 KDELRSTDKVRLGKSRLIEASSLNDSVNMRMKLGNLYKAF--HQNPGIItgsAVGCDPD-VFWSVI--PCLMDGHLMAFD 1953
Cdd:cd23192      8 KDELRPVEKIAEGKRRLLWGCDVGVTLVAAAAFGPVADALkaVCPTGPI---AVGINMDsEDVEVIfeRLSGFRYHYCLD 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1954 YSNFDASLSP-VWFECLEkVLTKLGFKHSsLIQTICHTHH-----IFKDEIYVVEGGMPSGCSGTSIFNSMINNIIIRTL 2027
Cdd:cd23192     85 YSKWDSTQSPaVTAAAID-ILADLSEETP-LRDSVVETLSsppmgIFDDVIFVTKRGLPSGMPFTSVINSLNHWLLFSAA 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2028 VLDAYK------GIDLDKLKILAYGDDLIVSYPYELD---PEVLATLgKKYGLTITPPDKTEKFSKITWDNLTFLKRYFR 2098
Cdd:cd23192    163 VLKAYElvgiytGNVFDEADFFTYGDDGVYAMPPATAsvmDEIIENL-KSYGLKPTAADKTENPDIPPLQGPVFLKRTFV 241

                          250       260       270
                   ....*....|....*....|....*....|....*..
gi 2099546876 2099 SDeqfPFLVHPVMPMQDIYESIRWTKDPkNTQDHVRS 2135
Cdd:cd23192    242 RT---PGGWRALLDRSSILRQLYWVKGP-NTHDWTEP 274

Aquamavirus_RdRp

cd23220

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

1829-2154

3.61e-25

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: 109.03 E-value: 3.61e-25

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1829 PIDITTSAGYPYVslGIKKRDILN----RETQDVEKMKLYLDKYGIDLPLVTYIKDELRSTDKVRLGKSRLIEASSLNDS 1904
Cdd:cd23220     11 PLNFNGTAGAKYP--GMNRRQLLLplnpQVRDDVVKLAGDVGNGTATVVFETFMKDELRPKEKIESGKTRIVESCPLDYL 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1905 VNMRMKLGNLYKAFHQNPGIITGSAVGCDPDVFWSVIPCLMDGHLMAFDYSNFDASLSPVWFE-------CLEKVLTKLG 1977
Cdd:cd23220     89 LLYRMVMLKSMIWWYNSDCIKTGVAPGMNVYTDFVPMVKQFKKIKYCLDFSAYDSTLSDEILAagvevlaCTSAVPSYVR 168

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1978 FKHSSLIQTichtHHIFKDEIYVVEGGMPSGCSGTSIFNSMINNIIIRTLVldayKGIDLDKLKILAYGDDLIVSYPYEL 2057
Cdd:cd23220    169 KLHAPIICS----HHWHNNVVDLVLGGMPSGAPCTSVLNSIVNVLMARYIC----ALMDIDYPVMVAYGDDNVVSFDEEI 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2058 DPEVLATLGK-KYGLTITPPDKTEKFSKITwdNLTFLKRYFR--SDEQFPFlvhPVMPMQDIYESIRWTKDPKNTQDHVR 2134
Cdd:cd23220    241 DIERMVSLYKtEFGVTATNHDKTPVPRPMA--NPVFLKRRLRfnPDLNIQF---PVLPLGEMIDRMCWTRGPEHLSDQTF 315

                          330       340
                   ....*....|....*....|
gi 2099546876 2135 SLCMLAWHSGEKEYNDFTQK 2154
Cdd:cd23220    316 SFAIELAGYGKQVYTHIRDA 335

Pico_P1A

pfam02226

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

2-69

1.08e-21

Pssm-ID: 308053 Cd Length: 68 Bit Score: 90.51 E-value: 1.08e-21

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2099546876    2 GAQVSTQKSGSHENQNILTNGSNQTFTVINYYKDAASSSSAGQSFSMDPSKFTEPVKDLMLKGAPALN 69
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 68

Marnaviridae_RdRp

cd23195

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

1879-2101

1.32e-17

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: 85.96 E-value: 1.32e-17

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1879 KDELRSTDKvrlGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPgIITGSAVGCD---PDvfWSvipCLMDgHLMAF--- 1952
Cdd:cd23195      8 KDEPTKLTK---DKVRVFQAAPVALQLLVRKYFLPIARFLQMNP-LLSECAVGINaqsPE--WE---ELYE-HLTKFged 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1953 -----DYSNFDASLSPVW----FECLEKVLTKLGfKHSS--------LIQTICHTHHIFKDEIYVVEGGMPSGCSGTSIF 2015
Cdd:cd23195     78 riiagDYSKYDKRMSAQLilaaFKILIDIAAKSG-GYSEedlkimrgIATDIAYPLVDFNGDLIQFFGSNPSGHPLTVII 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2016 NSMINNIIIRTlvldAYKGIDLDKLK--------ILAYGDDLI--VSYPYEL-DPEVLATLGKKYGLTITPPDKTEKFSK 2084
Cdd:cd23195    157 NSIVNSLYMRY----AYYSLYPEKEVppfrdvvaLMTYGDDNImsVSPGYPWfNHTSIAEFLAKIGIKYTMADKEAESVP 232

                          250
                   ....*....|....*...
gi 2099546876 2085 -ITWDNLTFLKRYFRSDE 2101
Cdd:cd23195    233 fIHISEADFLKRKFVFDP 250

P3A

pfam08727

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

1434-1483

2.97e-17

Pssm-ID: 400873 Cd Length: 59 Bit Score: 77.47 E-value: 2.97e-17

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2099546876 1434 YKDLEIDICNTPPPECINDLLKSVDSEEVREYCKKKKWIIP-----QIPTNIDRA 1483
Cdd:pfam08727    5 GIDLKIDIKTSPPPEAIADLLQAVDSPEIIDYCEDKGWIVNipaecQIERDIGIA 59

Secoviridae_RdRp

cd23196

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

1953-2157

1.93e-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: 73.57 E-value: 1.93e-13

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1953 DYSNFDASLSPVWFECLEKVLTKL-GFKHSSLIQT-----ICHTHHIFKDEIYVVEGGMPSGCSGTSIFNSMINNIIIRT 2026
Cdd:cd23196     86 DYSRFDGLLSHQVYVWIADMINRLyGDGDEAKARRnllmmFCGRRSICGRQVYMVRGGMPSGCALTVIINSIFNEILIRY 165

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2027 lvldAYKGI-------DLDKL-KILAYGDDLIVSY-----PYeLDPEVLATLGKKYGLTITppDKTEKFSKI----TWDN 2089
Cdd:cd23196    166 ----VYRKVvprparnNFNKYvRLVVYGDDNLISVkeeiiPY-FDGPVIKKEMAKVGVTIT--DGTDKTSPTlerkPLES 238

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2099546876 2090 LTFLKRYFRsdEQFPFLVHPVMPMQDIYESIRWTKDPKNTQD-----HVRSLCMLAWHSGEKEYNDFTQKIRT 2157
Cdd:cd23196    239 LDFLKRGFR--VQSDGLVVAPLDKTSLYSRLHYVTAGGDGMYslyilNDNNKSFLEEHVDHPEFTEFRNRVVS 309

ps-ssRNAv_RdRp-like

cd23167

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

1948-2054

2.22e-10

Pssm-ID: 438017 [Multi-domain] Cd Length: 73 Bit Score: 58.50 E-value: 2.22e-10

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1948 HLMAFDYSNFDASLSPVWFEClekvltklgfkhssliqtichthhifkdeiyvvegGMPSGCSGTSIFNSMINNIIIRTL 2027
Cdd:cd23167      1 HVVESDYSGFDSSISPDLLKA-----------------------------------GQPSGSPNTSADNSLINLLLARLA 45

                           90       100
                   ....*....|....*....|....*...
gi 2099546876 2028 VLDAYKGIDLDK-LKILAYGDDLIVSYP 2054
Cdd:cd23167     46 LRKACGRAEFLNsVGILVYGDDSLVSVP 73

Iflaviridae_RdRp

cd23197

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

1873-2153

1.85e-09

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Iflaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Iflaviridae, order Picornavirales. Iflaviridae is a family of small non-enveloped viruses with (+)ssRNA genomes of approximately 9-11 kilobases in length encoding a single polyprotein. All members infect arthropod hosts with the majority infecting insects. Beneficial and pest insects serve as hosts and infections can be symptomless (Nilaparvata lugens honeydew virus 1), cause developmental abnormalities (deformed wing virus, Varroa destructor virus 1, sacbrood virus), behavioral changes (deformed wing virus, Varroa destructor virus 1, slow bee paralysis virus, sacbrood virus) and premature mortality (deformed wing virus, Varroa destructor virus 1, slow bee paralysis virus, infectious flacherie virus, sacbrood virus). RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438047 Cd Length: 319 Bit Score: 61.42 E-value: 1.85e-09

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1873 PLVTYIKDELRSTDKVR-LGKSRLIEASSLNDSVNMRMKLGNLYKAFHQNPgIITGSAVGCDPD-VFWS--VIPCLMDGH 1948
Cdd:cd23197      7 VYWAHLKDELRPSEKLRrFGGTRVFSVPPLELVLNSRRFLLPFMDAFQSFP-IEAHHAIGLNPNsGDWRrlRDTLLEKGP 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1949 -LMAFDYSNFDASLSpvwFECLEK---VLTKLGFKH-------SSLIQTICHTHH----IFKDEIYVVEGGMPSGCSGTS 2013
Cdd:cd23197     86 cLLQMDYKNYSDAIP---KECVAKafhIIVDYYRKWhcltveiENALKTLFLDTAdaelLVYGDVFKVNNGVLAGHPMTS 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2014 IFNSMINniiirtLVLDAYKGIDLDKLK---------ILAYGDDLIVSYPYELDPE----VLATLGKKYGLTITPPDKTE 2080
Cdd:cd23197    163 VVNSVVN------LILMNYMWIKITRRRaseffkltyIIVMGDDVVISLPKQLTEEfdcrKICAEFAKYDIKVTDSEKNL 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2081 KFSKITWDNL---TFLKRYFRSDEQFPFLVHPVMPMQDIYESIRW-TKDPKN---TQDHVRSLCMLAWHSGEKEYNDFTQ 2153
Cdd:cd23197    237 TGEPKPYDSFdkfEFLSRGFSDCDAYPDITFAPVKTIALFDCPLWiSKGQDEeeqTIQAIQAGLLLAFDHGPEFFGKYKQ 316

Polycipiviridae_RdRp

cd23198

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

1879-2155

1.96e-07

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: 55.11 E-value: 1.96e-07

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1879 KDELRSTDKVrLG------KSRLIEASSLNDSVNMRMKLGNLYKAFHQ--------NPGIitgSAVGcdPDvfWSVIPCL 1944
Cdd:cd23198      8 KDELRPIYKA-LGdpqtppKTRSVTCMNVYYILAWRRVTLDFWASMHRaadgnfpfCPGI---NPEG--PD--WNRLYHY 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1945 MDGHLMA--FDYSNFDASLSP-VWFECLEKVLTKLGFKHSS----LIQTI------CHTHhiFKDEIYVVEGGMPSGCSG 2011
Cdd:cd23198     80 LNRHPNAvdFDVSNWDGHLPAeLFYAVLDIIKTVLGLKPNSpnakVIYSIltevmnCHIQ--FEDIIYQKLRGLISGFPG 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2012 TSIFNSMINNIIIRTLVLDAYKGIDLDK--------LKILAYGDDLIVSYPYELDP----EVLATLGKKYGLTITPPDKT 2079
Cdd:cd23198    158 TAEVNTLAHWLLIYYIYLYLAQNTIYDMtitaflrnVSAIFYGDDIIITISDEILHwfngKTIQRMYEEHGYPVTSAAKD 237

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2080 EK--FSKITWDnLTFLKRYFRsdEQFPFLVHPVMPMQDIYESIRWTKDPKNTQDHVRSLCMLAWH----SGEKEYNDFTQ 2153
Cdd:cd23198    238 TEipESKPLSD-CQFLKSSWN--PILPGYYIRKMDIEVVYDLVYWVRAKEHPRDQFYSNYHDALRilfgHGEQVFEAFRE 314


                   ..
gi 2099546876 2154 KI 2155
Cdd:cd23198    315 QV 316

ps-ssRNAv_Nodaviridae_RdRp

cd23173

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

1953-2097

2.30e-07

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: 54.05 E-value: 2.30e-07

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1953 DYSNFDASLSPVWFECLEKVLTKLGFK----------HSSLIQTICHTHHIFKdeiYVVEGGMPSGCSGTSIFNSMINNI 2022
Cdd:cd23173     89 DYSRFDGTISEWLRRNVEFAAYLRWFHpeyraellklLDAEINCPARTKTGVK---YDPGVSRLSGSPTTTDGNTIINAF 165

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2023 I----IRTLVLD---AYKGIDldklkiLAYGDDLIVSYPYeldPEVLATLGKKYGLTItppdKTEKFSKitWDNLTFLKR 2095
Cdd:cd23173    166 VsycaLRETGYSpeeAFALLG------LYYGDDGLSDNLP---AEALEKVAKDLGLKL----KIEVVRP--GQPVTFLGR 230


                   ..
gi 2099546876 2096 YF 2097
Cdd:cd23173    231 VF 232

Calici_coat

pfam00915

Calicivirus coat protein;

428-554

5.29e-07

Calicivirus coat protein;

Pssm-ID: 459994 Cd Length: 291 Bit Score: 53.74 E-value: 5.29e-07

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876  428 LGEIAQYYTHWSGSLRISLMYTGPALSSAKLILAYTPPGAQgPTNRKDAMLGTHVVWDIGLQSTIIMTIPWTSGVQFRYT 507
Cdd:pfam00915   96 LLHLSQMYNGWSGGMRVRFMVAGSGVFGGKLAASVIPPGVE-PITSASMLQFPHVLFDARQLEPVIFTIPDLRNTLFHNM 174

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 2099546876  508 DPDTYTSAgyLSCWYQTSLILPPNTTGQVHLLSFISACP--DFKLRLMK 554
Cdd:pfam00915  175 DRNTDTTR--LVIMVYNPLINPGGTGDSSVCAVTVETRPspDFNFLLLK 221

Solinviviridae_RdRp

cd23199

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

1929-2156

6.86e-07

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: 53.51 E-value: 6.86e-07

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1929 AVGCDP-----DVFwsvIPCLMDGHLMAFDYSNFDAS----LSPVWFECLEKVLTKLGFKHSSLIQTICHTHHIFKDEIY 1999
Cdd:cd23199     72 AVGCNPyatfhKFA---TKFFKFKNFFSCDYKNFDRTipkcVFEDFRDMLIQANPHMKNEIYACFQTIIDRIQVSGNSIL 148

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2000 VVEGGMPSGCSGTSIFNSMINNI--------IIRTLVLDAYKGIDLDKLKI--LAYGDDLIVSYPYELDPEV-LATLGKK 2068
Cdd:cd23199    149 LVHGGMPSGCVPTAPLNSKVNDImiytayvnILRRADRGDITSYRYYRDLVcrLFYGDDVIIAVDDSIADIFnCQTLSEE 228

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2069 ----YGLTITPPDKTEKFSKI-TWDNLTFLKRYFRSDEQFPFLVHPVMPMQDIYESIRWTK--DPKNTQDHVRSLCMLAW 2141
Cdd:cd23199    229 mkilFGMNMTDGSKSDIIPKFeTIETLSFISRFFRPLKHQENFIVGALKKISIQTHFYYATddTPEHFGQVFKTIQEEAA 308

                          250
                   ....*....|....*
gi 2099546876 2142 HSGEKEYNDFTQKIR 2156
Cdd:cd23199    309 LWEEEYFNKIQSYIQ 323

ps-ssRNAv_Astroviridae_RdRp

cd23172

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

1952-2061

9.92e-07

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

Pssm-ID: 438022 Cd Length: 243 Bit Score: 52.09 E-value: 9.92e-07

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1952 FDYSNFDASLsPVW---------FECLEKVLTKLGFK-HSSLIQTICHTHHIFKD-EIYVVEGGMPSGCSGTSIFNSMIn 2020
Cdd:cd23172     85 FDWTRFDGTI-PAElfrhirklrWSFLDPEKTEENRKvYDWYVHNLLNRYVLLPTgEVTRVTKGNPSGQISTTMDNCMV- 162

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 2099546876 2021 NIIIRTLVLdAY----KGIDLDKL----KILAYGDDLIVSYPYELDPEV 2061
Cdd:cd23172    163 NTFLTAFEF-AYvygpKTGTLKELwdnyDTIVYGDDRLSGYPSLPDPYV 210

ps-ssRNAv_EoPV-like_RdRp

cd23171

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

1879-2098

2.94e-04

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

Pssm-ID: 438021 Cd Length: 239 Bit Score: 44.89 E-value: 2.94e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1879 KDELrstdkVRLGK-SRLIEASSLNDSVNMRMKLGNLYKAF-HQNPGIitgsAVGCD-PDVFWSVIPCLMDgHLMAFDYS 1955
Cdd:cd23171     21 KDEL-----LKPGKdTRLINGAPLHHTLDMRRYLMEFFAAItTINNKI----AVGIDvHSGDWALIHGGAD-DVVDEDYS 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1956 NFDASLSPVWFECLEKVLTKLGFKH-----------SSLIQTICHTHHIFKDEIYVVEGGMPSGCSGTSIFNSMINNIII 2024
Cdd:cd23171     91 GFGPGFHSQWLDVIRRIAVAWCKHHktvdpeyenvvRCLIRELQNAYHVAGDLVYQVLCGSPSGAFATDRINSLANLCYH 170

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2099546876 2025 RTLVLDAYKGI-DLDKLKILAYGDDLI---VSYPYELDPEVLATLgkkyGLTITPPDKTEKfskitwdnlTFLKRYFR 2098
Cdd:cd23171    171 CLCYLRKYGTLtGFWSHYLLVYGDDTRrreTAYTGDEFQDCMASI----GITVNRDKSGVT---------SFLKRQFI 235

dsRNAv_Picobirnaviridae_RdRp

cd23185

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

1953-2100

8.29e-04

catalytic core domain of RNA-dependent RNA polymerase (RdRp) of the family Picobirnaviridae of positive-sense double-stranded RNA [(+)dsRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Picobirnaviridae, order Durnavirales. Picobirnaviridae is a family of viruses with bi-segmented (rarely unsegmented) double-stranded RNA (dsRNA) genomes comprising about 4.4 kbp in total, with small, non-enveloped spherical virions. The family includes one genus (Picobirnavirus) grouping three genetic clusters with high sequence variability, two defined by viruses infecting vertebrates and a third with viruses found in invertebrates. Picobirnaviruses have been identified in feces of humans, rabbits, and a variety of other species of mammals, reptiles, birds, and invertebrates. The pathogenicity of picobirnaviruses has not been established; studies conducted with immunocompromised persons suggest that they are opportunistic pathogens that may cause diarrhea. A published phylogenetic tree constructed for RdRps of RNA viruses in the realm Riboviria, showed that picobirnaviruses are embedded in the branch of diverse (+)RNA viruses; sometimes they are collectively referred to as the picornavirus supergroup. The RdRp structure of double-stranded RNA picobirnavirus is highly homologous to the RdRp of (+)ssRNA 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: 438035 Cd Length: 444 Bit Score: 44.40 E-value: 8.29e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1953 DYSNFDASLSPVWFECLEKVLTKLGFK--HSSLIQTICHTHHI----FKDEIYVVEGGMPSGCSGT----SIFNsminni 2022
Cdd:cd23185    212 DFSKFDQHFNPDLQLAAFDVLKYLFQEqyWEWLDEVFPIKYNIplvySDGKIRTGKHGMGSGSGGTnfdeTLFH------ 285

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2023 iiRTLVLDAykGIDLDKLKIL---AYGDDLIVSYPYElDPEVLATLGKKYGLTITpPDKTEKfSKitwDNLTFLKRYFRS 2099
Cdd:cd23185    286 --RALQYEA--AIKNGSLLNPnsqCLGDDGVLSYPGI-TVEDVVRSYTSHGLEMN-PDKQYV-SK---DDCTYLQRWHHR 355


                   .
gi 2099546876 2100 D 2100
Cdd:cd23185    356 D 356

RVT_1

pfam00078

Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...

1948-2084

1.09e-03

Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.

Pssm-ID: 395031 [Multi-domain] Cd Length: 189 Bit Score: 42.29 E-value: 1.09e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1948 HLMAFDYSN-FDAslspVWFECLEKVLTKLGFKHSSLIQTICHTHHIFkdeiyvVEGGMPSGC-SGTSIFNSMINNIIIR 2025
Cdd:pfam00078   55 WFLKLDLKKaFDQ----VPLDELDRKLTAFTTPPININWNGELSGGRY------EWKGLPQGLvLSPALFQLFMNELLRP 124

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2099546876 2026 tlvLDAYKGIdldklKILAYGDDLIVSY--PYELD--PEVLATLGKKYGLTItPPDKTEKFSK 2084
Cdd:pfam00078  125 ---LRKRAGL-----TLVRYADDILIFSksEEEHQeaLEEVLEWLKESGLKI-NPEKTQFFLK 178

RdRP_4

pfam02123

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

1937-2075

5.88e-03

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: 41.68 E-value: 5.88e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1937 FWSVIPCLMDGH-LMAFDYSNFD-----ASLSPVwFECLEKVLTKlgFKHSSLIQTIC-----HTHHIFKDEIYVVEGGM 2005
Cdd:pfam02123  286 FDWSVQDWKRGGvSLMLDYDDFNsqhstESMRAV-FERLRRRLPD--EPAEAADWLVCsmdsmYQLSDGTLLAQRVPGTL 362

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 2006 PSGCSGTSIFNSMINNIIIRTLvldayKGIDLDKLKILAYGDDLIVSYPYELDPEVLATLGKKYGLTITP 2075
Cdd:pfam02123  363 KSGHRATTFINSVLNCAYAELA-----GAPWADVPTSIHMGDDVLEGLRTPADATSLLDKYARLGFKVNP 427

AAA

cd00009

The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...

1219-1349

6.76e-03

Pssm-ID: 99707 [Multi-domain] Cd Length: 151 Bit Score: 39.44 E-value: 6.76e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099546876 1219 QRTEPVCVLIHGTPGSGKSLTTSIVGRALAE------YFNSS----VYSLPPDPKHFDGYQQQE--------VVIMDDLN 1280
Cdd:cd00009     15 ELPPPKNLLLYGPPGTGKTTLARAIANELFRpgapflYLNASdlleGLVVAELFGHFLVRLLFElaekakpgVLFIDEID 94

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2099546876 1281 qnpdgqdiSMFCQMVSSVDFIppMANLDNKGMLFTSNFVLASTNSNTLSPPtilnPEALARRFGFDLDI 1349
Cdd:cd00009     95 --------SLSRGAQNALLRV--LETLNDLRIDRENVRVIGATNRPLLGDL----DRALYDRLDIRIVI 149

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