NCBI Conserved Domain Search

Conserved domains on [gi|2099547076|gb|UBI50869|]

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polyprotein [rhinovirus A20]

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 ...

1716-2166

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: 718.15 E-value: 0e+00

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1716 VKECNLYSIHTPSNTKLQPSVFHDIFPGSKEPAVLSCRDPRLEVDLDESIFSKYKGNESIEITQNMLTAAAHYTAQLSTL 1795
Cdd:cd23213      1 NKEVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1796 DINPKPLSLEESVYGIEGLEALDLHTSAGYPYTACGIKKKDLI-PKDKNLTKLKDAIEKYGLDLPMITFLKDELRKPEKI 1874
Cdd:cd23213     81 DIDTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILnKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKV 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1875 KTGKTRIIEASSLNDTVQFRMAFGNLFSKFHQNPGIVTGSAVGCDPEVFWSKIPVMLDGdCLMAFDYTNYDGSLNPVWFK 1954
Cdd:cd23213    161 EKGKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDG-SLFAFDYTGYDASLSPVWFR 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1955 LLSIVLNDLGFPGE--LVNKLCNSKHIYKTTYYEVEGGMPSGCAGTSIFNTIINNIIIRTLVLDAYKFINLDKLKILAYG 2032
Cdd:cd23213    240 ALKMVLEKGYSEEAvsLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYG 319

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2033 DDVIFSYPFDLDMKELAGEGIKYGLSITPADKSDTFRKLDYNNATFLKRGFKQDEKYGFLIHPIYPETEVWESIRWTKNP 2112
Cdd:cd23213    320 DDVIASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDP 399

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2099547076 2113 RNMQEHVLSLCHLMWHNGKDKYKHFVDKIRSVSAGRALYIPPYEVLLHEWYEKF 2166
Cdd:cd23213    400 RNTQDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453

Pico_P2A

pfam00947

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

882-1008

2.51e-65

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

Pssm-ID: 395757 Cd Length: 127 Bit Score: 217.25 E-value: 2.51e-65

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  882 NLHLCEPENLNDSTLICYSSDLVIYRTNTTGDDMIPTCDCTQATYYCKHKDRYYPINVKKHQWYEIQESEYYPKHIQYNI 961
Cdd:pfam00947    1 NRHLATHEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 2099547076  962 LIGEGPCEPGDCGGKLLCKHGVIGIVTAGGDNHVAFIDLRDFQVAEE 1008
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVRDLLWLEE 127

Rhv

pfam00073

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

93-301

1.70e-60

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: 205.24 E-value: 1.70e-60

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076   93 TSQDIANAVVGYGVWPQYLPPDDASAIDKPTHPDISSNRFYTLESKEWTGESKGW-WWKLPDALKNMGIFGENLFYHFLG 171
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFfWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  172 RAGYTVHVQCNASKFHQGTLIVAAIPEHQlayigkgsvtvgynhTHPGETgrmiggftnnnsrqpsdenwlncdgTLLGN 251
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPPGA---------------PPPGSR-------------------------DYLWQ 120

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 2099547076  252 ITIYPHQYINLRSNNSATLILPYVNAVPMDSMVRHNNWSIVIIPISKLQY 301
Cdd:pfam00073  121 ATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGNWTLVVAGWVPLNY 170

Peptidase_C3 super family

cl02893

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

1525-1690

5.28e-56

3C cysteine protease (picornain 3C); Picornaviral proteins are expressed as a single polyprotein which is cleaved by the viral 3C cysteine protease.

The actual alignment was detected with superfamily member pfam00548:

Pssm-ID: 278947 Cd Length: 174 Bit Score: 192.66 E-value: 5.28e-56

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1525 GPQEEFGRSLIKHNTCVVTTDNGKFTGL--GIYDNIMIIPTHADTGKEVEIDGIKTQVDD-AYDLHNSQGIKLEITVLKL 1601
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1602 HRNEKFRDIRKYIPETEDDYPECHLALVANQQEPTILEVGDCCSYGNI-LLSGNQTARMIKYNYPTKSGFCGGVLYKI-- 1678
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVVIAKve 160

                          170
                   ....*....|....
gi 2099547076 1679 --GLVLGIHVGGNG 1690
Cdd:pfam00548  161 gnGKILGMHIAGNG 174

Rhv

pfam00073

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

359-524

4.83e-50

Pssm-ID: 395026 Cd Length: 170 Bit Score: 175.19 E-value: 4.83e-50

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  359 FHPTKEIFIPGKVNNLSEICQVDSMIPINNTIAAKNTTGMYTVRVSQQTQPAQEIFSILVDVASQpiATTLIGEIASYYT 438
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFFWWKLPLALL--SMGLLGRLLRYHT 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  439 HWTGSLRFSFMFCGTANTSLKLLIAYTPPGVPKPENRQK---AMLSTHVVWDVGLQSTVSMVVPWVSASHYRYTTPD--- 512
Cdd:pfam00073   79 YYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRDYlwqATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDgnw 158

                          170
                   ....*....|..
gi 2099547076  513 TYSQAGYITCWY 524
Cdd:pfam00073  159 TLVVAGWVPLNY 170

Rhv

pfam00073

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

616-779

1.05e-45

Pssm-ID: 395026 Cd Length: 170 Bit Score: 162.87 E-value: 1.05e-45

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  616 PEDMVETRYVITDQTRDEMSVESFLGRSGCiaiihTDLDHEAEQY--------NAPGKNFSQWKITI--KEMAQIRRKCE 685
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAP-----VQPDVQGERFytldstdwTSLSKGFFWWKLPLalLSMGLLGRLLR 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  686 LFTYLRFDSEITIVATvaalGQDNGHVVLQYMYVPPGAPIPKTRDdYTWQSGTNASVFWQQG-QPYPRFTIPFMSIASAY 764
Cdd:pfam00073   76 YHTYYRGGLEVTVQFN----GSKFHQGKLLVAYVPPGAPPPGSRD-YLWQATLNPHQFWNLGlNSSARLSVPYISIAHYY 150

                          170
                   ....*....|....*
gi 2099547076  765 YMFYDGYEDDKGSVY 779
Cdd:pfam00073  151 STFYDGNWTLVVAGW 165

Pico_P2B super family

cl03260

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

1009-1105

1.13e-42

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: 151.71 E-value: 1.13e-42

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1009 QGISDYVHTLGEAFGAGFV----DNIKEQIQTINPINKITSKIVKWTIRIVSAITIIIRNNADPHTIVATLALLGCSGSP 1084
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTqqisDKIKELTNFINPTSKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|.
gi 2099547076 1085 WRFIKEKVCNWLQLVYVHKES 1105
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

5.08e-40

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

Pssm-ID: 308053 Cd Length: 68 Bit Score: 142.90 E-value: 5.08e-40

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2099547076    2 GAQVSRQNVGTHSTQNTVSNGSSLNYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLMKDIPTLQ 69
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 68

RNA_helicase

pfam00910

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

1224-1320

7.33e-39

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

Pssm-ID: 459992 Cd Length: 102 Bit Score: 140.82 E-value: 7.33e-39

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1224 VIFHGEPGTGKSITTSILARML-----TTESDIYSLPPSPKYFDGYDQQSVVIMDDIMQNPSGEDMSLFCQMVSSVPFIP 1298
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALlkklgLPKDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 2099547076 1299 PMADLPDKGKPFSSDYVLASTN 1320
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

P3A super family

cl07374

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

1422-1475

1.45e-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: 78.62 E-value: 1.45e-17

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2099547076 1422 AIFQG---PIDVVNKPPPPAIIDLLKSVRSPDVIKYCEENKWIV--PSDCKLERDLNYA 1475
Cdd:pfam08727    1 AIFQGidlKIDIKTSPPPEAIADLLQAVDSPEIIDYCEDKGWIVniPAECQIERDIGIA 59

SpoVK super family

cl33891

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...

1200-1245

5.93e-03

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];

The actual alignment was detected with superfamily member COG0464:

Pssm-ID: 440232 [Multi-domain] Cd Length: 397 Bit Score: 41.44 E-value: 5.93e-03

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 2099547076 1200 KRIKELLKRSQMILRTSKRTEPVGVIFHGEPGTGKSITTSILARML 1245
Cdd:COG0464    170 RELVALPLKRPELREEYGLPPPRGLLLYGPPGTGKTLLARALAGEL 215

Name

Accession

Description

Interval

E-value

Enterovirus_RdRp

cd23213

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

1716-2166

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: 718.15 E-value: 0e+00

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1716 VKECNLYSIHTPSNTKLQPSVFHDIFPGSKEPAVLSCRDPRLEVDLDESIFSKYKGNESIEITQNMLTAAAHYTAQLSTL 1795
Cdd:cd23213      1 NKEVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1796 DINPKPLSLEESVYGIEGLEALDLHTSAGYPYTACGIKKKDLI-PKDKNLTKLKDAIEKYGLDLPMITFLKDELRKPEKI 1874
Cdd:cd23213     81 DIDTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILnKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKV 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1875 KTGKTRIIEASSLNDTVQFRMAFGNLFSKFHQNPGIVTGSAVGCDPEVFWSKIPVMLDGdCLMAFDYTNYDGSLNPVWFK 1954
Cdd:cd23213    161 EKGKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDG-SLFAFDYTGYDASLSPVWFR 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1955 LLSIVLNDLGFPGE--LVNKLCNSKHIYKTTYYEVEGGMPSGCAGTSIFNTIINNIIIRTLVLDAYKFINLDKLKILAYG 2032
Cdd:cd23213    240 ALKMVLEKGYSEEAvsLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYG 319

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2033 DDVIFSYPFDLDMKELAGEGIKYGLSITPADKSDTFRKLDYNNATFLKRGFKQDEKYGFLIHPIYPETEVWESIRWTKNP 2112
Cdd:cd23213    320 DDVIASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDP 399

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2099547076 2113 RNMQEHVLSLCHLMWHNGKDKYKHFVDKIRSVSAGRALYIPPYEVLLHEWYEKF 2166
Cdd:cd23213    400 RNTQDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453

Pico_P2A

pfam00947

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

882-1008

2.51e-65

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

Pssm-ID: 395757 Cd Length: 127 Bit Score: 217.25 E-value: 2.51e-65

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  882 NLHLCEPENLNDSTLICYSSDLVIYRTNTTGDDMIPTCDCTQATYYCKHKDRYYPINVKKHQWYEIQESEYYPKHIQYNI 961
Cdd:pfam00947    1 NRHLATHEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 2099547076  962 LIGEGPCEPGDCGGKLLCKHGVIGIVTAGGDNHVAFIDLRDFQVAEE 1008
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVRDLLWLEE 127

Rhv

pfam00073

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

93-301

1.70e-60

Pssm-ID: 395026 Cd Length: 170 Bit Score: 205.24 E-value: 1.70e-60

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076   93 TSQDIANAVVGYGVWPQYLPPDDASAIDKPTHPDISSNRFYTLESKEWTGESKGW-WWKLPDALKNMGIFGENLFYHFLG 171
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFfWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  172 RAGYTVHVQCNASKFHQGTLIVAAIPEHQlayigkgsvtvgynhTHPGETgrmiggftnnnsrqpsdenwlncdgTLLGN 251
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPPGA---------------PPPGSR-------------------------DYLWQ 120

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 2099547076  252 ITIYPHQYINLRSNNSATLILPYVNAVPMDSMVRHNNWSIVIIPISKLQY 301
Cdd:pfam00073  121 ATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGNWTLVVAGWVPLNY 170

Peptidase_C3

pfam00548

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

1525-1690

5.28e-56

3C cysteine protease (picornain 3C); Picornaviral proteins are expressed as a single polyprotein which is cleaved by the viral 3C cysteine protease.

Pssm-ID: 278947 Cd Length: 174 Bit Score: 192.66 E-value: 5.28e-56

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1525 GPQEEFGRSLIKHNTCVVTTDNGKFTGL--GIYDNIMIIPTHADTGKEVEIDGIKTQVDD-AYDLHNSQGIKLEITVLKL 1601
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1602 HRNEKFRDIRKYIPETEDDYPECHLALVANQQEPTILEVGDCCSYGNI-LLSGNQTARMIKYNYPTKSGFCGGVLYKI-- 1678
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVVIAKve 160

                          170
                   ....*....|....
gi 2099547076 1679 --GLVLGIHVGGNG 1690
Cdd:pfam00548  161 gnGKILGMHIAGNG 174

Rhv

pfam00073

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

359-524

4.83e-50

Pssm-ID: 395026 Cd Length: 170 Bit Score: 175.19 E-value: 4.83e-50

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  359 FHPTKEIFIPGKVNNLSEICQVDSMIPINNTIAAKNTTGMYTVRVSQQTQPAQEIFSILVDVASQpiATTLIGEIASYYT 438
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFFWWKLPLALL--SMGLLGRLLRYHT 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  439 HWTGSLRFSFMFCGTANTSLKLLIAYTPPGVPKPENRQK---AMLSTHVVWDVGLQSTVSMVVPWVSASHYRYTTPD--- 512
Cdd:pfam00073   79 YYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRDYlwqATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDgnw 158

                          170
                   ....*....|..
gi 2099547076  513 TYSQAGYITCWY 524
Cdd:pfam00073  159 TLVVAGWVPLNY 170

Rhv

pfam00073

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

616-779

1.05e-45

Pssm-ID: 395026 Cd Length: 170 Bit Score: 162.87 E-value: 1.05e-45

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  616 PEDMVETRYVITDQTRDEMSVESFLGRSGCiaiihTDLDHEAEQY--------NAPGKNFSQWKITI--KEMAQIRRKCE 685
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAP-----VQPDVQGERFytldstdwTSLSKGFFWWKLPLalLSMGLLGRLLR 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  686 LFTYLRFDSEITIVATvaalGQDNGHVVLQYMYVPPGAPIPKTRDdYTWQSGTNASVFWQQG-QPYPRFTIPFMSIASAY 764
Cdd:pfam00073   76 YHTYYRGGLEVTVQFN----GSKFHQGKLLVAYVPPGAPPPGSRD-YLWQATLNPHQFWNLGlNSSARLSVPYISIAHYY 150

                          170
                   ....*....|....*
gi 2099547076  765 YMFYDGYEDDKGSVY 779
Cdd:pfam00073  151 STFYDGNWTLVVAGW 165

RdRP_1

pfam00680

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

1734-2143

4.95e-45

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: 170.67 E-value: 4.95e-45

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1734 PSVFHDIFPGSKEPAVLSCRDPR-------LEVDLDESIFSKY-KGNESIEITQNML--TAAAHYTAQLSTLDINPKPLS 1803
Cdd:pfam00680    2 PTERHLVAIPAYVPASLGPEDPRwarsylnTDPYVDDIKKYSRpKLPGPADERDKLLnrSAAKMVLSELRGVPKKANSTL 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1804 LEESVY-GIEGLEALDLHTSAGYPYTACGIKKKDLIPKDKNLT-------KLKDAIEKYGLDLPM----ITFLKDELRKP 1871
Cdd:pfam00680   82 IVYRAIdGVEQIDPLNWDTSAGYPYVGLGGKKGDLIEHLKDGTearelaeRLAADWEVLQNGTPLklvyQTCLKDELRPL 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1872 EKIKTGKTRIIEASSLNDTVQFRMAFGNLFSKFHQNPGIVTgSAVGCDPevFWSKIPVMLD-----GDCLMAFDYTNYDG 1946
Cdd:pfam00680  162 EKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHP-IQVGINP--FDRGWPRLLRrlarfGDYVYELDYSGFDS 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1947 SLNPVWFKLLSIVLNDL-GFP------GELVNKLCNSKH-IYKTTYYEVEGGMPSGCAGTSIFNTIINNIIIRTLVL--- 2015
Cdd:pfam00680  239 SVPPWLIRFAFEILRELlGFPsnvkewRAILELLIYTPIaLPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYALLksl 318

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2016 --DAYKFINLDKLKILA-YGDDVIF--SYPFDLDMKELAGEGIKYGLSITPADKSDTFRKlDYNNATFLKRGFKQDEkyg 2090
Cdd:pfam00680  319 enDGPRVCNLDKYFDFFtYGDDSLVavSPDFDPVLDRLSPHLKELGLTITPAKKTFPVSR-ELEEVSFLKRTFRKTP--- 394

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2099547076 2091 FLIHPIYPETEVWESIRWTKNPRNMQEHVLSLCHLMWHNGKDKYKHFVDKIRS 2143
Cdd:pfam00680  395 GGYRPPLDRKRILAQLEYIRSKPVPSGQLENIRAYASHHGYEFYRDLLYRFVE 447

rhv_like

cd00205

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

374-559

3.11e-43

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

Pssm-ID: 119412 Cd Length: 178 Bit Score: 156.02 E-value: 3.11e-43

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  374 LSEICQVDSMIPINNTIAAKNTTGMYTVRVSQQtqpaqeifsilvdVASQPIATTLIGEIASYYTHWTGSLRFSFMFCGT 453
Cdd:cd00205      1 VESFADRPTTVGTNNWNSSASGTQLFQWKLSPA-------------LGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGS 67

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  454 ANTSLKLLIAYTPPGVPKPEN---RQKAMLSTHVVWDVGLQSTVSMVVPWVSASHYRYTTPDTYSQA---GYITCWYQTN 527
Cdd:cd00205     68 KFHTGRLLVAYVPPGAPAPTTgdtRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDGYGPLnsfGTLVVRVLTP 147

                          170       180       190
                   ....*....|....*....|....*....|..
gi 2099547076  528 FIVPPNTPREADIICFVSGcKDFCLRMARDTN 559
Cdd:cd00205    148 LTVPSGAPTTVDITVYVRA-GDFELYGPRPPR 178

Pico_P2B

pfam01552

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

1009-1105

1.13e-42

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: 151.71 E-value: 1.13e-42

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1009 QGISDYVHTLGEAFGAGFV----DNIKEQIQTINPINKITSKIVKWTIRIVSAITIIIRNNADPHTIVATLALLGCSGSP 1084
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTqqisDKIKELTNFINPTSKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|.
gi 2099547076 1085 WRFIKEKVCNWLQLVYVHKES 1105
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

5.08e-40

Pssm-ID: 308053 Cd Length: 68 Bit Score: 142.90 E-value: 5.08e-40

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2099547076    2 GAQVSRQNVGTHSTQNTVSNGSSLNYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLMKDIPTLQ 69
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 68

RNA_helicase

pfam00910

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

1224-1320

7.33e-39

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

Pssm-ID: 459992 Cd Length: 102 Bit Score: 140.82 E-value: 7.33e-39

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1224 VIFHGEPGTGKSITTSILARML-----TTESDIYSLPPSPKYFDGYDQQSVVIMDDIMQNPSGEDMSLFCQMVSSVPFIP 1298
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALlkklgLPKDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 2099547076 1299 PMADLPDKGKPFSSDYVLASTN 1320
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

rhv_like

cd00205

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

636-825

3.22e-37

Pssm-ID: 119412 Cd Length: 178 Bit Score: 139.07 E-value: 3.22e-37

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  636 VESFLGRSGCIAIIHTDldheaeqYNAPGKNFSQWKIT------IKEMAQIRRKCELFTYLRFDSEITIVATvaalGQDN 709
Cdd:cd00205      1 VESFADRPTTVGTNNWN-------SSASGTQLFQWKLSpalgflLLQNTPLGALLSYFTYWRGDLEVTVQFN----GSKF 69

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  710 GHVVLQYMYVPPGAPIPKTrDDYTWQSGTNASVFWQ-QGQPYPRFTIPFMSIASAYYMFYDGYEddkgsvygsvVTNDMG 788
Cdd:cd00205     70 HTGRLLVAYVPPGAPAPTT-GDTRWQATLNPHVIWDlGTNSSVTFVVPYVSPTPYRSTRYDGYG----------PLNSFG 138

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 2099547076  789 TLCVRIVTEQQ-----THKVKITsrIFHKAKHISAWCPRAPR 825
Cdd:cd00205    139 TLVVRVLTPLTvpsgaPTTVDIT--VYVRAGDFELYGPRPPR 178

rhv_like

cd00205

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

129-329

2.45e-35

Pssm-ID: 119412 Cd Length: 178 Bit Score: 133.68 E-value: 2.45e-35

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  129 SNRFYTLESKEWTG---ESKGWWWKLPDA----LKNMGIFGENLFYHFLGRAGYTVHVQCNASKFHQGTLIVAAIPEHQL 201
Cdd:cd00205      5 ADRPTTVGTNNWNSsasGTQLFQWKLSPAlgflLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPPGAP 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  202 AYIgkgsvtvgynhthpgetgrmiggftnnnsrqpsdenwlncDGTLLGNITIYPHQYINLRSNNSATLILPYVNAVPMD 281
Cdd:cd00205     85 APT----------------------------------------TGDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYR 124

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2099547076  282 SMVRH------NNWSIVIIPISKLQYETGATPYVPITLSISPMCSEFSGARNNT 329
Cdd:cd00205    125 STRYDgygplnSFGTLVVRVLTPLTVPSGAPTTVDITVYVRAGDFELYGPRPPR 178

P3A

pfam08727

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

1422-1475

1.45e-17

Pssm-ID: 400873 Cd Length: 59 Bit Score: 78.62 E-value: 1.45e-17

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2099547076 1422 AIFQG---PIDVVNKPPPPAIIDLLKSVRSPDVIKYCEENKWIV--PSDCKLERDLNYA 1475
Cdd:pfam08727    1 AIFQGidlKIDIKTSPPPEAIADLLQAVDSPEIIDYCEDKGWIVniPAECQIERDIGIA 59

SpoVK

COG0464

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...

1200-1245

5.93e-03

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];

Pssm-ID: 440232 [Multi-domain] Cd Length: 397 Bit Score: 41.44 E-value: 5.93e-03

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 2099547076 1200 KRIKELLKRSQMILRTSKRTEPVGVIFHGEPGTGKSITTSILARML 1245
Cdd:COG0464    170 RELVALPLKRPELREEYGLPPPRGLLLYGPPGTGKTLLARALAGEL 215

RecA-like_protease

cd19481

proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...

1200-1245

9.02e-03

proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

Pssm-ID: 410889 [Multi-domain] Cd Length: 158 Bit Score: 39.19 E-value: 9.02e-03

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 2099547076 1200 KRIKELLK--RSQMILRTSKRTEPVGVIFHGEPGTGKSITTSILARML 1245
Cdd:cd19481      3 ASLREAVEapRRGSRLRRYGLGLPKGILLYGPPGTGKTLLAKALAGEL 50

Name

Accession

Description

Interval

E-value

Enterovirus_RdRp

cd23213

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

1716-2166

0e+00

Pssm-ID: 438063 Cd Length: 453 Bit Score: 718.15 E-value: 0e+00

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1716 VKECNLYSIHTPSNTKLQPSVFHDIFPGSKEPAVLSCRDPRLEVDLDESIFSKYKGNESIEITQNMLTAAAHYTAQLSTL 1795
Cdd:cd23213      1 NKEVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1796 DINPKPLSLEESVYGIEGLEALDLHTSAGYPYTACGIKKKDLI-PKDKNLTKLKDAIEKYGLDLPMITFLKDELRKPEKI 1874
Cdd:cd23213     81 DIDTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILnKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKV 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1875 KTGKTRIIEASSLNDTVQFRMAFGNLFSKFHQNPGIVTGSAVGCDPEVFWSKIPVMLDGdCLMAFDYTNYDGSLNPVWFK 1954
Cdd:cd23213    161 EKGKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDG-SLFAFDYTGYDASLSPVWFR 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1955 LLSIVLNDLGFPGE--LVNKLCNSKHIYKTTYYEVEGGMPSGCAGTSIFNTIINNIIIRTLVLDAYKFINLDKLKILAYG 2032
Cdd:cd23213    240 ALKMVLEKGYSEEAvsLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYG 319

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2033 DDVIFSYPFDLDMKELAGEGIKYGLSITPADKSDTFRKLDYNNATFLKRGFKQDEKYGFLIHPIYPETEVWESIRWTKNP 2112
Cdd:cd23213    320 DDVIASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDP 399

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2099547076 2113 RNMQEHVLSLCHLMWHNGKDKYKHFVDKIRSVSAGRALYIPPYEVLLHEWYEKF 2166
Cdd:cd23213    400 RNTQDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453

Sapelovirus_RdRp

cd23218

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

1808-2166

5.63e-150

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: 469.00 E-value: 5.63e-150

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1808 VYGIEGLEALDLHTSAGYPYTACGIKKKDLIP-KDKNLTKLKDAIEKYGLDLPMITFLKDELRKPEKIKTGKTRIIEASS 1886
Cdd:cd23218      3 VYGIDNLEGLDLNTSAGYPYNTMGIRKKDLIPpRGEPLSPLLKALDLHGYDLPFTTYLKDELRPKEKVKMGKTRLIECSS 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1887 LNDTVQFRMAFGNLFSKFHQNPGIVTGSAVGCDPEVFWSKIPVMLDGDCLMAFDYTNYDGSLNPVWFKLLSIVLNDLGFP 1966
Cdd:cd23218     83 LNDTIRMKRIFGRLFQTFHKNPGTYTGSAVGCNPDVHWSKFAEEGGMDNVCAFDYTNWDASLSPFWFDALKLFLSKLGYS 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1967 GE---LVNKLCNSKHIYKTTYYEVEGGMPSGCAGTSIFNTIINNIIIRTLVLDAYKFINLDKLKILAYGDDVIFSYPFDL 2043
Cdd:cd23218    163 ERdivLIDHLCYSNHIFKNEGYKVAGGMPSGCSGTSIFNSIINNIVVRTLVLLVYKGINLDELRILCYGDDLLVAYPYPL 242

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2044 DMKELAGEGIKYGLSITPADKSDTF---RKLdyNNATFLKRGFKQDEKYGFLIHPIYPETEVWESIRWTKNPRNMQEHVL 2120
Cdd:cd23218    243 DPNVLADLGKSLGLTMTPADKSDTFqgcTKL--TEVTFLKRSFVFDEEFPFLCHPVFPMEEVHESIRWTRNASTTQEHVT 320

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*.
gi 2099547076 2121 SLCHLMWHNGKDKYKHFVDKIRSVSAGRALYIPPYEVLLHEWYEKF 2166
Cdd:cd23218    321 SLCLLAWHNGEEVYEEFCEKIRSVPVGRALILPPYSQLRRSWLDMF 366

Rabovirus_RdRp

cd23230

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

1807-2166

2.73e-144

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: 453.19 E-value: 2.73e-144

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1807 SVYGIEGLEALDLHTSAGYPYTACGIKKKDLI-PKDKNLTKLKDAIEKYGLDLPMITFLKDELRKPEKIKTGKTRIIEAS 1885
Cdd:cd23230      1 AAYGIENLEGLDLNTSAGYPYVLNGIKKRDILdPETRDTTKLQECLDKYGVDLPFVTYLKDELRPLEKIKKGKTRLIECS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1886 SLNDTVQFRMAFGNLFSKFHQNPGIVTGSAVGCDPEVFWSKIPVMLDGDcLMAFDYTNYDGSLNPVWFKLLSIVLNDLGF 1965
Cdd:cd23230     81 SMNDTIRMKMMFGRLFATYHRNPGPITGSAVGCNPDIHWTKFRAEMHGE-IIAFDYSNYDASLNKVWFECLKMVLKNFGF 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1966 PgEL--VNKLCNSKHIYKTTYYEVEGGMPSGCAGTSIFNTIINNIIIRTLVLDAYKFINLDKLKILAYGDDVIFSYPFDL 2043
Cdd:cd23230    160 K-DLrpIDHIIRSRHIYKGIEYDVEGGMPSGCSGTSIFNSIINNIIIMTLVLDAYKGIDLEQLKIIAYGDDVIVTYPYPL 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2044 DMKELAGEGIKYGLSITPADKSDTFRKLDYNNATFLKRGFKQDEKYGFLIHPIYPETEVWESIRWTKNPRNMQEHVLSLC 2123
Cdd:cd23230    239 DAALLADCGKKYGLKMTPPDKSAEFKNVTWEDVTFLKRRFKPAKHYPFLIHPVFDQQEILESLRWTRNPAHTQEHVRSLA 318

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|...
gi 2099547076 2124 HLMWHNGKDKYKHFVDKIRSVSAGRALYIPPYEVLLHEWYEKF 2166
Cdd:cd23230    319 ELAWHSGRKSYEEFCNLVKSTNVGKACILPPYESFKRMWLDQF 361

ps-ssRNA_Picornaviridae

cd23193

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

1808-2142

1.26e-119

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: 382.28 E-value: 1.26e-119

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1808 VYGIEGLEALDLHTSAGYPYTACGIKKKDLIPKDKNLT------KLKDAIEKYGLDLPMITFLKDELRKPEKIKTGKTRI 1881
Cdd:cd23193      2 INGIDGLDPIDLNTSPGYPYTTQGLRRRDLIDNDKGGVsplleeEEQVLLDLDGPDVVFTTFLKDELRPKEKVKAGKTRV 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1882 IEASSLNDTVQFRMAFGNLFSKFHQNPGIVTGSAVGCDPEVFWSKIPVMLDGDCLMAFDYTNYDGSLNPVWFKLLSIVL- 1960
Cdd:cd23193     82 IEAAPLDYVIAGRMVFGRLFAQFHSNPGILTGSAVGCNPDTDWTRLFASLKQDNVYDLDYSGFDASLSSQLFEAAVEVLa 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1961 NDLGFPGELVN---KLCNSKHIYKTTYYEVEGGMPSGCAGTSIFNTIINNIIIRTLVLDAYKFiNLDKLKILAYGDDVIF 2037
Cdd:cd23193    162 ECHGDPELVLRylePIINSKHVVGDERYTVEGGMPSGCPCTSILNSICNNLVVRYALLETGKF-DPDEYYILAYGDDVLV 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2038 SYPFDLDMKELAGEGIKY-GLSITPADKSDTFRKLDYNNATFLKRGFKQDEKYgFLIHPIYPETEVWESIRWTKNPRNMQ 2116
Cdd:cd23193    241 STDEPIDPSDLAEFYKKYfGMTVTPADKSSDFPESSPIEDVFLKRRFFVPDGT-FLIHPVMDLETLEQSLMWCGRGGFFQ 319

                          330       340
                   ....*....|....*....|....*.
gi 2099547076 2117 EHVLSLCHLMWHNGKDKYKHFVDKIR 2142
Cdd:cd23193    320 QLLSSLCELALHHGPEEYERLVSKVR 345

Cosavirus_RdRp

cd23226

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

1724-2166

3.97e-72

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: 249.93 E-value: 3.97e-72

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1724 IHTPSNTKLQPSvfHDIFPGSKE--PAVLSCRDPRLE--VDLDESIFSKYKGNESIE----ITQNMLTAAAHYTAQLSTL 1795
Cdd:cd23226     12 VHVPRQSKLKRT--NATYPATGKygPAVLSKNDPRLDpdVDFDKVIFSKHVANVVIDedtsFWNALKMSAQIYAEKFKGV 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1796 DINPkpLSLEESVYGIEGLEALDLHTSAGYPYTACGIKKKDLIPK---DKNL-TKLKDAIEKYGLDLPMITFLKDELRKP 1871
Cdd:cd23226     90 DFSP--LTVEEAILGIPGLDRMDPNTASGLPYTKTRRQMIDFQEGkilDPELqERLDTWLSGKQPEMLYQTFLKDEIRPI 167

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1872 EKIKTGKTRIIEASSLNDTVQFRMAFGNLFSKFHQNPGIVTGSAVGCDPEVFWSKIPVMLDG-DCLMAFDYTNYDGSLNP 1950
Cdd:cd23226    168 EKVKAGKTRIIDVTPLDHVLAFRIVLGRFMAHFHNNYGFELGSAVGCDPDVAWANFGFALSSkKYQYDFDYSNFDASHSE 247

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1951 VWFKLLS--IVLNDLGFPGE---LVNKLCNSKHIYKTTYYEVEGGMPSGCAGTSIFNTIINNIIIRTLVLDAYKFINLDK 2025
Cdd:cd23226    248 SIFELLKqfVFTKDNGFDHRcslMIDSLVTSTHCYEDQRMTIRGGLPSGTSGTSVINTIINNIIFKAALYHTYSNFEWDD 327

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2026 LKILAYGDDVIFSYPFDLDMKELAGEGIKYGLSITPADKSDTFRKLDYNNATFLKRGFKqdeKYGFLIHPIYPETEVWES 2105
Cdd:cd23226    328 VQMLAYGDDIVAASDCLLDLDRVKYFMALIGYKITPADKGEKFIPKDMQNIQFLKRSFR---KVAGVWAPIMDLENLQAM 404

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2099547076 2106 IRWTKnPRNMQEHVLSLCHLMWHNGKDKYKHFVDKIrsVSAGraLYIPPYEVLLHEWYEKF 2166
Cdd:cd23226    405 LSWYK-PGTLQEKLDSVARLAHFCGEKVYDHLFTTF--VKDG--FQIKPWKQLHFEWLNRF 460

Aphthovirus_RdRp

cd23210

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

1724-2165

2.10e-71

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: 247.94 E-value: 2.10e-71

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1724 IHTPSNTKLQPSVFHDIFPGSKEPAVLSCRDPRLE--VDLDESIFSKYKGNESI--EITQNMLTAAAHYTAQL-STLDIN 1798
Cdd:cd23210      6 VHVMRKTKLAPTVAHGVFNPEFGPAALSNKDPRLNegVVLDEVIFSKHKGDTKMsaEDKALFRRCAADYASRLhSVLGTA 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1799 PKPLSLEESVYGIEGLEALDLHTSAGYPYTACGIKKKDLIPKDKNLTK-----LKDAIEKYGLDLPMITFLKDELRKPEK 1873
Cdd:cd23210     86 NAPLSIYEAIKGVDGLDAMEPDTAPGLPWALQGKRRGALIDFENGTVGpeveaALKLMEKREYKFACQTFLKDEIRPMEK 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1874 IKTGKTRIIEASSLNDTVQFRMAFGNLFSKFHQNPGIVTGSAVGCDPEVFWSKIPVMLDG-DCLMAFDYTNYDGSLNPvw 1952
Cdd:cd23210    166 VRAGKTRIVDVLPVEHILYTRMMIGRFCAQMHSNNGPQIGSAVGCNPDVDWQRFGTHFAQyRNVWDVDYSAFDANHCS-- 243

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1953 fKLLSIVLN-----DLGF-PGE--LVNKLCNSKHIYKTTYYEVEGGMPSGCAGTSIFNTIINNIIIRTLVLDAYKFINLD 2024
Cdd:cd23210    244 -DAMNIMFEevfrtEFGFhPNAewILKTLVNTEHAYENKRITVEGGMPSGCSATSIINTILNNIYVLYALRRHYEGVELD 322

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2025 KLKILAYGDDVIFSYPFDLDMKELAGEGIKYGLSITPADKSDTFRKLDY--NNATFLKRGFKQDEKYGFLiHPIYpETEV 2102
Cdd:cd23210    323 TYTMISYGDDIVVASDYDLDFEALKPHFKSLGQTITPADKSDKGFVLGHsiTDVTFLKRHFHMDYGTGFY-KPVM-ASKT 400

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2099547076 2103 WESIRWTKNPRNMQEHVLSLCHLMWHNGKDKYKHFVDKIRSVsagraLYIPPYEVLLHEWYEK 2165
Cdd:cd23210    401 LEAILSFARRGTIQEKLISVAGLAVHSGPDEYRRLFEPFQGL-----FEIPSYRSLYLRWVNA 458

Dicipivirus_RdRp

cd23222

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

1733-2162

1.34e-70

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: 245.27 E-value: 1.34e-70

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1733 QPSVFHDIFPGSKEPAVLSCRDPRL--EVDLDESIFSKYKGNESiEITQNMLTAAAHYTAQLSTLDINPK-PLSL-EESV 1808
Cdd:cd23222      1 KPSPVYGVYPVTKEPAPLKPTDRRIdeGVDFNEPVFGKYGADMK-EPFRNLDVGRDVVIARLKKVLPNKKfAPCTvSEAL 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1809 YGIEGLEALDLHTSAGYPYTACGIKKKDLIPKDKN-----LTKLKDAIE---KYGLDLPMITFLKDELRKPEKIKTGKTR 1880
Cdd:cd23222     80 NGKDGLPKLDLKQASGYPYNLSAIKRKHLIESDKDgfltaTPKLLADIEeskKHPEKFPYTSFLKDELRSVKKVKAGKTR 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1881 IIEASSLNDTVQFRMAFGNLFSKFHQNPGIVTGSAVGCDPEVFWSKI-PVMLDGDCLMAFDYTNYDGSLNPVWFKLLSIV 1959
Cdd:cd23222    160 VVEAGSLPVIVEGRMIFGNLFAYFNTHPGFETMAAVGCDPEVCWTDWyYKMREKAHTWDYDYTGFDGSIPSCSFDALADL 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1960 LNDLgFPGE-----LVNKLCNSKHIYKTTYYEVEGGMPSGCAGTSIFNTIINNiiirTLVLDAYKFI--NLDKLK--ILA 2030
Cdd:cd23222    240 LCEF-VENEddvrrYISNIKNSYHAYDGNLYLIEGAMPSGCAGTSVFNCLINA----MLCFSCFMDLepEMDPFEplLIA 314

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2031 YGDDVIFSYPFDLDMKELAgEGIKYG--LSITPADKSDTFR-KLDYNNATFLKRGFKQDEKYGfLIHPIYPETEVWESIR 2107
Cdd:cd23222    315 YGDDILVSSDHDLFPSRVS-EWMKANttFKITPADKGEIFNdDSDVSDVRFLKRLFVEDPVCE-LIHPVIETETLEPSLN 392

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2099547076 2108 WTkNPRNMQEHVLSLCHLMWHNGKDKYKHFVDKIRSVSAGRALYIP---PYEVLLHEW 2162
Cdd:cd23222    393 WC-HEGEFETKVDAISMLAFHHGPEYYRDWCKKLTDICEERNISPPglkPYSVHRNRW 449

Cardiovirus_RdRp

cd23211

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

1724-2166

5.06e-70

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: 243.98 E-value: 5.06e-70

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1724 IHTPSNTKLQPSVFHDIFPGSKEPAVLSCRDPRLEVDLDESIFSKYKGN-ESIEITQNMLtaAAHYTAQL-STLDINPKP 1801
Cdd:cd23211     12 VHVPRKTKLRRTVAHPVFQPKFEPAVLSKYDPRTDKDVDEVAFSKHTTNqESLPPVFRMV--AKEYANRVfTLLGKDNGR 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1802 LSLEESVYGIEGLEALDLHTSAGYPYTACGIKKKDLI--PKDKNLTKLKDAIEKYGL----DLPMITFLKDELRKPEKIK 1875
Cdd:cd23211     90 LTVEQAVLGLEGMDPMEKDTSPGLPYTQQGLRRTDVVdfETATMIPFLAEAHRKMVEgdysDVVYQSFLKDEIRPIEKVQ 169

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1876 TGKTRIIEASSLNDTVQFRMAFGNLFSKFHQNPGIVTGSAVGCDPEVFWSKIPVMLDG-DCLMAFDYTNYDGSLNPVWFK 1954
Cdd:cd23211    170 AAKTRIVDVPPFEHCILGRQLLGRFASKFQTNPGLELGSAIGCDPDVDWTAFAVALSGfKYVYDVDYSNFDSTHSTAMFE 249

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1955 LL--SIVLNDLGFP---GELVNKLCNSKHIYKTTYYEVEGGMPSGCAGTSIFNTIINNIIIRTLVLDAYKFINLDKLKIL 2029
Cdd:cd23211    250 LLieNFFTEENGFDpriGEYLRSLAVSRHAYEERRVLIRGGLPSGCAATSMLNTIMNNIIIRAGLYLTYKNFEFDDIKVL 329

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2030 AYGDDVIFSYPFDLDMKELAGEGIKYGLSITPADKSDTFRKLDY-NNATFLKRGFKQDEKYgfLIHPIYpETEVWESIRW 2108
Cdd:cd23211    330 SYGDDLLVATNYQIDFNLVKARLAKFGYKITPANKTSTFPLTSTlEDVVFLKRKFVKENSY--LYRPVM-DRENLKAMLS 406

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2099547076 2109 TKNPRNMQEHVLSLCHLMWHNGKDKYKHFVDKIRSVsagrALYIPPYEVLLHEWYEKF 2166
Cdd:cd23211    407 YYRPGTLKEKLTSIALLAVHSGKQVYDEIFAPFREV----GIVVPTYESVLYRWLSLF 460

Megrivirus_RdRp

cd23223

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

1738-2141

9.68e-69

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: 238.97 E-value: 9.68e-69

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1738 HDIFPGSKEPAVLSCRDPRLE--VDLDESIFSKYKGNES--IEITQNMLTAAAHYTAQLSTLDINPKP-LSLEESVYGIE 1812
Cdd:cd23223      2 YGAFPVTHGPAALTNKDKRLEegVDLDDVMFSKHVPDHPgwPTLEPAMSYVVEDLMHKLGFSKDEPVPmWTLEQAINGEG 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1813 GLEALDLHTSAGYPYTACGIKKKDLIPKDKN-------LTKLKDAIEKYGLDLPMITFLKDELRKPEKIKTGKTRIIEAS 1885
Cdd:cd23223     82 VMDGIDMGQSPGYPYNAQGRSRRSFFEWNGEkwqpteeLKKEVDHALKDPDDFYFSTFLKDELRPLEKVKAGKTRLVDGD 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1886 SLNDTVQFRMAFGNLFSKFHQNPGIVTGSAVGCDPEVFWSKI---------PVMLDgdclmaFDYTNYDGSLNPVWFKLL 1956
Cdd:cd23223    162 SLPRILAMRMVFGPLFEAMLRKNGPEIHSAVGCNPDTDWTRYyhemgpdsfPYCFD------LDYSCFDSTEPKIAFRLM 235

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1957 SIVLNDLgF---PGELVNKLCNSKHIYKTTYYEVEGGMPSGCAGTSIFNTIINNIIIRTLVLdAYKfINLDKLKILAYGD 2033
Cdd:cd23223    236 AKYLKPY-FsvdVTPFFEALATSKHVYGDKAYEMEGGMPSGCVGTSMFNCINNSAFIVSALI-ALK-ISPEDCAWICYGD 312

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2034 DVIFSypfdLDMKELAGEGIKY-----GLSITPADKSDTFRKLD-YNNATFLKRGFKQDEKYGFLIHPIYPETEVWESIR 2107
Cdd:cd23223    313 DVIIS----TDEKALSKRIADFyhkntNLVVTPASKSGDFPETStIYDVTFLKRFFQPDSHYPHLIHPYMPLEHLEQSVM 388

                          410       420       430
                   ....*....|....*....|....*....|....*
gi 2099547076 2108 W-TKNPrnMQEHVLSLCHLMWHNGKDKYKHFVDKI 2141
Cdd:cd23223    389 WqTDGP--FQQKLDSLCLLAFHAGGPDYREFVDAI 421

Mischivirus_RdRp

cd23227

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

1724-2166

2.93e-68

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: 239.08 E-value: 2.93e-68

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1724 IHTPSNTKLQPSVFHDIFPGSKEPAVLSCRDPRL--EVDLDESIFSKYKGNESiEITQNMLTAAAHYTAQLST-LDINPK 1800
Cdd:cd23227     12 IHVPRKTKLRKSPAYPIFKPDAGPAVLSKNDPRLaeGVDFDKQVFSKHSANQK-EYPKAFRRMARWYADRVFTyLGKDNG 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1801 PLSLEESVYGIEGLEALDLHTSAGYPYTACGIKKKDLIPKDKNL---TKLKDAIEKYG----LDLPMITFLKDELRKPEK 1873
Cdd:cd23227     91 PLSVKDAIKGIDNLDAMDPTTSPGLPYSAAGIKRTDLLDFDTGEiisPALRAEYNKYVsgdySDHVFQTFLKDEIRSEEK 170

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1874 IKTGKTRIIEASSLNDTVQFRMAFGNLFSKFHQNPGIVTGSAVGCDPEVFWSKIPVML-DGDCLMAFDYTNYDGSLNPVW 1952
Cdd:cd23227    171 IKAGKTRIVDVPSLAHVIIGRVLLGKFCSKFQASPGTELGSAIGCNPDWDWTYFAHQLmERQWCYDIDYSNFDSTHGTGM 250

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1953 FKLL--SIVLNDLGFPGEL---VNKLCNSKHIYKTTYYEVEGGMPSGCAGTSIFNTIINNIIIRTLVLDAYKFINLDKLK 2027
Cdd:cd23227    251 FELLidCFFTPENGFSPAVapyLRSLAFSKHAWMDKRYKIEGGLPSGCSATSVLNTVMNNIIIRALLSLTYKNFHPEDVL 330

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2028 ILAYGDDVIFSYPFDLD---MKELAGEGIKYGLsiTPADKSDTFRKLD-YNNATFLKRGFKQDEKYGFLIHPIYPETEVw 2103
Cdd:cd23227    331 VLAYGDDLLVASDYQLDfnrVREKAAEHTLYKL--TTANKAPDFPETStLLDCQFLKRKFVLHSTRNFIWRPVMDVTNL- 407

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2099547076 2104 ESIRWTKNPRNMQEHVLSLCHLMWHNGKDKYKHFVDKIRSVSagraLYIPPYEVLLHEWYEKF 2166
Cdd:cd23227    408 KTMLSFYKPNTLSEKLLSVAQLAFHSGYTVYEELFAPFKELQ----MTVPSWWYLEHEWEHNF 466

Pico_P2A

pfam00947

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

882-1008

2.51e-65

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

Pssm-ID: 395757 Cd Length: 127 Bit Score: 217.25 E-value: 2.51e-65

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  882 NLHLCEPENLNDSTLICYSSDLVIYRTNTTGDDMIPTCDCTQATYYCKHKDRYYPINVKKHQWYEIQESEYYPKHIQYNI 961
Cdd:pfam00947    1 NRHLATHEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 2099547076  962 LIGEGPCEPGDCGGKLLCKHGVIGIVTAGGDNHVAFIDLRDFQVAEE 1008
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVRDLLWLEE 127

Mosavirus_RdRp

cd23225

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

1815-2165

9.00e-61

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: 214.01 E-value: 9.00e-61

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1815 EALDLHTSAGYPYTACGIKKKDLIP-KDKN-------LTKLKDAIEKY--GLDLP-MITFLKDELRKPEKIKTGKTRIIE 1883
Cdd:cd23225     10 DAMDMTKAVGYPYCLDSIKRLDLVEiKETEngkvylpTERLVEETEKFftGEEKPkFVTFLKDEVRSNEKIKQGKTRIVD 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1884 ASSLNDTVQFRMAFGNLFSKFHQNPGIVTGSAVGCDPEVFWSKIPVMLDGDCLMAFDYTNYDGSLNPVWFKLLS--IVLN 1961
Cdd:cd23225     90 ASPFPYAIAGRMVMQNFMSNMMRCNGTEVGSAVGCDPDTEWTRYFFELCDRYVFDLDYKAFDSTHPTAMFNLLAerFFTE 169

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1962 DLGFPGE----LVNKLCNSKHIYKTTYYEVEGGMPSGCAGTSIFNTIINNIIIRTLVLDAYKF--INLDKLKILAYGDDV 2035
Cdd:cd23225    170 RNGFDQQavriFLNGLSDSDHVYEGKHFRIRGGLPSGCPCTSILNTVINNIIVRAAILGAYQIdtVDFQKFRMLAYGDDV 249

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2036 IFSYPFDLDMKELA---GEGIKYglSITPADKSDTF-RKLDYNNATFLKRGFKQDEKYGFLIHPIYPETEVWESIRWTKn 2111
Cdd:cd23225    250 VYATPQPIKPQDLAdwlHANTNY--KVTPASKAGTFpEESTIWDVTFLKRSFKPDEDHGHLIRPVMAVGNLKQMLSFMR- 326

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2099547076 2112 PRNMQEHVLSLCHLMWHNGKDKYKHFVDKIRSVSAGRAlyIPPYEVLLHEWYEK 2165
Cdd:cd23225    327 PGTFPDKVRSVAGLAVHCGEEDYNQLADAVALYVPGVS--MPAYKYMKACWYAK 378

Rhv

pfam00073

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

93-301

1.70e-60

Pssm-ID: 395026 Cd Length: 170 Bit Score: 205.24 E-value: 1.70e-60

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076   93 TSQDIANAVVGYGVWPQYLPPDDASAIDKPTHPDISSNRFYTLESKEWTGESKGW-WWKLPDALKNMGIFGENLFYHFLG 171
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFfWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  172 RAGYTVHVQCNASKFHQGTLIVAAIPEHQlayigkgsvtvgynhTHPGETgrmiggftnnnsrqpsdenwlncdgTLLGN 251
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPPGA---------------PPPGSR-------------------------DYLWQ 120

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 2099547076  252 ITIYPHQYINLRSNNSATLILPYVNAVPMDSMVRHNNWSIVIIPISKLQY 301
Cdd:pfam00073  121 ATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGNWTLVVAGWVPLNY 170

Rosavirus_RdRp

cd23221

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

1807-2166

2.76e-57

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: 204.00 E-value: 2.76e-57

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1807 SVYGIEGLEALDLHTSAGYPYTACGIKKKDL--------IPKDKnltkLKDAIEKYGLDLPM---ITFLKDELRKPEKIK 1875
Cdd:cd23221      1 AINGIDNMDGLDMNQSPGVPYVSEGVSRRSLfdcvdgqwVPRER----LASDIAQVSGDPSLghfATFLKDELRSTEKVA 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1876 TGKTRIIEASSLNDTVQFRMAFGNLFSKFHQNPGIVTGSAVGCDPEVFWSKIPVMLDGDC-LMAFDYTNYDGSLNPVWFK 1954
Cdd:cd23221     77 AGKTRVVEAGSLPHIIVGRKIFGNLFALFNSNPGFQTMCAVGCDPDVTWTELYHPLSAKTyVFDYDYSGFDGSVPSCCFD 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1955 LLSIVLNDLgFPGE-----LVNKLCNSKHIYKTTYYEVEGGMPSGCAGTSIFNTIINNiiirTLVLDAYKFI----NLDK 2025
Cdd:cd23221    157 ALADLLADF-VEGEedvrkYISSLKTSFHHYKGKLWRLDGAMPSGCCGTSVFNSLINA----MLLFSAFSQIcpdfRASE 231

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2026 LKILAYGDDVIFSYPFDLDMKELAGEGIKY-GLSITPADKSDTFR-KLDYNNATFLKRGFKQDEKYGFLIHPIYPETEVW 2103
Cdd:cd23221    232 PLLVAYGDDVLVGTDQPLFPSKVAEWVNSHtTFRITPADKGSVFNdESDIHSVQFLKRHFTPDPDFPALIHPTIDPDTYE 311

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2099547076 2104 ESIRWTKNPrNMQEHVLSLCHLMWHNGKDKYKHFVDKI--RSVSAGRAL-YIPPYEVLLHEWYEKF 2166
Cdd:cd23221    312 QSVMWQRTG-DFQETVNSLALLVFHRGPKSYSRWCESVtrKCVDGGYPPpFFPPFSLLRHQWLKKF 376

Kobuvirus_RdRp

cd23214

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

1730-2162

3.73e-57

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: 206.23 E-value: 3.73e-57

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1730 TKLQPSVFHDIFPGSKEPAVLSCRDPRLE--VDLDESIFSKYKGNESIEITQNMLTAAAHYTAQLSTLdinPKPLSLEES 1807
Cdd:cd23214      9 SRLGPSPAYGAFPVKKQPAPLTQKDDRLEdgIRLDDQLFLKHNKGDMDEPWPGLEAAADLYFSKFPTM---IRTLTQEEA 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1808 VYGIEGLEALDLHTSAGYPYTACGIKKKDLIPKDKN-----LTKLKDAIEKYGLDLPMI--TFLKDELRKPEKIKTGKTR 1880
Cdd:cd23214     86 INGTPNLEGLDMNQAAGYPWNTMGRSRRSLFVEVQPgiyvpKPELQAEIDKTLEDPDYFysTFLKDELRPTAKVTLGLTR 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1881 IIEASSLNDTVQFRMAFGNLFSKFHQNPGiVTGSAVGCDPEVFWSKIPVML-DGDCLMAFDYTNYDGSLNPVWFKLLSIV 1959
Cdd:cd23214    166 VVEAAPIHAIVAGRMLLGGLIEYMQARPG-KHGSAVGCNPDLHWTKFFYKFcHYPQVFDLDYKCFDATLPSCAFRIVEDH 244

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1960 LNDL-GFP--GELVNKLCNSKHIYKTTYYEVEGGMPSGCAGTSIFNTIINNIIIRTLVLDAYKFiNLDKLKILAYGDDVI 2036
Cdd:cd23214    245 LERLtGDErvTRYIESIRHSHHVYGNETYEMIGGNPSGCVGTSIINTIINNICVLSALIQHPDF-SPESFRILAYGDDVI 323

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2037 FSYPFDLDMKELAGEGIKYG-LSITPADKSDTFRKLD-YNNATFLKRGFKQDEKYGFLIHPIYPETEVWESIRWTKNPrN 2114
Cdd:cd23214    324 YGCDPPIHPSFIKEFYDKHTpLVVTPANKGSDFPETStIYDVTFLKRWFVPDDIRPFYIHPVMDPDTYEQSVMWLRDG-D 402

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2099547076 2115 MQEHVLSLCHLMWHNGKDKYKHFVDKIRSVSAGRALYIP---PYEVLLHEW 2162
Cdd:cd23214    403 FQDLVTSLCYLAFHSGPKTYDRWCTRVRDQVMKTTGFPPtflPYSYLQTRW 453

Teschovirus_RdRp

cd23212

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

1800-2138

8.55e-57

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: 201.77 E-value: 8.55e-57

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1800 KPLSLEESVYGIEGLEALDLHTSAGYPYTACGIKKKDLI-PKDKNLTKLKDAIEKYgLDLP-----MITFLKDELRKPEK 1873
Cdd:cd23212      9 EPLSVREAVEGIDGLDPMDMDKSPGLPYVKKGLRRTDLWnPKTGPSIELMAEINRY-LDYNydkhvFLTFLKDELRPKEK 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1874 IKTGKTRIIEASSLNDTVQFRMAFGNLFSKFHQNPGIVTGSAVGCDPEVFWSKIPVMLDGDCLMAFDYTNYDGSLNPVWF 1953
Cdd:cd23212     88 VQAGKTRVIDVAGFGHAIVGRMLFGRLFAFFHKNPGWNTGSAVGVNPDLAWTQIFYTAPSRNVLAMDYSGFDASHTSGMF 167

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1954 KLLSIVLNDLGFpGEL----VNKLCNSKHIYKTTYYEVEGGMPSGCAGTSIFNTIINNIIIRTlvldAYKFINLDKLKIL 2029
Cdd:cd23212    168 CILKHFLTTLGY-GTLqlsyIDSLCYSKHHWDDETYRLDGGLPSGCSGTTIFNTIMNNIVARA----AASYAAEGPVGIL 242

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2030 AYGDDVIFSYPFDLDMKELAGEGIKYGLSITPADKSDTFRKLDYNNATFLKRGFKQDekyGFLIHPIYPETEVWESIRWT 2109
Cdd:cd23212    243 CYGDDILVSSPEKFPVSDWLEFYSKTPYKVTAADKSEQIDWRDITQCTFLKRGFVLD---GSLVRPVMEEQHLAELLKWA 319

                          330       340
                   ....*....|....*....|....*....
gi 2099547076 2110 KnPRNMQEHVLSLCHLMWHNGKDKYKHFV 2138
Cdd:cd23212    320 R-PGTLQAKLLSIAQLAFHLPRQAYDRLM 347

Peptidase_C3

pfam00548

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

1525-1690

5.28e-56

3C cysteine protease (picornain 3C); Picornaviral proteins are expressed as a single polyprotein which is cleaved by the viral 3C cysteine protease.

Pssm-ID: 278947 Cd Length: 174 Bit Score: 192.66 E-value: 5.28e-56

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1525 GPQEEFGRSLIKHNTCVVTTDNGKFTGL--GIYDNIMIIPTHADTGKEVEIDGIKTQVDD-AYDLHNSQGIKLEITVLKL 1601
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1602 HRNEKFRDIRKYIPETEDDYPECHLALVANQQEPTILEVGDCCSYGNI-LLSGNQTARMIKYNYPTKSGFCGGVLYKI-- 1678
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVVIAKve 160

                          170
                   ....*....|....
gi 2099547076 1679 --GLVLGIHVGGNG 1690
Cdd:pfam00548  161 gnGKILGMHIAGNG 174

ps-ssRNAv-Picornavirales

cd23169

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

1861-2142

2.05e-54

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: 193.19 E-value: 2.05e-54

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1861 ITFLKDELRKPEKIKTGKTRIIEASSLNDTVQFRMAFGNLFSKFHQNPgIVTGSAVGCDPE-VFWSKIPVML--DGDCLM 1937
Cdd:cd23169      4 VDCLKDELRPIEKVKAGKTRLFSASPLDYTIAFRKYFGDFIAAFQKNR-IKLEHAVGINPDsVEWTRLYRRLlkKGPNIF 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1938 AFDYTNYDGSLNPVWF-KLLSIVLN--DLGFPGE-------LVNKLCNSKHIYKTTYYEVEGGMPSGCAGTSIFNTIINN 2007
Cdd:cd23169     83 AGDYSNFDGSLPPDVMeAAFDIINDwyDEYVDDEdervrkvLFEELINTIHLVGNLVYQVHGGNPSGNPLTTIINSIVNL 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2008 IIIRTLVLDAYKFINLDK----LKILAYGDDVIFS----YPFDLDMKELAGEGIKYGLSITPADKSDTFRKLD-YNNATF 2078
Cdd:cd23169    163 LYIRYAWLRITGLTSLSDfkknVRLVTYGDDVIISvsdeVKDEFNFVTISEFLKELGITYTDADKSGDIVPYRpLEEVTF 242

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2099547076 2079 LKRGFKQDEKYGFLIHPIyPETEVWESIRWTK---NPRNMQEHVLSLCHLMWH-NGKDKYKHFVDKIR 2142
Cdd:cd23169    243 LKRGFRPHPTPGLVLAPL-DLESIEEQLNWTRkedDLLEATIENARAALLLAFgHGPEYYNKFRQKLN 309

Rhv

pfam00073

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

359-524

4.83e-50

Pssm-ID: 395026 Cd Length: 170 Bit Score: 175.19 E-value: 4.83e-50

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  359 FHPTKEIFIPGKVNNLSEICQVDSMIPINNTIAAKNTTGMYTVRVSQQTQPAQEIFSILVDVASQpiATTLIGEIASYYT 438
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFFWWKLPLALL--SMGLLGRLLRYHT 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  439 HWTGSLRFSFMFCGTANTSLKLLIAYTPPGVPKPENRQK---AMLSTHVVWDVGLQSTVSMVVPWVSASHYRYTTPD--- 512
Cdd:pfam00073   79 YYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRDYlwqATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDgnw 158

                          170
                   ....*....|..
gi 2099547076  513 TYSQAGYITCWY 524
Cdd:pfam00073  159 TLVVAGWVPLNY 170

Fipivirus_RdRp

cd23229

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

1808-2162

3.26e-49

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: 181.16 E-value: 3.26e-49

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1808 VYGIEGLEALDLHTSAGYPYTACGIKKKDLIPKDKN--------LTKLKDAIEKYGLDLPM-------ITFLKDELRKPE 1872
Cdd:cd23229      2 VEGIPGMEGLDMKTSAGYPWCEQNQKKKDKIKLLAGknflvrplREVVHIVVDWYIMPPDMpkpeikyVVYLKDELLSSD 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1873 KIKTGKTRIIEASSLNDTVQFRMAFGNLFSKFH-QNP--GIVTGSAVGCDPEVFWSKIPVMLDGDCLMAFDYTNYDGSLN 1949
Cdd:cd23229     82 KVKMGRTRWICAAPVQLVCAWKKVFGRAIAAIHlESVtdGKSTGCAVGMDPETAWTDIALARPGWPVIALDYSNFDGSLQ 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1950 PvwFKLLS---IVLNDLGFPGELVNKLC----NSKHIYKTTYYEVEGGMPSGCAGTSIFNTIINNIiirTLVLDAYKFIN 2022
Cdd:cd23229    162 S--FVITGavrILGYIAGLPDGQSYRLAefvyDVKQIVGKYLYTTVGPLPSGCPSTSIIGSLCNVL---MLLYTLSHATG 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2023 L------DKLKILAYGDDV-IFSYP---FDLDMkeLAGEGIK-YGLSITPA-DKSDTFRKLDYNNATFLKRGFKQDEKYG 2090
Cdd:cd23229    237 QrysafrDWMHVVTYGDDVlVFVHPevvVVLDT--LAHEMYLvFGVTATDAtDKRAPPQLRELSNVTFLKRGFRQCSSVP 314

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2091 FLIHPIYPETEVWESIRWTKNPRNMQEHVLSLCHLMWHNGKDKYKHFVDKIRS------VSAGRALY--IPPYEVLLHEW 2162
Cdd:cd23229    315 FLVHPTMDKSTIYQMLAWKRKGTTLAENVKCAAEFMMHHGEEEYEDFVGVVKEcstligVDQRSKVYeeLCSYAELHDHW 394

RNA_dep_RNAP

cd01699

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

1847-2109

3.30e-48

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: 174.39 E-value: 3.30e-48

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1847 LKDAIEKY------GLDLPMITFLKDELRKPEKIKTGKTRIIEASSLNDTVQFRMAFGNLFSKFHQNpGIVTGSAVGCDP 1920
Cdd:cd01699      1 LEKAVESLedlpliRPDLVFTTFLKDELRPLEKVEAGKTRLIQPRPLDYNIALRMYLGPFEAKLMKN-RGGLPIAVGINP 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1921 EVF-WSKIPVMLD--GDCLMAFDYTNYDGSLNPVWFKLLSIVLNDLgFPG-------ELVNKLCNS-KHIYKTTYYEVEG 1989
Cdd:cd01699     80 YSRdWTILANKLRsfSPVAIALDYSRFDSSLSPQLLEAEHSIYNAL-YDDddelerrNLLRSLTNNsLHIGFNEVYKVRG 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1990 GMPSGCAGTSIFNTIINNIIIRTLVLDAYKFINLDKLKILAYGDDVIFSYPFDLD---MKELAGEGIKYGLSITPADKSD 2066
Cdd:cd01699    159 GRPSGDPLTSIGNSIINCILVRYAFRKLGGKSFFKNVRLLNYGDDCLLSVEKADDkfnLETLAEWLKEYGLTMTDEDKVE 238

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....
gi 2099547076 2067 T-FRKLdyNNATFLKRGFKQDEkyGFLIHPIYPETEVWESIRWT 2109
Cdd:cd01699    239 SpFRPL--EEVEFLKRRFVLDE--GGGWRAPLDPSSILSKLSWS 278

Rhv

pfam00073

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

616-779

1.05e-45

Pssm-ID: 395026 Cd Length: 170 Bit Score: 162.87 E-value: 1.05e-45

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  616 PEDMVETRYVITDQTRDEMSVESFLGRSGCiaiihTDLDHEAEQY--------NAPGKNFSQWKITI--KEMAQIRRKCE 685
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAP-----VQPDVQGERFytldstdwTSLSKGFFWWKLPLalLSMGLLGRLLR 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  686 LFTYLRFDSEITIVATvaalGQDNGHVVLQYMYVPPGAPIPKTRDdYTWQSGTNASVFWQQG-QPYPRFTIPFMSIASAY 764
Cdd:pfam00073   76 YHTYYRGGLEVTVQFN----GSKFHQGKLLVAYVPPGAPPPGSRD-YLWQATLNPHQFWNLGlNSSARLSVPYISIAHYY 150

                          170
                   ....*....|....*
gi 2099547076  765 YMFYDGYEDDKGSVY 779
Cdd:pfam00073  151 STFYDGNWTLVVAGW 165

RdRP_1

pfam00680

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

1734-2143

4.95e-45

Pssm-ID: 425815 Cd Length: 450 Bit Score: 170.67 E-value: 4.95e-45

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1734 PSVFHDIFPGSKEPAVLSCRDPR-------LEVDLDESIFSKY-KGNESIEITQNML--TAAAHYTAQLSTLDINPKPLS 1803
Cdd:pfam00680    2 PTERHLVAIPAYVPASLGPEDPRwarsylnTDPYVDDIKKYSRpKLPGPADERDKLLnrSAAKMVLSELRGVPKKANSTL 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1804 LEESVY-GIEGLEALDLHTSAGYPYTACGIKKKDLIPKDKNLT-------KLKDAIEKYGLDLPM----ITFLKDELRKP 1871
Cdd:pfam00680   82 IVYRAIdGVEQIDPLNWDTSAGYPYVGLGGKKGDLIEHLKDGTearelaeRLAADWEVLQNGTPLklvyQTCLKDELRPL 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1872 EKIKTGKTRIIEASSLNDTVQFRMAFGNLFSKFHQNPGIVTgSAVGCDPevFWSKIPVMLD-----GDCLMAFDYTNYDG 1946
Cdd:pfam00680  162 EKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHP-IQVGINP--FDRGWPRLLRrlarfGDYVYELDYSGFDS 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1947 SLNPVWFKLLSIVLNDL-GFP------GELVNKLCNSKH-IYKTTYYEVEGGMPSGCAGTSIFNTIINNIIIRTLVL--- 2015
Cdd:pfam00680  239 SVPPWLIRFAFEILRELlGFPsnvkewRAILELLIYTPIaLPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYALLksl 318

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2016 --DAYKFINLDKLKILA-YGDDVIF--SYPFDLDMKELAGEGIKYGLSITPADKSDTFRKlDYNNATFLKRGFKQDEkyg 2090
Cdd:pfam00680  319 enDGPRVCNLDKYFDFFtYGDDSLVavSPDFDPVLDRLSPHLKELGLTITPAKKTFPVSR-ELEEVSFLKRTFRKTP--- 394

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2099547076 2091 FLIHPIYPETEVWESIRWTKNPRNMQEHVLSLCHLMWHNGKDKYKHFVDKIRS 2143
Cdd:pfam00680  395 GGYRPPLDRKRILAQLEYIRSKPVPSGQLENIRAYASHHGYEFYRDLLYRFVE 447

Passerivirus_RdRp

cd23224

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

1806-2164

2.48e-43

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: 163.72 E-value: 2.48e-43

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1806 ESVYGIEGLEALDLHTSAGYPYTACgIKKKDLIPKD-----KNLTKLKDAIEK--YGLDLPMITFLKDELRKPEKIKTGK 1878
Cdd:cd23224      1 EAINGTPLLDGLDMKQSPGYPWSLT-TNRRSLFTQDetgkyYPVPELEEAVLAclENPDYFYTTHLKDELRPVEKALAGK 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1879 TRIIEASSLNDTVQFRMAFGNLFSKFHQNPGiVTGSAVGCDPEVFWSKIPVMLDGDC-LMAFDYTNYDGSLNPVWFKLLS 1957
Cdd:cd23224     80 TRLIEAAPIHAIIAGRMLLGGLFEYMHARPG-EHGSAVGCDPDYHWTPFFHSFDEFSqVWALDYSCFDSTLPSCCFDLIA 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1958 IVLNDL--GFPG-------ELVNKLCNSKHIYKTTYYEVEGGMPSGCAGTSIFNTIINNIIIRTLVLDAYKFiNLDKLKI 2028
Cdd:cd23224    159 QKLAKIitPGEGiapdaivKYIRSISISKHVFGNEAYLMVGGNPSGCVGTSILNSMINNCVLISAFLTQKDF-NPNQMRI 237

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2029 LAYGDDVIFSYPFDLD---MKELAGEGIKygLSITPADKSDTFRklDYN---NATFLKRGFKQDEKYGFLIHPIYPETEV 2102
Cdd:cd23224    238 LTYGDDVLYATNPPIHprvVKKFFDENTT--LIVTPATKAGDFP--DEStiwDVTFLKRYFVPDEIRPWYVHPVIEPATY 313

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2099547076 2103 WESIRWTKNPrNMQEHVLSLCHLMWHNGKDKYKHFVDKIRSVSAGRALY--IPPYEVLLHEWYE 2164
Cdd:cd23224    314 EQSVMWTRGG-DFQDVVTSLSFLAHHAGPTNYMIWEEKVRKAAAAKGVSlnILPYSYLQHRWML 376

rhv_like

cd00205

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

374-559

3.11e-43

Pssm-ID: 119412 Cd Length: 178 Bit Score: 156.02 E-value: 3.11e-43

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  374 LSEICQVDSMIPINNTIAAKNTTGMYTVRVSQQtqpaqeifsilvdVASQPIATTLIGEIASYYTHWTGSLRFSFMFCGT 453
Cdd:cd00205      1 VESFADRPTTVGTNNWNSSASGTQLFQWKLSPA-------------LGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGS 67

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  454 ANTSLKLLIAYTPPGVPKPEN---RQKAMLSTHVVWDVGLQSTVSMVVPWVSASHYRYTTPDTYSQA---GYITCWYQTN 527
Cdd:cd00205     68 KFHTGRLLVAYVPPGAPAPTTgdtRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDGYGPLnsfGTLVVRVLTP 147

                          170       180       190
                   ....*....|....*....|....*....|..
gi 2099547076  528 FIVPPNTPREADIICFVSGcKDFCLRMARDTN 559
Cdd:cd00205    148 LTVPSGAPTTVDITVYVRA-GDFELYGPRPPR 178

Pico_P2B

pfam01552

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

1009-1105

1.13e-42

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: 151.71 E-value: 1.13e-42

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1009 QGISDYVHTLGEAFGAGFV----DNIKEQIQTINPINKITSKIVKWTIRIVSAITIIIRNNADPHTIVATLALLGCSGSP 1084
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTqqisDKIKELTNFINPTSKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|.
gi 2099547076 1085 WRFIKEKVCNWLQLVYVHKES 1105
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

5.08e-40

Pssm-ID: 308053 Cd Length: 68 Bit Score: 142.90 E-value: 5.08e-40

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2099547076    2 GAQVSRQNVGTHSTQNTVSNGSSLNYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLMKDIPTLQ 69
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 68

Hepatovirus_RdRp

cd23215

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

1801-2143

1.04e-39

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: 155.01 E-value: 1.04e-39

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1801 PLSLEESVYGIEGLEALDLHTSAGYPYTACGIKKKDLIPKDKNLT------KLKDAIE--------KYGLDLPMITFLKD 1866
Cdd:cd23215     64 FFDLEQAITGVPGMDAINMDSSPGYPYVQEKLTKSDLIWLDDNGEllgmhpRLAQRILfnltmmdnGNDLDVVYTTCPKD 143

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1867 ELRKPEKIKTGKTRIIEASSLNDTVQFRMAFGNLFSKFHQNPGIVTGSAVGCDPEVFWSKI-PVMLD-GDCLMAFDYTNY 1944
Cdd:cd23215    144 ELRPLEKVLESKTRAIDACPLDFTIICRMFWGPAISYFQLNPGFHTGVAVGIDPDRDWDALfKTMIRfGDYGIDLDFSSF 223

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1945 DGSLNPVWFKLLSIVLNDLGFPGE-----LVNKLCNSKHIYKTTYYEVEGGMPSGCAGTSIFNTIINNIIIRTLVLDAYK 2019
Cdd:cd23215    224 DASLSPFMIREACRVLSELSGVPDhqgqaLINTIIYSKHLLYNLCYHVCGSMPSGSPCTSLLNSIVNNVNLYYVFSKIFK 303

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2020 ---FINLDKLKILAYGDDVIFSYPFDLDMKELAGEGIK-------YGLSITPADKSDTfRKLDYNNATFLKRGFKQDEKY 2089
Cdd:cd23215    304 kspVFFYDAVKFLCYGDDVLIVFSRDLEIKNLDKLGQRiqdefklLGMTATSADKGEP-QVVPVSELTFLKRSFNLIEDR 382

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2099547076 2090 gflIHPIYPETEVWESIRWTKNPRNMQEHVLSLCHLMWHNGKDKYKHFVDKIRS 2143
Cdd:cd23215    383 ---FRPAISEKTIWSLVAWQRSNAEFEQNLDTACWFAFMHGYDFYQNFYLQLQS 433

RNA_helicase

pfam00910

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

1224-1320

7.33e-39

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

Pssm-ID: 459992 Cd Length: 102 Bit Score: 140.82 E-value: 7.33e-39

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1224 VIFHGEPGTGKSITTSILARML-----TTESDIYSLPPSPKYFDGYDQQSVVIMDDIMQNPSGEDMSLFCQMVSSVPFIP 1298
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALlkklgLPKDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 2099547076 1299 PMADLPDKGKPFSSDYVLASTN 1320
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

rhv_like

cd00205

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

636-825

3.22e-37

Pssm-ID: 119412 Cd Length: 178 Bit Score: 139.07 E-value: 3.22e-37

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  636 VESFLGRSGCIAIIHTDldheaeqYNAPGKNFSQWKIT------IKEMAQIRRKCELFTYLRFDSEITIVATvaalGQDN 709
Cdd:cd00205      1 VESFADRPTTVGTNNWN-------SSASGTQLFQWKLSpalgflLLQNTPLGALLSYFTYWRGDLEVTVQFN----GSKF 69

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  710 GHVVLQYMYVPPGAPIPKTrDDYTWQSGTNASVFWQ-QGQPYPRFTIPFMSIASAYYMFYDGYEddkgsvygsvVTNDMG 788
Cdd:cd00205     70 HTGRLLVAYVPPGAPAPTT-GDTRWQATLNPHVIWDlGTNSSVTFVVPYVSPTPYRSTRYDGYG----------PLNSFG 138

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 2099547076  789 TLCVRIVTEQQ-----THKVKITsrIFHKAKHISAWCPRAPR 825
Cdd:cd00205    139 TLVVRVLTPLTvpsgaPTTVDIT--VYVRAGDFELYGPRPPR 178

Parechovirus_RdRp

cd23217

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

1807-2160

5.29e-36

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: 141.93 E-value: 5.29e-36

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1807 SVYGIEGLEALDLHTSAGYPYTACGIKKKDLI---PKDKNLTKLKDAIEK----YGLDLP---MITFLKDELRKPEKIKT 1876
Cdd:cd23217      1 AVLGTSHLNSLDLSTSPGYKYVKSGYKKRDLLslePFSVSPQLEKDVKDKlhavYKGNQPttiFNACLKDELRKLDKIAQ 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1877 GKTRIIEASSLNDTVQFRMAFGNLFSKFHQNPGIVTGSAVGCDPEVFWS-KIPVMLDGDCLMafDYTNYDGSLNPVWFKL 1955
Cdd:cd23217     81 GKTRCIEACSIDYVIAYRVVMSSLYEAIYQTPCQELGLAVGMNPWTDWDfMINALNPYNYGL--DYSSYDGSLSEMLMWE 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1956 LSIVLNDLGFPGELVNKL----CNSKHIYKTTYYEVEGGMPSGCAGTSIFNTIINNIIIRTLvldAY-KFINLDKLKILa 2030
Cdd:cd23217    159 AVEVLAYCHESPDLVMQLhkpvINSDHVVMDERWLVHGGMPSGSPCTTVLNSICNLLVCIYL---AYlQSPGIECLPIV- 234

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2031 YGDDVIFSYPFDLDMKELAGEGIK-YGLSITPADKSDTFRKLDYNNATFLKRGFKQDEKYGFLIHPIYPETEVwESIRWT 2109
Cdd:cd23217    235 YGDDVIFSVSSEIDPEYLVSSAADsFGMEVTGSDKDEPPSLLPRMEVEFLKRTTGYFPGSTYKVGALDLETME-QHIMWM 313

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2099547076 2110 KNPRNMQEHVLSLCHLMWHNGKDKYKHFVDKIRSVSAGRALYIPPYEVLLH 2160
Cdd:cd23217    314 KNLSTFPQQLQSFENELCLHGKDIYDDYKKIFNPYLKEWNITMDDYDVVIH 364

rhv_like

cd00205

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

129-329

2.45e-35

Pssm-ID: 119412 Cd Length: 178 Bit Score: 133.68 E-value: 2.45e-35

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  129 SNRFYTLESKEWTG---ESKGWWWKLPDA----LKNMGIFGENLFYHFLGRAGYTVHVQCNASKFHQGTLIVAAIPEHQL 201
Cdd:cd00205      5 ADRPTTVGTNNWNSsasGTQLFQWKLSPAlgflLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPPGAP 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  202 AYIgkgsvtvgynhthpgetgrmiggftnnnsrqpsdenwlncDGTLLGNITIYPHQYINLRSNNSATLILPYVNAVPMD 281
Cdd:cd00205     85 APT----------------------------------------TGDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYR 124

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2099547076  282 SMVRH------NNWSIVIIPISKLQYETGATPYVPITLSISPMCSEFSGARNNT 329
Cdd:cd00205    125 STRYDgygplnSFGTLVVRVLTPLTVPSGAPTTVDITVYVRAGDFELYGPRPPR 178

Crohivirus_RdRp

cd23232

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

1804-2156

3.82e-35

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: 139.47 E-value: 3.82e-35

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1804 LEESVYGIEGLEALDLHTSAGYPYTACGIKKKDLIPKDK------------NLTKLKDAIEKygLDLPMITFLKDELRKP 1871
Cdd:cd23232      1 IEEACFEEGDEHALDLKTSPGFKYVQMGLKKTDLVNRPNkfihpilrndvrLIFDEMAKGQM--PVVTFTAHLKDELRKL 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1872 EKIKTGKTRIIEASSLNDTVQFRMAFGNLFSKFHQNPGIVTGSAVGCDPEVFWSKIPVMLDgDCLMAFDYTNYDGSLNPV 1951
Cdd:cd23232     79 EKIRSGKTRCIEACDFDYTVAHKMMFGTLYKAIYDTPGIITGLAVGMNPWKDWELIQQSLF-KYNYDFDYKTFDGSLSRE 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1952 WFKLLSIVLNDLGFPGELVNKL----CNSKHIYKTTYYEVEGGMPSGCAGTSIFNTIINNIIIRTLVLDAYKfinlDKLK 2027
Cdd:cd23232    158 LMLHAVDILSACVENDEMAKLMlsvvVESVHLVLDQKWNVSGGMPSGSPCTTVLNSVCNLIVSSTIADMCTE----GDFK 233

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2028 ILAYGDDVIFSYPFDLD---MKELAGEgiKYGLSITPADKSDTFRKLDYNNATFLKRGFKQDEKYGFLIHPIYPETeVWE 2104
Cdd:cd23232    234 ILVYGDDLIISSTAPLDcdrFKTLVEL--HYGMEVTPGDKGDEFKVKDREQVSFLKRVTRKFPGTNYRVGALDLDT-VKQ 310

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2099547076 2105 SIRWTKNPRNMQEHVLSLCHLMWHNGKDKYKHFVDKIRSVSAGRALYIPPYE 2156
Cdd:cd23232    311 HLMWCKSYSSFKQQLDSALMEVAMHGEETYNGFLTEIKTKLDKFKIYPPKFK 362

Dicistroviridae_RdRp

cd23194

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

1863-2142

7.42e-31

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: 125.31 E-value: 7.42e-31

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1863 FLKDELRKPEKIKTGKTRIIEASSLNDTVQFRMAFGNLFSKFHQNPgIVTGSAVGCDP---EvfWSKIPVML--DGDCLM 1937
Cdd:cd23194     11 TLKDERRPIEKVDAGKTRVFSAGPMDYTIAFRMYFLGFVAHLMRNR-IDNEIAVGTNVyslD--WDKLARKLlsKGDKVI 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1938 AFDYTNYDGSLNP-VWFKLLSIVLN--DLGFPGELVNK-----LCNSKHIYKTTYYEVEGGMPSGCAGTS---------I 2000
Cdd:cd23194     88 AGDFSNFDGSLNPqILWAILDIINEwyDDGEENALIRRvlwedIVNSVHICGGYVYQWTHSQPSGNPLTAiinsiynsiI 167

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2001 FNTIINNIIIRTLVLDAYKFinLDKLKILAYGDDVIFSYP----FDLDMKELAGEGIKYGLSITPADKSDT---FRKLDy 2073
Cdd:cd23194    168 MRYVYLLLTKEAGLMTMSDF--NKHVSMVSYGDDNVINVSdevsEWFNQLTITEAMAEIGMTYTDETKTGEivpYRSLE- 244

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2099547076 2074 nNATFLKRGFKQDEKYGFLIHPIYPETeVWESIRWTKNPRNMQE----------HVLSLcHlmwhnGKDKYKHFVDKIR 2142
Cdd:cd23194    245 -EVSFLKRGFRYDDDLGRWVAPLDLDT-ILEMPNWVRKGKDPEEitkqnvenalRELSL-H-----GEEVFDKWAPKIR 315

Limnipivirus_RdRp

cd23228

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

1813-2157

1.31e-29

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: 123.45 E-value: 1.31e-29

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1813 GLEALDLHTSAGYPYTACGIKKKDL--IPKDKNLT---KLKDAIEKYgLDL------PMITF---LKDELRKPEKIKTGK 1878
Cdd:cd23228      6 GTNPIDKNTSPGLKYTRDGLKKSDLytIDEDGNVVvsdMLRADVEAW-EELiqsggyPTTLFtacLKDELRSDEKVALGK 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1879 TRIIEASSLNDTVQFRMAFGNLFSKFHQNPGIVTGSAVGCDPEVFWSKIPVMLDG-DCLMAFDYTNYDGSLNPVWFKLLS 1957
Cdd:cd23228     85 TRVIEAAELDYVVAYRMYMSSIYSDLYNAYAGDTGIAAGINPPADGHRLREELSQyDSFLALDYSRFDGSLPEMLMRAAV 164

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1958 IVLNDLGFPGELVNKL----CNSKHIYKTTYYEVEGGMPSGCAGTSifntiINNIIIRTLVLD---------AYKFINLD 2024
Cdd:cd23228    165 EILADLHEDPDLVRRLhetvIISKHLVVDEDWTVKGGMPSGSPCTT-----VLNCICNLLVLEyaflvhfgvYEDDDGVG 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2025 KLK----ILAYGDDVIFSY---PFDLDMKELAGEGikYGLSITPADKSDTFRKLDYNNATFLKRGFK--QDEKYGFLIHP 2095
Cdd:cd23228    240 LPQcdylSVVYGDDCIVAYngmEMGLAFAETIEDT--FGMEVTPASKVGDHFNVELHEVEFLKRKFFafETEEYDRIALR 317

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2099547076 2096 IyPETEVWESIRWTKNPRNMQEHVLSLCHLMWHNGKDKYKHFVDKIRSVSAGRALYI--PPYEV 2157
Cdd:cd23228    318 L-SENTIVQSLMWMRNLKTFPDQVQSLMMELSAWGKEKYDKLRDTCKRRLAKQNLQVtvPGYDI 380

Kunsagivirus_RdRp

cd23219

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

1804-2134

1.67e-28

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: 119.20 E-value: 1.67e-28

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1804 LEESVYgiEGLEALDLHTSAGYPYTacGIKKKDLI--------PKDKN-LTKLKDAIEKYGLD-LPMITFLKDELRKPEK 1873
Cdd:cd23219      1 IEEAVF--DTVTPMDHTASAGPKYP--GTKRSELIdfqnriisDRLRNdVLELQFRGTSGGAGeVKFSSFLKDELRPLSK 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1874 IKTGKTRIIEASSLNDTVQFRMAFGNLFSKFHQNPGIVTGSAVGCDpeVFWSKIPVMLD-GDCLMAFDYTNYDGSLNP-- 1950
Cdd:cd23219     77 IRSGDTRVVECSSLDYTVAFRMQFLRVLQMCYGSDPTLTGLAPGMN--VYTDMLPLCTSlYDYNLCLDFSKYDSRLPLqv 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1951 --VWFKLLSIVLNDLGFPGELVNKLCNSKHIYKTTYYEVEGGMPSGCAGTSIFNTIInniiirTLVLDAYKFINLD---K 2025
Cdd:cd23219    155 mhRVAQLISNLTPDPQVSMRLFQPIIISTHIVGSYEVVVEGGMPSGCPITTIMNSVC------NVVMTSYAMLLLDpdsD 228

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2026 LKILAYGDDVIFSY--PFDLDM--KELAGEgikYGLSITPADKSDTFRKLDYNNATFLKRGFKQDEKYGFLIhPIYPETE 2101
Cdd:cd23219    229 FWPVAYGDDNIVSTrkPIDTELfcSILNEE---FGMILTGADKTTTVQAVPPMSVDFLKRRLRYTPEFPLPV-PVLPLDS 304

                          330       340       350
                   ....*....|....*....|....*....|...
gi 2099547076 2102 VWESIRWTKNPRNMQEHVLSLCHLMWHNGKDKY 2134
Cdd:cd23219    305 MLSRICWCKGETEFKDQLESFSYELALYGQEVY 337

Avisivirus_RdRp

cd23231

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

1817-2149

8.40e-23

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: 102.66 E-value: 8.40e-23

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1817 LDLHTSAGYPYTacGIKKKDLIPKDK------NLTKLKDAIEKYGLDLPMITFLKDELRKPEKIKTGKTRIIEASSLNDT 1890
Cdd:cd23231     11 IDWGTSPGDKYK--GKTKAQLVDDKKfkadvmNLVRFNGDPNREPPDVYFTTYLKDELRPKEKAKAGKTRVISAASFDYT 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1891 VQFRMAFGNLFSKFHQNpGIVTGSAVGCDP-----EVFWSKIPVMLdgdCLmafDYTNYDGSLNPVWFKLLSIVLNDLGF 1965
Cdd:cd23231     89 IACRMVFGPILRQLFAW-GREFGFGPGLNPythfdELYDKILPFVI---CL---DYSGFDGSLSSELMFHAAQVIACFSE 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1966 PGELVNKLC----NSKHIYKTTYYEVEGGMPSGCAGTSIFNTIINNIIIRTLVLDAYKFInlDKLKILAYGDDVIFSypf 2041
Cdd:cd23231    162 KPEAIMASAeltiGSTERVSDEVWYVYGGMPSGSPWTTTLNTICNLLMCYTYLLDMGHCW--SETFVVAYGDDVVIS--- 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2042 dLDMKELAgEGI------KYGLSITPADKSDTFRKLDYNNATFLKRGFKQDEkygFL--IHPIYPETEVWESIRWTKNpr 2113
Cdd:cd23231    237 -ANIKHNL-EGIeqwfktKFGATVTPSDKQGKITWTTKNNMEFLKRRPKQLD---FLpkIVGALDLDNMLDRIQWTKG-- 309

                          330       340       350
                   ....*....|....*....|....*....|....*.
gi 2099547076 2114 NMQEHVLSLCHLMWHNGKDKYkhfvDKIRSVSAGRA 2149
Cdd:cd23231    310 HFQDQLNSFYLELALHGRETY----NEIRAKLAPRA 341

Caliciviridae_RdRp

cd23192

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

1864-2115

3.61e-22

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: 99.65 E-value: 3.61e-22

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1864 LKDELRKPEKIKTGKTRIIEASSLNDTVQFRMAFGNLFSKFHQNPGiVTGSAVGCDPEVfwSKIPVM----LDGDCLMAF 1939
Cdd:cd23192      7 LKDELRPVEKIAEGKRRLLWGCDVGVTLVAAAAFGPVADALKAVCP-TGPIAVGINMDS--EDVEVIferlSGFRYHYCL 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1940 DYTNYDGSLNPVWFKLLSIVLNDLGFPGELVNKLCNSKH-----IYKTTYYEVEGGMPSGCAGTSIFNTIINNIIIRTLV 2014
Cdd:cd23192     84 DYSKWDSTQSPAVTAAAIDILADLSEETPLRDSVVETLSsppmgIFDDVIFVTKRGLPSGMPFTSVINSLNHWLLFSAAV 163

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2015 LDAYKFINL------DKLKILAYGDDVIFSYP--FDLDMKELAGEGIKYGLSITPADKSDTFRKLDYNNATFLKRGFKQD 2086
Cdd:cd23192    164 LKAYELVGIytgnvfDEADFFTYGDDGVYAMPpaTASVMDEIIENLKSYGLKPTAADKTENPDIPPLQGPVFLKRTFVRT 243

                          250       260
                   ....*....|....*....|....*....
gi 2099547076 2087 ekyGFLIHPIYPETEVWESIRWTKNPRNM 2115
Cdd:cd23192    244 ---PGGWRALLDRSSILRQLYWVKGPNTH 269

Aalivirus_RdRp

cd23216

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

1817-2134

5.89e-22

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: 99.74 E-value: 5.89e-22

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1817 LDLHTSAGYPYTacGIKKKDLIPKDKNLTKLKDAIEkyGLDLPMITFLKDELRKPEKIKTGKTRIIEASSLNDTVQFRMA 1896
Cdd:cd23216     12 IDWQTSPGLKYK--GRTKADLVQDPKFKEDVKEILA--GKPTFFTTYLKDELRSIEKIANGNTRAIEAANFDHVVAWRQV 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1897 FGNLFSKFHQNPGIVTGSAVGCDPEVFWSKIPVMLDGDcLMAFDYTNYDGSLNPVWFKLLSIVLNDLGFPGELVnklcns 1976
Cdd:cd23216     88 MGNIVKQLFSDHDRVTGFAPGMNPYTHFDSLMDQVKWN-VLALDFKKFDGSLSPQVMEEAVDILASFHDMPQMV------ 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1977 KHIYKTTYYE----------VEGGMPSGCAGTSIFNTIINNIIIRTLVLDayKFINLDKLKILAYGDDVIFS---YPFDL 2043
Cdd:cd23216    161 VDIHKHTIYStnvvsdetwfVEGGMCSGSPCTTVLNTICNLLVNTTILLS--EGIQPDNFYIAAYGDDTIISvdgLSSSL 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2044 DMKELAGEGIK--YGLSITPADKSDTFRKLDYNNATFLKRgfkqdeKYGFlihpiYPETE----------VWESIRWTKN 2111
Cdd:cd23216    239 PDPKIMQQKYKewFGMTVTSADKGSEITWDTRNHVQFLKR------RPGF-----FPGTQkvvgvldlesMMEHIAWTKG 307

                          330       340
                   ....*....|....*....|...
gi 2099547076 2112 prNMQEHVLSLCHLMWHNGKDKY 2134
Cdd:cd23216    308 --SFQDQLNSFYQELVLHGEQVY 328

Aquamavirus_RdRp

cd23220

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

1817-2136

4.46e-19

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: 90.92 E-value: 4.46e-19

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1817 LDLHTSAGYPYTacGIKKKDLI----PKDKN-LTKLKDAIEKYGLDLPMITFLKDELRKPEKIKTGKTRIIEASSLNDTV 1891
Cdd:cd23220     12 LNFNGTAGAKYP--GMNRRQLLlplnPQVRDdVVKLAGDVGNGTATVVFETFMKDELRPKEKIESGKTRIVESCPLDYLL 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1892 QFRMAFGNLFSKFHQNPGIVTGSAVGCDpeVFWSKIPVMLDGD----CLmafDYTNYDGSLN----PVWFKLLSIVLNDL 1963
Cdd:cd23220     90 LYRMVMLKSMIWWYNSDCIKTGVAPGMN--VYTDFVPMVKQFKkikyCL---DFSAYDSTLSdeilAAGVEVLACTSAVP 164

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1964 GFPGELVNKLCNSKHIYKTTYYEVEGGMPSGCAGTSIFNTIINNIIIRTLVldayKFINLDKLKILAYGDDVIFSYPFDL 2043
Cdd:cd23220    165 SYVRKLHAPIICSHHWHNNVVDLVLGGMPSGAPCTSVLNSIVNVLMARYIC----ALMDIDYPVMVAYGDDNVVSFDEEI 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2044 DMKELAG-EGIKYGLSITPADKSDTFRKLdyNNATFLKRG--FKQDEKYGFlihPIYPETEVWESIRWTKNPRNMQEHVL 2120
Cdd:cd23220    241 DIERMVSlYKTEFGVTATNHDKTPVPRPM--ANPVFLKRRlrFNPDLNIQF---PVLPLGEMIDRMCWTRGPEHLSDQTF 315

                          330
                   ....*....|....*.
gi 2099547076 2121 SLCHLMWHNGKDKYKH 2136
Cdd:cd23220    316 SFAIELAGYGKQVYTH 331

P3A

pfam08727

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

1422-1475

1.45e-17

Pssm-ID: 400873 Cd Length: 59 Bit Score: 78.62 E-value: 1.45e-17

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2099547076 1422 AIFQG---PIDVVNKPPPPAIIDLLKSVRSPDVIKYCEENKWIV--PSDCKLERDLNYA 1475
Cdd:pfam08727    1 AIFQGidlKIDIKTSPPPEAIADLLQAVDSPEIIDYCEDKGWIVniPAECQIERDIGIA 59

Secoviridae_RdRp

cd23196

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

1864-2143

5.85e-13

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Secoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Secoviridae, order Picornavirales. Members of the family Secoviridae are non-enveloped viruses with mono- or bipartite (RNA-1 and RNA-2) linear (+)ssRNA genomes of 9 to 13.7 kilobases in total. Secoviruses are related to picornaviruses and are classified in the order Picornavirales. The majority of known members infect dicotyledonous plants and many are important plant pathogens (e.g., grapevine fanleaf virus and rice tungro spherical virus). The Secoviridae includes 8 genera (Comovirus, Fabavirus, Nepovirus, Cheravirus, Sadwavirus, Torradovirus, Sequivirus, and Waikavirus) as well as unassigned species (strawberry latent ringspot virus-MEN 454, strawberry mottle virus-Thompson, black raspberry necrosis virus- 1, chocolate lily virus A-KP2, and Dioscorea mosaic associated virus-goiana). RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438046 Cd Length: 309 Bit Score: 72.03 E-value: 5.85e-13

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1864 LKDELRKPEK-IKTGKTRIIEASSLNDTVQFRMAFGNlFSKFHQNPGIVTGSAVGCDP-EVFWSKIPVML--DGDCLMAF 1939
Cdd:cd23196      7 PKDERLKKRKvLEKPKTRLFDVLPMEYNLLLRKYFLN-FVRFIQANRHRLPCQVGINPySREWTTLYDRLaeKSDTALNC 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1940 DYTNYDGSLN----PVWFKLLSIVLNDLGFPGELVNKL---CNSKHIYKTTYYEVEGGMPSGCAGTsifnTIINNIIIRT 2012
Cdd:cd23196     86 DYSRFDGLLShqvyVWIADMINRLYGDGDEAKARRNLLmmfCGRRSICGRQVYMVRGGMPSGCALT----VIINSIFNEI 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2013 LVLDAYKFI-------NLDKL-KILAYGDD-------VIFSYpFDLDM--KELAgegiKYGLSITPA-DKSD---TFRKL 2071
Cdd:cd23196    162 LIRYVYRKVvprparnNFNKYvRLVVYGDDnlisvkeEIIPY-FDGPVikKEMA----KVGVTITDGtDKTSptlERKPL 236

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2099547076 2072 DynNATFLKRGFKQDEKyGFLIHPIyPETEVWESIRWTkNPRNMQEHVLSLCH------LMWHNGKDKYKHFVDKIRS 2143
Cdd:cd23196    237 E--SLDFLKRGFRVQSD-GLVVAPL-DKTSLYSRLHYV-TAGGDGMYSLYILNdnnksfLEEHVDHPEFTEFRNRVVS 309

Marnaviridae_RdRp

cd23195

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

1864-2090

2.70e-12

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: 70.17 E-value: 2.70e-12

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1864 LKDELRKPEKiktGKTRIIEASSLNDTVQFRMAFGNLFSKFHQNPgIVTGSAVGCD---PEvfWSKIPVML---DGDCLM 1937
Cdd:cd23195      7 LKDEPTKLTK---DKVRVFQAAPVALQLLVRKYFLPIARFLQMNP-LLSECAVGINaqsPE--WEELYEHLtkfGEDRII 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1938 AFDYTNYDGSLNPVW----FK-LLSIVLNDLGFPGE-------LVNKLCNSKHIYKTTYYEVEGGMPSGCAGtsifntii 2005
Cdd:cd23195     81 AGDYSKYDKRMSAQLilaaFKiLIDIAAKSGGYSEEdlkimrgIATDIAYPLVDFNGDLIQFFGSNPSGHPL-------- 152

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2006 nniiirTLVLD----------AYKFINLDKLK--------ILAYGDDVIFS----YPFdLDMKELAGEGIKYGLSITPAD 2063
Cdd:cd23195    153 ------TVIINsivnslymryAYYSLYPEKEVppfrdvvaLMTYGDDNIMSvspgYPW-FNHTSIAEFLAKIGIKYTMAD 225

                          250       260
                   ....*....|....*....|....*...
gi 2099547076 2064 KSDTFRK-LDYNNATFLKRGFKQDEKYG 2090
Cdd:cd23195    226 KEAESVPfIHISEADFLKRKFVFDPELG 253

Iflaviridae_RdRp

cd23197

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

1859-2099

7.52e-08

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: 56.41 E-value: 7.52e-08

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1859 PMITFLKDELRKPEKIKT-GKTRIIEASSLNDTVQFRMAFGNLFSKFHQNPgIVTGSAVGCDPE-VFWSKI--PVMLDGD 1934
Cdd:cd23197      7 VYWAHLKDELRPSEKLRRfGGTRVFSVPPLELVLNSRRFLLPFMDAFQSFP-IEAHHAIGLNPNsGDWRRLrdTLLEKGP 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1935 CLMAFDYTNYDGSLnPVWF--KLLSIVLNDLGFPGELVNKLCNskhIYKTTY--------------YEVEGGMPSGCAGT 1998
Cdd:cd23197     86 CLLQMDYKNYSDAI-PKECvaKAFHIIVDYYRKWHCLTVEIEN---ALKTLFldtadaellvygdvFKVNNGVLAGHPMT 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1999 SIFNTIInniiirTLVLDAYKFINLDKLK---------ILAYGDDVIFSYPFDL----DMKELAGEGIKYGLSITPADKS 2065
Cdd:cd23197    162 SVVNSVV------NLILMNYMWIKITRRRaseffkltyIIVMGDDVVISLPKQLteefDCRKICAEFAKYDIKVTDSEKN 235

                          250       260       270
                   ....*....|....*....|....*....|....*..
gi 2099547076 2066 DTFRKLDYNNA---TFLKRGFKqdekygflIHPIYPE 2099
Cdd:cd23197    236 LTGEPKPYDSFdkfEFLSRGFS--------DCDAYPD 264

Calici_coat

pfam00915

Calicivirus coat protein;

415-513

3.59e-04

Calicivirus coat protein;

Pssm-ID: 459994 Cd Length: 291 Bit Score: 44.88 E-value: 3.59e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076  415 SILVDVASQPIATTLIGEIASYYTHWTGSLRFSFMFCGTANTSLKLLIAYTPPGVpKPENRQKAMLSTHVVWDVGLQSTV 494
Cdd:pfam00915   81 KVLFDQSLGPHLNPFLLHLSQMYNGWSGGMRVRFMVAGSGVFGGKLAASVIPPGV-EPITSASMLQFPHVLFDARQLEPV 159

                           90
                   ....*....|....*....
gi 2099547076  495 SMVVPWVSASHYRYTTPDT 513
Cdd:pfam00915  160 IFTIPDLRNTLFHNMDRNT 178

RdRP_4

pfam02123

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

1871-2093

2.22e-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: 42.83 E-value: 2.22e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1871 PEKIKTGKTRIIEASSLNDTVQFRM-------AFGNlfSKFHQNPGivTGSAVGcdpevFWSKIPVMLDGDCLMAFDYTN 1943
Cdd:pfam02123  236 SMKLEHGKSRAIYACDTRSYLAFEYllapvekAWAN--KSVILNPG--EGDISG-----FDWSVQDWKRGGVSLMLDYDD 306

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1944 YD-----GSLNPVWFKLLSIVLNDlgfPGELVNKLCNS-KHIY-----KTTYYEVEGGMPSGCAGTSIFNTiinniiirt 2012
Cdd:pfam02123  307 FNsqhstESMRAVFERLRRRLPDE---PAEAADWLVCSmDSMYqlsdgTLLAQRVPGTLKSGHRATTFINS--------- 374

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2013 lVLD-AYKFI----NLDKLKILAYGDDVIFSYPFDLDMKELAGEGIKYGLSITPADKSDTFRkldynNATFLKRGFKQDE 2087
Cdd:pfam02123  375 -VLNcAYAELagapWADVPTSIHMGDDVLEGLRTPADATSLLDKYARLGFKVNPSKQSVGHT-----IAEFLRVAFCSHE 448


                   ....*.
gi 2099547076 2088 KYGFLI 2093
Cdd:pfam02123  449 VRGYLA 454

Polycipiviridae_RdRp

cd23198

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

1863-2141

2.67e-03

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: 42.40 E-value: 2.67e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1863 FLKDELRKPEKI-----KTGKTRIIEASSLNDTVQFRMAFGNLFSKFHQ--------NPGIvtgsavgcDPE-------- 1921
Cdd:cd23198      6 FPKDELRPIYKAlgdpqTPPKTRSVTCMNVYYILAWRRVTLDFWASMHRaadgnfpfCPGI--------NPEgpdwnrly 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1922 VFWSKIPVMLDgdclmaFDYTNYDGSLNPVWF----KLLSIVLNDLgfPGELVNKLCNS-------KHI-YKTTYYEVEG 1989
Cdd:cd23198     78 HYLNRHPNAVD------FDVSNWDGHLPAELFyavlDIIKTVLGLK--PNSPNAKVIYSiltevmnCHIqFEDIIYQKLR 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1990 GMPSGCAGTSifntiinniIIRTLV---LDAYKFINLDKLKI--------------LAYGDDVIFSYPFDL----DMKEL 2048
Cdd:cd23198    150 GLISGFPGTA---------EVNTLAhwlLIYYIYLYLAQNTIydmtitaflrnvsaIFYGDDIIITISDEIlhwfNGKTI 220

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2049 AGEGIKYGLSITPADKSD--TFRKlDYNNATFLKRGFKQdekygflIHPIY-----PETEVWESIRWTK---NPRN-MQE 2117
Cdd:cd23198    221 QRMYEEHGYPVTSAAKDTeiPESK-PLSDCQFLKSSWNP-------ILPGYyirkmDIEVVYDLVYWVRakeHPRDqFYS 292

                          330       340
                   ....*....|....*....|....
gi 2099547076 2118 HVLSLCHLMWHNGKDKYKHFVDKI 2141
Cdd:cd23198    293 NYHDALRILFGHGEQVFEAFREQV 316

Nora-virus_RdRp

cd23200

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

1864-2142

5.53e-03

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

Pssm-ID: 438050 Cd Length: 306 Bit Score: 41.06 E-value: 5.53e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1864 LKDELRKPEKIKTGKTRIIEASSLNDTVQFRMAFGNLFSKFHQnPGIVTGSAVGCDPE-VFWSKIPV-MLDGDCLMAFDY 1941
Cdd:cd23200      7 LKDQPIKIAQAKSGRTRVFHCIPVDLILFSGALYGPYKEAYTK-AGLKCYHAVGIDPKsVGWQQLATyMTKHPNYFDADY 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 1942 TNYDGSLNPVWFK-LLSIVLNdlgfpgeLVNKLCNSKH----------------IYKTTYYEVEGGMPSGCAGTSIFNTI 2004
Cdd:cd23200     86 KNYDKYLHRQVFKaVRKIQRS-------VIQQVCPDKWdkaraveeldaidtyvVDYQTVYKTNRGNKSGSYTTTIDNCL 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2005 INNI------IIRTLVLDAYKFinLDKLKILAYGDDVIfsypfdldmKELAGEGI-KY------------GLSITPADKS 2065
Cdd:cd23200    159 ANDIyglyawVKTTGLRSLWDY--RQNVSSVAFGDDII---------KSVSDEYKdKYnyctyrdvlnatGHIMTPGSKD 227

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2099547076 2066 DTFRKLDY-NNATFLKRGFKQdeKYGFLIHPIYPET----EVWESIRWTKNP--RNM-QEHVLSLchLMWhnGKDKYKHF 2137
Cdd:cd23200    228 GEEKPFTSfENLQFLKRGFKL--ENGMVLAPLLQRSiegpFVWTDIREDQITvwVNLvQEQLIEA--ALW--GEEYYNEL 301


                   ....*
gi 2099547076 2138 VDKIR 2142
Cdd:cd23200    302 CQKLK 306

SpoVK

COG0464

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...

1200-1245

5.93e-03

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];

Pssm-ID: 440232 [Multi-domain] Cd Length: 397 Bit Score: 41.44 E-value: 5.93e-03

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 2099547076 1200 KRIKELLKRSQMILRTSKRTEPVGVIFHGEPGTGKSITTSILARML 1245
Cdd:COG0464    170 RELVALPLKRPELREEYGLPPPRGLLLYGPPGTGKTLLARALAGEL 215

RecA-like_protease

cd19481

proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...

1200-1245

9.02e-03

Pssm-ID: 410889 [Multi-domain] Cd Length: 158 Bit Score: 39.19 E-value: 9.02e-03

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 2099547076 1200 KRIKELLK--RSQMILRTSKRTEPVGVIFHGEPGTGKSITTSILARML 1245
Cdd:cd19481      3 ASLREAVEapRRGSRLRRYGLGLPKGILLYGPPGTGKTLLAKALAGEL 50

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