NCBI Conserved Domain Search

Conserved domains on [gi|1147809662|ref|YP_009344963|]

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polyprotein [Enterovirus AN12]

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 ...

1721-2173

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: 833.33 E-value: 0e+00

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1721 SKDAGYPIINAPTKTKLHPSVFFDIFPGEKEPAVLHKKDKRLEVDFEEALFSKYIGNIHKPVTEEMEIAIDHYANQLKQL 1800
Cdd:cd23213      1 NKEVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1801 DIDPTPISMEDAIYGTEGLEALDLGTSAGYPYVALGIKKRDILNKETRDVTKMQQCIDKYGLNLPMVTYVKDELRSKEKV 1880
Cdd:cd23213     81 DIDTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKV 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1881 KKGKSRLIEASSLNDSVAMRCAFGNLYKAFHTNPGTLTGCAVGCNPETFWSKIPVMMDGELFGFDYTAYDASLSPVWFQC 1960
Cdd:cd23213    161 EKGKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDGSLFAFDYTGYDASLSPVWFRA 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1961 LYLLLEKIGFGHCKHFIDQLCCSNHLFMDKRYVVVGGMPSGCSGTSIFNSMINNIIIRTLVLTVYKNIDLDDLKIIAYGD 2040
Cdd:cd23213    241 LKMVLEKGYSEEAVSLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYGD 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2041 DVIASYPFELDAKLLADAGKSFGLIMTPPDKSSEFVKLTWDNVTFLKRSFVKDERFPFLIHPVMKMSDIHESIRWTKDAK 2120
Cdd:cd23213    321 DVIASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDPR 400

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1147809662 2121 STQDHVRSLCLLAWHCGQEQYEEFLEKIRSVPVGRALSLPSFKALQRSWYDSF 2173
Cdd:cd23213    401 NTQDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453

Pico_P2A

pfam00947

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

858-984

1.17e-74

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

Pssm-ID: 395757 Cd Length: 127 Bit Score: 244.21 E-value: 1.17e-74

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  858 NRHLADCVDWQNLVWESYERDLLVTRVDAHGCDQIARCDCRAGVYYCKSRMKHYPVVVTPPSLVHVDKNDYYPERYQSHV 937
Cdd:pfam00947    1 NRHLATHEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1147809662  938 ALGIGFAEPGDCGGLLRCEHGVMGILTAGGNNLVAFADIRDLLWIED 984
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVRDLLWLEE 127

Rhv

pfam00073

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

93-285

2.64e-57

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: 195.99 E-value: 2.64e-57

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662   93 TTQEAANICVGYGEWPSHLDDHDATAVDRPTHPGVSCERFYTLPSVEWTNTWKG-QYWKLPNALTETGMFGQNAQFHYLY 171
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGfFWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  172 RGGWAVHVQCNATKFHQGLLLVVMIPEcvvnlrGAPPINKTQpgengreieepflldsgeALGNALIYPHQWINLRTNNA 251
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPP------GAPPPGSRD------------------YLWQATLNPHQFWNLGLNSS 136

                          170       180       190
                   ....*....|....*....|....*....|....
gi 1147809662  252 ATIIVPYVNAIPMDSAIRHSNWTLMVIPVTELAY 285
Cdd:pfam00073  137 ARLSVPYISIAHYYSTFYDGNWTLVVAGWVPLNY 170

Peptidase_C3 super family

cl02893

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

1530-1695

8.07e-49

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: 171.86 E-value: 8.07e-49

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1530 GPLLDFAMSLLKKNIRTVVTKTGEFTGL--GVYDTFMVLPRHAMAHGEVEVDGKKVEIED-AYDLNDTTQTSLELTVIKL 1606
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1607 KQNEKFRDIRSLIPDQISETTEALVIVNTSAYPNLFMPVGAVKDYGYL-NLAGRPTHRTLMYNFPTRAGQCGGVAVSM-- 1683
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVVIAKve 160

                          170
                   ....*....|....
gi 1147809662 1684 --GKVIGIHIGGNG 1695
Cdd:pfam00548  161 gnGKILGMHIAGNG 174

Rhv

pfam00073

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

343-514

2.38e-45

Pssm-ID: 395026 Cd Length: 170 Bit Score: 162.10 E-value: 2.38e-45

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  343 FEPSPEIHIPAEVRNLLEIVQVESMVEANNL-ADVEGAKRYNIPLNVQTGMDAQIFALNVDpgrDGPLQHTLLGIYTRYF 421
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVqPDVQGERFYTLDSTDWTSLSKGFFWWKLP---LALLSMGLLGRLLRYH 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  422 TQWSGSLEFTFMFTGTFMTTGKILIAYTPPGAAVPASR---REAMLGTHVVWDFGLQSSITLVVPWISAAHFRgtdSTST 498
Cdd:pfam00073   78 TYYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRdylWQATLNPHQFWNLGLNSSARLSVPYISIAHYY---STFY 154

                          170
                   ....*....|....*.
gi 1147809662  499 LYKYKYYEAGVITGWY 514
Cdd:pfam00073  155 DGNWTLVVAGWVPLNY 170

RNA_helicase

pfam00910

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

1213-1311

1.34e-40

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

Pssm-ID: 459992 Cd Length: 102 Bit Score: 145.83 E-value: 1.34e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1213 CLIHGTPGTGKSLATTIIGRKIAEYENSG---VYSLPPDPDHFDGYQEQAVVIMDDLHQNPDGKDMSLFCQMVSTTPFVV 1289
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKKLGLPkdsVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 1147809662 1290 PMAALEDKGRLFTSKYVLASTN 1311
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

Pico_P2B super family

cl03260

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

989-1089

9.05e-35

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

The actual alignment was detected with superfamily member pfam01552:

Pssm-ID: 279840 Cd Length: 101 Bit Score: 128.99 E-value: 9.05e-35

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  989 QGLTDYVQSLGNAFGAGFTDEISNYVGQVRDMMVGSDTVVEKIVRNIIKLLSALVIVVRNRSDIVTVTATLSLLGCSGSP 1068
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTQQISDKIKELTNFINPTSKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|.
gi 1147809662 1069 WRWLKAKICSILGINMAQKQA 1089
Cdd:pfam01552   81 WQFLKEKACAVLEIPYVHKQG 101

rhv_like

cd00205

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

622-805

9.36e-33

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: 125.97 E-value: 9.36e-33

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  622 LESFYGRSSLVGMPSLNPGDT---VTEWIINFGE------FVQLRAKLCLFTYMRFDIEFTIVATAysatgdpiSDPTYI 692
Cdd:cd00205      1 VESFADRPTTVGTNNWNSSASgtqLFQWKLSPALgflllqNTPLGALLSYFTYWRGDLEVTVQFNG--------SKFHTG 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  693 TYQVMYVPPGASAPTdQDTYQWQSGANPSLLSRVGDVPAA-FSVPFMGTANAYSYAYDGYAffnttdhldygvlPSNYLG 771
Cdd:cd00205     73 RLLVAYVPPGAPAPT-TGDTRWQATLNPHVIWDLGTNSSVtFVVPYVSPTPYRSTRYDGYG-------------PLNSFG 138

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|
gi 1147809662  772 SMYFRTLER------VTQKIRFRIYAKPKHVRAWVPRAPR 805
Cdd:cd00205    139 TLVVRVLTPltvpsgAPTTVDITVYVRAGDFELYGPRPPR 178

Pico_P1A super family

cl03490

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

2-69

1.40e-20

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

The actual alignment was detected with superfamily member pfam02226:

Pssm-ID: 308053 Cd Length: 68 Bit Score: 87.43 E-value: 1.40e-20

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1147809662    2 GGQFSKNTAGSHTTGTYAAGGSTIHYTNINYYENAASSSLNKQDLTQDPTKFTQPVVDVIKESAVPLK 69
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 68

P3A super family

cl07374

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

1418-1478

1.20e-13

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: 67.45 E-value: 1.20e-13

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1147809662 1418 GPPEFRPLRIDVsEETPAPPAIADLLASVDSEDVREYCRQKGWIVQerITKE-SLERNVSRA 1478
Cdd:pfam08727    1 AIFQGIDLKIDI-KTSPPPEAIADLLQAVDSPEIIDYCEDKGWIVN--IPAEcQIERDIGIA 59

Name

Accession

Description

Interval

E-value

Enterovirus_RdRp

cd23213

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

1721-2173

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: 833.33 E-value: 0e+00

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1721 SKDAGYPIINAPTKTKLHPSVFFDIFPGEKEPAVLHKKDKRLEVDFEEALFSKYIGNIHKPVTEEMEIAIDHYANQLKQL 1800
Cdd:cd23213      1 NKEVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1801 DIDPTPISMEDAIYGTEGLEALDLGTSAGYPYVALGIKKRDILNKETRDVTKMQQCIDKYGLNLPMVTYVKDELRSKEKV 1880
Cdd:cd23213     81 DIDTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKV 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1881 KKGKSRLIEASSLNDSVAMRCAFGNLYKAFHTNPGTLTGCAVGCNPETFWSKIPVMMDGELFGFDYTAYDASLSPVWFQC 1960
Cdd:cd23213    161 EKGKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDGSLFAFDYTGYDASLSPVWFRA 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1961 LYLLLEKIGFGHCKHFIDQLCCSNHLFMDKRYVVVGGMPSGCSGTSIFNSMINNIIIRTLVLTVYKNIDLDDLKIIAYGD 2040
Cdd:cd23213    241 LKMVLEKGYSEEAVSLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYGD 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2041 DVIASYPFELDAKLLADAGKSFGLIMTPPDKSSEFVKLTWDNVTFLKRSFVKDERFPFLIHPVMKMSDIHESIRWTKDAK 2120
Cdd:cd23213    321 DVIASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDPR 400

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1147809662 2121 STQDHVRSLCLLAWHCGQEQYEEFLEKIRSVPVGRALSLPSFKALQRSWYDSF 2173
Cdd:cd23213    401 NTQDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453

Pico_P2A

pfam00947

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

858-984

1.17e-74

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

Pssm-ID: 395757 Cd Length: 127 Bit Score: 244.21 E-value: 1.17e-74

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  858 NRHLADCVDWQNLVWESYERDLLVTRVDAHGCDQIARCDCRAGVYYCKSRMKHYPVVVTPPSLVHVDKNDYYPERYQSHV 937
Cdd:pfam00947    1 NRHLATHEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1147809662  938 ALGIGFAEPGDCGGLLRCEHGVMGILTAGGNNLVAFADIRDLLWIED 984
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVRDLLWLEE 127

Rhv

pfam00073

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

93-285

2.64e-57

Pssm-ID: 395026 Cd Length: 170 Bit Score: 195.99 E-value: 2.64e-57

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662   93 TTQEAANICVGYGEWPSHLDDHDATAVDRPTHPGVSCERFYTLPSVEWTNTWKG-QYWKLPNALTETGMFGQNAQFHYLY 171
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGfFWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  172 RGGWAVHVQCNATKFHQGLLLVVMIPEcvvnlrGAPPINKTQpgengreieepflldsgeALGNALIYPHQWINLRTNNA 251
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPP------GAPPPGSRD------------------YLWQATLNPHQFWNLGLNSS 136

                          170       180       190
                   ....*....|....*....|....*....|....
gi 1147809662  252 ATIIVPYVNAIPMDSAIRHSNWTLMVIPVTELAY 285
Cdd:pfam00073  137 ARLSVPYISIAHYYSTFYDGNWTLVVAGWVPLNY 170

RdRP_1

pfam00680

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

1738-2150

1.37e-49

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: 183.77 E-value: 1.37e-49

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1738 HPSVFFDIFPGEKEPAVLHKKDKRLEVDFEeaLFSKYIGNIHK--------PVTEEMEIAID----HYANQLKQLD--ID 1803
Cdd:pfam00680    1 SPTERHLVAIPAYVPASLGPEDPRWARSYL--NTDPYVDDIKKysrpklpgPADERDKLLNRsaakMVLSELRGVPkkAN 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1804 PTPISMEDAIYGtEGLEALDLGTSAGYPYVALGIKKRDILNKETRDVT------KMQQCIDKYGLNLPMV----TYVKDE 1873
Cdd:pfam00680   79 STLIVYRAIDGV-EQIDPLNWDTSAGYPYVGLGGKKGDLIEHLKDGTEarelaeRLAADWEVLQNGTPLKlvyqTCLKDE 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1874 LRSKEKVKKGKSRLIEASSLNDSVAMRCAFGNLYKAFHTNPGTLTgCAVGCNPETF-WSKIPVMMDGE---LFGFDYTAY 1949
Cdd:pfam00680  158 LRPLEKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHP-IQVGINPFDRgWPRLLRRLARFgdyVYELDYSGF 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1950 DASLSPvWF--QCLYLLLEKIGF----GHCKHFIDQLCCSNHLFMD-KRYVVVGGMPSGCSGTSIFNSMINNIIIRTLvl 2022
Cdd:pfam00680  237 DSSVPP-WLirFAFEILRELLGFpsnvKEWRAILELLIYTPIALPNgTVFKKTGGLPSGSPFTSIINSIVNYLLILYA-- 313

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2023 tVYKNIDLDDLKI---------IAYGDDVIA--SYPFELDAKLLADAGKSFGLIMTPPDKSSEFVKlTWDNVTFLKRSFV 2091
Cdd:pfam00680  314 -LLKSLENDGPRVcnldkyfdfFTYGDDSLVavSPDFDPVLDRLSPHLKELGLTITPAKKTFPVSR-ELEEVSFLKRTFR 391

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1147809662 2092 KDerfPFLIHPVMKMSDIHESIRWTKDAKSTQDHVRSLCLLAWHCGQEQYEEFLEKIRS 2150
Cdd:pfam00680  392 KT---PGGYRPPLDRKRILAQLEYIRSKPVPSGQLENIRAYASHHGYEFYRDLLYRFVE 447

Peptidase_C3

pfam00548

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

1530-1695

8.07e-49

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: 171.86 E-value: 8.07e-49

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1530 GPLLDFAMSLLKKNIRTVVTKTGEFTGL--GVYDTFMVLPRHAMAHGEVEVDGKKVEIED-AYDLNDTTQTSLELTVIKL 1606
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1607 KQNEKFRDIRSLIPDQISETTEALVIVNTSAYPNLFMPVGAVKDYGYL-NLAGRPTHRTLMYNFPTRAGQCGGVAVSM-- 1683
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVVIAKve 160

                          170
                   ....*....|....
gi 1147809662 1684 --GKVIGIHIGGNG 1695
Cdd:pfam00548  161 gnGKILGMHIAGNG 174

Rhv

pfam00073

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

343-514

2.38e-45

Pssm-ID: 395026 Cd Length: 170 Bit Score: 162.10 E-value: 2.38e-45

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  343 FEPSPEIHIPAEVRNLLEIVQVESMVEANNL-ADVEGAKRYNIPLNVQTGMDAQIFALNVDpgrDGPLQHTLLGIYTRYF 421
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVqPDVQGERFYTLDSTDWTSLSKGFFWWKLP---LALLSMGLLGRLLRYH 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  422 TQWSGSLEFTFMFTGTFMTTGKILIAYTPPGAAVPASR---REAMLGTHVVWDFGLQSSITLVVPWISAAHFRgtdSTST 498
Cdd:pfam00073   78 TYYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRdylWQATLNPHQFWNLGLNSSARLSVPYISIAHYY---STFY 154

                          170
                   ....*....|....*.
gi 1147809662  499 LYKYKYYEAGVITGWY 514
Cdd:pfam00073  155 DGNWTLVVAGWVPLNY 170

RNA_helicase

pfam00910

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

1213-1311

1.34e-40

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

Pssm-ID: 459992 Cd Length: 102 Bit Score: 145.83 E-value: 1.34e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1213 CLIHGTPGTGKSLATTIIGRKIAEYENSG---VYSLPPDPDHFDGYQEQAVVIMDDLHQNPDGKDMSLFCQMVSTTPFVV 1289
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKKLGLPkdsVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 1147809662 1290 PMAALEDKGRLFTSKYVLASTN 1311
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

rhv_like

cd00205

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

389-549

1.65e-40

Pssm-ID: 119412 Cd Length: 178 Bit Score: 148.31 E-value: 1.65e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  389 QTGMDAQIFALNVDPG-RDGPLQHTLLGIYTRYFTQWSGSLEFTFMFTGTFMTTGKILIAYTPPGAAVPA---SRREAML 464
Cdd:cd00205     18 SSASGTQLFQWKLSPAlGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPPGAPAPTtgdTRWQATL 97

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  465 GTHVVWDFGLQSSITLVVPWISAAHFRGTDSTSTLYkykYYEAGVITGWYQTNMITPPDFPQTASIVAFVAAqSNFSLRI 544
Cdd:cd00205     98 NPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDGYGP---LNSFGTLVVRVLTPLTVPSGAPTTVDITVYVRA-GDFELYG 173


                   ....*
gi 1147809662  545 QKDRP 549
Cdd:cd00205    174 PRPPR 178

rhv_like

cd00205

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

125-313

6.08e-40

Pssm-ID: 119412 Cd Length: 178 Bit Score: 146.77 E-value: 6.08e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  125 PGVSCERFYTLPSVEWTNTWKGQ---YWKLPNALT----ETGMFGQNAQFHYLYRGGWAVHVQCNATKFHQGLLLVVMIP 197
Cdd:cd00205      1 VESFADRPTTVGTNNWNSSASGTqlfQWKLSPALGflllQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  198 EcvvnlrGAPPINKTQPgengreieepflldsgeaLGNALIYPHQWINLRTNNAATIIVPYVNAIPMDSAIRH------S 271
Cdd:cd00205     81 P------GAPAPTTGDT------------------RWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDgygplnS 136

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 1147809662  272 NWTLMVIPVTELAYAANTSPLVPITVTLAPMCTEFGGLRAAS 313
Cdd:cd00205    137 FGTLVVRVLTPLTVPSGAPTTVDITVYVRAGDFELYGPRPPR 178

Pico_P2B

pfam01552

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

989-1089

9.05e-35

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

Pssm-ID: 279840 Cd Length: 101 Bit Score: 128.99 E-value: 9.05e-35

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  989 QGLTDYVQSLGNAFGAGFTDEISNYVGQVRDMMVGSDTVVEKIVRNIIKLLSALVIVVRNRSDIVTVTATLSLLGCSGSP 1068
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTQQISDKIKELTNFINPTSKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|.
gi 1147809662 1069 WRWLKAKICSILGINMAQKQA 1089
Cdd:pfam01552   81 WQFLKEKACAVLEIPYVHKQG 101

rhv_like

cd00205

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

622-805

9.36e-33

Pssm-ID: 119412 Cd Length: 178 Bit Score: 125.97 E-value: 9.36e-33

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  622 LESFYGRSSLVGMPSLNPGDT---VTEWIINFGE------FVQLRAKLCLFTYMRFDIEFTIVATAysatgdpiSDPTYI 692
Cdd:cd00205      1 VESFADRPTTVGTNNWNSSASgtqLFQWKLSPALgflllqNTPLGALLSYFTYWRGDLEVTVQFNG--------SKFHTG 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  693 TYQVMYVPPGASAPTdQDTYQWQSGANPSLLSRVGDVPAA-FSVPFMGTANAYSYAYDGYAffnttdhldygvlPSNYLG 771
Cdd:cd00205     73 RLLVAYVPPGAPAPT-TGDTRWQATLNPHVIWDLGTNSSVtFVVPYVSPTPYRSTRYDGYG-------------PLNSFG 138

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|
gi 1147809662  772 SMYFRTLER------VTQKIRFRIYAKPKHVRAWVPRAPR 805
Cdd:cd00205    139 TLVVRVLTPltvpsgAPTTVDITVYVRAGDFELYGPRPPR 178

Rhv

pfam00073

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

605-750

1.48e-26

Pssm-ID: 395026 Cd Length: 170 Bit Score: 108.17 E-value: 1.48e-26

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  605 MIETRHVVATHGVAETSLESFYGRSSLV-------GMPSLNPGDTVTE------WIINFG--EFVQLRAKLCLFTYMRFD 669
Cdd:pfam00073    4 TPETRTVGYGKNPLELAVENFLGRDAPVqpdvqgeRFYTLDSTDWTSLskgffwWKLPLAllSMGLLGRLLRYHTYYRGG 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  670 IEFTIVATAysatgdpiSDPTYITYQVMYVPPGASAPTDQDtYQWQSGANPSLLSRVG-DVPAAFSVPFMGTANAYSYAY 748
Cdd:pfam00073   84 LEVTVQFNG--------SKFHQGKLLVAYVPPGAPPPGSRD-YLWQATLNPHQFWNLGlNSSARLSVPYISIAHYYSTFY 154


                   ..
gi 1147809662  749 DG 750
Cdd:pfam00073  155 DG 156

Pico_P1A

pfam02226

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

2-69

1.40e-20

Pssm-ID: 308053 Cd Length: 68 Bit Score: 87.43 E-value: 1.40e-20

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1147809662    2 GGQFSKNTAGSHTTGTYAAGGSTIHYTNINYYENAASSSLNKQDLTQDPTKFTQPVVDVIKESAVPLK 69
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 68

P3A

pfam08727

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

1418-1478

1.20e-13

Pssm-ID: 400873 Cd Length: 59 Bit Score: 67.45 E-value: 1.20e-13

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1147809662 1418 GPPEFRPLRIDVsEETPAPPAIADLLASVDSEDVREYCRQKGWIVQerITKE-SLERNVSRA 1478
Cdd:pfam08727    1 AIFQGIDLKIDI-KTSPPPEAIADLLQAVDSPEIIDYCEDKGWIVN--IPAEcQIERDIGIA 59

Name

Accession

Description

Interval

E-value

Enterovirus_RdRp

cd23213

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

1721-2173

0e+00

Pssm-ID: 438063 Cd Length: 453 Bit Score: 833.33 E-value: 0e+00

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1721 SKDAGYPIINAPTKTKLHPSVFFDIFPGEKEPAVLHKKDKRLEVDFEEALFSKYIGNIHKPVTEEMEIAIDHYANQLKQL 1800
Cdd:cd23213      1 NKEVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1801 DIDPTPISMEDAIYGTEGLEALDLGTSAGYPYVALGIKKRDILNKETRDVTKMQQCIDKYGLNLPMVTYVKDELRSKEKV 1880
Cdd:cd23213     81 DIDTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKV 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1881 KKGKSRLIEASSLNDSVAMRCAFGNLYKAFHTNPGTLTGCAVGCNPETFWSKIPVMMDGELFGFDYTAYDASLSPVWFQC 1960
Cdd:cd23213    161 EKGKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDGSLFAFDYTGYDASLSPVWFRA 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1961 LYLLLEKIGFGHCKHFIDQLCCSNHLFMDKRYVVVGGMPSGCSGTSIFNSMINNIIIRTLVLTVYKNIDLDDLKIIAYGD 2040
Cdd:cd23213    241 LKMVLEKGYSEEAVSLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYGD 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2041 DVIASYPFELDAKLLADAGKSFGLIMTPPDKSSEFVKLTWDNVTFLKRSFVKDERFPFLIHPVMKMSDIHESIRWTKDAK 2120
Cdd:cd23213    321 DVIASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDPR 400

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1147809662 2121 STQDHVRSLCLLAWHCGQEQYEEFLEKIRSVPVGRALSLPSFKALQRSWYDSF 2173
Cdd:cd23213    401 NTQDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453

Rabovirus_RdRp

cd23230

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

1812-2173

1.55e-175

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: 539.47 E-value: 1.55e-175

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1812 AIYGTEGLEALDLGTSAGYPYVALGIKKRDILNKETRDVTKMQQCIDKYGLNLPMVTYVKDELRSKEKVKKGKSRLIEAS 1891
Cdd:cd23230      1 AAYGIENLEGLDLNTSAGYPYVLNGIKKRDILDPETRDTTKLQECLDKYGVDLPFVTYLKDELRPLEKIKKGKTRLIECS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1892 SLNDSVAMRCAFGNLYKAFHTNPGTLTGCAVGCNPETFWSKIPVMMDGELFGFDYTAYDASLSPVWFQCLYLLLEKIGFG 1971
Cdd:cd23230     81 SMNDTIRMKMMFGRLFATYHRNPGPITGSAVGCNPDIHWTKFRAEMHGEIIAFDYSNYDASLNKVWFECLKMVLKNFGFK 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1972 HCKHfIDQLCCSNHLFMDKRYVVVGGMPSGCSGTSIFNSMINNIIIRTLVLTVYKNIDLDDLKIIAYGDDVIASYPFELD 2051
Cdd:cd23230    161 DLRP-IDHIIRSRHIYKGIEYDVEGGMPSGCSGTSIFNSIINNIIIMTLVLDAYKGIDLEQLKIIAYGDDVIVTYPYPLD 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2052 AKLLADAGKSFGLIMTPPDKSSEFVKLTWDNVTFLKRSFVKDERFPFLIHPVMKMSDIHESIRWTKDAKSTQDHVRSLCL 2131
Cdd:cd23230    240 AALLADCGKKYGLKMTPPDKSAEFKNVTWEDVTFLKRRFKPAKHYPFLIHPVFDQQEILESLRWTRNPAHTQEHVRSLAE 319

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|..
gi 1147809662 2132 LAWHCGQEQYEEFLEKIRSVPVGRALSLPSFKALQRSWYDSF 2173
Cdd:cd23230    320 LAWHSGRKSYEEFCNLVKSTNVGKACILPPYESFKRMWLDQF 361

Sapelovirus_RdRp

cd23218

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

1811-2173

1.85e-165

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

Pssm-ID: 438068 Cd Length: 366 Bit Score: 512.14 E-value: 1.85e-165

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1811 DAIYGTEGLEALDLGTSAGYPYVALGIKKRDILNKETRDVTKMQQCIDKYGLNLPMVTYVKDELRSKEKVKKGKSRLIEA 1890
Cdd:cd23218      1 DVVYGIDNLEGLDLNTSAGYPYNTMGIRKKDLIPPRGEPLSPLLKALDLHGYDLPFTTYLKDELRPKEKVKMGKTRLIEC 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1891 SSLNDSVAMRCAFGNLYKAFHTNPGTLTGCAVGCNPETFWSKIPVMMDGE-LFGFDYTAYDASLSPVWFQCLYLLLEKIG 1969
Cdd:cd23218     81 SSLNDTIRMKRIFGRLFQTFHKNPGTYTGSAVGCNPDVHWSKFAEEGGMDnVCAFDYTNWDASLSPFWFDALKLFLSKLG 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1970 FGHCK-HFIDQLCCSNHLFMDKRYVVVGGMPSGCSGTSIFNSMINNIIIRTLVLTVYKNIDLDDLKIIAYGDDVIASYPF 2048
Cdd:cd23218    161 YSERDiVLIDHLCYSNHIFKNEGYKVAGGMPSGCSGTSIFNSIINNIVVRTLVLLVYKGINLDELRILCYGDDLLVAYPY 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2049 ELDAKLLADAGKSFGLIMTPPDKSSEF---VKLTwdNVTFLKRSFVKDERFPFLIHPVMKMSDIHESIRWTKDAKSTQDH 2125
Cdd:cd23218    241 PLDPNVLADLGKSLGLTMTPADKSDTFqgcTKLT--EVTFLKRSFVFDEEFPFLCHPVFPMEEVHESIRWTRNASTTQEH 318

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*...
gi 1147809662 2126 VRSLCLLAWHCGQEQYEEFLEKIRSVPVGRALSLPSFKALQRSWYDSF 2173
Cdd:cd23218    319 VTSLCLLAWHNGEEVYEEFCEKIRSVPVGRALILPPYSQLRRSWLDMF 366

ps-ssRNA_Picornaviridae

cd23193

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

1812-2149

5.92e-138

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: 434.28 E-value: 5.92e-138

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1812 AIYGTEGLEALDLGTSAGYPYVALGIKKRDILNKETRDVT-----KMQQCIDKYGLNLPMVTYVKDELRSKEKVKKGKSR 1886
Cdd:cd23193      1 AINGIDGLDPIDLNTSPGYPYTTQGLRRRDLIDNDKGGVSplleeEEQVLLDLDGPDVVFTTFLKDELRPKEKVKAGKTR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1887 LIEASSLNDSVAMRCAFGNLYKAFHTNPGTLTGCAVGCNPETFWSKIPVMM-DGELFGFDYTAYDASLSPVWFQCL-YLL 1964
Cdd:cd23193     81 VIEAAPLDYVIAGRMVFGRLFAQFHSNPGILTGSAVGCNPDTDWTRLFASLkQDNVYDLDYSGFDASLSSQLFEAAvEVL 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1965 LEKIGFGH-CKHFIDQLCCSNHLFMDKRYVVVGGMPSGCSGTSIFNSMINNIIIRTLVLTVYKnIDLDDLKIIAYGDDVI 2043
Cdd:cd23193    161 AECHGDPElVLRYLEPIINSKHVVGDERYTVEGGMPSGCPCTSILNSICNNLVVRYALLETGK-FDPDEYYILAYGDDVL 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2044 ASYPFELDAKLLADAGKS-FGLIMTPPDKSSEFVKLTWDNVTFLKRSFVKDERFpFLIHPVMKMSDIHESIRWTKDAKST 2122
Cdd:cd23193    240 VSTDEPIDPSDLAEFYKKyFGMTVTPADKSSDFPESSPIEDVFLKRRFFVPDGT-FLIHPVMDLETLEQSLMWCGRGGFF 318

                          330       340
                   ....*....|....*....|....*..
gi 1147809662 2123 QDHVRSLCLLAWHCGQEQYEEFLEKIR 2149
Cdd:cd23193    319 QQLLSSLCELALHHGPEEYERLVSKVR 345

Mischivirus_RdRp

cd23227

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

1727-2173

1.75e-80

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: 274.52 E-value: 1.75e-80

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1727 PIINAPTKTKLHPSVFFDIFPGEKEPAVLHKKDKRL--EVDFEEALFSKYIGNiHKPVTEEMEIAIDHYANQL-KQLDID 1803
Cdd:cd23227     10 PRIHVPRKTKLRKSPAYPIFKPDAGPAVLSKNDPRLaeGVDFDKQVFSKHSAN-QKEYPKAFRRMARWYADRVfTYLGKD 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1804 PTPISMEDAIYGTEGLEALDLGTSAGYPYVALGIKKRDILNKETRDVT------KMQQCIDKYGLNLPMVTYVKDELRSK 1877
Cdd:cd23227     89 NGPLSVKDAIKGIDNLDAMDPTTSPGLPYSAAGIKRTDLLDFDTGEIIspalraEYNKYVSGDYSDHVFQTFLKDEIRSE 168

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1878 EKVKKGKSRLIEASSLNDSVAMRCAFGNLYKAFHTNPGTLTGCAVGCNPETFWSKIP--VMMDGELFGFDYTAYDASLSP 1955
Cdd:cd23227    169 EKIKAGKTRIVDVPSLAHVIIGRVLLGKFCSKFQASPGTELGSAIGCNPDWDWTYFAhqLMERQWCYDIDYSNFDSTHGT 248

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1956 VWFQCLY--LLLEKIGFG-HCKHFIDQLCCSNHLFMDKRYVVVGGMPSGCSGTSIFNSMINNIIIRTLVLTVYKNIDLDD 2032
Cdd:cd23227    249 GMFELLIdcFFTPENGFSpAVAPYLRSLAFSKHAWMDKRYKIEGGLPSGCSATSVLNTVMNNIIIRALLSLTYKNFHPED 328

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2033 LKIIAYGDDVIASYPFELDAKLLADAGKSFGLI-MTPPDKSSEFVKL-TWDNVTFLKRSFVKDERFPFLIHPVMKMSDIH 2110
Cdd:cd23227    329 VLVLAYGDDLLVASDYQLDFNRVREKAAEHTLYkLTTANKAPDFPETsTLLDCQFLKRKFVLHSTRNFIWRPVMDVTNLK 408

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1147809662 2111 ESIRWTKdAKSTQDHVRSLCLLAWHCGQEQYEEFLEKIRSVpvgrALSLPSFKALQRSWYDSF 2173
Cdd:cd23227    409 TMLSFYK-PNTLSEKLLSVAQLAFHSGYTVYEELFAPFKEL----QMTVPSWWYLEHEWEHNF 466

Dicipivirus_RdRp

cd23222

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

1739-2169

1.81e-79

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: 271.08 E-value: 1.81e-79

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1739 PSVFFDIFPGEKEPAVLHKKDKRL--EVDFEEALFSKYIGNIHKP---VTEEMEIAIdhyaNQLKQLDidPT----PISM 1809
Cdd:cd23222      2 PSPVYGVYPVTKEPAPLKPTDRRIdeGVDFNEPVFGKYGADMKEPfrnLDVGRDVVI----ARLKKVL--PNkkfaPCTV 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1810 EDAIYGTEGLEALDLGTSAGYPYVALGIKKRDILNKET--------RDVTKMQQCiDKYGLNLPMVTYVKDELRSKEKVK 1881
Cdd:cd23222     76 SEALNGKDGLPKLDLKQASGYPYNLSAIKRKHLIESDKdgfltatpKLLADIEES-KKHPEKFPYTSFLKDELRSVKKVK 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1882 KGKSRLIEASSLNDSVAMRCAFGNLYKAFHTNPGTLTGCAVGCNPETFWSKI--PVMMDGELFGFDYTAYDASLSPVWFQ 1959
Cdd:cd23222    155 AGKTRVVEAGSLPVIVEGRMIFGNLFAYFNTHPGFETMAAVGCDPEVCWTDWyyKMREKAHTWDYDYTGFDGSIPSCSFD 234

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1960 CLY-LLLEKI-GFGHCKHFIDQLCCSNHLFMDKRYVVVGGMPSGCSGTSIFNSMINNIIIRTLVLTVYKNIDLDDLKIIA 2037
Cdd:cd23222    235 ALAdLLCEFVeNEDDVRRYISNIKNSYHAYDGNLYLIEGAMPSGCAGTSVFNCLINAMLCFSCFMDLEPEMDPFEPLLIA 314

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2038 YGDDVIASYPFEL-DAKLLADAGKSFGLIMTPPDKSSEFVKLT-WDNVTFLKRSFVKDERFPfLIHPVMKMSDIHESIRW 2115
Cdd:cd23222    315 YGDDILVSSDHDLfPSRVSEWMKANTTFKITPADKGEIFNDDSdVSDVRFLKRLFVEDPVCE-LIHPVIETETLEPSLNW 393

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1147809662 2116 TkDAKSTQDHVRSLCLLAWHCGQEQYEEFLEKIRSVPVGRALSLPSFKAL---QRSW 2169
Cdd:cd23222    394 C-HEGEFETKVDAISMLAFHHGPEYYRDWCKKLTDICEERNISPPGLKPYsvhRNRW 449

Megrivirus_RdRp

cd23223

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

1745-2148

3.40e-79

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: 269.40 E-value: 3.40e-79

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1745 IFPGEKEPAVLHKKDKRLE--VDFEEALFSKYIGNihKPVTEEMEIAIDHYANQL-KQLDIDPT-PISM---EDAIYGTE 1817
Cdd:cd23223      4 AFPVTHGPAALTNKDKRLEegVDLDDVMFSKHVPD--HPGWPTLEPAMSYVVEDLmHKLGFSKDePVPMwtlEQAINGEG 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1818 GLEALDLGTSAGYPYVALGIKKRDILN------KETRDVTKMQQCIDKYGLNLPMVTYVKDELRSKEKVKKGKSRLIEAS 1891
Cdd:cd23223     82 VMDGIDMGQSPGYPYNAQGRSRRSFFEwngekwQPTEELKKEVDHALKDPDDFYFSTFLKDELRPLEKVKAGKTRLVDGD 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1892 SLNDSVAMRCAFGNLYKAFHTNPGTLTGCAVGCNPETFWSKIPVMMDGE----LFGFDYTAYDASLSPVWFQCLYLLLEK 1967
Cdd:cd23223    162 SLPRILAMRMVFGPLFEAMLRKNGPEIHSAVGCNPDTDWTRYYHEMGPDsfpyCFDLDYSCFDSTEPKIAFRLMAKYLKP 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1968 IGFGHCKHFIDQLCCSNHLFMDKRYVVVGGMPSGCSGTSIFNSMINNIIIRTLVLTVykNIDLDDLKIIAYGDDVIASYP 2047
Cdd:cd23223    242 YFSVDVTPFFEALATSKHVYGDKAYEMEGGMPSGCVGTSMFNCINNSAFIVSALIAL--KISPEDCAWICYGDDVIISTD 319

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2048 FELDAKLLAD-AGKSFGLIMTPPDKSSEFVKL-TWDNVTFLKRSFVKDERFPFLIHPVMKMSDIHESIRWTKDAKsTQDH 2125
Cdd:cd23223    320 EKALSKRIADfYHKNTNLVVTPASKSGDFPETsTIYDVTFLKRFFQPDSHYPHLIHPYMPLEHLEQSVMWQTDGP-FQQK 398

                          410       420
                   ....*....|....*....|...
gi 1147809662 2126 VRSLCLLAWHCGQEQYEEFLEKI 2148
Cdd:cd23223    399 LDSLCLLAFHAGGPDYREFVDAI 421

Cardiovirus_RdRp

cd23211

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

1727-2173

3.95e-78

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

Pssm-ID: 438061 Cd Length: 460 Bit Score: 267.48 E-value: 3.95e-78

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1727 PIINAPTKTKLHPSVFFDIFPGEKEPAVLHKKDKRLEVDFEEALFSKYIGNIHK--PVteeMEIAIDHYANQL-KQLDID 1803
Cdd:cd23211     10 PVVHVPRKTKLRRTVAHPVFQPKFEPAVLSKYDPRTDKDVDEVAFSKHTTNQESlpPV---FRMVAKEYANRVfTLLGKD 86

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1804 PTPISMEDAIYGTEGLEALDLGTSAGYPYVALGIKKRDILNKETRDVT-----KMQQCIDKYGLNLPMVTYVKDELRSKE 1878
Cdd:cd23211     87 NGRLTVEQAVLGLEGMDPMEKDTSPGLPYTQQGLRRTDVVDFETATMIpflaeAHRKMVEGDYSDVVYQSFLKDEIRPIE 166

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1879 KVKKGKSRLIEASSLNDSVAMRCAFGNLYKAFHTNPGTLTGCAVGCNPETFWSKIPVMMDG--ELFGFDYTAYDASLSPV 1956
Cdd:cd23211    167 KVQAAKTRIVDVPPFEHCILGRQLLGRFASKFQTNPGLELGSAIGCDPDVDWTAFAVALSGfkYVYDVDYSNFDSTHSTA 246

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1957 WFQCLY--LLLEKIGFG-HCKHFIDQLCCSNHLFMDKRYVVVGGMPSGCSGTSIFNSMINNIIIRTLVLTVYKNIDLDDL 2033
Cdd:cd23211    247 MFELLIenFFTEENGFDpRIGEYLRSLAVSRHAYEERRVLIRGGLPSGCAATSMLNTIMNNIIIRAGLYLTYKNFEFDDI 326

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2034 KIIAYGDDVIASYPFELDAKLLADAGKSFGLIMTPPDKSSEF-VKLTWDNVTFLKRSFVKDErfPFLIHPVMKMSDIHES 2112
Cdd:cd23211    327 KVLSYGDDLLVATNYQIDFNLVKARLAKFGYKITPANKTSTFpLTSTLEDVVFLKRKFVKEN--SYLYRPVMDRENLKAM 404

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1147809662 2113 IRWTKDAkSTQDHVRSLCLLAWHCGQEQYEEFLEKIRSVPVgralSLPSFKALQRSWYDSF 2173
Cdd:cd23211    405 LSYYRPG-TLKEKLTSIALLAVHSGKQVYDEIFAPFREVGI----VVPTYESVLYRWLSLF 460

Cosavirus_RdRp

cd23226

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

1727-2173

9.64e-78

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: 266.11 E-value: 9.64e-78

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1727 PIINAPTKTKLHPSVFFDIFPGEKEPAVLHKKDKRLE--VDFEEALFSKYIGNI----HKPVTEEMEIAIDHYANQLKql 1800
Cdd:cd23226     10 PRVHVPRQSKLKRTNATYPATGKYGPAVLSKNDPRLDpdVDFDKVIFSKHVANVvideDTSFWNALKMSAQIYAEKFK-- 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1801 DIDPTPISMEDAIYGTEGLEALDLGTSAGYPYVAlgiKKRDILNKETRDV--TKMQQCIDKYGLN----LPMVTYVKDEL 1874
Cdd:cd23226     88 GVDFSPLTVEEAILGIPGLDRMDPNTASGLPYTK---TRRQMIDFQEGKIldPELQERLDTWLSGkqpeMLYQTFLKDEI 164

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1875 RSKEKVKKGKSRLIEASSLNDSVAMRCAFGNLYKAFHTNPGTLTGCAVGCNPETFWSKIPVMMDGE--LFGFDYTAYDAS 1952
Cdd:cd23226    165 RPIEKVKAGKTRIIDVTPLDHVLAFRIVLGRFMAHFHNNYGFELGSAVGCDPDVAWANFGFALSSKkyQYDFDYSNFDAS 244

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1953 LSPVWFQCL--YLLLEKIGFGH-CKHFIDQLCCSNHLFMDKRYVVVGGMPSGCSGTSIFNSMINNIIIRTLVLTVYKNID 2029
Cdd:cd23226    245 HSESIFELLkqFVFTKDNGFDHrCSLMIDSLVTSTHCYEDQRMTIRGGLPSGTSGTSVINTIINNIIFKAALYHTYSNFE 324

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2030 LDDLKIIAYGDDVIASYPFELDAKLLADAGKSFGLIMTPPDKSSEFVKLTWDNVTFLKRSFVKderFPFLIHPVMKMSDI 2109
Cdd:cd23226    325 WDDVQMLAYGDDIVAASDCLLDLDRVKYFMALIGYKITPADKGEKFIPKDMQNIQFLKRSFRK---VAGVWAPIMDLENL 401

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1147809662 2110 HESIRWTKDAkSTQDHVRSLCLLAWHCGQEQYEEFLEKIrsvpVGRALSLPSFKALQRSWYDSF 2173
Cdd:cd23226    402 QAMLSWYKPG-TLQEKLDSVARLAHFCGEKVYDHLFTTF----VKDGFQIKPWKQLHFEWLNRF 460

Pico_P2A

pfam00947

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

858-984

1.17e-74

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

Pssm-ID: 395757 Cd Length: 127 Bit Score: 244.21 E-value: 1.17e-74

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  858 NRHLADCVDWQNLVWESYERDLLVTRVDAHGCDQIARCDCRAGVYYCKSRMKHYPVVVTPPSLVHVDKNDYYPERYQSHV 937
Cdd:pfam00947    1 NRHLATHEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1147809662  938 ALGIGFAEPGDCGGLLRCEHGVMGILTAGGNNLVAFADIRDLLWIED 984
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVRDLLWLEE 127

Mosavirus_RdRp

cd23225

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

1812-2170

4.93e-73

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: 249.45 E-value: 4.93e-73

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1812 AIYGTEGLEALDLGTSAGYPYVALGIKKRDILN-KETRD------VTKMQQCIDKY--GLNLP-MVTYVKDELRSKEKVK 1881
Cdd:cd23225      2 AMNGDGISDAMDMTKAVGYPYCLDSIKRLDLVEiKETENgkvylpTERLVEETEKFftGEEKPkFVTFLKDEVRSNEKIK 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1882 KGKSRLIEASSLNDSVAMRCAFGNLYKAFHTNPGTLTGCAVGCNPETFWSKIPV-MMDGELFGFDYTAYDASLSPVWFQC 1960
Cdd:cd23225     82 QGKTRIVDASPFPYAIAGRMVMQNFMSNMMRCNGTEVGSAVGCDPDTEWTRYFFeLCDRYVFDLDYKAFDSTHPTAMFNL 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1961 L--YLLLEKIGFGH-CKH-FIDQLCCSNHLFMDKRYVVVGGMPSGCSGTSIFNSMINNIIIRTLVLTVYK--NIDLDDLK 2034
Cdd:cd23225    162 LaeRFFTERNGFDQqAVRiFLNGLSDSDHVYEGKHFRIRGGLPSGCPCTSILNTVINNIIVRAAILGAYQidTVDFQKFR 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2035 IIAYGDDVIASYPFELDAKLLAD-AGKSFGLIMTPPDKSSEFVKLT--WDnVTFLKRSFVKDERFPFLIHPVMKMSDIHE 2111
Cdd:cd23225    242 MLAYGDDVVYATPQPIKPQDLADwLHANTNYKVTPASKAGTFPEEStiWD-VTFLKRSFKPDEDHGHLIRPVMAVGNLKQ 320

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1147809662 2112 SIRWTKDAkSTQDHVRSLCLLAWHCGQEQYEEFLEKIRSVPVGraLSLPSFKALQRSWY 2170
Cdd:cd23225    321 MLSFMRPG-TFPDKVRSVAGLAVHCGEEDYNQLADAVALYVPG--VSMPAYKYMKACWY 376

Kobuvirus_RdRp

cd23214

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

1727-2149

1.98e-72

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: 250.92 E-value: 1.98e-72

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1727 PIINAPTKTKLHPSVFFDIFPGEKEPAVLHKKDKRLE--VDFEEALFSKY-IGNIHKPvTEEMEIAIDHYANQLkqldid 1803
Cdd:cd23214      1 PGVNVNRKSRLGPSPAYGAFPVKKQPAPLTQKDDRLEdgIRLDDQLFLKHnKGDMDEP-WPGLEAAADLYFSKF------ 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1804 PTPI---SMEDAIYGTEGLEALDLGTSAGYPYVALGIKKRDILNKETRDV----TKMQQCIDKYGLNLPMV--TYVKDEL 1874
Cdd:cd23214     74 PTMIrtlTQEEAINGTPNLEGLDMNQAAGYPWNTMGRSRRSLFVEVQPGIyvpkPELQAEIDKTLEDPDYFysTFLKDEL 153

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1875 RSKEKVKKGKSRLIEASSLNDSVAMRCAFGNLYKAFHTNPGTlTGCAVGCNPETFWSKI--PVMMDGELFGFDYTAYDAS 1952
Cdd:cd23214    154 RPTAKVTLGLTRVVEAAPIHAIVAGRMLLGGLIEYMQARPGK-HGSAVGCNPDLHWTKFfyKFCHYPQVFDLDYKCFDAT 232

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1953 LSPVWFQCLYLLLEKI-GFGHCKHFIDQLCCSNHLFMDKRYVVVGGMPSGCSGTSIFNSMINNIIIRTlVLTVYKNIDLD 2031
Cdd:cd23214    233 LPSCAFRIVEDHLERLtGDERVTRYIESIRHSHHVYGNETYEMIGGNPSGCVGTSIINTIINNICVLS-ALIQHPDFSPE 311

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2032 DLKIIAYGDDVI-ASYPFELDAKLLADAGKSFGLIMTPPDKSSEFVKL-TWDNVTFLKRSFVKDERFPFLIHPVMKMSDI 2109
Cdd:cd23214    312 SFRILAYGDDVIyGCDPPIHPSFIKEFYDKHTPLVVTPANKGSDFPETsTIYDVTFLKRWFVPDDIRPFYIHPVMDPDTY 391

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|
gi 1147809662 2110 HESIRWTKDAkSTQDHVRSLCLLAWHCGQEQYEEFLEKIR 2149
Cdd:cd23214    392 EQSVMWLRDG-DFQDLVTSLCYLAFHSGPKTYDRWCTRVR 430

ps-ssRNAv-Picornavirales

cd23169

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

1867-2149

4.57e-72

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: 244.04 E-value: 4.57e-72

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1867 VTYVKDELRSKEKVKKGKSRLIEASSLNDSVAMRCAFGNLYKAFHTNPGTLtGCAVGCNPE-TFWSKI--------PVMM 1937
Cdd:cd23169      4 VDCLKDELRPIEKVKAGKTRLFSASPLDYTIAFRKYFGDFIAAFQKNRIKL-EHAVGINPDsVEWTRLyrrllkkgPNIF 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1938 DGelfgfDYTAYDASLSPVWFQCLYLLLEKIGFGHC--------KHFIDQLCCSNHLFMDKRYVVVGGMPSGCSGTSIFN 2009
Cdd:cd23169     83 AG-----DYSNFDGSLPPDVMEAAFDIINDWYDEYVddedervrKVLFEELINTIHLVGNLVYQVHGGNPSGNPLTTIIN 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2010 SMINNIIIRTLVLTVYKNIDLDD----LKIIAYGDDVIAS----YPFELDAKLLADAGKSFGLIMTPPDKSSEFVKL-TW 2080
Cdd:cd23169    158 SIVNLLYIRYAWLRITGLTSLSDfkknVRLVTYGDDVIISvsdeVKDEFNFVTISEFLKELGITYTDADKSGDIVPYrPL 237

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1147809662 2081 DNVTFLKRSFVKDErFPFLIHPVMKMSDIHESIRWTK---DAKSTQDHVRSLCLLAWH-CGQEQYEEFLEKIR 2149
Cdd:cd23169    238 EEVTFLKRGFRPHP-TPGLVLAPLDLESIEEQLNWTRkedDLLEATIENARAALLLAFgHGPEYYNKFRQKLN 309

Aphthovirus_RdRp

cd23210

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

1729-2169

2.57e-69

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

Pssm-ID: 438060 Cd Length: 458 Bit Score: 241.77 E-value: 2.57e-69

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1729 INAPTKTKLHPSVFFDIFPGEKEPAVLHKKDKRLE--VDFEEALFSKYIGNihKPVTEE-----MEIAIDHYANQLKQLD 1801
Cdd:cd23210      6 VHVMRKTKLAPTVAHGVFNPEFGPAALSNKDPRLNegVVLDEVIFSKHKGD--TKMSAEdkalfRRCAADYASRLHSVLG 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1802 IDPTPISMEDAIYGTEGLEALDLGTSAGYPYVALGIKKRDILNKETRDV---TKMQ-QCIDKYGLNLPMVTYVKDELRSK 1877
Cdd:cd23210     84 TANAPLSIYEAIKGVDGLDAMEPDTAPGLPWALQGKRRGALIDFENGTVgpeVEAAlKLMEKREYKFACQTFLKDEIRPM 163

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1878 EKVKKGKSRLIEASSLNDSVAMRCAFGNLYKAFHTNPGTLTGCAVGCNPETFWSKIPVMMDG--ELFGFDYTAYDASLSP 1955
Cdd:cd23210    164 EKVRAGKTRIVDVLPVEHILYTRMMIGRFCAQMHSNNGPQIGSAVGCNPDVDWQRFGTHFAQyrNVWDVDYSAFDANHCS 243

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1956 VWFQCL--YLLLEKIGFG-HCKHFIDQLCCSNHLFMDKRYVVVGGMPSGCSGTSIFNSMINNIIIRTLVLTVYKNIDLDD 2032
Cdd:cd23210    244 DAMNIMfeEVFRTEFGFHpNAEWILKTLVNTEHAYENKRITVEGGMPSGCSATSIINTILNNIYVLYALRRHYEGVELDT 323

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2033 LKIIAYGDDVIASYPFELDAKLLADAGKSFGLIMTPPDKSSEFVKL--TWDNVTFLKRSFVKDERFPFLiHPVMKMSDIh 2110
Cdd:cd23210    324 YTMISYGDDIVVASDYDLDFEALKPHFKSLGQTITPADKSDKGFVLghSITDVTFLKRHFHMDYGTGFY-KPVMASKTL- 401

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1147809662 2111 ESIRWTKDAKSTQDHVRSLCLLAWHCGQEQYEEFLEkirsvPVGRALSLPSFKALQRSW 2169
Cdd:cd23210    402 EAILSFARRGTIQEKLISVAGLAVHSGPDEYRRLFE-----PFQGLFEIPSYRSLYLRW 455

Rosavirus_RdRp

cd23221

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

1812-2173

9.23e-63

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: 220.18 E-value: 9.23e-63

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1812 AIYGTEGLEALDLGTSAGYPYVALGIKKRDILN-------KETRDVTKMQQCIDKYGLNlPMVTYVKDELRSKEKVKKGK 1884
Cdd:cd23221      1 AINGIDNMDGLDMNQSPGVPYVSEGVSRRSLFDcvdgqwvPRERLASDIAQVSGDPSLG-HFATFLKDELRSTEKVAAGK 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1885 SRLIEASSLNDSVAMRCAFGNLYKAFHTNPGTLTGCAVGCNPETFWSKI--PVMMDGELFGFDYTAYDASLSPVWFQCLY 1962
Cdd:cd23221     80 TRVVEAGSLPHIIVGRKIFGNLFALFNSNPGFQTMCAVGCDPDVTWTELyhPLSAKTYVFDYDYSGFDGSVPSCCFDALA 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1963 LLLEKI--GFGHCKHFIDQLCCSNHLFMDKRYVVVGGMPSGCSGTSIFNSMINNIIIRTLVLTVYKNIDLDDLKIIAYGD 2040
Cdd:cd23221    160 DLLADFveGEEDVRKYISSLKTSFHHYKGKLWRLDGAMPSGCCGTSVFNSLINAMLLFSAFSQICPDFRASEPLLVAYGD 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2041 DVIASYPFELDAKLLAD-AGKSFGLIMTPPDKSSEFVKLT-WDNVTFLKRSFVKDERFPFLIHPVMKMSDIHESIRWTKd 2118
Cdd:cd23221    240 DVLVGTDQPLFPSKVAEwVNSHTTFRITPADKGSVFNDESdIHSVQFLKRHFTPDPDFPALIHPTIDPDTYEQSVMWQR- 318

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1147809662 2119 AKSTQDHVRSLCLLAWHCGQEQYEEFLEKI--RSVPVGRALS-LPSFKALQRSWYDSF 2173
Cdd:cd23221    319 TGDFQETVNSLALLVFHRGPKSYSRWCESVtrKCVDGGYPPPfFPPFSLLRHQWLKKF 376

RNA_dep_RNAP

cd01699

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

1864-2116

6.86e-62

RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage. RdRp catalyzes synthesis of the RNA strand complementary to a given RNA template. RdRps of many viruses are products of processing of polyproteins. Some RdRps consist of one polypeptide chain, and others are complexes of several subunits. The domain organization and the 3D structure of the catalytic center of a wide range of RdRps, including those with a low overall sequence homology, are conserved. The catalytic center is formed by several motifs containing a number of conserved amino acid residues. This subfamily represents the RNA-dependent RNA polymerases from all positive-strand RNA eukaryotic viruses with no DNA stage.

Pssm-ID: 238843 [Multi-domain] Cd Length: 278 Bit Score: 213.68 E-value: 6.86e-62

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1864 LPMVTYVKDELRSKEKVKKGKSRLIEASSLNDSVAMRCAFGNLYKAFHTNPGTLtGCAVGCNPE-TFWSKIPVMMDGEL- 1941
Cdd:cd01699     18 LVFTTFLKDELRPLEKVEAGKTRLIQPRPLDYNIALRMYLGPFEAKLMKNRGGL-PIAVGINPYsRDWTILANKLRSFSp 96

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1942 --FGFDYTAYDASLSPVWFQCLYLLLEKIGFGH----CKHFIDQLCCSN-HLFMDKRYVVVGGMPSGCSGTSIFNSMINN 2014
Cdd:cd01699     97 vaIALDYSRFDSSLSPQLLEAEHSIYNALYDDDdeleRRNLLRSLTNNSlHIGFNEVYKVRGGRPSGDPLTSIGNSIINC 176

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2015 IIIRTLVLTVYKNIDLDDLKIIAYGDDVIASYPFELD---AKLLADAGKSFGLIMTPPDKSSEFVKlTWDNVTFLKRSFV 2091
Cdd:cd01699    177 ILVRYAFRKLGGKSFFKNVRLLNYGDDCLLSVEKADDkfnLETLAEWLKEYGLTMTDEDKVESPFR-PLEEVEFLKRRFV 255

                          250       260
                   ....*....|....*....|....*
gi 1147809662 2092 KDErfPFLIHPVMKMSDIHESIRWT 2116
Cdd:cd01699    256 LDE--GGGWRAPLDPSSILSKLSWS 278

Rhv

pfam00073

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

93-285

2.64e-57

Pssm-ID: 395026 Cd Length: 170 Bit Score: 195.99 E-value: 2.64e-57

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662   93 TTQEAANICVGYGEWPSHLDDHDATAVDRPTHPGVSCERFYTLPSVEWTNTWKG-QYWKLPNALTETGMFGQNAQFHYLY 171
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGfFWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  172 RGGWAVHVQCNATKFHQGLLLVVMIPEcvvnlrGAPPINKTQpgengreieepflldsgeALGNALIYPHQWINLRTNNA 251
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPP------GAPPPGSRD------------------YLWQATLNPHQFWNLGLNSS 136

                          170       180       190
                   ....*....|....*....|....*....|....
gi 1147809662  252 ATIIVPYVNAIPMDSAIRHSNWTLMVIPVTELAY 285
Cdd:pfam00073  137 ARLSVPYISIAHYYSTFYDGNWTLVVAGWVPLNY 170

Teschovirus_RdRp

cd23212

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

1806-2145

5.83e-56

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: 199.46 E-value: 5.83e-56

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1806 PISMEDAIYGTEGLEALDLGTSAGYPYVALGIKKRDILNKETRDVTKMQQCIDKY-GLNLP---MVTYVKDELRSKEKVK 1881
Cdd:cd23212     10 PLSVREAVEGIDGLDPMDMDKSPGLPYVKKGLRRTDLWNPKTGPSIELMAEINRYlDYNYDkhvFLTFLKDELRPKEKVQ 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1882 KGKSRLIEASSLNDSVAMRCAFGNLYKAFHTNPGTLTGCAVGCNPETFWSKIPVMMDGE-LFGFDYTAYDASLSPVWFQC 1960
Cdd:cd23212     90 AGKTRVIDVAGFGHAIVGRMLFGRLFAFFHKNPGWNTGSAVGVNPDLAWTQIFYTAPSRnVLAMDYSGFDASHTSGMFCI 169

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1961 LYLLLEKIGFGHCK-HFIDQLCCSNHLFMDKRYVVVGGMPSGCSGTSIFNSMINNIIIRTLVLTVYKnidlDDLKIIAYG 2039
Cdd:cd23212    170 LKHFLTTLGYGTLQlSYIDSLCYSKHHWDDETYRLDGGLPSGCSGTTIFNTIMNNIVARAAASYAAE----GPVGILCYG 245

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2040 DDVIASYPFELDAKLLADAGKSFGLIMTPPDKSSEfvkLTWDNV---TFLKRSFVKDERfpfLIHPVMKMSDIHESIRWT 2116
Cdd:cd23212    246 DDILVSSPEKFPVSDWLEFYSKTPYKVTAADKSEQ---IDWRDItqcTFLKRGFVLDGS---LVRPVMEEQHLAELLKWA 319

                          330       340
                   ....*....|....*....|....*....
gi 1147809662 2117 KDAkSTQDHVRSLCLLAWHCGQEQYEEFL 2145
Cdd:cd23212    320 RPG-TLQAKLLSIAQLAFHLPRQAYDRLM 347

Passerivirus_RdRp

cd23224

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

1811-2169

1.49e-53

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: 193.38 E-value: 1.49e-53

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1811 DAIYGTEGLEALDLGTSAGYPYvALGIKKRDILNKET----RDVTKMQQ----CIDKygLNLPMVTYVKDELRSKEKVKK 1882
Cdd:cd23224      1 EAINGTPLLDGLDMKQSPGYPW-SLTTNRRSLFTQDEtgkyYPVPELEEavlaCLEN--PDYFYTTHLKDELRPVEKALA 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1883 GKSRLIEASSLNDSVAMRCAFGNLYKAFHTNPGTLtGCAVGCNPETFWSKIPVMMD--GELFGFDYTAYDASLSPVWFQC 1960
Cdd:cd23224     78 GKTRLIEAAPIHAIIAGRMLLGGLFEYMHARPGEH-GSAVGCDPDYHWTPFFHSFDefSQVWALDYSCFDSTLPSCCFDL 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1961 LYLLLEKI-----GFGH--CKHFIDQLCCSNHLFMDKRYVVVGGMPSGCSGTSIFNSMINNIIIRTLVLTvYKNIDLDDL 2033
Cdd:cd23224    157 IAQKLAKIitpgeGIAPdaIVKYIRSISISKHVFGNEAYLMVGGNPSGCVGTSILNSMINNCVLISAFLT-QKDFNPNQM 235

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2034 KIIAYGDDVI-ASYPFELDAKLLADAGKSFGLIMTPPDKSSEFVKLT--WDnVTFLKRSFVKDERFPFLIHPVMKMSDIH 2110
Cdd:cd23224    236 RILTYGDDVLyATNPPIHPRVVKKFFDENTTLIVTPATKAGDFPDEStiWD-VTFLKRYFVPDEIRPWYVHPVIEPATYE 314

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1147809662 2111 ESIRWTKDAkSTQDHVRSLCLLAWHCGQEQYEEFLEKIRSVPVGRALsLPS---FKALQRSW 2169
Cdd:cd23224    315 QSVMWTRGG-DFQDVVTSLSFLAHHAGPTNYMIWEEKVRKAAAAKGV-SLNilpYSYLQHRW 374

RdRP_1

pfam00680

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

1738-2150

1.37e-49

Pssm-ID: 425815 Cd Length: 450 Bit Score: 183.77 E-value: 1.37e-49

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1738 HPSVFFDIFPGEKEPAVLHKKDKRLEVDFEeaLFSKYIGNIHK--------PVTEEMEIAID----HYANQLKQLD--ID 1803
Cdd:pfam00680    1 SPTERHLVAIPAYVPASLGPEDPRWARSYL--NTDPYVDDIKKysrpklpgPADERDKLLNRsaakMVLSELRGVPkkAN 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1804 PTPISMEDAIYGtEGLEALDLGTSAGYPYVALGIKKRDILNKETRDVT------KMQQCIDKYGLNLPMV----TYVKDE 1873
Cdd:pfam00680   79 STLIVYRAIDGV-EQIDPLNWDTSAGYPYVGLGGKKGDLIEHLKDGTEarelaeRLAADWEVLQNGTPLKlvyqTCLKDE 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1874 LRSKEKVKKGKSRLIEASSLNDSVAMRCAFGNLYKAFHTNPGTLTgCAVGCNPETF-WSKIPVMMDGE---LFGFDYTAY 1949
Cdd:pfam00680  158 LRPLEKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHP-IQVGINPFDRgWPRLLRRLARFgdyVYELDYSGF 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1950 DASLSPvWF--QCLYLLLEKIGF----GHCKHFIDQLCCSNHLFMD-KRYVVVGGMPSGCSGTSIFNSMINNIIIRTLvl 2022
Cdd:pfam00680  237 DSSVPP-WLirFAFEILRELLGFpsnvKEWRAILELLIYTPIALPNgTVFKKTGGLPSGSPFTSIINSIVNYLLILYA-- 313

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2023 tVYKNIDLDDLKI---------IAYGDDVIA--SYPFELDAKLLADAGKSFGLIMTPPDKSSEFVKlTWDNVTFLKRSFV 2091
Cdd:pfam00680  314 -LLKSLENDGPRVcnldkyfdfFTYGDDSLVavSPDFDPVLDRLSPHLKELGLTITPAKKTFPVSR-ELEEVSFLKRTFR 391

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1147809662 2092 KDerfPFLIHPVMKMSDIHESIRWTKDAKSTQDHVRSLCLLAWHCGQEQYEEFLEKIRS 2150
Cdd:pfam00680  392 KT---PGGYRPPLDRKRILAQLEYIRSKPVPSGQLENIRAYASHHGYEFYRDLLYRFVE 447

Peptidase_C3

pfam00548

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

1530-1695

8.07e-49

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: 171.86 E-value: 8.07e-49

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1530 GPLLDFAMSLLKKNIRTVVTKTGEFTGL--GVYDTFMVLPRHAMAHGEVEVDGKKVEIED-AYDLNDTTQTSLELTVIKL 1606
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDpEVELVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1607 KQNEKFRDIRSLIPDQISETTEALVIVNTSAYPNLFMPVGAVKDYGYL-NLAGRPTHRTLMYNFPTRAGQCGGVAVSM-- 1683
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVVIAKve 160

                          170
                   ....*....|....
gi 1147809662 1684 --GKVIGIHIGGNG 1695
Cdd:pfam00548  161 gnGKILGMHIAGNG 174

Parechovirus_RdRp

cd23217

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

1812-2151

1.06e-47

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: 175.83 E-value: 1.06e-47

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1812 AIYGTEGLEALDLGTSAGYPYVALGIKKRDILNKETRDVTKM------QQCIDKYGLNLP---MVTYVKDELRSKEKVKK 1882
Cdd:cd23217      1 AVLGTSHLNSLDLSTSPGYKYVKSGYKKRDLLSLEPFSVSPQlekdvkDKLHAVYKGNQPttiFNACLKDELRKLDKIAQ 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1883 GKSRLIEASSLNDSVAMRCAFGNLYKAFHTNPGTLTGCAVGCNPETFWSKIPVMMDGELFGFDYTAYDASLSPvwfQCLY 1962
Cdd:cd23217     81 GKTRCIEACSIDYVIAYRVVMSSLYEAIYQTPCQELGLAVGMNPWTDWDFMINALNPYNYGLDYSSYDGSLSE---MLMW 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1963 LLLEKIGFGH-----CKHFIDQLCCSNHLFMDKRYVVVGGMPSGCSGTSIFNSMINNIIIRtlVLTVYKNIDLDDLKIIa 2037
Cdd:cd23217    158 EAVEVLAYCHespdlVMQLHKPVINSDHVVMDERWLVHGGMPSGSPCTTVLNSICNLLVCI--YLAYLQSPGIECLPIV- 234

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2038 YGDDVIASYPFELDA-KLLADAGKSFGLIMTPPDKSSEFVKLTWDNVTFLKRsfvKDERFPFLIHPVMKMS--DIHESIR 2114
Cdd:cd23217    235 YGDDVIFSVSSEIDPeYLVSSAADSFGMEVTGSDKDEPPSLLPRMEVEFLKR---TTGYFPGSTYKVGALDleTMEQHIM 311

                          330       340       350
                   ....*....|....*....|....*....|....*...
gi 1147809662 2115 WTKDAKSTQDHVRS-LCLLAWHcGQEQYEEFLEKIRSV 2151
Cdd:cd23217    312 WMKNLSTFPQQLQSfENELCLH-GKDIYDDYKKIFNPY 348

Rhv

pfam00073

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

343-514

2.38e-45

Pssm-ID: 395026 Cd Length: 170 Bit Score: 162.10 E-value: 2.38e-45

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  343 FEPSPEIHIPAEVRNLLEIVQVESMVEANNL-ADVEGAKRYNIPLNVQTGMDAQIFALNVDpgrDGPLQHTLLGIYTRYF 421
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVqPDVQGERFYTLDSTDWTSLSKGFFWWKLP---LALLSMGLLGRLLRYH 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  422 TQWSGSLEFTFMFTGTFMTTGKILIAYTPPGAAVPASR---REAMLGTHVVWDFGLQSSITLVVPWISAAHFRgtdSTST 498
Cdd:pfam00073   78 TYYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRdylWQATLNPHQFWNLGLNSSARLSVPYISIAHYY---STFY 154

                          170
                   ....*....|....*.
gi 1147809662  499 LYKYKYYEAGVITGWY 514
Cdd:pfam00073  155 DGNWTLVVAGWVPLNY 170

Fipivirus_RdRp

cd23229

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

1813-2169

3.18e-45

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: 169.60 E-value: 3.18e-45

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1813 IYGTEGLEALDLGTSAGYPYVALGIKKRDILnKETRDVTKMQ--------QCIDKY----GLNLPMVTYV---KDELRSK 1877
Cdd:cd23229      2 VEGIPGMEGLDMKTSAGYPWCEQNQKKKDKI-KLLAGKNFLVrplrevvhIVVDWYimppDMPKPEIKYVvylKDELLSS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1878 EKVKKGKSRLIEASSLNDSVAMRCAFGNLYKAFHT-NP--GTLTGCAVGCNPETFWSKIPVMMDG-ELFGFDYTAYDASL 1953
Cdd:cd23229     81 DKVKMGRTRWICAAPVQLVCAWKKVFGRAIAAIHLeSVtdGKSTGCAVGMDPETAWTDIALARPGwPVIALDYSNFDGSL 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1954 SPvwFQ---CLYLL--LEKIGFGHCKHFIDQLCCSNHLFMDKRYVVVGGMPSGCSGTSIFNSMINniiIRTLVLTVYKNI 2028
Cdd:cd23229    161 QS--FVitgAVRILgyIAGLPDGQSYRLAEFVYDVKQIVGKYLYTTVGPLPSGCPSTSIIGSLCN---VLMLLYTLSHAT 235

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2029 DL------DDLKIIAYGDDVIA--SYPFELDAKLLADAG-KSFGLIMT-PPDKSSEFVKLTWDNVTFLKRSFVKDERFPF 2098
Cdd:cd23229    236 GQrysafrDWMHVVTYGDDVLVfvHPEVVVVLDTLAHEMyLVFGVTATdATDKRAPPQLRELSNVTFLKRGFRQCSSVPF 315

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1147809662 2099 LIHPVMKMSDIHESIRWTKDAKSTQDHVRSLCLLAWHCGQEQYEEFLEKIRS------VPVGRAL--SLPSFKALQRSW 2169
Cdd:cd23229    316 LVHPTMDKSTIYQMLAWKRKGTTLAENVKCAAEFMMHHGEEEYEDFVGVVKEcstligVDQRSKVyeELCSYAELHDHW 394

RNA_helicase

pfam00910

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

1213-1311

1.34e-40

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

Pssm-ID: 459992 Cd Length: 102 Bit Score: 145.83 E-value: 1.34e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1213 CLIHGTPGTGKSLATTIIGRKIAEYENSG---VYSLPPDPDHFDGYQEQAVVIMDDLHQNPDGKDMSLFCQMVSTTPFVV 1289
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKKLGLPkdsVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 1147809662 1290 PMAALEDKGRLFTSKYVLASTN 1311
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102

rhv_like

cd00205

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

389-549

1.65e-40

Pssm-ID: 119412 Cd Length: 178 Bit Score: 148.31 E-value: 1.65e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  389 QTGMDAQIFALNVDPG-RDGPLQHTLLGIYTRYFTQWSGSLEFTFMFTGTFMTTGKILIAYTPPGAAVPA---SRREAML 464
Cdd:cd00205     18 SSASGTQLFQWKLSPAlGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPPGAPAPTtgdTRWQATL 97

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  465 GTHVVWDFGLQSSITLVVPWISAAHFRGTDSTSTLYkykYYEAGVITGWYQTNMITPPDFPQTASIVAFVAAqSNFSLRI 544
Cdd:cd00205     98 NPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDGYGP---LNSFGTLVVRVLTPLTVPSGAPTTVDITVYVRA-GDFELYG 173


                   ....*
gi 1147809662  545 QKDRP 549
Cdd:cd00205    174 PRPPR 178

Hepatovirus_RdRp

cd23215

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

1752-2150

2.56e-40

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

Pssm-ID: 438065 Cd Length: 464 Bit Score: 156.93 E-value: 2.56e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1752 PAVLhKKDKRLEVDFEEALFSKYigniHKPVTEEMEI---AIDHYANQLKQLDIDPT-PISMEDAIYGTEGLEALDLGTS 1827
Cdd:cd23215     11 PAVM-PYQRNVEIDPMAVMLSKY----SLPIVEEPVDykdVVVFYQNKILGKDILYDeFFDLEQAITGVPGMDAINMDSS 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1828 AGYPYVALGIKKRDIL----------------NKETRDVTKMQQCIDkygLNLPMVTYVKDELRSKEKVKKGKSRLIEAS 1891
Cdd:cd23215     86 PGYPYVQEKLTKSDLIwlddngellgmhprlaQRILFNLTMMDNGND---LDVVYTTCPKDELRPLEKVLESKTRAIDAC 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1892 SLNDSVAMRCAFGNLYKAFHTNPGTLTGCAVGCNPETFWSKIPVMMDgeLFG-----FDYTAYDASLSPVWFQCLYLLLE 1966
Cdd:cd23215    163 PLDFTIICRMFWGPAISYFQLNPGFHTGVAVGIDPDRDWDALFKTMI--RFGdygidLDFSSFDASLSPFMIREACRVLS 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1967 KIGfGHCKHF----IDQLCCSNHLFMDKRYVVVGGMPSGCSGTSIFNSMINNIIIRTLVLTVYKNIDL---DDLKIIAYG 2039
Cdd:cd23215    241 ELS-GVPDHQgqalINTIIYSKHLLYNLCYHVCGSMPSGSPCTSLLNSIVNNVNLYYVFSKIFKKSPVffyDAVKFLCYG 319

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2040 DDVIASYPFELDAKLLADAG-------KSFGLIMTPPDKSSEFVKLTWDnVTFLKRSF--VKDErfpflIHPVMKMSDIH 2110
Cdd:cd23215    320 DDVLIVFSRDLEIKNLDKLGqriqdefKLLGMTATSADKGEPQVVPVSE-LTFLKRSFnlIEDR-----FRPAISEKTIW 393

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|
gi 1147809662 2111 ESIRWTKDAKSTQDHVRSLCLLAWHCGQEQYEEFLEKIRS 2150
Cdd:cd23215    394 SLVAWQRSNAEFEQNLDTACWFAFMHGYDFYQNFYLQLQS 433

rhv_like

cd00205

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

125-313

6.08e-40

Pssm-ID: 119412 Cd Length: 178 Bit Score: 146.77 E-value: 6.08e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  125 PGVSCERFYTLPSVEWTNTWKGQ---YWKLPNALT----ETGMFGQNAQFHYLYRGGWAVHVQCNATKFHQGLLLVVMIP 197
Cdd:cd00205      1 VESFADRPTTVGTNNWNSSASGTqlfQWKLSPALGflllQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  198 EcvvnlrGAPPINKTQPgengreieepflldsgeaLGNALIYPHQWINLRTNNAATIIVPYVNAIPMDSAIRH------S 271
Cdd:cd00205     81 P------GAPAPTTGDT------------------RWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDgygplnS 136

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 1147809662  272 NWTLMVIPVTELAYAANTSPLVPITVTLAPMCTEFGGLRAAS 313
Cdd:cd00205    137 FGTLVVRVLTPLTVPSGAPTTVDITVYVRAGDFELYGPRPPR 178

Crohivirus_RdRp

cd23232

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

1809-2163

4.04e-37

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

Pssm-ID: 438082 Cd Length: 373 Bit Score: 145.24 E-value: 4.04e-37

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1809 MEDAIYGTEGLEALDLGTSAGYPYVALGIKKRDILNKET--------RDVTKMQQCIDKYG-LNLPMVTYVKDELRSKEK 1879
Cdd:cd23232      1 IEEACFEEGDEHALDLKTSPGFKYVQMGLKKTDLVNRPNkfihpilrNDVRLIFDEMAKGQmPVVTFTAHLKDELRKLEK 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1880 VKKGKSRLIEASSLNDSVAMRCAFGNLYKAFHTNPGTLTGCAVGCNPETFWSKIPVMMDGELFGFDYTAYDASLSPVWF- 1958
Cdd:cd23232     81 IRSGKTRCIEACDFDYTVAHKMMFGTLYKAIYDTPGIITGLAVGMNPWKDWELIQQSLFKYNYDFDYKTFDGSLSRELMl 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1959 ---QCLYLLLEKIGFGhcKHFIDQLCCSNHLFMDKRYVVVGGMPSGCSGTSIFNSMINNIIIRTLVLTVYKNidldDLKI 2035
Cdd:cd23232    161 havDILSACVENDEMA--KLMLSVVVESVHLVLDQKWNVSGGMPSGSPCTTVLNSVCNLIVSSTIADMCTEG----DFKI 234

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2036 IAYGDDVIASYPFELDAKLLADAGK-SFGLIMTPPDKSSEFVKLTWDNVTFLKRsfvKDERFP---FLIHpVMKMSDIHE 2111
Cdd:cd23232    235 LVYGDDLIISSTAPLDCDRFKTLVElHYGMEVTPGDKGDEFKVKDREQVSFLKR---VTRKFPgtnYRVG-ALDLDTVKQ 310

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1147809662 2112 SIRWTKDAKSTQDHVRSLCL-LAWHcGQEQYEEFLEKIRSVPVGRALSLPSFK 2163
Cdd:cd23232    311 HLMWCKSYSSFKQQLDSALMeVAMH-GEETYNGFLTEIKTKLDKFKIYPPKFK 362

Kunsagivirus_RdRp

cd23219

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

1809-2142

7.32e-37

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: 143.47 E-value: 7.32e-37

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1809 MEDAIYGTegLEALDLGTSAGYPYValGIKKRDILNKETR--------DVTKMQQCIDKYGLN-LPMVTYVKDELRSKEK 1879
Cdd:cd23219      1 IEEAVFDT--VTPMDHTASAGPKYP--GTKRSELIDFQNRiisdrlrnDVLELQFRGTSGGAGeVKFSSFLKDELRPLSK 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1880 VKKGKSRLIEASSLNDSVAMRCAFGNLYKAFHTNPGTLTGCAVGCNPETFWSKIPVMMDGELFGFDYTAYDASLSP---- 1955
Cdd:cd23219     77 IRSGDTRVVECSSLDYTVAFRMQFLRVLQMCYGSDPTLTGLAPGMNVYTDMLPLCTSLYDYNLCLDFSKYDSRLPLqvmh 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1956 VWFQCLYLLLEKIGFghCKHFIDQLCCSNHLFMDKRYVVVGGMPSGCSGTSIFNSMINNIIIRTLVLTVYKNIdldDLKI 2035
Cdd:cd23219    157 RVAQLISNLTPDPQV--SMRLFQPIIISTHIVGSYEVVVEGGMPSGCPITTIMNSVCNVVMTSYAMLLLDPDS---DFWP 231

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2036 IAYGDDVIASYPFELDAKLLADAGKS-FGLIMTPPDKSSEFVKLTWDNVTFLKRSFVKDERFPFLIhPVMKMSDIHESIR 2114
Cdd:cd23219    232 VAYGDDNIVSTRKPIDTELFCSILNEeFGMILTGADKTTTVQAVPPMSVDFLKRRLRYTPEFPLPV-PVLPLDSMLSRIC 310

                          330       340
                   ....*....|....*....|....*...
gi 1147809662 2115 WTKDAKSTQDHVRSLCLLAWHCGQEQYE 2142
Cdd:cd23219    311 WCKGETEFKDQLESFSYELALYGQEVYE 338

Dicistroviridae_RdRp

cd23194

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

1871-2149

3.94e-35

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: 137.63 E-value: 3.94e-35

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1871 KDELRSKEKVKKGKSRLIEASSLNDSVAMRCAFGnlykAF--H------TNpgtltGCAVGCNPETF-WSKI-------- 1933
Cdd:cd23194     13 KDERRPIEKVDAGKTRVFSAGPMDYTIAFRMYFL----GFvaHlmrnriDN-----EIAVGTNVYSLdWDKLarkllskg 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1934 PVMMDGelfgfDYTAYDASLSPvwfQCLYLLLEKI----GFGHCKHFIDQ-----LCCSNHLFMDKRYVVVGGMPSGCSG 2004
Cdd:cd23194     84 DKVIAG-----DFSNFDGSLNP---QILWAILDIInewyDDGEENALIRRvlwedIVNSVHICGGYVYQWTHSQPSGNPL 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2005 TSIFNSMINNIIIRTLVLTVYKNIDLDDLK-------IIAYGDDVIASYPFELDAK----LLADAGKSFGLIMTPPDKSS 2073
Cdd:cd23194    156 TAIINSIYNSIIMRYVYLLLTKEAGLMTMSdfnkhvsMVSYGDDNVINVSDEVSEWfnqlTITEAMAEIGMTYTDETKTG 235

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2074 EFVKL-TWDNVTFLKRSFVKDERFPFLIHPvMKMSDIHESIRWTKDAKS----TQDHVRSlCL--LAWHcGQEQYEEFLE 2146
Cdd:cd23194    236 EIVPYrSLEEVSFLKRGFRYDDDLGRWVAP-LDLDTILEMPNWVRKGKDpeeiTKQNVEN-ALreLSLH-GEEVFDKWAP 312


                   ...
gi 1147809662 2147 KIR 2149
Cdd:cd23194    313 KIR 315

Pico_P2B

pfam01552

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

989-1089

9.05e-35

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

Pssm-ID: 279840 Cd Length: 101 Bit Score: 128.99 E-value: 9.05e-35

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  989 QGLTDYVQSLGNAFGAGFTDEISNYVGQVRDMMVGSDTVVEKIVRNIIKLLSALVIVVRNRSDIVTVTATLSLLGCSGSP 1068
Cdd:pfam01552    1 QGISDYIEHLGAAFGSGFTQQISDKIKELTNFINPTSKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCDASP 80

                           90       100
                   ....*....|....*....|.
gi 1147809662 1069 WRWLKAKICSILGINMAQKQA 1089
Cdd:pfam01552   81 WQFLKEKACAVLEIPYVHKQG 101

Limnipivirus_RdRp

cd23228

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

1812-2164

4.72e-33

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: 133.85 E-value: 4.72e-33

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1812 AIYGTeGLEALDLGTSAGYPYVALGIKKRD---ILNKET--------RDVTKMQQCIDKYGLNLPMVTYV-KDELRSKEK 1879
Cdd:cd23228      1 AITGA-GTNPIDKNTSPGLKYTRDGLKKSDlytIDEDGNvvvsdmlrADVEAWEELIQSGGYPTTLFTAClKDELRSDEK 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1880 VKKGKSRLIEASSLNDSVAMRCAFGNLYKAFHTNPGTLTGCAVGCNPETFWSKIPVMMD--GELFGFDYTAYDASLSPVW 1957
Cdd:cd23228     80 VALGKTRVIEAAELDYVVAYRMYMSSIYSDLYNAYAGDTGIAAGINPPADGHRLREELSqyDSFLALDYSRFDGSLPEML 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1958 FQCLYLLL-------EKIGFGHckhfiDQLCCSNHLFMDKRYVVVGGMPSGCSGTSIFNSMINNIIIRTLVLT---VYKN 2027
Cdd:cd23228    160 MRAAVEILadlhedpDLVRRLH-----ETVIISKHLVVDEDWTVKGGMPSGSPCTTVLNCICNLLVLEYAFLVhfgVYED 234

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2028 ID-----LDDLKIIAYGDDVIASY-PFELDAKLLADAGKSFGLIMTPPDKSSEFVKLTWDNVTFLKRSFVK--DERFPFL 2099
Cdd:cd23228    235 DDgvglpQCDYLSVVYGDDCIVAYnGMEMGLAFAETIEDTFGMEVTPASKVGDHFNVELHEVEFLKRKFFAfeTEEYDRI 314

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1147809662 2100 IhpvMKMSD--IHESIRWTKDAKSTQDHVRSLC--LLAWhcGQEQYEEFLEKIRSVPVGRAL--SLPSFKA 2164
Cdd:cd23228    315 A---LRLSEntIVQSLMWMRNLKTFPDQVQSLMmeLSAW--GKEKYDKLRDTCKRRLAKQNLqvTVPGYDI 380

rhv_like

cd00205

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

622-805

9.36e-33

Pssm-ID: 119412 Cd Length: 178 Bit Score: 125.97 E-value: 9.36e-33

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  622 LESFYGRSSLVGMPSLNPGDT---VTEWIINFGE------FVQLRAKLCLFTYMRFDIEFTIVATAysatgdpiSDPTYI 692
Cdd:cd00205      1 VESFADRPTTVGTNNWNSSASgtqLFQWKLSPALgflllqNTPLGALLSYFTYWRGDLEVTVQFNG--------SKFHTG 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  693 TYQVMYVPPGASAPTdQDTYQWQSGANPSLLSRVGDVPAA-FSVPFMGTANAYSYAYDGYAffnttdhldygvlPSNYLG 771
Cdd:cd00205     73 RLLVAYVPPGAPAPT-TGDTRWQATLNPHVIWDLGTNSSVtFVVPYVSPTPYRSTRYDGYG-------------PLNSFG 138

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|
gi 1147809662  772 SMYFRTLER------VTQKIRFRIYAKPKHVRAWVPRAPR 805
Cdd:cd00205    139 TLVVRVLTPltvpsgAPTTVDITVYVRAGDFELYGPRPPR 178

Avisivirus_RdRp

cd23231

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

1822-2148

4.82e-30

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: 124.23 E-value: 4.82e-30

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1822 LDLGTSAGYPYValGIKKRDILNKET--RDVTKMQQC---IDKYGLNLPMVTYVKDELRSKEKVKKGKSRLIEASSLNDS 1896
Cdd:cd23231     11 IDWGTSPGDKYK--GKTKAQLVDDKKfkADVMNLVRFngdPNREPPDVYFTTYLKDELRPKEKAKAGKTRVISAASFDYT 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1897 VAMRCAFGNLYKAFHTNpGTLTGCAVGCNPETFWSKIPVMMDGELFGFDYTAYDASLS-PVWFQCLYLLLekigfghCKH 1975
Cdd:cd23231     89 IACRMVFGPILRQLFAW-GREFGFGPGLNPYTHFDELYDKILPFVICLDYSGFDGSLSsELMFHAAQVIA-------CFS 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1976 FIDQLCC--------SNHLFMDKRYVVVGGMPSGCSGTSIFNSMINNIIIRTLVLtvYKNIDLDDLKIIAYGDDVIASYP 2047
Cdd:cd23231    161 EKPEAIMasaeltigSTERVSDEVWYVYGGMPSGSPWTTTLNTICNLLMCYTYLL--DMGHCWSETFVVAYGDDVVISAN 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2048 FELDAKLLADAGKS-FGLIMTPPDKSSefvKLTW---DNVTFLKRSFVKDERFPFLIHpVMKMSDIHESIRWTKDakSTQ 2123
Cdd:cd23231    239 IKHNLEGIEQWFKTkFGATVTPSDKQG---KITWttkNNMEFLKRRPKQLDFLPKIVG-ALDLDNMLDRIQWTKG--HFQ 312

                          330       340
                   ....*....|....*....|....*.
gi 1147809662 2124 DHVRSLCL-LAWHcGQEQYEEFLEKI 2148
Cdd:cd23231    313 DQLNSFYLeLALH-GRETYNEIRAKL 337

Aalivirus_RdRp

cd23216

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

1868-2129

1.84e-28

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: 119.00 E-value: 1.84e-28

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1868 TYVKDELRSKEKVKKGKSRLIEASSLNDSVAMRCAFGNLYKAFHTNPGTLTGCAVGCNPETFWSKIPVMMDGELFGFDYT 1947
Cdd:cd23216     53 TYLKDELRSIEKIANGNTRAIEAANFDHVVAWRQVMGNIVKQLFSDHDRVTGFAPGMNPYTHFDSLMDQVKWNVLALDFK 132

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1948 AYDASLSPvwfqclYLLLEKIGFGHCKHFIDQLCCSNH--------LFMDKRYVVVGGMPSGCSGTSIFNSMINNIIIRT 2019
Cdd:cd23216    133 KFDGSLSP------QVMEEAVDILASFHDMPQMVVDIHkhtiystnVVSDETWFVEGGMCSGSPCTTVLNTICNLLVNTT 206

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2020 LVLTvyKNIDLDDLKIIAYGDDVIAS---YPFEL-DAKLLADAGKS-FGLIMTPPDKSSEfvkLTWD---NVTFLKRsfv 2091
Cdd:cd23216    207 ILLS--EGIQPDNFYIAAYGDDTIISvdgLSSSLpDPKIMQQKYKEwFGMTVTSADKGSE---ITWDtrnHVQFLKR--- 278

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|
gi 1147809662 2092 KDERFPFL--IHPVMKMSDIHESIRWTKDakSTQDHVRSL 2129
Cdd:cd23216    279 RPGFFPGTqkVVGVLDLESMMEHIAWTKG--SFQDQLNSF 316

Caliciviridae_RdRp

cd23192

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

1871-2146

1.01e-27

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

Pssm-ID: 438042 Cd Length: 310 Bit Score: 115.82 E-value: 1.01e-27

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1871 KDELRSKEKVKKGKSRLIEASSLNDSVAMRCAFGNLYKAFHTNPGTlTGCAVGCNPE-TFWSkipvMMDGELFGF----- 1944
Cdd:cd23192      8 KDELRPVEKIAEGKRRLLWGCDVGVTLVAAAAFGPVADALKAVCPT-GPIAVGINMDsEDVE----VIFERLSGFryhyc 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1945 -DYTAYDASLSPVwfqclylLLekigfghcKHFIDQLC--CSNH----------------LFMDKRYVVVGGMPSGCSGT 2005
Cdd:cd23192     83 lDYSKWDSTQSPA-------VT--------AAAIDILAdlSEETplrdsvvetlssppmgIFDDVIFVTKRGLPSGMPFT 147

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2006 SIFNSMINNIII------RTLVLTVYKNIDLDDLKIIAYGDDVIASYPFELDAKL--LADAGKSFGLIMTPPDKSSEFVK 2077
Cdd:cd23192    148 SVINSLNHWLLFsaavlkAYELVGIYTGNVFDEADFFTYGDDGVYAMPPATASVMdeIIENLKSYGLKPTAADKTENPDI 227

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2078 LTWDNVTFLKRSFVKDerfPFLIHPVMKMSDIHESIRWTKdAKSTQDH---------------VRSLCL-LAWHcGQEQY 2141
Cdd:cd23192    228 PPLQGPVFLKRTFVRT---PGGWRALLDRSSILRQLYWVK-GPNTHDWteppteidheartvqLENVLLeAAQH-GPEFY 302


                   ....*
gi 1147809662 2142 EEFLE 2146
Cdd:cd23192    303 EKVLK 307

Rhv

pfam00073

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

605-750

1.48e-26

Pssm-ID: 395026 Cd Length: 170 Bit Score: 108.17 E-value: 1.48e-26

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  605 MIETRHVVATHGVAETSLESFYGRSSLV-------GMPSLNPGDTVTE------WIINFG--EFVQLRAKLCLFTYMRFD 669
Cdd:pfam00073    4 TPETRTVGYGKNPLELAVENFLGRDAPVqpdvqgeRFYTLDSTDWTSLskgffwWKLPLAllSMGLLGRLLRYHTYYRGG 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  670 IEFTIVATAysatgdpiSDPTYITYQVMYVPPGASAPTDQDtYQWQSGANPSLLSRVG-DVPAAFSVPFMGTANAYSYAY 748
Cdd:pfam00073   84 LEVTVQFNG--------SKFHQGKLLVAYVPPGAPPPGSRD-YLWQATLNPHQFWNLGlNSSARLSVPYISIAHYYSTFY 154


                   ..
gi 1147809662  749 DG 750
Cdd:pfam00073  155 DG 156

Aquamavirus_RdRp

cd23220

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

1809-2141

1.38e-22

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: 101.32 E-value: 1.38e-22

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1809 MEDAIYGTEGLEALDLGTSAGYPyvalGIKKRDIL---NKETRD-VTKMQQCIDKYGLNLPMVTYVKDELRSKEKVKKGK 1884
Cdd:cd23220      1 LNEAINSSESPLNFNGTAGAKYP----GMNRRQLLlplNPQVRDdVVKLAGDVGNGTATVVFETFMKDELRPKEKIESGK 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1885 SRLIEASSLNDSVAMRCAFGNLYKAFHTNPGTLTGCAVGCNPETFWSKIPVMMDGELFGFDYTAYDASLSPvwfQCLYLL 1964
Cdd:cd23220     77 TRIVESCPLDYLLLYRMVMLKSMIWWYNSDCIKTGVAPGMNVYTDFVPMVKQFKKIKYCLDFSAYDSTLSD---EILAAG 153

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1965 LEKIGF-----GHCKHFIDQLCCSNHLFMDKRYVVVGGMPSGCSGTSIFNSMINNIIIRTLVLTvyknIDLDDLKIIAYG 2039
Cdd:cd23220    154 VEVLACtsavpSYVRKLHAPIICSHHWHNNVVDLVLGGMPSGAPCTSVLNSIVNVLMARYICAL----MDIDYPVMVAYG 229

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2040 DDVIASYPFELDAKLLADAGKS-FGLIMTPPDKSSefVKLTWDNVTFLKRS--FVKDERFPFlihPVMKMSDIHESIRWT 2116
Cdd:cd23220    230 DDNVVSFDEEIDIERMVSLYKTeFGVTATNHDKTP--VPRPMANPVFLKRRlrFNPDLNIQF---PVLPLGEMIDRMCWT 304

                          330       340
                   ....*....|....*....|....*
gi 1147809662 2117 KDAKSTQDHVRSLCLLAWHCGQEQY 2141
Cdd:cd23220    305 RGPEHLSDQTFSFAIELAGYGKQVY 329

Marnaviridae_RdRp

cd23195

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

1871-2149

8.28e-22

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: 98.29 E-value: 8.28e-22

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1871 KDELRSKEKvkkGKSRLIEASSLNDSVAMRCAFGNLYKAFHTNPgTLTGCAVGCN---PEtfWSKIP--VMMDGE--LFG 1943
Cdd:cd23195      8 KDEPTKLTK---DKVRVFQAAPVALQLLVRKYFLPIARFLQMNP-LLSECAVGINaqsPE--WEELYehLTKFGEdrIIA 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1944 FDYTAYDASLSPVW----FQCLYLLLEK------------------IGFGHCKHFIDqlccsnhLFMdkryvVVGGMPSG 2001
Cdd:cd23195     82 GDYSKYDKRMSAQLilaaFKILIDIAAKsggyseedlkimrgiatdIAYPLVDFNGD-------LIQ-----FFGSNPSG 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2002 CSGTSIFNSMINNIIIRTLVLTVYKNIDLDDLK----IIAYGDDVIAS----YPFeLDAKLLADAGKSFGLIMTPPDKSS 2073
Cdd:cd23195    150 HPLTVIINSIVNSLYMRYAYYSLYPEKEVPPFRdvvaLMTYGDDNIMSvspgYPW-FNHTSIAEFLAKIGIKYTMADKEA 228

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2074 EFVK-LTWDNVTFLKRSFVKDERFPFLIHPVMKMSdIHESIRWTKDAKS-TQDHVRSLCL------LAWHcGQEQYEEFL 2145
Cdd:cd23195    229 ESVPfIHISEADFLKRKFVFDPELGVYVGPLDEDS-IFKSLHCYLKSKVlTPEEQAAQNIdgalreWFFH-GREVYEKRR 306


                   ....
gi 1147809662 2146 EKIR 2149
Cdd:cd23195    307 EQLK 310

Pico_P1A

pfam02226

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

2-69

1.40e-20

Pssm-ID: 308053 Cd Length: 68 Bit Score: 87.43 E-value: 1.40e-20

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1147809662    2 GGQFSKNTAGSHTTGTYAAGGSTIHYTNINYYENAASSSLNKQDLTQDPTKFTQPVVDVIKESAVPLK 69
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ 68

P3A

pfam08727

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

1418-1478

1.20e-13

Pssm-ID: 400873 Cd Length: 59 Bit Score: 67.45 E-value: 1.20e-13

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1147809662 1418 GPPEFRPLRIDVsEETPAPPAIADLLASVDSEDVREYCRQKGWIVQerITKE-SLERNVSRA 1478
Cdd:pfam08727    1 AIFQGIDLKIDI-KTSPPPEAIADLLQAVDSPEIIDYCEDKGWIVN--IPAEcQIERDIGIA 59

Secoviridae_RdRp

cd23196

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

1870-2150

5.19e-12

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: 69.34 E-value: 5.19e-12

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1870 VKDELRSKEKV-KKGKSRLIEASSLNDSVAMRCAFGNLYKAFHTNPGTLTgCAVGCNPETF-WSKIPVMM---DGELFGF 1944
Cdd:cd23196      7 PKDERLKKRKVlEKPKTRLFDVLPMEYNLLLRKYFLNFVRFIQANRHRLP-CQVGINPYSReWTTLYDRLaekSDTALNC 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1945 DYTAYDASLSpvwfQCLYlllekigfGHCKHFIDQLCCSNH-------LFM----------DKRYVVVGGMPSGCSGTSI 2007
Cdd:cd23196     86 DYSRFDGLLS----HQVY--------VWIADMINRLYGDGDeakarrnLLMmfcgrrsicgRQVYMVRGGMPSGCALTVI 153

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2008 FNSMINNIIIR----TLVLTVYKNIDLDDLKIIAYGDD-------VIASYpfeLDAKLLADAGKSFGLIMTP-PDKSS-- 2073
Cdd:cd23196    154 INSIFNEILIRyvyrKVVPRPARNNFNKYVRLVVYGDDnlisvkeEIIPY---FDGPVIKKEMAKVGVTITDgTDKTSpt 230

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2074 -EFVKLtwDNVTFLKRSFVKDERfpFLIHPVMKMSDIHESIRWTKDAKSTQD-----HVRSLCLLAWHCGQEQYEEFLEK 2147
Cdd:cd23196    231 lERKPL--ESLDFLKRGFRVQSD--GLVVAPLDKTSLYSRLHYVTAGGDGMYslyilNDNNKSFLEEHVDHPEFTEFRNR 306


                   ...
gi 1147809662 2148 IRS 2150
Cdd:cd23196    307 VVS 309

Nora-virus_RdRp

cd23200

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

1870-2149

1.11e-08

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: 59.16 E-value: 1.11e-08

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1870 VKDELRSKEKVKKGKSRLIEASSLNDSVAMRCAFGNlYKAFHTNPGTLTGCAVGCNPETF-WSKIPVMMDGELFGFD--Y 1946
Cdd:cd23200      7 LKDQPIKIAQAKSGRTRVFHCIPVDLILFSGALYGP-YKEAYTKAGLKCYHAVGIDPKSVgWQQLATYMTKHPNYFDadY 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1947 TAYDASLSPVWFQCLYLLLEKIgfghckhfIDQLCCSNhlFMDKRYV---------VVG---------GMPSGCSGTSIF 2008
Cdd:cd23200     86 KNYDKYLHRQVFKAVRKIQRSV--------IQQVCPDK--WDKARAVeeldaidtyVVDyqtvyktnrGNKSGSYTTTID 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2009 NSMINNII-----IRTLVLTVYKNIdLDDLKIIAYGDDVIASYPFELDAKL----LADAGKSFGLIMTPPDKSSEFVKLT 2079
Cdd:cd23200    156 NCLANDIYglyawVKTTGLRSLWDY-RQNVSSVAFGDDIIKSVSDEYKDKYnyctYRDVLNATGHIMTPGSKDGEEKPFT 234

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2080 -WDNVTFLKRSFVKDErfPFLIHPVMKMSdIHESIRWTkDAKST---------QDHVRSLCLlaWhcGQEQYEEFLEKIR 2149
Cdd:cd23200    235 sFENLQFLKRGFKLEN--GMVLAPLLQRS-IEGPFVWT-DIREDqitvwvnlvQEQLIEAAL--W--GEEYYNELCQKLK 306

ps-ssRNAv_RdRp-like

cd23167

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

1941-2047

4.99e-08

Pssm-ID: 438017 [Multi-domain] Cd Length: 73 Bit Score: 51.96 E-value: 4.99e-08

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1941 LFGFDYTAYDASLSPVWFQClylllekigfghckhfidqlccsnhlfmdkryvvvgGMPSGCSGTSIFNSMINNIIIRTL 2020
Cdd:cd23167      2 VVESDYSGFDSSISPDLLKA------------------------------------GQPSGSPNTSADNSLINLLLARLA 45

                           90       100
                   ....*....|....*....|....*...
gi 1147809662 2021 VLTVYKNID-LDDLKIIAYGDDVIASYP 2047
Cdd:cd23167     46 LRKACGRAEfLNSVGILVYGDDSLVSVP 73

Iflaviridae_RdRp

cd23197

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

1865-2144

3.10e-06

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: 51.41 E-value: 3.10e-06

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1865 PMVTYVKDELRSKEKVKK-GKSRLIEASSLNDSVAMRCAFGNLYKAFHTNPGTLTGcAVGCNPETF-WSKI--PVMMDGE 1940
Cdd:cd23197      7 VYWAHLKDELRPSEKLRRfGGTRVFSVPPLELVLNSRRFLLPFMDAFQSFPIEAHH-AIGLNPNSGdWRRLrdTLLEKGP 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1941 -LFGFDYTAYDASLSpvwFQCLYLLLEKIGFGHCKH---------FIDQLC----CSNHLFMDKRYVVVGGMPSGCSGTS 2006
Cdd:cd23197     86 cLLQMDYKNYSDAIP---KECVAKAFHIIVDYYRKWhcltveienALKTLFldtaDAELLVYGDVFKVNNGVLAGHPMTS 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2007 IFNSMINniiirtLVLTVYKNIDLDDLK---------IIAYGDDVIASYPFEL----DAKLLADAGKSFGLIMTPPDKSS 2073
Cdd:cd23197    163 VVNSVVN------LILMNYMWIKITRRRaseffkltyIIVMGDDVVISLPKQLteefDCRKICAEFAKYDIKVTDSEKNL 236

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1147809662 2074 EFVKLTWDNV---TFLKRSFVKDERFPFLIHPVMKMSDIHESIRW-TKDA---KSTQDHVRSLCLLAWHCGQEQYEEF 2144
Cdd:cd23197    237 TGEPKPYDSFdkfEFLSRGFSDCDAYPDITFAPVKTIALFDCPLWiSKGQdeeEQTIQAIQAGLLLAFDHGPEFFGKY 314

Polycipiviridae_RdRp

cd23198

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

1871-2148

3.83e-04

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Polycipiviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Polycipiviridae (polycistronic picorna-like viruses), order Picornavirales. Polycipiviridae is a family of picorna-like viruses with non-segmented, linear, (+)ssRNA genomes of approximately 10-12 kb. Their genomes are polycistronic, with four (or more) consecutive 5'-proximal open reading frames (ORFs) encoding structural (and possibly other) proteins and a long 3' ORF encoding the replication polyprotein. Members of species within the family are typically found in ants, with Apple picorna-like virus 1 and the unnamed Polycipiviridae virus in fruit bat stool as exceptions. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438048 Cd Length: 317 Bit Score: 45.10 E-value: 3.83e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1871 KDELRSKEKV-----KKGKSRLIEASSLNDSVAMRCAFGNLYKAFH-TNPGTLTGCAvGCNPE--------TFWSKIPVM 1936
Cdd:cd23198      8 KDELRPIYKAlgdpqTPPKTRSVTCMNVYYILAWRRVTLDFWASMHrAADGNFPFCP-GINPEgpdwnrlyHYLNRHPNA 86

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1937 MDgelfgFDYTAYDASLSPVWF--------------------QCLYLLLEKIGFGHCKHfidqlccSNHLFMDKRyvvvg 1996
Cdd:cd23198     87 VD-----FDVSNWDGHLPAELFyavldiiktvlglkpnspnaKVIYSILTEVMNCHIQF-------EDIIYQKLR----- 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1997 GMPSGCSGTSIFNSMINNIIIRTLVLTVYKNIDLDD--------LKIIAYGDDVIASYPFEL----DAKLLADAGKSFGL 2064
Cdd:cd23198    150 GLISGFPGTAEVNTLAHWLLIYYIYLYLAQNTIYDMtitaflrnVSAIFYGDDIIITISDEIlhwfNGKTIQRMYEEHGY 229

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 2065 IMTPPDKSSEFVKLT-WDNVTFLKRSFvkDERFPFLIHPVMKMSDIHESIRWTKDAKSTQDHVRSLCLLAWHC----GQE 2139
Cdd:cd23198    230 PVTSAAKDTEIPESKpLSDCQFLKSSW--NPILPGYYIRKMDIEVVYDLVYWVRAKEHPRDQFYSNYHDALRIlfghGEQ 307


                   ....*....
gi 1147809662 2140 QYEEFLEKI 2148
Cdd:cd23198    308 VFEAFREQV 316

Calici_coat

pfam00915

Calicivirus coat protein;

407-494

1.13e-03

Calicivirus coat protein;

Pssm-ID: 459994 Cd Length: 291 Bit Score: 43.34 E-value: 1.13e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662  407 GPLQHTLLGIYTRYFTQWSGSLEFTFMFTGTFMTTGKILIAYTPPGAAvPASRREAMLGTHVVWDFGLQSSITLVVPWIS 486
Cdd:pfam00915   89 GPHLNPFLLHLSQMYNGWSGGMRVRFMVAGSGVFGGKLAASVIPPGVE-PITSASMLQFPHVLFDARQLEPVIFTIPDLR 167


                   ....*...
gi 1147809662  487 AAHFRGTD 494
Cdd:pfam00915  168 NTLFHNMD 175

RdRP_4

pfam02123

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

1863-2064

2.10e-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: 2.10e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1863 NLPMVTYVKDELRSKEKVKKGKSRLIEASSLNDSVAM-------RCAFGNlyKAFHTNPGTLtGCAvgcnpeTFWSKIPV 1935
Cdd:pfam02123  222 NNEIAWWGSVPSKPSMKLEHGKSRAIYACDTRSYLAFeyllapvEKAWAN--KSVILNPGEG-DIS------GFDWSVQD 292

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1936 MMDGE-LFGFDYTAYD-----ASLSPVwFQCLyllleKIGFGHCKH-FIDQLCCSnhlfMDKRYV----------VVGGM 1998
Cdd:pfam02123  293 WKRGGvSLMLDYDDFNsqhstESMRAV-FERL-----RRRLPDEPAeAADWLVCS----MDSMYQlsdgtllaqrVPGTL 362

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1147809662 1999 PSGCSGTSIFNSMINNIIIRTLVLTVyknidLDDLKIIAYGDDVIASYPFELDAKLLADAGKSFGL 2064
Cdd:pfam02123  363 KSGHRATTFINSVLNCAYAELAGAPW-----ADVPTSIHMGDDVLEGLRTPADATSLLDKYARLGF 423

Solinviviridae_RdRp

cd23199

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

1920-2090

4.70e-03

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

Pssm-ID: 438049 Cd Length: 323 Bit Score: 41.57 E-value: 4.70e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1920 CAVGCNPETFWSKIPVMMD--GELFGFDYTAYDAS----LSPVWFQCLYLL---LEKIGFGHCKHFIDQLCCS-NHLFMd 1989
Cdd:cd23199     71 CAVGCNPYATFHKFATKFFkfKNFFSCDYKNFDRTipkcVFEDFRDMLIQAnphMKNEIYACFQTIIDRIQVSgNSILL- 149

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1147809662 1990 kryvVVGGMPSGCSGTSIFNSMINNIIIRTLVLTVYKNIDLD-----DLKII-----AYGDDVIASY-----PFELDAKL 2054
Cdd:cd23199    150 ----VHGGMPSGCVPTAPLNSKVNDIMIYTAYVNILRRADRGditsyRYYRDlvcrlFYGDDVIIAVddsiaDIFNCQTL 225

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 1147809662 2055 LADAGKSFGLIMTPPDKSSEFVKL-TWDNVTFLKRSF 2090
Cdd:cd23199    226 SEEMKILFGMNMTDGSKSDIIPKFeTIETLSFISRFF 262

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