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Conserved domains on  [gi|1737293894|gb|QEO75975|]
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polyprotein [rhinovirus C19]

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 ...
 1705-2155 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: 737.03  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1705 VREEGIKPVNTPTHTKLRPSVFYDVFPGCKEPAALSNNDPRLETNLDDAVLAKYKGNPKVEFNEFIQVAVDHYAAQLYPL 1784
Cdd:cd23213      1 NKEVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1785 DINPSPISIEQAVYGYPNLEPLDLTTSAGYPYTTLGVKKRDIFNKQSRDVVKMQELLDKYGVDLPYVTYLKDELRAPEKI 1864
Cdd:cd23213     81 DIDTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKV 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1865 RSGKTRIIEAASVNDTVNFRMIYGNLFSMFHANPGIQTGSAVGCNPDTFWSQLYSTMGGHLLAFDYTNYDGSIHPIWFDA 1944
Cdd:cd23213    161 EKGKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDGSLFAFDYTGYDASLSPVWFRA 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1945 LGKVL--DQLGFPGHLMKRLNSTRHIYKNAFYITEGGMPSGICGTSIFNTMINNIIIRTLVIQTYKHIDLDKLRIVAYGD 2022
Cdd:cd23213    241 LKMVLekGYSEEAVSLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYGD 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2023 DVIASYPELLDPQEIANTAKVYGLTITPADKSATFKPITWENVTFLKRGFRPDKRYPFLVHPIYSMSDIFESIRWTKDPK 2102
Cdd:cd23213    321 DVIASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDPR 400

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1737293894 2103 NTQDHVRSLCLMAWHNGEAEYNNFLSKIRSVSVGRTLELPPYSYLYQQWVDNF 2155
Cdd:cd23213    401 NTQDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
 91-298 3.34e-55

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: 190.22  E-value: 3.34e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894   91 TTQDSLNTILAYGEWPSYLSDLDATSVDKPSHPETSSDRFYTLESVNWESGSKGW-WWKFPDALKDMGMFGQNMYHHSMG 169
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFfWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  170 RFGALIHVQCNATKFHSGCLLIMVVPEHQlayigaegvkvryehTHPGERghtlrdsrdrstnnpddnpfymcngTLLGN 249
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPPGA---------------PPPGSR-------------------------DYLWQ 120

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 1737293894  250 GMIYPHQMINLRTNNSATIVIPYINCIPMDNMLRHNNFSLVIVPIVPLR 298
Cdd:pfam00073  121 ATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGNWTLVVAGWVPLN 169
Pico_P2A super family cl03031
Picornavirus core protein 2A; This protein is a protease, involved in cleavage of the ...
 866-983 2.18e-48

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


The actual alignment was detected with superfamily member pfam00947:

Pssm-ID: 395757  Cd Length: 127  Bit Score: 168.71  E-value: 2.18e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  866 NAHLTTASD--DTILLAITADLQVDAAHEPGPDYIPDCDCTEGCYYSKSLDRYIPVQCVAHDWYPIEESSYYPKHIQYNI 943
Cdd:pfam00947    1 NRHLATHEDwhNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1737293894  944 LLGEGHCQPGDCGGKLLCKHGVIGIITAGGEDHVAFTDLR 983
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVR 120
RNA_helicase pfam00910
RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...
 1214-1310 9.62e-41

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: 146.21  E-value: 9.62e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1214 LMIHGPPGCGKSLVTTVIARGLAT-----EGDIYSLPPNPKHFDGYNQQKVVIMDDVGQNPDGEDLSTFCQMVSTADFHV 1288
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKklglpKDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 1737293894 1289 PMAALEDKGRSFTSDFVLASTN 1310
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102
Peptidase_C3 super family cl02893
3C cysteine protease (picornain 3C); Picornaviral proteins are expressed as a single ...
 1514-1679 1.39e-39

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: 145.67  E-value: 1.39e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1514 GPEHEFMYALIKRNCHIVETDKGEFNML--GIYDNCAVLPTHANCGDSLLLNGIKTPILKQQI-ITDLNDTDTEITIIWL 1590
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDPEVeLVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1591 DRNEKFRDIRRFLPESIQEWDHMRLATNVSKFPMFFADVGSVTPYGEI-NLSGNPTCRLLKYDYPTRPGQCGGVI----G 1665
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVViakvE 160

                          170
                   ....*....|....
gi 1737293894 1666 NTGHIIGIHVGGNG 1679
Cdd:pfam00548  161 GNGKILGMHIAGNG 174
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
 367-531 6.86e-39

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: 143.61  E-value: 6.86e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  367 YSPTKEIHIPGKIDNMLHIAMVDSLIPINNQQSHAGQVAMYNVQVFKRSDTDLILALpLQMDNTLFATTLLGEVLNYFGN 446
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFFW-WKLPLALLSMGLLGRLLRYHTY 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  447 WSGSIKVTFMCVCDSFSSGKFLVAYTPPGGGVPTNR---KEAMLGTHLIWDLGLQSSCTLVAPWMSSTFYRRTKGDA--- 520
Cdd:pfam00073   80 YRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRdylWQATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGnwt 159

                          170
                   ....*....|.
gi 1737293894  521 YTSGGYITLWY 531
Cdd:pfam00073  160 LVVAGWVPLNY 170
Pico_P2B super family cl03260
Picornavirus 2B protein; Poliovirus infection leads to drastic alterations in membrane ...
 992-1092 4.35e-30

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


The actual alignment was detected with superfamily member pfam01552:

Pssm-ID: 279840  Cd Length: 101  Bit Score: 115.51  E-value: 4.35e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  992 QGpIGNYINQLGTAFGDGFTT----AIKSQLDMLGNTvcDQLTGKVIKWLVRVISAITIMVRNSSDIPTVLATLALLGCH 1067
Cdd:pfam01552    1 QG-ISDYIEHLGAAFGSGFTQqisdKIKELTNFINPT--SKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCD 77

                           90       100
                   ....*....|....*....|....*
gi 1737293894 1068 TSPWSFLKDKVCKWLGIPApARKQG 1092
Cdd:pfam01552   78 ASPWQFLKEKACAVLEIPY-VHKQG 101
Pico_P1A super family cl03490
Picornavirus coat protein (VP4); VP1, VP2, VP3 and VP4 for the basic unit that forms the ...
 2-67 1.53e-28

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: 110.15  E-value: 1.53e-28
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1737293894    2 GAQVSKQNVGSHENSVSASNGSVIKYFNINYYKDSASSGLTKQDFSQDPSKFTQPLVDTLTNPALM 67
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPT 66
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 642-810 6.99e-27

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: 109.41  E-value: 6.99e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  642 IENFLGRSSLWA----ELSLGNKKFCKWDISFQEQ------AHIRKKMEWFTYVRFDMEVTVVTNN---HSL-MQIMFIP 707
Cdd:cd00205      1 VESFADRPTTVGtnnwNSSASGTQLFQWKLSPALGflllqnTPLGALLSYFTYWRGDLEVTVQFNGskfHTGrLLVAYVP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  708 PGIDPPSTHDDkKWNGASNPSVFYQPKSGFP-RFTIPFTGLGAAYYIFYDGYDENkagnvnygisatNDMGTLCFRSL-- 784
Cdd:cd00205     81 PGAPAPTTGDT-RWQATLNPHVIWDLGTNSSvTFVVPYVSPTPYRSTRYDGYGPL------------NSFGTLVVRVLtp 147

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1737293894  785 -----EEAQGTDIKVYIKPKHITAWCPRAPR 810
Cdd:cd00205    148 ltvpsGAPTTVDITVYVRAGDFELYGPRPPR 178
 
Name Accession Description Interval E-value
Enterovirus_RdRp cd23213
RNA-dependent RNA polymerase (RdRp) in the Enterovirus genus of positive-sense single-stranded ...
 1705-2155 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: 737.03  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1705 VREEGIKPVNTPTHTKLRPSVFYDVFPGCKEPAALSNNDPRLETNLDDAVLAKYKGNPKVEFNEFIQVAVDHYAAQLYPL 1784
Cdd:cd23213      1 NKEVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1785 DINPSPISIEQAVYGYPNLEPLDLTTSAGYPYTTLGVKKRDIFNKQSRDVVKMQELLDKYGVDLPYVTYLKDELRAPEKI 1864
Cdd:cd23213     81 DIDTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKV 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1865 RSGKTRIIEAASVNDTVNFRMIYGNLFSMFHANPGIQTGSAVGCNPDTFWSQLYSTMGGHLLAFDYTNYDGSIHPIWFDA 1944
Cdd:cd23213    161 EKGKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDGSLFAFDYTGYDASLSPVWFRA 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1945 LGKVL--DQLGFPGHLMKRLNSTRHIYKNAFYITEGGMPSGICGTSIFNTMINNIIIRTLVIQTYKHIDLDKLRIVAYGD 2022
Cdd:cd23213    241 LKMVLekGYSEEAVSLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYGD 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2023 DVIASYPELLDPQEIANTAKVYGLTITPADKSATFKPITWENVTFLKRGFRPDKRYPFLVHPIYSMSDIFESIRWTKDPK 2102
Cdd:cd23213    321 DVIASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDPR 400

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1737293894 2103 NTQDHVRSLCLMAWHNGEAEYNNFLSKIRSVSVGRTLELPPYSYLYQQWVDNF 2155
Cdd:cd23213    401 NTQDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
 91-298 3.34e-55

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: 190.22  E-value: 3.34e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894   91 TTQDSLNTILAYGEWPSYLSDLDATSVDKPSHPETSSDRFYTLESVNWESGSKGW-WWKFPDALKDMGMFGQNMYHHSMG 169
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFfWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  170 RFGALIHVQCNATKFHSGCLLIMVVPEHQlayigaegvkvryehTHPGERghtlrdsrdrstnnpddnpfymcngTLLGN 249
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPPGA---------------PPPGSR-------------------------DYLWQ 120

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 1737293894  250 GMIYPHQMINLRTNNSATIVIPYINCIPMDNMLRHNNFSLVIVPIVPLR 298
Cdd:pfam00073  121 ATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGNWTLVVAGWVPLN 169
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
 1723-2132 2.21e-54

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: 198.02  E-value: 2.21e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1723 PSVFYDVFPGCKEPAALSNNDPRLETNL--DDAV---LAKYKGNPKVE-----FNEFIQVAVDHYAAQLYPLDINPSPIS 1792
Cdd:pfam00680    2 PTERHLVAIPAYVPASLGPEDPRWARSYlnTDPYvddIKKYSRPKLPGpaderDKLLNRSAAKMVLSELRGVPKKANSTL 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1793 IEQAVY-GYPNLEPLDLTTSAGYPYTTLGVKKRDIFN-------------KQSRDVVKMQELLDKYGVdlpYVTYLKDEL 1858
Cdd:pfam00680   82 IVYRAIdGVEQIDPLNWDTSAGYPYVGLGGKKGDLIEhlkdgtearelaeRLAADWEVLQNGTPLKLV---YQTCLKDEL 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1859 RAPEKIRSGKTRIIEAASVNDTVNFRMIYGNLFSMFHANPGIQTgSAVGCNP-DTFWSQLYSTM---GGHLLAFDYTNYD 1934
Cdd:pfam00680  159 RPLEKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHP-IQVGINPfDRGWPRLLRRLarfGDYVYELDYSGFD 237

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1935 GSIHPIWFDALGKVLDQL-GFPGH------LMKRLNSTRH-IYKNAFYITEGGMPSGICGTSIFNTMINNIIIRTLVI-- 2004
Cdd:pfam00680  238 SSVPPWLIRFAFEILRELlGFPSNvkewraILELLIYTPIaLPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYALLks 317

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2005 ---QTYKHIDLDK-LRIVAYGDDVIASYPELLDP--QEIANTAKVYGLTITPADKSAT-FKPItwENVTFLKRGFRPDkr 2077
Cdd:pfam00680  318 lenDGPRVCNLDKyFDFFTYGDDSLVAVSPDFDPvlDRLSPHLKELGLTITPAKKTFPvSREL--EEVSFLKRTFRKT-- 393

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1737293894 2078 yPFLVHPIYSMSDIFESIRWTKDPKNTQDHVRSLCLMAWHNGEAEYNNFLSKIRS 2132
Cdd:pfam00680  394 -PGGYRPPLDRKRILAQLEYIRSKPVPSGQLENIRAYASHHGYEFYRDLLYRFVE 447
Pico_P2A pfam00947
Picornavirus core protein 2A; This protein is a protease, involved in cleavage of the ...
 866-983 2.18e-48

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


Pssm-ID: 395757  Cd Length: 127  Bit Score: 168.71  E-value: 2.18e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  866 NAHLTTASD--DTILLAITADLQVDAAHEPGPDYIPDCDCTEGCYYSKSLDRYIPVQCVAHDWYPIEESSYYPKHIQYNI 943
Cdd:pfam00947    1 NRHLATHEDwhNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1737293894  944 LLGEGHCQPGDCGGKLLCKHGVIGIITAGGEDHVAFTDLR 983
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVR 120
RNA_helicase pfam00910
RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...
 1214-1310 9.62e-41

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: 146.21  E-value: 9.62e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1214 LMIHGPPGCGKSLVTTVIARGLAT-----EGDIYSLPPNPKHFDGYNQQKVVIMDDVGQNPDGEDLSTFCQMVSTADFHV 1288
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKklglpKDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 1737293894 1289 PMAALEDKGRSFTSDFVLASTN 1310
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102
Peptidase_C3 pfam00548
3C cysteine protease (picornain 3C); Picornaviral proteins are expressed as a single ...
 1514-1679 1.39e-39

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: 145.67  E-value: 1.39e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1514 GPEHEFMYALIKRNCHIVETDKGEFNML--GIYDNCAVLPTHANCGDSLLLNGIKTPILKQQI-ITDLNDTDTEITIIWL 1590
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDPEVeLVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1591 DRNEKFRDIRRFLPESIQEWDHMRLATNVSKFPMFFADVGSVTPYGEI-NLSGNPTCRLLKYDYPTRPGQCGGVI----G 1665
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVViakvE 160

                          170
                   ....*....|....
gi 1737293894 1666 NTGHIIGIHVGGNG 1679
Cdd:pfam00548  161 GNGKILGMHIAGNG 174
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
 367-531 6.86e-39

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: 143.61  E-value: 6.86e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  367 YSPTKEIHIPGKIDNMLHIAMVDSLIPINNQQSHAGQVAMYNVQVFKRSDTDLILALpLQMDNTLFATTLLGEVLNYFGN 446
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFFW-WKLPLALLSMGLLGRLLRYHTY 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  447 WSGSIKVTFMCVCDSFSSGKFLVAYTPPGGGVPTNR---KEAMLGTHLIWDLGLQSSCTLVAPWMSSTFYRRTKGDA--- 520
Cdd:pfam00073   80 YRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRdylWQATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGnwt 159

                          170
                   ....*....|.
gi 1737293894  521 YTSGGYITLWY 531
Cdd:pfam00073  160 LVVAGWVPLNY 170
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 385-565 3.08e-38

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


Pssm-ID: 119412  Cd Length: 178  Bit Score: 141.76  E-value: 3.08e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  385 IAMVDSLIPINNQQSHAGQVAMYNVQvfkrsdtdlilaLPLQMDNTLFATTLLGEVLNYFGNWSGSIKVTFMCVCDSFSS 464
Cdd:cd00205      4 FADRPTTVGTNNWNSSASGTQLFQWK------------LSPALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHT 71

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  465 GKFLVAYTPPGGGVPTN---RKEAMLGTHLIWDLGLQSSCTLVAPWMSSTFYRRTKGDAY---TSGGYITLWYQTDFI-P 537
Cdd:cd00205     72 GRLLVAYVPPGAPAPTTgdtRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDGYgplNSFGTLVVRVLTPLTvP 151

                          170       180
                   ....*....|....*....|....*...
gi 1737293894  538 SSSGGVGTILATCSACpDLSVRMMRDTP 565
Cdd:cd00205    152 SGAPTTVDITVYVRAG-DFELYGPRPPR 178
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 123-322 1.37e-32

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


Pssm-ID: 119412  Cd Length: 178  Bit Score: 125.59  E-value: 1.37e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  123 PETSSDRFYTLESVNWE---SGSKGWWWKFPDA----LKDMGMFGQNMYHHSMGRFGALIHVQCNATKFHSGCLLIMVVP 195
Cdd:cd00205      1 VESFADRPTTVGTNNWNssaSGTQLFQWKLSPAlgflLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  196 EHQLAYIgaegvkvryehthpgerghtlrdsrdrstnnpddnpfymcNGTLLGNGMIYPHQMINLRTNNSATIVIPYINC 275
Cdd:cd00205     81 PGAPAPT----------------------------------------TGDTRWQATLNPHVIWDLGTNSSVTFVVPYVSP 120

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1737293894  276 IPMDNMLRH-----NNF-SLVIVPIVPLRPGNSGAPILPITVTIAPYKSEFSG 322
Cdd:cd00205    121 TPYRSTRYDgygplNSFgTLVVRVLTPLTVPSGAPTTVDITVYVRAGDFELYG 173
Pico_P2B pfam01552
Picornavirus 2B protein; Poliovirus infection leads to drastic alterations in membrane ...
 992-1092 4.35e-30

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


Pssm-ID: 279840  Cd Length: 101  Bit Score: 115.51  E-value: 4.35e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  992 QGpIGNYINQLGTAFGDGFTT----AIKSQLDMLGNTvcDQLTGKVIKWLVRVISAITIMVRNSSDIPTVLATLALLGCH 1067
Cdd:pfam01552    1 QG-ISDYIEHLGAAFGSGFTQqisdKIKELTNFINPT--SKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCD 77

                           90       100
                   ....*....|....*....|....*
gi 1737293894 1068 TSPWSFLKDKVCKWLGIPApARKQG 1092
Cdd:pfam01552   78 ASPWQFLKEKACAVLEIPY-VHKQG 101
Pico_P1A pfam02226
Picornavirus coat protein (VP4); VP1, VP2, VP3 and VP4 for the basic unit that forms the ...
 2-67 1.53e-28

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


Pssm-ID: 308053  Cd Length: 68  Bit Score: 110.15  E-value: 1.53e-28
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1737293894    2 GAQVSKQNVGSHENSVSASNGSVIKYFNINYYKDSASSGLTKQDFSQDPSKFTQPLVDTLTNPALM 67
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPT 66
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 642-810 6.99e-27

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: 109.41  E-value: 6.99e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  642 IENFLGRSSLWA----ELSLGNKKFCKWDISFQEQ------AHIRKKMEWFTYVRFDMEVTVVTNN---HSL-MQIMFIP 707
Cdd:cd00205      1 VESFADRPTTVGtnnwNSSASGTQLFQWKLSPALGflllqnTPLGALLSYFTYWRGDLEVTVQFNGskfHTGrLLVAYVP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  708 PGIDPPSTHDDkKWNGASNPSVFYQPKSGFP-RFTIPFTGLGAAYYIFYDGYDENkagnvnygisatNDMGTLCFRSL-- 784
Cdd:cd00205     81 PGAPAPTTGDT-RWQATLNPHVIWDLGTNSSvTFVVPYVSPTPYRSTRYDGYGPL------------NSFGTLVVRVLtp 147

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1737293894  785 -----EEAQGTDIKVYIKPKHITAWCPRAPR 810
Cdd:cd00205    148 ltvpsGAPTTVDITVYVRAGDFELYGPRPPR 178
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
 622-757 4.88e-23

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: 98.15  E-value: 4.88e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  622 PADTIETRYVINNHTNNEAIIENFLGRSSL-----------------WAELSlgnKKFCKWDISFQEQAH--IRKKMEWF 682
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPvqpdvqgerfytldstdWTSLS---KGFFWWKLPLALLSMglLGRLLRYH 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  683 TYVRFDMEVTVVTN----NHSLMQIMFIPPGIDPPSTHdDKKWNGASNPSVFYQPKSG-FPRFTIPFTGLGAAYYIFYDG 757
Cdd:pfam00073   78 TYYRGGLEVTVQFNgskfHQGKLLVAYVPPGAPPPGSR-DYLWQATLNPHQFWNLGLNsSARLSVPYISIAHYYSTFYDG 156
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 1194-1329 4.13e-03

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


Pssm-ID: 99707 [Multi-domain]  Cd Length: 151  Bit Score: 39.82  E-value: 4.13e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1194 HKELKQLQcyKRTKRTEPVCLMIHGPPGCGKSLVTTVIARGLA--------------TEGDIYSLPPNPKHFDG------ 1253
Cdd:cd00009      4 EEAIEALR--EALELPPPKNLLLYGPPGTGKTTLARAIANELFrpgapflylnasdlLEGLVVAELFGHFLVRLlfelae 81

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1737293894 1254 YNQQKVVIMDDVGQNPDGedlstfcqmVSTADFHVpMAALEDKGRSFTSDFVLASTNLASLvpqtVQTPEALLRRF 1329
Cdd:cd00009     82 KAKPGVLFIDEIDSLSRG---------AQNALLRV-LETLNDLRIDRENVRVIGATNRPLL----GDLDRALYDRL 143
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 1197-1238 8.70e-03

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


Pssm-ID: 440232 [Multi-domain]  Cd Length: 397  Bit Score: 41.05  E-value: 8.70e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1737293894 1197 LKQLQCYKRTKRTEPVCLMIHGPPGCGKSLVttviARGLATE 1238
Cdd:COG0464    177 LKRPELREEYGLPPPRGLLLYGPPGTGKTLL----ARALAGE 214
 
Name Accession Description Interval E-value
Enterovirus_RdRp cd23213
RNA-dependent RNA polymerase (RdRp) in the Enterovirus genus of positive-sense single-stranded ...
 1705-2155 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: 737.03  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1705 VREEGIKPVNTPTHTKLRPSVFYDVFPGCKEPAALSNNDPRLETNLDDAVLAKYKGNPKVEFNEFIQVAVDHYAAQLYPL 1784
Cdd:cd23213      1 NKEVGRPNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLKVDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQLATL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1785 DINPSPISIEQAVYGYPNLEPLDLTTSAGYPYTTLGVKKRDIFNKQSRDVVKMQELLDKYGVDLPYVTYLKDELRAPEKI 1864
Cdd:cd23213     81 DIDTEQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDTSKMKKYLDKYGLDLPMVTYVKDELRSKDKV 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1865 RSGKTRIIEAASVNDTVNFRMIYGNLFSMFHANPGIQTGSAVGCNPDTFWSQLYSTMGGHLLAFDYTNYDGSIHPIWFDA 1944
Cdd:cd23213    161 EKGKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTGSAVGCDPDTFWSKIPILLDGSLFAFDYTGYDASLSPVWFRA 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1945 LGKVL--DQLGFPGHLMKRLNSTRHIYKNAFYITEGGMPSGICGTSIFNTMINNIIIRTLVIQTYKHIDLDKLRIVAYGD 2022
Cdd:cd23213    241 LKMVLekGYSEEAVSLIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDLDELKMIAYGD 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2023 DVIASYPELLDPQEIANTAKVYGLTITPADKSATFKPITWENVTFLKRGFRPDKRYPFLVHPIYSMSDIFESIRWTKDPK 2102
Cdd:cd23213    321 DVIASYPHPIDCSLLARTGKEYGLTMTPADKSPCFNEVNWENVTFLKRGFRADEQYPFLIHPVMPMKEIHESIRWTKDPR 400

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1737293894 2103 NTQDHVRSLCLMAWHNGEAEYNNFLSKIRSVSVGRTLELPPYSYLYQQWVDNF 2155
Cdd:cd23213    401 NTQDHVRSLCLLAWHNGEEEYEKFVSKIRSVPVGRALALPNYSTLRRNWLDSF 453
Rabovirus_RdRp cd23230
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Rabovirus of ...
 1796-2155 6.02e-166

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: 513.28  E-value: 6.02e-166
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1796 AVYGYPNLEPLDLTTSAGYPYTTLGVKKRDIFNKQSRDVVKMQELLDKYGVDLPYVTYLKDELRAPEKIRSGKTRIIEAA 1875
Cdd:cd23230      1 AAYGIENLEGLDLNTSAGYPYVLNGIKKRDILDPETRDTTKLQECLDKYGVDLPFVTYLKDELRPLEKIKKGKTRLIECS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1876 SVNDTVNFRMIYGNLFSMFHANPGIQTGSAVGCNPDTFWSQLYSTMGGHLLAFDYTNYDGSIHPIWFDALGKVLDQLGFp 1955
Cdd:cd23230     81 SMNDTIRMKMMFGRLFATYHRNPGPITGSAVGCNPDIHWTKFRAEMHGEIIAFDYSNYDASLNKVWFECLKMVLKNFGF- 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1956 gHLMKRLN---STRHIYKNAFYITEGGMPSGICGTSIFNTMINNIIIRTLVIQTYKHIDLDKLRIVAYGDDVIASYPELL 2032
Cdd:cd23230    160 -KDLRPIDhiiRSRHIYKGIEYDVEGGMPSGCSGTSIFNSIINNIIIMTLVLDAYKGIDLEQLKIIAYGDDVIVTYPYPL 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2033 DPQEIANTAKVYGLTITPADKSATFKPITWENVTFLKRGFRPDKRYPFLVHPIYSMSDIFESIRWTKDPKNTQDHVRSLC 2112
Cdd:cd23230    239 DAALLADCGKKYGLKMTPPDKSAEFKNVTWEDVTFLKRRFKPAKHYPFLIHPVFDQQEILESLRWTRNPAHTQEHVRSLA 318

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|...
gi 1737293894 2113 LMAWHNGEAEYNNFLSKIRSVSVGRTLELPPYSYLYQQWVDNF 2155
Cdd:cd23230    319 ELAWHSGRKSYEEFCNLVKSTNVGKACILPPYESFKRMWLDQF 361
Sapelovirus_RdRp cd23218
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Sapelovirus of ...
 1797-2155 4.84e-154

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: 480.55  E-value: 4.84e-154
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1797 VYGYPNLEPLDLTTSAGYPYTTLGVKKRDIFNKQSRDVVKMQELLDKYGVDLPYVTYLKDELRAPEKIRSGKTRIIEAAS 1876
Cdd:cd23218      3 VYGIDNLEGLDLNTSAGYPYNTMGIRKKDLIPPRGEPLSPLLKALDLHGYDLPFTTYLKDELRPKEKVKMGKTRLIECSS 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1877 VNDTVNFRMIYGNLFSMFHANPGIQTGSAVGCNPDTFWSQLYSTMG-GHLLAFDYTNYDGSIHPIWFDALGKVLDQLGFP 1955
Cdd:cd23218     83 LNDTIRMKRIFGRLFQTFHKNPGTYTGSAVGCNPDVHWSKFAEEGGmDNVCAFDYTNWDASLSPFWFDALKLFLSKLGYS 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1956 GH---LMKRLNSTRHIYKNAFYITEGGMPSGICGTSIFNTMINNIIIRTLVIQTYKHIDLDKLRIVAYGDDVIASYPELL 2032
Cdd:cd23218    163 ERdivLIDHLCYSNHIFKNEGYKVAGGMPSGCSGTSIFNSIINNIVVRTLVLLVYKGINLDELRILCYGDDLLVAYPYPL 242

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2033 DPQEIANTAKVYGLTITPADKSATFKPIT-WENVTFLKRGFRPDKRYPFLVHPIYSMSDIFESIRWTKDPKNTQDHVRSL 2111
Cdd:cd23218    243 DPNVLADLGKSLGLTMTPADKSDTFQGCTkLTEVTFLKRSFVFDEEFPFLCHPVFPMEEVHESIRWTRNASTTQEHVTSL 322

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....
gi 1737293894 2112 CLMAWHNGEAEYNNFLSKIRSVSVGRTLELPPYSYLYQQWVDNF 2155
Cdd:cd23218    323 CLLAWHNGEEVYEEFCEKIRSVPVGRALILPPYSQLRRSWLDMF 366
ps-ssRNA_Picornaviridae cd23193
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Picornaviridae of ...
 1796-2131 5.64e-137

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: 431.59  E-value: 5.64e-137
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1796 AVYGYPNLEPLDLTTSAGYPYTTLGVKKRDIFNKQSRD-----VVKMQELLDKYGVDLPYVTYLKDELRAPEKIRSGKTR 1870
Cdd:cd23193      1 AINGIDGLDPIDLNTSPGYPYTTQGLRRRDLIDNDKGGvspllEEEEQVLLDLDGPDVVFTTFLKDELRPKEKVKAGKTR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1871 IIEAASVNDTVNFRMIYGNLFSMFHANPGIQTGSAVGCNPDTFWSQLYSTMGG-HLLAFDYTNYDGSIHPIWFDALGKVL 1949
Cdd:cd23193     81 VIEAAPLDYVIAGRMVFGRLFAQFHSNPGILTGSAVGCNPDTDWTRLFASLKQdNVYDLDYSGFDASLSSQLFEAAVEVL 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1950 -DQLGFPGHLMKRLNST---RHIYKNAFYITEGGMPSGICGTSIFNTMINNIIIRTLVIQTYkHIDLDKLRIVAYGDDVI 2025
Cdd:cd23193    161 aECHGDPELVLRYLEPIinsKHVVGDERYTVEGGMPSGCPCTSILNSICNNLVVRYALLETG-KFDPDEYYILAYGDDVL 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2026 ASYPELLDPQEIANTAKVY-GLTITPADKSATFKPITWENVTFLKRGFRPDKRYpFLVHPIYSMSDIFESIRWTKDPKNT 2104
Cdd:cd23193    240 VSTDEPIDPSDLAEFYKKYfGMTVTPADKSSDFPESSPIEDVFLKRRFFVPDGT-FLIHPVMDLETLEQSLMWCGRGGFF 318

                          330       340
                   ....*....|....*....|....*..
gi 1737293894 2105 QDHVRSLCLMAWHNGEAEYNNFLSKIR 2131
Cdd:cd23193    319 QQLLSSLCELALHHGPEEYERLVSKVR 345
Dicipivirus_RdRp cd23222
RNA-dependent RNA polymerase (RdRp) in the genus Dicipivirus of positive-sense single-stranded ...
 1722-2152 2.20e-80

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: 273.39  E-value: 2.20e-80
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1722 RPSVFYDVFPGCKEPAALSNNDPRL--ETNLDDAVLAKYKGNPKVEFNEfIQVAVDHYAAQLYPLDINP--SPISIEQAV 1797
Cdd:cd23222      1 KPSPVYGVYPVTKEPAPLKPTDRRIdeGVDFNEPVFGKYGADMKEPFRN-LDVGRDVVIARLKKVLPNKkfAPCTVSEAL 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1798 YGYPNLEPLDLTTSAGYPYTTLGVKKRDI-------FNKQSRDVVKMQELLDKYGVDLPYVTYLKDELRAPEKIRSGKTR 1870
Cdd:cd23222     80 NGKDGLPKLDLKQASGYPYNLSAIKRKHLiesdkdgFLTATPKLLADIEESKKHPEKFPYTSFLKDELRSVKKVKAGKTR 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1871 IIEAASVNDTVNFRMIYGNLFSMFHANPGIQTGSAVGCNPDTFWSQLYSTM--GGHLLAFDYTNYDGSIHPIWFDALGKV 1948
Cdd:cd23222    160 VVEAGSLPVIVEGRMIFGNLFAYFNTHPGFETMAAVGCDPEVCWTDWYYKMreKAHTWDYDYTGFDGSIPSCSFDALADL 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1949 LDQLGFPGHLMKR----LNSTRHIYKNAFYITEGGMPSGICGTSIFNTMINNIIIRTLVIQTYKHIDLDKLRIVAYGDDV 2024
Cdd:cd23222    240 LCEFVENEDDVRRyisnIKNSYHAYDGNLYLIEGAMPSGCAGTSVFNCLINAMLCFSCFMDLEPEMDPFEPLLIAYGDDI 319

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2025 IASYPELLDPQEIAN-TAKVYGLTITPADKSATFKPIT-WENVTFLKRGFRPDKRYPfLVHPIYSMSDIFESIRWTkDPK 2102
Cdd:cd23222    320 LVSSDHDLFPSRVSEwMKANTTFKITPADKGEIFNDDSdVSDVRFLKRLFVEDPVCE-LIHPVIETETLEPSLNWC-HEG 397

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1737293894 2103 NTQDHVRSLCLMAWHNGEAEYNNFLSKIRSVSVGRTLELP---PYSYLYQQWV 2152
Cdd:cd23222    398 EFETKVDAISMLAFHHGPEYYRDWCKKLTDICEERNISPPglkPYSVHRNRWL 450
Cosavirus_RdRp cd23226
RNA-dependent RNA polymerase (RdRp) in the genus Cosavirus of positive-sense single-stranded ...
 1713-2155 2.81e-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: 267.65  E-value: 2.81e-78
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1713 VNTPTHTKL-RPSVFYDVFPgCKEPAALSNNDPRLE--TNLDDAVLAKYKGNPKVE----FNEFIQVAVDHYAAQLYPLD 1785
Cdd:cd23226     12 VHVPRQSKLkRTNATYPATG-KYGPAVLSKNDPRLDpdVDFDKVIFSKHVANVVIDedtsFWNALKMSAQIYAEKFKGVD 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1786 InpSPISIEQAVYGYPNLEPLDLTTSAGYPYTTlgvKKRDIFNKQSRDVV--KMQELLDKY----GVDLPYVTYLKDELR 1859
Cdd:cd23226     91 F--SPLTVEEAILGIPGLDRMDPNTASGLPYTK---TRRQMIDFQEGKILdpELQERLDTWlsgkQPEMLYQTFLKDEIR 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1860 APEKIRSGKTRIIEAASVNDTVNFRMIYGNLFSMFHANPGIQTGSAVGCNPDTFWSQLYSTMGG--HLLAFDYTNYDGSi 1937
Cdd:cd23226    166 PIEKVKAGKTRIIDVTPLDHVLAFRIVLGRFMAHFHNNYGFELGSAVGCDPDVAWANFGFALSSkkYQYDFDYSNFDAS- 244

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1938 HPIwfdALGKVLDQLGFPGH---------LMKRLNSTRHIYKNAFYITEGGMPSGICGTSIFNTMINNIIIRTLVIQTYK 2008
Cdd:cd23226    245 HSE---SIFELLKQFVFTKDngfdhrcslMIDSLVTSTHCYEDQRMTIRGGLPSGTSGTSVINTIINNIIFKAALYHTYS 321

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2009 HIDLDKLRIVAYGDDVIASYPELLDPQEIANTAKVYGLTITPADKSATFKPITWENVTFLKRGFRpdkRYPFLVHPIYSM 2088
Cdd:cd23226    322 NFEWDDVQMLAYGDDIVAASDCLLDLDRVKYFMALIGYKITPADKGEKFIPKDMQNIQFLKRSFR---KVAGVWAPIMDL 398

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1737293894 2089 SDIFESIRWTKdPKNTQDHVRSLCLMAWHNGEAEYNNFLSKIrsvsVGRTLELPPYSYLYQQWVDNF 2155
Cdd:cd23226    399 ENLQAMLSWYK-PGTLQEKLDSVARLAHFCGEKVYDHLFTTF----VKDGFQIKPWKQLHFEWLNRF 460
Megrivirus_RdRp cd23223
RNA-dependent RNA polymerase (RdRp) in the genus Megrivirus of positive-sense single-stranded ...
 1727-2130 1.15e-77

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


Pssm-ID: 438073  Cd Length: 432  Bit Score: 265.17  E-value: 1.15e-77
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1727 YDVFPGCKEPAALSNNDPRLE--TNLDDAVLAKYKGNPKVEFNefIQVAVDHYAAQL-YPLDINPS-PISI---EQAVYG 1799
Cdd:cd23223      2 YGAFPVTHGPAALTNKDKRLEegVDLDDVMFSKHVPDHPGWPT--LEPAMSYVVEDLmHKLGFSKDePVPMwtlEQAING 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1800 YPNLEPLDLTTSAGYPYTTLGVKKRDIF---NKQSRDVVKMQELLD---KYGVDLPYVTYLKDELRAPEKIRSGKTRIIE 1873
Cdd:cd23223     80 EGVMDGIDMGQSPGYPYNAQGRSRRSFFewnGEKWQPTEELKKEVDhalKDPDDFYFSTFLKDELRPLEKVKAGKTRLVD 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1874 AASVNDTVNFRMIYGNLFSMFHANPGIQTGSAVGCNPDTFWSQLYSTMG----GHLLAFDYTNYDGSIHPIWFDALGKVL 1949
Cdd:cd23223    160 GDSLPRILAMRMVFGPLFEAMLRKNGPEIHSAVGCNPDTDWTRYYHEMGpdsfPYCFDLDYSCFDSTEPKIAFRLMAKYL 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1950 dQLGF---PGHLMKRLNSTRHIYKNAFYITEGGMPSGICGTSIFNTMINNIIIRTLVIQTykHIDLDKLRIVAYGDDVIA 2026
Cdd:cd23223    240 -KPYFsvdVTPFFEALATSKHVYGDKAYEMEGGMPSGCVGTSMFNCINNSAFIVSALIAL--KISPEDCAWICYGDDVII 316

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2027 SYPELLDPQEIAN-TAKVYGLTITPADKSATFKPI-TWENVTFLKRGFRPDKRYPFLVHPIYSMSDIFESIRWTKDPKnT 2104
Cdd:cd23223    317 STDEKALSKRIADfYHKNTNLVVTPASKSGDFPETsTIYDVTFLKRFFQPDSHYPHLIHPYMPLEHLEQSVMWQTDGP-F 395

                          410       420
                   ....*....|....*....|....*.
gi 1737293894 2105 QDHVRSLCLMAWHNGEAEYNNFLSKI 2130
Cdd:cd23223    396 QQKLDSLCLLAFHAGGPDYREFVDAI 421
Kobuvirus_RdRp cd23214
RNA-dependent RNA polymerase (RdRp) in the Kobuvirus genus of positive-sense single-stranded ...
 1713-2153 3.70e-77

RNA-dependent RNA polymerase (RdRp) in the Kobuvirus genus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Kobuvirus genus within the family Picornaviridae, order Picornavirales. Kobuviruses are small, icosahedral and spherical viruses, with a (+)ssRNA genome. Unlike other picornaviruses, Kobuvirus capsids show a distinctive lumpy morphology when observed by electron microscopy; "kobu" means "knob" in Japanese. There are six species (Aichivirus A-F) in this genus. Initially, the genus Kobuvirus was divided into three species: Aichivirus A (AiVA, formerly Aichi virus), Aichivirus B (AivB, formerly Bovine kobuvirus) and Aichivirus C (AiVC, formerly Porcine kobuvirus) each possessing a single serotype. Canine kobuvirus belong to species Aichivirus A. Aichi virus infects humans, while bovine kobuvirus, porcine kobuvirus and canine kobuvirus infects cattle, swine, dogs and cats, respectively. Kobuviruses have also been detected in black goats, rabbits, European roller, and bats. RdRps are multi-domain proteins that play a pivotal role in enterovirus replication. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of kobuviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438064  Cd Length: 459  Bit Score: 264.40  E-value: 3.70e-77
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1713 VNTPTHTKLRPSVFYDVFPGCKEPAALSNNDPRLE--TNLDDAVLAKYKGNPKVEFNEFIQVAVDHYAAQlYPLDINPsp 1790
Cdd:cd23214      3 VNVNRKSRLGPSPAYGAFPVKKQPAPLTQKDDRLEdgIRLDDQLFLKHNKGDMDEPWPGLEAAADLYFSK-FPTMIRT-- 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1791 ISIEQAVYGYPNLEPLDLTTSAGYPYTTLGVKKRDIFNKQSRDVV----KMQELLDKYGVDLPYV--TYLKDELRAPEKI 1864
Cdd:cd23214     80 LTQEEAINGTPNLEGLDMNQAAGYPWNTMGRSRRSLFVEVQPGIYvpkpELQAEIDKTLEDPDYFysTFLKDELRPTAKV 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1865 RSGKTRIIEAASVNDTVNFRMIYGNLFSMFHANPGiQTGSAVGCNPDTFWSQLYSTMGGHLLAF--DYTNYDGSIHPIWF 1942
Cdd:cd23214    160 TLGLTRVVEAAPIHAIVAGRMLLGGLIEYMQARPG-KHGSAVGCNPDLHWTKFFYKFCHYPQVFdlDYKCFDATLPSCAF 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1943 DALGKVLDQL-GFP--GHLMKRLNSTRHIYKNAFYITEGGMPSGICGTSIFNTMINNIIIRTLVIQtykHIDL--DKLRI 2017
Cdd:cd23214    239 RIVEDHLERLtGDErvTRYIESIRHSHHVYGNETYEMIGGNPSGCVGTSIINTIINNICVLSALIQ---HPDFspESFRI 315

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2018 VAYGDDVIASYPELLDPQEIANTAKVYG-LTITPADKSATFKPI-TWENVTFLKRGFRPDKRYPFLVHPIYSMSDIFESI 2095
Cdd:cd23214    316 LAYGDDVIYGCDPPIHPSFIKEFYDKHTpLVVTPANKGSDFPETsTIYDVTFLKRWFVPDDIRPFYIHPVMDPDTYEQSV 395

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1737293894 2096 RWTKDpKNTQDHVRSLCLMAWHNGEAEYNNFLSKIRSVSVGRTLELP---PYSYLYQQWVD 2153
Cdd:cd23214    396 MWLRD-GDFQDLVTSLCYLAFHSGPKTYDRWCTRVRDQVMKTTGFPPtflPYSYLQTRWLN 455
ps-ssRNAv-Picornavirales cd23169
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of ...
 1849-2131 2.94e-74

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: 250.59  E-value: 2.94e-74
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1849 PYVTYLKDELRAPEKIRSGKTRIIEAASVNDTVNFRMIYGNLFSMFHANPgIQTGSAVGCNPD-TFWSQLYSTM---GGH 1924
Cdd:cd23169      2 IFVDCLKDELRPIEKVKAGKTRLFSASPLDYTIAFRKYFGDFIAAFQKNR-IKLEHAVGINPDsVEWTRLYRRLlkkGPN 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1925 LLAFDYTNYDGSIHPIWFDALGKVL----DQLGFPGH------LMKRLNSTRHIYKNAFYITEGGMPSGICGTSIFNTMI 1994
Cdd:cd23169     81 IFAGDYSNFDGSLPPDVMEAAFDIIndwyDEYVDDEDervrkvLFEELINTIHLVGNLVYQVHGGNPSGNPLTTIINSIV 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1995 NNIIIRTLVIQTYKHIDLDK----LRIVAYGDDVIAS----YPELLDPQEIANTAKVYGLTITPADKSATFKP-ITWENV 2065
Cdd:cd23169    161 NLLYIRYAWLRITGLTSLSDfkknVRLVTYGDDVIISvsdeVKDEFNFVTISEFLKELGITYTDADKSGDIVPyRPLEEV 240

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2066 TFLKRGFRPDkRYPFLVHPIYSMSDIFESIRWTK---DPKNTQDHVRSLCLMAWH-NGEAEYNNFLSKIR 2131
Cdd:cd23169    241 TFLKRGFRPH-PTPGLVLAPLDLESIEEQLNWTRkedDLLEATIENARAALLLAFgHGPEYYNKFRQKLN 309
Aphthovirus_RdRp cd23210
RNA-dependent RNA polymerase (RdRp) in the Aphthovirus genus of positive-sense single-stranded ...
 1713-2152 7.89e-72

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: 249.09  E-value: 7.89e-72
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1713 VNTPTHTKLRPSVFYDVFPGCKEPAALSNNDPRLE--TNLDDAVLAKYKGNPKVEFNE---FIQVAVDhYAAQLYP-LDI 1786
Cdd:cd23210      6 VHVMRKTKLAPTVAHGVFNPEFGPAALSNKDPRLNegVVLDEVIFSKHKGDTKMSAEDkalFRRCAAD-YASRLHSvLGT 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1787 NPSPISIEQAVYGYPNLEPLDLTTSAGYPYTTLGVKKRDIF---NKQSRDVVKMQ-ELLDKYGVDLPYVTYLKDELRAPE 1862
Cdd:cd23210     85 ANAPLSIYEAIKGVDGLDAMEPDTAPGLPWALQGKRRGALIdfeNGTVGPEVEAAlKLMEKREYKFACQTFLKDEIRPME 164

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1863 KIRSGKTRIIEAASVNDTVNFRMIYGNLFSMFHANPGIQTGSAVGCNPDTFWSQLystmGGHL------LAFDYTNYDGS 1936
Cdd:cd23210    165 KVRAGKTRIVDVLPVEHILYTRMMIGRFCAQMHSNNGPQIGSAVGCNPDVDWQRF----GTHFaqyrnvWDVDYSAFDAN 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1937 iHPIwfDALGKVLDQL-----GF-PG--HLMKRLNSTRHIYKNAFYITEGGMPSGICGTSIFNTMINNIIIRTLVIQTYK 2008
Cdd:cd23210    241 -HCS--DAMNIMFEEVfrtefGFhPNaeWILKTLVNTEHAYENKRITVEGGMPSGCSATSIINTILNNIYVLYALRRHYE 317

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2009 HIDLDKLRIVAYGDDVIASYPELLDPQEIANTAKVYGLTITPADKSATFK--PITWENVTFLKRGFRPDKRYPFLvHPIY 2086
Cdd:cd23210    318 GVELDTYTMISYGDDIVVASDYDLDFEALKPHFKSLGQTITPADKSDKGFvlGHSITDVTFLKRHFHMDYGTGFY-KPVM 396

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1737293894 2087 SmSDIFESIRWTKDPKNTQDHVRSLCLMAWHNGEAEYNNFLSKIRSVsvgrtLELPPYSYLYQQWV 2152
Cdd:cd23210    397 A-SKTLEAILSFARRGTIQEKLISVAGLAVHSGPDEYRRLFEPFQGL-----FEIPSYRSLYLRWV 456
Cardiovirus_RdRp cd23211
RNA-dependent RNA polymerase (RdRp) in the Cardiovirus genus of positive-sense single-stranded ...
 1713-2155 8.46e-72

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: 248.99  E-value: 8.46e-72
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1713 VNTPTHTKLRPSVFYDVFPGCKEPAALSNNDPRLETNLDDAVLAKYKGNpKVEFNEFIQVAVDHYAAQLYP-LDINPSPI 1791
Cdd:cd23211     12 VHVPRKTKLRRTVAHPVFQPKFEPAVLSKYDPRTDKDVDEVAFSKHTTN-QESLPPVFRMVAKEYANRVFTlLGKDNGRL 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1792 SIEQAVYGYPNLEPLDLTTSAGYPYTTLGVKKRDIFNKQSRDVV-----KMQELLDKYGVDLPYVTYLKDELRAPEKIRS 1866
Cdd:cd23211     91 TVEQAVLGLEGMDPMEKDTSPGLPYTQQGLRRTDVVDFETATMIpflaeAHRKMVEGDYSDVVYQSFLKDEIRPIEKVQA 170

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1867 GKTRIIEAASVNDTVNFRMIYGNLFSMFHANPGIQTGSAVGCNPDTFWSQLYSTMGGHLLAFD--YTNYDGSIHPIWFDA 1944
Cdd:cd23211    171 AKTRIVDVPPFEHCILGRQLLGRFASKFQTNPGLELGSAIGCDPDVDWTAFAVALSGFKYVYDvdYSNFDSTHSTAMFEL 250

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1945 LGKVL--DQLGFP---GHLMKRLNSTRHIYKNAFYITEGGMPSGICGTSIFNTMINNIIIRTLVIQTYKHIDLDKLRIVA 2019
Cdd:cd23211    251 LIENFftEENGFDpriGEYLRSLAVSRHAYEERRVLIRGGLPSGCAATSMLNTIMNNIIIRAGLYLTYKNFEFDDIKVLS 330

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2020 YGDDVIASYPELLDPQEIANTAKVYGLTITPADKSATFKPI-TWENVTFLKRGFRpdKRYPFLVHPIYSMSDIFESIRWT 2098
Cdd:cd23211    331 YGDDLLVATNYQIDFNLVKARLAKFGYKITPANKTSTFPLTsTLEDVVFLKRKFV--KENSYLYRPVMDRENLKAMLSYY 408

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1737293894 2099 KdPKNTQDHVRSLCLMAWHNGEAEYNNFLSKIRSVSVgrtlELPPYSYLYQQWVDNF 2155
Cdd:cd23211    409 R-PGTLKEKLTSIALLAVHSGKQVYDEIFAPFREVGI----VVPTYESVLYRWLSLF 460
Rosavirus_RdRp cd23221
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Rosavirus of ...
 1796-2155 2.12e-70

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: 242.13  E-value: 2.12e-70
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1796 AVYGYPNLEPLDLTTSAGYPYTTLGVKKRDIFNKQSRDVVKMQELLDKYG---VDlP----YVTYLKDELRAPEKIRSGK 1868
Cdd:cd23221      1 AINGIDNMDGLDMNQSPGVPYVSEGVSRRSLFDCVDGQWVPRERLASDIAqvsGD-PslghFATFLKDELRSTEKVAAGK 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1869 TRIIEAASVNDTVNFRMIYGNLFSMFHANPGIQTGSAVGCNPDTFWSQLYSTMGGHLLAF--DYTNYDGSIHPIWFDALG 1946
Cdd:cd23221     80 TRVVEAGSLPHIIVGRKIFGNLFALFNSNPGFQTMCAVGCDPDVTWTELYHPLSAKTYVFdyDYSGFDGSVPSCCFDALA 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1947 KVLDQLGFPGHLMKR----LNSTRHIYKNAFYITEGGMPSGICGTSIFNTMINNIIIRTLVIQTYKHIDLDKLRIVAYGD 2022
Cdd:cd23221    160 DLLADFVEGEEDVRKyissLKTSFHHYKGKLWRLDGAMPSGCCGTSVFNSLINAMLLFSAFSQICPDFRASEPLLVAYGD 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2023 DVIASYPELLDPQEIA---NTAKVYglTITPADKSATFKPIT-WENVTFLKRGFRPDKRYPFLVHPIYSMSDIFESIRWT 2098
Cdd:cd23221    240 DVLVGTDQPLFPSKVAewvNSHTTF--RITPADKGSVFNDESdIHSVQFLKRHFTPDPDFPALIHPTIDPDTYEQSVMWQ 317

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2099 KdPKNTQDHVRSLCLMAWHNGEAEYNNFLSKI--RSVSVGRTLE-LPPYSYLYQQWVDNF 2155
Cdd:cd23221    318 R-TGDFQETVNSLALLVFHRGPKSYSRWCESVtrKCVDGGYPPPfFPPFSLLRHQWLKKF 376
Mischivirus_RdRp cd23227
RNA-dependent RNA polymerase (RdRp) in the genus Mischivirus of positive-sense single-stranded ...
 1713-2155 9.66e-70

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: 243.31  E-value: 9.66e-70
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1713 VNTPTHTKLRPSVFYDVFPGCKEPAALSNNDPRL--ETNLDDAVLAKYKGNPKVEFNEFIQVAvDHYAAQLYP-LDINPS 1789
Cdd:cd23227     12 IHVPRKTKLRKSPAYPIFKPDAGPAVLSKNDPRLaeGVDFDKQVFSKHSANQKEYPKAFRRMA-RWYADRVFTyLGKDNG 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1790 PISIEQAVYGYPNLEPLDLTTSAGYPYTTLGVKKRDIFNKQSRDV------VKMQELLDKYGVDLPYVTYLKDELRAPEK 1863
Cdd:cd23227     91 PLSVKDAIKGIDNLDAMDPTTSPGLPYSAAGIKRTDLLDFDTGEIispalrAEYNKYVSGDYSDHVFQTFLKDEIRSEEK 170

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1864 IRSGKTRIIEAASVNDTVNFRMIYGNLFSMFHANPGIQTGSAVGCNPDTFWSQLYSTMGGHLLAF--DYTNYDGSIHPIW 1941
Cdd:cd23227    171 IKAGKTRIVDVPSLAHVIIGRVLLGKFCSKFQASPGTELGSAIGCNPDWDWTYFAHQLMERQWCYdiDYSNFDSTHGTGM 250

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1942 FDALGKVL--DQLGFPGHL---MKRLNSTRHIYKNAFYITEGGMPSGICGTSIFNTMINNIIIRTLVIQTYKHIDLDKLR 2016
Cdd:cd23227    251 FELLIDCFftPENGFSPAVapyLRSLAFSKHAWMDKRYKIEGGLPSGCSATSVLNTVMNNIIIRALLSLTYKNFHPEDVL 330

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2017 IVAYGDDVIASYPELLD---PQEIANTAKVYGLTItpADKSATFKPI-TWENVTFLKRGFRPDKRYPFLVHPIYSMSDIF 2092
Cdd:cd23227    331 VLAYGDDLLVASDYQLDfnrVREKAAEHTLYKLTT--ANKAPDFPETsTLLDCQFLKRKFVLHSTRNFIWRPVMDVTNLK 408

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1737293894 2093 ESIRWTKdPKNTQDHVRSLCLMAWHNGEAEYNNFLSKIRSVSvgrtLELPPYSYLYQQWVDNF 2155
Cdd:cd23227    409 TMLSFYK-PNTLSEKLLSVAQLAFHSGYTVYEELFAPFKELQ----MTVPSWWYLEHEWEHNF 466
Mosavirus_RdRp cd23225
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Mosavirus of ...
 1804-2151 9.96e-69

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


Pssm-ID: 438075  Cd Length: 378  Bit Score: 237.12  E-value: 9.96e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1804 EPLDLTTSAGYPYTTLGVKKRDIFN---KQSRDVV----KMQELLDKY--GVDLP-YVTYLKDELRAPEKIRSGKTRIIE 1873
Cdd:cd23225     10 DAMDMTKAVGYPYCLDSIKRLDLVEikeTENGKVYlpteRLVEETEKFftGEEKPkFVTFLKDEVRSNEKIKQGKTRIVD 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1874 AASVNDTVNFRMIYGNLFSMFHANPGIQTGSAVGCNPDTFWSQ-LYSTMGGHLLAFDYTNYDgSIHPI-WFDALGK--VL 1949
Cdd:cd23225     90 ASPFPYAIAGRMVMQNFMSNMMRCNGTEVGSAVGCDPDTEWTRyFFELCDRYVFDLDYKAFD-STHPTaMFNLLAErfFT 168

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1950 DQLGFPGH----LMKRLNSTRHIYKNAFYITEGGMPSGICGTSIFNTMINNIIIRTLVIQTYK--HIDLDKLRIVAYGDD 2023
Cdd:cd23225    169 ERNGFDQQavriFLNGLSDSDHVYEGKHFRIRGGLPSGCPCTSILNTVINNIIVRAAILGAYQidTVDFQKFRMLAYGDD 248

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2024 VIASYPELLDPQEIA---NTAKVYglTITPADKSATF-KPITWENVTFLKRGFRPDKRYPFLVHPIYSMSDIFESIRWTK 2099
Cdd:cd23225    249 VVYATPQPIKPQDLAdwlHANTNY--KVTPASKAGTFpEESTIWDVTFLKRSFKPDEDHGHLIRPVMAVGNLKQMLSFMR 326

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1737293894 2100 dPKNTQDHVRSLCLMAWHNGEAEYNNFLSKIRSVSVGrtLELPPYSYLYQQW 2151
Cdd:cd23225    327 -PGTFPDKVRSVAGLAVHCGEEDYNQLADAVALYVPG--VSMPAYKYMKACW 375
Passerivirus_RdRp cd23224
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Passerivirus of ...
 1795-2152 1.28e-60

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: 213.80  E-value: 1.28e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1795 QAVYGYPNLEPLDLTTSAGYPYTtLGVKKRDIFNK----QSRDVVKMQE--LLDKYGVDLPYVTYLKDELRAPEKIRSGK 1868
Cdd:cd23224      1 EAINGTPLLDGLDMKQSPGYPWS-LTTNRRSLFTQdetgKYYPVPELEEavLACLENPDYFYTTHLKDELRPVEKALAGK 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1869 TRIIEAASVNDTVNFRMIYGNLFSMFHANPGiQTGSAVGCNPDTFWSQLYSTMG--GHLLAFDYTNYDGSIHPIWFDALG 1946
Cdd:cd23224     80 TRLIEAAPIHAIIAGRMLLGGLFEYMHARPG-EHGSAVGCDPDYHWTPFFHSFDefSQVWALDYSCFDSTLPSCCFDLIA 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1947 KVLDQL--GFPG-------HLMKRLNSTRHIYKNAFYITEGGMPSGICGTSIFNTMINNIIIRTLVIqTYKHIDLDKLRI 2017
Cdd:cd23224    159 QKLAKIitPGEGiapdaivKYIRSISISKHVFGNEAYLMVGGNPSGCVGTSILNSMINNCVLISAFL-TQKDFNPNQMRI 237

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2018 VAYGDDVIASYPELLDPQEIA-----NTAkvygLTITPADKSATF--KPITWEnVTFLKRGFRPDKRYPFLVHPIYSMSD 2090
Cdd:cd23224    238 LTYGDDVLYATNPPIHPRVVKkffdeNTT----LIVTPATKAGDFpdESTIWD-VTFLKRYFVPDEIRPWYVHPVIEPAT 312

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1737293894 2091 IFESIRWTKDpKNTQDHVRSLCLMAWHNGEAEYNNFLSKIRSVSVGRTLeLP---PYSYLYQQWV 2152
Cdd:cd23224    313 YEQSVMWTRG-GDFQDVVTSLSFLAHHAGPTNYMIWEEKVRKAAAAKGV-SLnilPYSYLQHRWM 375
Fipivirus_RdRp cd23229
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Fipivirus of ...
 1797-2151 3.76e-58

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: 206.97  E-value: 3.76e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1797 VYGYPNLEPLDLTTSAGYPYTTLGVKKRDIFnKQSRDVVKMQELLDKYGV---------------DLPYVTYLKDELRAP 1861
Cdd:cd23229      2 VEGIPGMEGLDMKTSAGYPWCEQNQKKKDKI-KLLAGKNFLVRPLREVVHivvdwyimppdmpkpEIKYVVYLKDELLSS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1862 EKIRSGKTRIIEAASVNDTVNFRMIYGNLFSMFH-ANP--GIQTGSAVGCNPDTFWSQLYSTMGG-HLLAFDYTNYDGSI 1937
Cdd:cd23229     81 DKVKMGRTRWICAAPVQLVCAWKKVFGRAIAAIHlESVtdGKSTGCAVGMDPETAWTDIALARPGwPVIALDYSNFDGSL 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1938 HPIWFDALGKVLDQL-GFPGHLMKRLNS----TRHIYKNAFYITEGGMPSGICGTSIFNTMINNIIIR-TLVI---QTYK 2008
Cdd:cd23229    161 QSFVITGAVRILGYIaGLPDGQSYRLAEfvydVKQIVGKYLYTTVGPLPSGCPSTSIIGSLCNVLMLLyTLSHatgQRYS 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2009 HIDlDKLRIVAYGDDVIA----SYPELLDpQEIANTAKVYGLTITPA-DKSATFKPITWENVTFLKRGFRPDKRYPFLVH 2083
Cdd:cd23229    241 AFR-DWMHVVTYGDDVLVfvhpEVVVVLD-TLAHEMYLVFGVTATDAtDKRAPPQLRELSNVTFLKRGFRQCSSVPFLVH 318

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1737293894 2084 PIYSMSDIFESIRWTKDPKNTQDHVRSLCLMAWHNGEAEYNNFLSKIRSVS-----VGRTL---ELPPYSYLYQQW 2151
Cdd:cd23229    319 PTMDKSTIYQMLAWKRKGTTLAENVKCAAEFMMHHGEEEYEDFVGVVKECStligvDQRSKvyeELCSYAELHDHW 394
RNA_dep_RNAP cd01699
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
 1838-2098 2.86e-57

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: 200.20  E-value: 2.86e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1838 QELLDKYGV------DLPYVTYLKDELRAPEKIRSGKTRIIEAASVNDTVNFRMIYGNLFSMFHANpGIQTGSAVGCNPD 1911
Cdd:cd01699      2 EKAVESLEDlplirpDLVFTTFLKDELRPLEKVEAGKTRLIQPRPLDYNIALRMYLGPFEAKLMKN-RGGLPIAVGINPY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1912 -TFWSQLYSTM---GGHLLAFDYTNYDGSIHPIWFDALGKVLDQL-GFPGHLMKR------LNSTRHIYKNAFYITEGGM 1980
Cdd:cd01699     81 sRDWTILANKLrsfSPVAIALDYSRFDSSLSPQLLEAEHSIYNALyDDDDELERRnllrslTNNSLHIGFNEVYKVRGGR 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1981 PSGICGTSIFNTMINNIIIRTLVIQTYKHIDLDKLRIVAYGDDVIASYP---ELLDPQEIANTAKVYGLTITPADKSaTF 2057
Cdd:cd01699    161 PSGDPLTSIGNSIINCILVRYAFRKLGGKSFFKNVRLLNYGDDCLLSVEkadDKFNLETLAEWLKEYGLTMTDEDKV-ES 239

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|.
gi 1737293894 2058 KPITWENVTFLKRGFRPDKryPFLVHPIYSMSDIFESIRWT 2098
Cdd:cd01699    240 PFRPLEEVEFLKRRFVLDE--GGGWRAPLDPSSILSKLSWS 278
Teschovirus_RdRp cd23212
RNA-dependent RNA polymerase (RdRp) in the Teschovirus genus of positive-sense single-stranded ...
 1790-2128 3.70e-57

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


Pssm-ID: 438062  Cd Length: 354  Bit Score: 202.93  E-value: 3.70e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1790 PISIEQAVYGYPNLEPLDLTTSAGYPYTTLGVKKRDIFNKQSRDVVKMQELLDKYgVDLPY-----VTYLKDELRAPEKI 1864
Cdd:cd23212     10 PLSVREAVEGIDGLDPMDMDKSPGLPYVKKGLRRTDLWNPKTGPSIELMAEINRY-LDYNYdkhvfLTFLKDELRPKEKV 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1865 RSGKTRIIEAASVNDTVNFRMIYGNLFSMFHANPGIQTGSAVGCNPDTFWSQL-YSTMGGHLLAFDYTNYDGSIHPIWFD 1943
Cdd:cd23212     89 QAGKTRVIDVAGFGHAIVGRMLFGRLFAFFHKNPGWNTGSAVGVNPDLAWTQIfYTAPSRNVLAMDYSGFDASHTSGMFC 168

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1944 ALGKVLDQLGFPGHLMKRLNS---TRHIYKNAFYITEGGMPSGICGTSIFNTMINNIIIRTLViqtyKHIDLDKLRIVAY 2020
Cdd:cd23212    169 ILKHFLTTLGYGTLQLSYIDSlcySKHHWDDETYRLDGGLPSGCSGTTIFNTIMNNIVARAAA----SYAAEGPVGILCY 244

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2021 GDDVIASYPELLDPQEIANTAKVYGLTITPADKSatfKPITWENV---TFLKRGFRPDKRypfLVHPIYSMSDIFESIRW 2097
Cdd:cd23212    245 GDDILVSSPEKFPVSDWLEFYSKTPYKVTAADKS---EQIDWRDItqcTFLKRGFVLDGS---LVRPVMEEQHLAELLKW 318

                          330       340       350
                   ....*....|....*....|....*....|.
gi 1737293894 2098 TKdPKNTQDHVRSLCLMAWHNGEAEYNNFLS 2128
Cdd:cd23212    319 AR-PGTLQAKLLSIAQLAFHLPRQAYDRLML 348
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
 91-298 3.34e-55

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: 190.22  E-value: 3.34e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894   91 TTQDSLNTILAYGEWPSYLSDLDATSVDKPSHPETSSDRFYTLESVNWESGSKGW-WWKFPDALKDMGMFGQNMYHHSMG 169
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFfWWKLPLALLSMGLLGRLLRYHTYY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  170 RFGALIHVQCNATKFHSGCLLIMVVPEHQlayigaegvkvryehTHPGERghtlrdsrdrstnnpddnpfymcngTLLGN 249
Cdd:pfam00073   81 RGGLEVTVQFNGSKFHQGKLLVAYVPPGA---------------PPPGSR-------------------------DYLWQ 120

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 1737293894  250 GMIYPHQMINLRTNNSATIVIPYINCIPMDNMLRHNNFSLVIVPIVPLR 298
Cdd:pfam00073  121 ATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGNWTLVVAGWVPLN 169
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
 1723-2132 2.21e-54

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: 198.02  E-value: 2.21e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1723 PSVFYDVFPGCKEPAALSNNDPRLETNL--DDAV---LAKYKGNPKVE-----FNEFIQVAVDHYAAQLYPLDINPSPIS 1792
Cdd:pfam00680    2 PTERHLVAIPAYVPASLGPEDPRWARSYlnTDPYvddIKKYSRPKLPGpaderDKLLNRSAAKMVLSELRGVPKKANSTL 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1793 IEQAVY-GYPNLEPLDLTTSAGYPYTTLGVKKRDIFN-------------KQSRDVVKMQELLDKYGVdlpYVTYLKDEL 1858
Cdd:pfam00680   82 IVYRAIdGVEQIDPLNWDTSAGYPYVGLGGKKGDLIEhlkdgtearelaeRLAADWEVLQNGTPLKLV---YQTCLKDEL 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1859 RAPEKIRSGKTRIIEAASVNDTVNFRMIYGNLFSMFHANPGIQTgSAVGCNP-DTFWSQLYSTM---GGHLLAFDYTNYD 1934
Cdd:pfam00680  159 RPLEKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHP-IQVGINPfDRGWPRLLRRLarfGDYVYELDYSGFD 237

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1935 GSIHPIWFDALGKVLDQL-GFPGH------LMKRLNSTRH-IYKNAFYITEGGMPSGICGTSIFNTMINNIIIRTLVI-- 2004
Cdd:pfam00680  238 SSVPPWLIRFAFEILRELlGFPSNvkewraILELLIYTPIaLPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYALLks 317

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2005 ---QTYKHIDLDK-LRIVAYGDDVIASYPELLDP--QEIANTAKVYGLTITPADKSAT-FKPItwENVTFLKRGFRPDkr 2077
Cdd:pfam00680  318 lenDGPRVCNLDKyFDFFTYGDDSLVAVSPDFDPvlDRLSPHLKELGLTITPAKKTFPvSREL--EEVSFLKRTFRKT-- 393

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1737293894 2078 yPFLVHPIYSMSDIFESIRWTKDPKNTQDHVRSLCLMAWHNGEAEYNNFLSKIRS 2132
Cdd:pfam00680  394 -PGGYRPPLDRKRILAQLEYIRSKPVPSGQLENIRAYASHHGYEFYRDLLYRFVE 447
Pico_P2A pfam00947
Picornavirus core protein 2A; This protein is a protease, involved in cleavage of the ...
 866-983 2.18e-48

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


Pssm-ID: 395757  Cd Length: 127  Bit Score: 168.71  E-value: 2.18e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  866 NAHLTTASD--DTILLAITADLQVDAAHEPGPDYIPDCDCTEGCYYSKSLDRYIPVQCVAHDWYPIEESSYYPKHIQYNI 943
Cdd:pfam00947    1 NRHLATHEDwhNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPTLIEIEASEYYPARYQSHL 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1737293894  944 LLGEGHCQPGDCGGKLLCKHGVIGIITAGGEDHVAFTDLR 983
Cdd:pfam00947   81 LLGVGPAEPGDCGGILRCQHGVIGIVTAGGEGHVAFADVR 120
Hepatovirus_RdRp cd23215
RNA-dependent RNA polymerase (RdRp) in the genus Hepatovirus of positive-sense single-stranded ...
 1790-2153 1.14e-44

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: 170.03  E-value: 1.14e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1790 PISIEQAVYGYPNLEPLDLTTSAGYPYTTLGVKKRD-IFNKQSRDVVKMQELLDKY------------GVDLPYVTYLKD 1856
Cdd:cd23215     64 FFDLEQAITGVPGMDAINMDSSPGYPYVQEKLTKSDlIWLDDNGELLGMHPRLAQRilfnltmmdngnDLDVVYTTCPKD 143

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1857 ELRAPEKIRSGKTRIIEAASVNDTVNFRMIYGNLFSMFHANPGIQTGSAVGCNPDTFWSQLYSTM---GGHLLAFDYTNY 1933
Cdd:cd23215    144 ELRPLEKVLESKTRAIDACPLDFTIICRMFWGPAISYFQLNPGFHTGVAVGIDPDRDWDALFKTMirfGDYGIDLDFSSF 223

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1934 DGSIHPIWFDALGKVLDQL-GFPGHLMKRLNST----RHIYKNAFYITEGGMPSGICGTSIFNTMINNIIIRTLVIQTYK 2008
Cdd:cd23215    224 DASLSPFMIREACRVLSELsGVPDHQGQALINTiiysKHLLYNLCYHVCGSMPSGSPCTSLLNSIVNNVNLYYVFSKIFK 303

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2009 HIDL---DKLRIVAYGDDVIASYPELLD-------PQEIANTAKVYGLTITPADKSA-TFKPITweNVTFLKRGFR--PD 2075
Cdd:cd23215    304 KSPVffyDAVKFLCYGDDVLIVFSRDLEiknldklGQRIQDEFKLLGMTATSADKGEpQVVPVS--ELTFLKRSFNliED 381

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2076 KrypflVHPIYSMSDIFESIRWTKDPKNTQDHVRSLCLMAWHNGEAEYNNFLSKIRSVSVGRTLE--LPPYSYLYQQWVD 2153
Cdd:cd23215    382 R-----FRPAISEKTIWSLVAWQRSNAEFEQNLDTACWFAFMHGYDFYQNFYLQLQSCLEKEMIDyrLKSYEWWRMRFED 456
Parechovirus_RdRp cd23217
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Parechovirus of ...
 1796-2133 8.05e-41

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: 155.80  E-value: 8.05e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1796 AVYGYPNLEPLDLTTSAGYPYTTLGVKKRDIFNKQSRDVVKM------QELLDKYGVDLP---YVTYLKDELRAPEKIRS 1866
Cdd:cd23217      1 AVLGTSHLNSLDLSTSPGYKYVKSGYKKRDLLSLEPFSVSPQlekdvkDKLHAVYKGNQPttiFNACLKDELRKLDKIAQ 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1867 GKTRIIEAASVNDTVNFRMIYGNLFSMFHANPGIQTGSAVGCNPDTFWSQLYSTMGGHLLAFDYTNYDGSIHP--IWF-- 1942
Cdd:cd23217     81 GKTRCIEACSIDYVIAYRVVMSSLYEAIYQTPCQELGLAVGMNPWTDWDFMINALNPYNYGLDYSSYDGSLSEmlMWEav 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1943 DALGKVLDQLGFPGHLMKRLNSTRHIYKNAFYITEGGMPSGICGTSIFNTMINNIIIRTLVIQtyKHIDLDKLRIVaYGD 2022
Cdd:cd23217    161 EVLAYCHESPDLVMQLHKPVINSDHVVMDERWLVHGGMPSGSPCTTVLNSICNLLVCIYLAYL--QSPGIECLPIV-YGD 237

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2023 DVIASYPELLDPQEIANT-AKVYGLTITPADKSATFKPITWENVTFLKR--GFRPDKRYpfLVHPIySMSDIFESIRWTK 2099
Cdd:cd23217    238 DVIFSVSSEIDPEYLVSSaADSFGMEVTGSDKDEPPSLLPRMEVEFLKRttGYFPGSTY--KVGAL-DLETMEQHIMWMK 314

                          330       340       350
                   ....*....|....*....|....*....|....*...
gi 1737293894 2100 D----PKNTQDHVRSLCLmawhNGEAEYNNFLSKIRSV 2133
Cdd:cd23217    315 NlstfPQQLQSFENELCL----HGKDIYDDYKKIFNPY 348
RNA_helicase pfam00910
RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...
 1214-1310 9.62e-41

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: 146.21  E-value: 9.62e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1214 LMIHGPPGCGKSLVTTVIARGLAT-----EGDIYSLPPNPKHFDGYNQQKVVIMDDVGQNPDGEDLSTFCQMVSTADFHV 1288
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKklglpKDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80

                           90       100
                   ....*....|....*....|..
gi 1737293894 1289 PMAALEDKGRSFTSDFVLASTN 1310
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102
Dicistroviridae_RdRp cd23194
RNA-dependent RNA polymerase (RdRp) in the family Dicistroviridae of positive-sense ...
 1845-2131 1.56e-40

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: 153.42  E-value: 1.56e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1845 GVDLP--YVTYLKDELRAPEKIRSGKTRIIEAASVNDTVNFRMIYGNLFS-MFHANpgIQTGSAVGCNPDTF-WSQLYST 1920
Cdd:cd23194      1 GIRLPhvFVDTLKDERRPIEKVDAGKTRVFSAGPMDYTIAFRMYFLGFVAhLMRNR--IDNEIAVGTNVYSLdWDKLARK 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1921 M---GGHLLAFDYTNYDGSIHPIWFDALGKVLDQLGFPGH--------LMKRLNSTRHIYKNAFYITEGGMPSGICGTSI 1989
Cdd:cd23194     79 LlskGDKVIAGDFSNFDGSLNPQILWAILDIINEWYDDGEenalirrvLWEDIVNSVHICGGYVYQWTHSQPSGNPLTAI 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1990 FNTMINNIIIRT--------LVIQTYKHIDlDKLRIVAYGDDVIASYPELLDP----QEIANTAKVYGLTITPADKSAT- 2056
Cdd:cd23194    159 INSIYNSIIMRYvyllltkeAGLMTMSDFN-KHVSMVSYGDDNVINVSDEVSEwfnqLTITEAMAEIGMTYTDETKTGEi 237

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2057 --FKPItwENVTFLKRGFRPDKRYPFLVHPIySMSDIFESIRWTK---DPK-NTQDHVRSlCLMAW-HNGEAEYNNFLSK 2129
Cdd:cd23194    238 vpYRSL--EEVSFLKRGFRYDDDLGRWVAPL-DLDTILEMPNWVRkgkDPEeITKQNVEN-ALRELsLHGEEVFDKWAPK 313


                   ..
gi 1737293894 2130 IR 2131
Cdd:cd23194    314 IR 315
Avisivirus_RdRp cd23231
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Avisivirus of ...
 1803-2130 1.61e-40

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: 154.66  E-value: 1.61e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1803 LEPLDLTTSAGYPYTtlGVKKRDIFNKQS--RDVVKMQE---LLDKYGVDLPYVTYLKDELRAPEKIRSGKTRIIEAASV 1877
Cdd:cd23231      8 LLPIDWGTSPGDKYK--GKTKAQLVDDKKfkADVMNLVRfngDPNREPPDVYFTTYLKDELRPKEKAKAGKTRVISAASF 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1878 NDTVNFRMIYGNLFSMFHANpGIQTGSAVGCNPDTFWSQLYSTMGGHLLAFDYTNYDGSI-HPIWFDALGKVLDQLGFPG 1956
Cdd:cd23231     86 DYTIACRMVFGPILRQLFAW-GREFGFGPGLNPYTHFDELYDKILPFVICLDYSGFDGSLsSELMFHAAQVIACFSEKPE 164

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1957 HLMK----RLNSTRHIYKNAFYITeGGMPSGICGTSIFNTMINNIIIRTLVIqtYKHIDLDKLRIVAYGDDVIASYPELL 2032
Cdd:cd23231    165 AIMAsaelTIGSTERVSDEVWYVY-GGMPSGSPWTTTLNTICNLLMCYTYLL--DMGHCWSETFVVAYGDDVVISANIKH 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2033 DPQEIANTAKV-YGLTITPADKSATFKPITWENVTFLKRgfRPdKRYPFLVHPI--YSMSDIFESIRWTKDpkNTQDHVR 2109
Cdd:cd23231    242 NLEGIEQWFKTkFGATVTPSDKQGKITWTTKNNMEFLKR--RP-KQLDFLPKIVgaLDLDNMLDRIQWTKG--HFQDQLN 316

                          330       340
                   ....*....|....*....|..
gi 1737293894 2110 SLCL-MAWHnGEAEYNNFLSKI 2130
Cdd:cd23231    317 SFYLeLALH-GRETYNEIRAKL 337
Crohivirus_RdRp cd23232
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Crohivirus of ...
 1793-2144 2.02e-40

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


Pssm-ID: 438082  Cd Length: 373  Bit Score: 154.87  E-value: 2.02e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1793 IEQAVYGYPNLEPLDLTTSAGYPYTTLGVKKRDIFNKQS--------RDVVKMQELLDKYG-VDLPYVTYLKDELRAPEK 1863
Cdd:cd23232      1 IEEACFEEGDEHALDLKTSPGFKYVQMGLKKTDLVNRPNkfihpilrNDVRLIFDEMAKGQmPVVTFTAHLKDELRKLEK 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1864 IRSGKTRIIEAASVNDTVNFRMIYGNLFSMFHANPGIQTGSAVGCNPDTFWSQLYSTMGGHLLAFDYTNYDGSIHPIWF- 1942
Cdd:cd23232     81 IRSGKTRCIEACDFDYTVAHKMMFGTLYKAIYDTPGIITGLAVGMNPWKDWELIQQSLFKYNYDFDYKTFDGSLSRELMl 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1943 ---DALGKVLDQLGFPGHLMKRLNSTRHIYKNAFYITEGGMPSGICGTSIFNTMINNIIIRTLVIQTYKhidlDKLRIVA 2019
Cdd:cd23232    161 havDILSACVENDEMAKLMLSVVVESVHLVLDQKWNVSGGMPSGSPCTTVLNSVCNLIVSSTIADMCTE----GDFKILV 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2020 YGDDVIASYPELLDPQEIANTAK-VYGLTITPADKSATFKPITWENVTFLKrgfRPDKRYP---FLVHPIySMSDIFESI 2095
Cdd:cd23232    237 YGDDLIISSTAPLDCDRFKTLVElHYGMEVTPGDKGDEFKVKDREQVSFLK---RVTRKFPgtnYRVGAL-DLDTVKQHL 312

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*....
gi 1737293894 2096 RWTKDPKNTQDHVRSLCLMAWHNGEAEYNNFLSKIRSVSVGRTLELPPY 2144
Cdd:cd23232    313 MWCKSYSSFKQQLDSALMEVAMHGEETYNGFLTEIKTKLDKFKIYPPKF 361
Limnipivirus_RdRp cd23228
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Limnipivirus of ...
 1805-2146 6.47e-40

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: 153.88  E-value: 6.47e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1805 PLDLTTSAGYPYTTLGVKKRDIF-----------NKQSRDVVKMQELLDKYG-VDLPYVTYLKDELRAPEKIRSGKTRII 1872
Cdd:cd23228      9 PIDKNTSPGLKYTRDGLKKSDLYtidedgnvvvsDMLRADVEAWEELIQSGGyPTTLFTACLKDELRSDEKVALGKTRVI 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1873 EAASVNDTVNFRMIYGNLFSMFHANPGIQTGSAVGCNPDTFWSQLYSTMGGH--LLAFDYTNYDGSIHPIWFDALGKVLD 1950
Cdd:cd23228     89 EAAELDYVVAYRMYMSSIYSDLYNAYAGDTGIAAGINPPADGHRLREELSQYdsFLALDYSRFDGSLPEMLMRAAVEILA 168

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1951 QLGFPGHLMKRLNST----RHIYKNAFYITEGGMPSGICGTSIFNTMINNIIIRTLVIQT----YKHIDLDKLR----IV 2018
Cdd:cd23228    169 DLHEDPDLVRRLHETviisKHLVVDEDWTVKGGMPSGSPCTTVLNCICNLLVLEYAFLVHfgvyEDDDGVGLPQcdylSV 248

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2019 AYGDDVIASY--PEL-LDPQEIANTAkvYGLTITPADKSATFKPITWENVTFLKRGF-----RPDKRYPFLVhpiySMSD 2090
Cdd:cd23228    249 VYGDDCIVAYngMEMgLAFAETIEDT--FGMEVTPASKVGDHFNVELHEVEFLKRKFfafetEEYDRIALRL----SENT 322

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1737293894 2091 IFESIRWTKDPKNTQDHVRSLC--LMAWhnGEAEYNNFLSKIRSVSVGRTLELPPYSY 2146
Cdd:cd23228    323 IVQSLMWMRNLKTFPDQVQSLMmeLSAW--GKEKYDKLRDTCKRRLAKQNLQVTVPGY 378
Peptidase_C3 pfam00548
3C cysteine protease (picornain 3C); Picornaviral proteins are expressed as a single ...
 1514-1679 1.39e-39

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: 145.67  E-value: 1.39e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1514 GPEHEFMYALIKRNCHIVETDKGEFNML--GIYDNCAVLPTHANCGDSLLLNGIKTPILKQQI-ITDLNDTDTEITIIWL 1590
Cdd:pfam00548    1 GPGDDFAESMLKQNAVPVTTSKGVFTCCatGVYDNVILLPRHAEPGLTIVLDGKVVTISDPEVeLVDQEGMPLDAAIVKL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1591 DRNEKFRDIRRFLPESIQEWDHMRLATNVSKFPMFFADVGSVTPYGEI-NLSGNPTCRLLKYDYPTRPGQCGGVI----G 1665
Cdd:pfam00548   81 KRNEKFKDIRKHLPNRITKGNPVVLLINNNEQGRIYVPVGAVTHSGGIkTLDGTTTPRTISYNAPTKAGMCGGVViakvE 160

                          170
                   ....*....|....
gi 1737293894 1666 NTGHIIGIHVGGNG 1679
Cdd:pfam00548  161 GNGKILGMHIAGNG 174
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
 367-531 6.86e-39

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: 143.61  E-value: 6.86e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  367 YSPTKEIHIPGKIDNMLHIAMVDSLIPINNQQSHAGQVAMYNVQVFKRSDTDLILALpLQMDNTLFATTLLGEVLNYFGN 446
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFFW-WKLPLALLSMGLLGRLLRYHTY 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  447 WSGSIKVTFMCVCDSFSSGKFLVAYTPPGGGVPTNR---KEAMLGTHLIWDLGLQSSCTLVAPWMSSTFYRRTKGDA--- 520
Cdd:pfam00073   80 YRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRdylWQATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDGnwt 159

                          170
                   ....*....|.
gi 1737293894  521 YTSGGYITLWY 531
Cdd:pfam00073  160 LVVAGWVPLNY 170
Kunsagivirus_RdRp cd23219
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Kunsagivirus of ...
 1793-2110 1.15e-38

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: 148.86  E-value: 1.15e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1793 IEQAVYGypNLEPLDLTTSAGYPYTtlGVKKRDIFNKQSR--------DVVKMQELLDKYGVD-LPYVTYLKDELRAPEK 1863
Cdd:cd23219      1 IEEAVFD--TVTPMDHTASAGPKYP--GTKRSELIDFQNRiisdrlrnDVLELQFRGTSGGAGeVKFSSFLKDELRPLSK 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1864 IRSGKTRIIEAASVNDTVNFRMIYGNLFSMFHANPGIQTGSAVGCNPDTFWSQLYSTMGGHLLAFDYTNYDGSIHPIWFD 1943
Cdd:cd23219     77 IRSGDTRVVECSSLDYTVAFRMQFLRVLQMCYGSDPTLTGLAPGMNVYTDMLPLCTSLYDYNLCLDFSKYDSRLPLQVMH 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1944 ALGKVLDQLGFPGHLMKR-----LNSTrHIYKNAFYITEGGMPSGICGTSIFNTMINNIIIRTLVIQTYKHIDldkLRIV 2018
Cdd:cd23219    157 RVAQLISNLTPDPQVSMRlfqpiIIST-HIVGSYEVVVEGGMPSGCPITTIMNSVCNVVMTSYAMLLLDPDSD---FWPV 232

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2019 AYGDDVIASYPELLDPQEIANT-AKVYGLTITPADKSATFKPITWENVTFLKRGFRPDKRYPFLVhPIYSMSDIFESIRW 2097
Cdd:cd23219    233 AYGDDNIVSTRKPIDTELFCSIlNEEFGMILTGADKTTTVQAVPPMSVDFLKRRLRYTPEFPLPV-PVLPLDSMLSRICW 311

                          330
                   ....*....|...
gi 1737293894 2098 TKDPKNTQDHVRS 2110
Cdd:cd23219    312 CKGETEFKDQLES 324
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 385-565 3.08e-38

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


Pssm-ID: 119412  Cd Length: 178  Bit Score: 141.76  E-value: 3.08e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  385 IAMVDSLIPINNQQSHAGQVAMYNVQvfkrsdtdlilaLPLQMDNTLFATTLLGEVLNYFGNWSGSIKVTFMCVCDSFSS 464
Cdd:cd00205      4 FADRPTTVGTNNWNSSASGTQLFQWK------------LSPALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHT 71

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  465 GKFLVAYTPPGGGVPTN---RKEAMLGTHLIWDLGLQSSCTLVAPWMSSTFYRRTKGDAY---TSGGYITLWYQTDFI-P 537
Cdd:cd00205     72 GRLLVAYVPPGAPAPTTgdtRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDGYgplNSFGTLVVRVLTPLTvP 151

                          170       180
                   ....*....|....*....|....*...
gi 1737293894  538 SSSGGVGTILATCSACpDLSVRMMRDTP 565
Cdd:cd00205    152 SGAPTTVDITVYVRAG-DFELYGPRPPR 178
Aalivirus_RdRp cd23216
RNA-dependent RNA polymerase (RdRp) in the genus Aalivirus of positive-sense single-stranded ...
 1805-2132 2.07e-33

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: 133.25  E-value: 2.07e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1805 PLDLTTSAGYPYTtlGVKKRDIFNKQS-RDVVKMqeLLDkyGVDLPYVTYLKDELRAPEKIRSGKTRIIEAASVNDTVNF 1883
Cdd:cd23216     11 PIDWQTSPGLKYK--GRTKADLVQDPKfKEDVKE--ILA--GKPTFFTTYLKDELRSIEKIANGNTRAIEAANFDHVVAW 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1884 RMIYGNLFSMFHANPGIQTGSAVGCNPDTFWSQLYSTMGGHLLAFDYTNYDGSIHPIWFDALGKVLDQLGFPGHLMKRLN 1963
Cdd:cd23216     85 RQVMGNIVKQLFSDHDRVTGFAPGMNPYTHFDSLMDQVKWNVLALDFKKFDGSLSPQVMEEAVDILASFHDMPQMVVDIH 164

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1964 S----TRHIYKNAFYITEGGMPSGICGTSIFNTMINNIIIRTLVIQtyKHIDLDKLRIVAYGDDVIASY----PELLDPQ 2035
Cdd:cd23216    165 KhtiySTNVVSDETWFVEGGMCSGSPCTTVLNTICNLLVNTTILLS--EGIQPDNFYIAAYGDDTIISVdglsSSLPDPK 242

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2036 EIANTAKV-YGLTITPADKSATFKPITWENVTFLKR--GFRPDKRYpflVHPIYSMSDIFESIRWTKDpkNTQDHVRSLC 2112
Cdd:cd23216    243 IMQQKYKEwFGMTVTSADKGSEITWDTRNHVQFLKRrpGFFPGTQK---VVGVLDLESMMEHIAWTKG--SFQDQLNSFY 317

                          330       340
                   ....*....|....*....|
gi 1737293894 2113 LMAWHNGEAEYNNFLSKIRS 2132
Cdd:cd23216    318 QELVLHGEQVYMTVRQTLKS 337
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 123-322 1.37e-32

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


Pssm-ID: 119412  Cd Length: 178  Bit Score: 125.59  E-value: 1.37e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  123 PETSSDRFYTLESVNWE---SGSKGWWWKFPDA----LKDMGMFGQNMYHHSMGRFGALIHVQCNATKFHSGCLLIMVVP 195
Cdd:cd00205      1 VESFADRPTTVGTNNWNssaSGTQLFQWKLSPAlgflLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  196 EHQLAYIgaegvkvryehthpgerghtlrdsrdrstnnpddnpfymcNGTLLGNGMIYPHQMINLRTNNSATIVIPYINC 275
Cdd:cd00205     81 PGAPAPT----------------------------------------TGDTRWQATLNPHVIWDLGTNSSVTFVVPYVSP 120

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1737293894  276 IPMDNMLRH-----NNF-SLVIVPIVPLRPGNSGAPILPITVTIAPYKSEFSG 322
Cdd:cd00205    121 TPYRSTRYDgygplNSFgTLVVRVLTPLTVPSGAPTTVDITVYVRAGDFELYG 173
Pico_P2B pfam01552
Picornavirus 2B protein; Poliovirus infection leads to drastic alterations in membrane ...
 992-1092 4.35e-30

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


Pssm-ID: 279840  Cd Length: 101  Bit Score: 115.51  E-value: 4.35e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  992 QGpIGNYINQLGTAFGDGFTT----AIKSQLDMLGNTvcDQLTGKVIKWLVRVISAITIMVRNSSDIPTVLATLALLGCH 1067
Cdd:pfam01552    1 QG-ISDYIEHLGAAFGSGFTQqisdKIKELTNFINPT--SKIGEKLIKNLIKIISALIIITRNSEDPQTVIATLALLGCD 77

                           90       100
                   ....*....|....*....|....*
gi 1737293894 1068 TSPWSFLKDKVCKWLGIPApARKQG 1092
Cdd:pfam01552   78 ASPWQFLKEKACAVLEIPY-VHKQG 101
Caliciviridae_RdRp cd23192
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Caliciviridae of ...
 1854-2125 9.97e-30

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: 121.60  E-value: 9.97e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1854 LKDELRAPEKIRSGKTRIIEAASVNDTVNFRMIYGNLFSMFHANPGIqTGSAVGCNPD-TFWSQLYSTM--GGHLLAFDY 1930
Cdd:cd23192      7 LKDELRPVEKIAEGKRRLLWGCDVGVTLVAAAAFGPVADALKAVCPT-GPIAVGINMDsEDVEVIFERLsgFRYHYCLDY 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1931 TNYDGSIHPIWFDALGKVLDQLGFPGHL----MKRLNSTRHIYKNA-FYITEGGMPSGICGTSIFNTMINNIIIRTLVIQ 2005
Cdd:cd23192     86 SKWDSTQSPAVTAAAIDILADLSEETPLrdsvVETLSSPPMGIFDDvIFVTKRGLPSGMPFTSVINSLNHWLLFSAAVLK 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2006 TYKHIDL------DKLRIVAYGDDVIASYPELL--DPQEIANTAKVYGLTITPADKSATFKPITWENVTFLKRGFRPDkr 2077
Cdd:cd23192    166 AYELVGIytgnvfDEADFFTYGDDGVYAMPPATasVMDEIIENLKSYGLKPTAADKTENPDIPPLQGPVFLKRTFVRT-- 243

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1737293894 2078 yPFLVHPIYSMSDIFESIRWTKDPkNTQDH---------------VRSLCLMAWHNGEAEYNN 2125
Cdd:cd23192    244 -PGGWRALLDRSSILRQLYWVKGP-NTHDWteppteidheartvqLENVLLEAAQHGPEFYEK 304
Aquamavirus_RdRp cd23220
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Aquamavirus of ...
 1805-2125 2.32e-29

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: 121.35  E-value: 2.32e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1805 PLDLTTSAGYPYTtlGVKKRDIFNKQS----RDVVKMQELLDKYGVDLPYVTYLKDELRAPEKIRSGKTRIIEAASVNDT 1880
Cdd:cd23220     11 PLNFNGTAGAKYP--GMNRRQLLLPLNpqvrDDVVKLAGDVGNGTATVVFETFMKDELRPKEKIESGKTRIVESCPLDYL 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1881 VNFRMIYGNLFSMFHANPGIQTGSAVGCNPDTFWSQLYSTMGGHLLAFDYTNYDGSIHPIWFDALGKVLDQLGFPGHLMK 1960
Cdd:cd23220     89 LLYRMVMLKSMIWWYNSDCIKTGVAPGMNVYTDFVPMVKQFKKIKYCLDFSAYDSTLSDEILAAGVEVLACTSAVPSYVR 168

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1961 RLNS----TRHIYKNAFYITEGGMPSGICGTSIFNTMINNIIIRTLVIQtykhIDLDKLRIVAYGDDVIASYPELLDPQE 2036
Cdd:cd23220    169 KLHApiicSHHWHNNVVDLVLGGMPSGAPCTSVLNSIVNVLMARYICAL----MDIDYPVMVAYGDDNVVSFDEEIDIER 244

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2037 IANTAKV-YGLTITPADKSATFKPITweNVTFLKRGFR--PDKRYPFlvhPIYSMSDIFESIRWTKDPKNTQDHVRSLCL 2113
Cdd:cd23220    245 MVSLYKTeFGVTATNHDKTPVPRPMA--NPVFLKRRLRfnPDLNIQF---PVLPLGEMIDRMCWTRGPEHLSDQTFSFAI 319

                          330
                   ....*....|..
gi 1737293894 2114 MAWHNGEAEYNN 2125
Cdd:cd23220    320 ELAGYGKQVYTH 331
Pico_P1A pfam02226
Picornavirus coat protein (VP4); VP1, VP2, VP3 and VP4 for the basic unit that forms the ...
 2-67 1.53e-28

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


Pssm-ID: 308053  Cd Length: 68  Bit Score: 110.15  E-value: 1.53e-28
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1737293894    2 GAQVSKQNVGSHENSVSASNGSVIKYFNINYYKDSASSGLTKQDFSQDPSKFTQPLVDTLTNPALM 67
Cdd:pfam02226    1 GAQVSRQNVGTHSTQNRVSNGSSINYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPT 66
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 642-810 6.99e-27

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: 109.41  E-value: 6.99e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  642 IENFLGRSSLWA----ELSLGNKKFCKWDISFQEQ------AHIRKKMEWFTYVRFDMEVTVVTNN---HSL-MQIMFIP 707
Cdd:cd00205      1 VESFADRPTTVGtnnwNSSASGTQLFQWKLSPALGflllqnTPLGALLSYFTYWRGDLEVTVQFNGskfHTGrLLVAYVP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  708 PGIDPPSTHDDkKWNGASNPSVFYQPKSGFP-RFTIPFTGLGAAYYIFYDGYDENkagnvnygisatNDMGTLCFRSL-- 784
Cdd:cd00205     81 PGAPAPTTGDT-RWQATLNPHVIWDLGTNSSvTFVVPYVSPTPYRSTRYDGYGPL------------NSFGTLVVRVLtp 147

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1737293894  785 -----EEAQGTDIKVYIKPKHITAWCPRAPR 810
Cdd:cd00205    148 ltvpsGAPTTVDITVYVRAGDFELYGPRPPR 178
Marnaviridae_RdRp cd23195
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Marnaviridae of ...
 1854-2131 1.64e-24

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: 106.38  E-value: 1.64e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1854 LKDElraPEKIRSGKTRIIEAASVNDTVNFRMIYGNLFSMFHANPgIQTGSAVGCN---PDtfWSQLYSTMGGH----LL 1926
Cdd:cd23195      7 LKDE---PTKLTKDKVRVFQAAPVALQLLVRKYFLPIARFLQMNP-LLSECAVGINaqsPE--WEELYEHLTKFgedrII 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1927 AFDYTNYDGSIHPIWFDALGKVLDQLgfpghLMKRLN-STRHIYK---------NAFYITEG-------GMPSGICGTSI 1989
Cdd:cd23195     81 AGDYSKYDKRMSAQLILAAFKILIDI-----AAKSGGySEEDLKImrgiatdiaYPLVDFNGdliqffgSNPSGHPLTVI 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1990 FNTMINNIIIRTLVIQTYKHIDLDKLR----IVAYGDDVIAS----YPElLDPQEIANTAKVYGLTITPADKSATFKP-I 2060
Cdd:cd23195    156 INSIVNSLYMRYAYYSLYPEKEVPPFRdvvaLMTYGDDNIMSvspgYPW-FNHTSIAEFLAKIGIKYTMADKEAESVPfI 234

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1737293894 2061 TWENVTFLKRGFRPDKRYPFLVHPIySMSDIFESIRWTKDPKN-TQDHVRSLCL------MAWHnGEAEYNNFLSKIR 2131
Cdd:cd23195    235 HISEADFLKRKFVFDPELGVYVGPL-DEDSIFKSLHCYLKSKVlTPEEQAAQNIdgalreWFFH-GREVYEKRREQLK 310
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
 622-757 4.88e-23

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: 98.15  E-value: 4.88e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  622 PADTIETRYVINNHTNNEAIIENFLGRSSL-----------------WAELSlgnKKFCKWDISFQEQAH--IRKKMEWF 682
Cdd:pfam00073    1 TTQTPETRTVGYGKNPLELAVENFLGRDAPvqpdvqgerfytldstdWTSLS---KGFFWWKLPLALLSMglLGRLLRYH 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894  683 TYVRFDMEVTVVTN----NHSLMQIMFIPPGIDPPSTHdDKKWNGASNPSVFYQPKSG-FPRFTIPFTGLGAAYYIFYDG 757
Cdd:pfam00073   78 TYYRGGLEVTVQFNgskfHQGKLLVAYVPPGAPPPGSR-DYLWQATLNPHQFWNLGLNsSARLSVPYISIAHYYSTFYDG 156
Iflaviridae_RdRp cd23197
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Iflaviridae of ...
 1849-2097 2.22e-16

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: 82.61  E-value: 2.22e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1849 PYVTYLKDELRAPEKIRS-GKTRIIEAASVNDTVNFRMIYGNLFSMFHANPgIQTGSAVGCNPDTF-WSQLYSTM---GG 1923
Cdd:cd23197      7 VYWAHLKDELRPSEKLRRfGGTRVFSVPPLELVLNSRRFLLPFMDAFQSFP-IEAHHAIGLNPNSGdWRRLRDTLlekGP 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1924 HLLAFDYTNYDgsihpiwfDALGKVLDQLGFpgHLMKRLNSTRH--------IYKNAFYITE--------------GGMP 1981
Cdd:cd23197     86 CLLQMDYKNYS--------DAIPKECVAKAF--HIIVDYYRKWHcltveienALKTLFLDTAdaellvygdvfkvnNGVL 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1982 SGICGTSIFNTMINniiirtLVIQTYKHIDLDKLR---------IVAYGDDVIASYPELLDPQ----EIANTAKVYGLTI 2048
Cdd:cd23197    156 AGHPMTSVVNSVVN------LILMNYMWIKITRRRaseffkltyIIVMGDDVVISLPKQLTEEfdcrKICAEFAKYDIKV 229

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1737293894 2049 TPADKSATFKPITWENV---TFLKRGFRPDKRYPFLVHPIYSMSDIFESIRW 2097
Cdd:cd23197    230 TDSEKNLTGEPKPYDSFdkfEFLSRGFSDCDAYPDITFAPVKTIALFDCPLW 281
Secoviridae_RdRp cd23196
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Secoviridae of ...
 1844-2132 2.16e-15

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: 79.35  E-value: 2.16e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1844 YGVDLPyvtylKDELRAPEK-IRSGKTRIIEAASVNDTVNFRMIYGNLFSMFHANPgIQTGSAVGCNPDTF-WSQLYSTM 1921
Cdd:cd23196      2 NCVECP-----KDERLKKRKvLEKPKTRLFDVLPMEYNLLLRKYFLNFVRFIQANR-HRLPCQVGINPYSReWTTLYDRL 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1922 ---GGHLLAFDYTNYDGSI-HPI---WFDALGKVL---DQLGFPGHLMKRLNSTRHIYKNAFYITEGGMPSGICGTSIFN 1991
Cdd:cd23196     76 aekSDTALNCDYSRFDGLLsHQVyvwIADMINRLYgdgDEAKARRNLLMMFCGRRSICGRQVYMVRGGMPSGCALTVIIN 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1992 TMINNIIIRTLviqtYKHI-------DLDKL-RIVAYGDD-VIASYPELL---DPQEIANTAKVYGLTITP-ADKSA--- 2055
Cdd:cd23196    156 SIFNEILIRYV----YRKVvprparnNFNKYvRLVVYGDDnLISVKEEIIpyfDGPVIKKEMAKVGVTITDgTDKTSptl 231

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2056 TFKPItwENVTFLKRGFR--PDKRYpflVHPIySMSDIFESIRWTKDPKNTQD-----HVRSLCLMAWHNGEAEYNNFLS 2128
Cdd:cd23196    232 ERKPL--ESLDFLKRGFRvqSDGLV---VAPL-DKTSLYSRLHYVTAGGDGMYslyilNDNNKSFLEEHVDHPEFTEFRN 305


                   ....
gi 1737293894 2129 KIRS 2132
Cdd:cd23196    306 RVVS 309
Nora-virus_RdRp cd23200
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in a novel picorna-like ...
 1854-2072 7.18e-13

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: 71.87  E-value: 7.18e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1854 LKDELRAPEKIRSGKTRIIEAASVNDTVNFRMIYGNLFSMFHaNPGIQTGSAVGCNPDTF-WSQLYSTMGGHLLAF--DY 1930
Cdd:cd23200      7 LKDQPIKIAQAKSGRTRVFHCIPVDLILFSGALYGPYKEAYT-KAGLKCYHAVGIDPKSVgWQQLATYMTKHPNYFdaDY 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1931 TNYDGSIHPIWFDALGKVL---------DQLGFPGHLMKRLNSTRHIYKNA-FYITEGGMPSGICGTSIFNTMINNIIIR 2000
Cdd:cd23200     86 KNYDKYLHRQVFKAVRKIQrsviqqvcpDKWDKARAVEELDAIDTYVVDYQtVYKTNRGNKSGSYTTTIDNCLANDIYGL 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2001 TLVIQTYKHIDLDKLRI----VAYGDDVIAS----YPELLDPQEIANTAKVYGLTITPADKSATFKPIT-WENVTFLKRG 2071
Cdd:cd23200    166 YAWVKTTGLRSLWDYRQnvssVAFGDDIIKSvsdeYKDKYNYCTYRDVLNATGHIMTPGSKDGEEKPFTsFENLQFLKRG 245


                   .
gi 1737293894 2072 F 2072
Cdd:cd23200    246 F 246
Polycipiviridae_RdRp cd23198
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Polycipiviridae of ...
 1855-2130 7.95e-10

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: 62.43  E-value: 7.95e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1855 KDELRAPEKIRSG-----KTRIIEAASVNDTVNFRMIYGNLFSMFHA--------NPGIqtgsavgcNPD-TFWSQLYST 1920
Cdd:cd23198      8 KDELRPIYKALGDpqtppKTRSVTCMNVYYILAWRRVTLDFWASMHRaadgnfpfCPGI--------NPEgPDWNRLYHY 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1921 MGGH--LLAFDYTNYDGSIHPIWFDALGKVL-DQLGFPGH----------LMKRLNStrHI-YKNAFYITEGGMPSGICG 1986
Cdd:cd23198     80 LNRHpnAVDFDVSNWDGHLPAELFYAVLDIIkTVLGLKPNspnakviysiLTEVMNC--HIqFEDIIYQKLRGLISGFPG 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1987 TSIFNTMINNIII-----RTLVIQTYKHIDLDKLRIVA---YGDDVIASYPE----LLDPQEIANTAKVYGLTITPADKS 2054
Cdd:cd23198    158 TAEVNTLAHWLLIyyiylYLAQNTIYDMTITAFLRNVSaifYGDDIIITISDeilhWFNGKTIQRMYEEHGYPVTSAAKD 237

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 2055 ---ATFKPITweNVTFLKRGFRPdkrypflVHPIY-----SMSDIFESIRWTKDPKNTQDHVRSLCLMAWH----NGEAE 2122
Cdd:cd23198    238 teiPESKPLS--DCQFLKSSWNP-------ILPGYyirkmDIEVVYDLVYWVRAKEHPRDQFYSNYHDALRilfgHGEQV 308


                   ....*...
gi 1737293894 2123 YNNFLSKI 2130
Cdd:cd23198    309 FEAFREQV 316
Solinviviridae_RdRp cd23199
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Solinviviridae of ...
 1905-2073 2.90e-08

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: 57.75  E-value: 2.90e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1905 AVGCNPDTFWSQLYSTMG--GHLLAFDYTNYDGSIHP----IWFDALGKVLDQLGFPGHLMKRlnSTRH---IYKNAFYI 1975
Cdd:cd23199     72 AVGCNPYATFHKFATKFFkfKNFFSCDYKNFDRTIPKcvfeDFRDMLIQANPHMKNEIYACFQ--TIIDriqVSGNSILL 149

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1976 TEGGMPSGICGTSIFNTMINNIIIRTLVIQTYKHIDLDKLRI----------VAYGDDVIASYPE----LLDPQEIAN-T 2040
Cdd:cd23199    150 VHGGMPSGCVPTAPLNSKVNDIMIYTAYVNILRRADRGDITSyryyrdlvcrLFYGDDVIIAVDDsiadIFNCQTLSEeM 229

                          170       180       190
                   ....*....|....*....|....*....|....
gi 1737293894 2041 AKVYGLTITPADKSATFKPI-TWENVTFLKRGFR 2073
Cdd:cd23199    230 KILFGMNMTDGSKSDIIPKFeTIETLSFISRFFR 263
ps-ssRNAv_RdRp-like cd23167
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
 1924-2029 4.49e-08

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.


Pssm-ID: 438017 [Multi-domain]  Cd Length: 73  Bit Score: 51.96  E-value: 4.49e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1924 HLLAFDYTNYDGSIHPIWFDAlgkvldqlgfpghlmkrlnstrhiyknafyitegGMPSGICGTSIFNTMINNIIIRTLV 2003
Cdd:cd23167      1 HVVESDYSGFDSSISPDLLKA----------------------------------GQPSGSPNTSADNSLINLLLARLAL 46

                           90       100
                   ....*....|....*....|....*..
gi 1737293894 2004 IQTYKHIDLDK-LRIVAYGDDVIASYP 2029
Cdd:cd23167     47 RKACGRAEFLNsVGILVYGDDSLVSVP 73
RdRP_4 pfam02123
Viral RNA-directed RNA-polymerase; This family includes RNA-dependent RNA polymerase proteins ...
 1745-2073 7.90e-08

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: 57.09  E-value: 7.90e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1745 RLETNLDDAVLAKYKGNPKVEFNEFIQVAVDHYAA------QLYPLDINPSPIS------IEQAVYGYPnLEPLDLTTSA 1812
Cdd:pfam02123  122 RGVTNVDWEEEAKNRVDLAVVCRLVLLPMEELRAHidavldELVVRRGLCDPIRlfvknePLWCVNGHP-DHKLREGRLR 200

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1813 GYP----YTTLGvkKRDIFNKQSRDvvkmqelldkyGVDLPYVTYLKdelrAPEKIRSGKTRIIEAASVNDTVNFRMIYg 1888
Cdd:pfam02123  201 LLSsvslVDQLV--RRMLFEPQNNN-----------EIAWWGSVPSK----PSMKLEHGKSRAIYACDTRSYLAFEYLL- 262

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1889 NLF------SMFHANPGiqTGSAVGcnpdtFWSQLY-STMGGHLLAFDYTNYDgSIHPIW-----FDALGKVLDQlgFPG 1956
Cdd:pfam02123  263 APVekawanKSVILNPG--EGDISG-----FDWSVQdWKRGGVSLMLDYDDFN-SQHSTEsmravFERLRRRLPD--EPA 332

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1957 HLMKRL-NSTRHIY-----KNAFYITEGGMPSGICGTSIFNTMINNIIIRTLVIQtykhiDLDKLRIVAYGDDVIASYPE 2030
Cdd:pfam02123  333 EAADWLvCSMDSMYqlsdgTLLAQRVPGTLKSGHRATTFINSVLNCAYAELAGAP-----WADVPTSIHMGDDVLEGLRT 407

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|...
gi 1737293894 2031 LLDPQEIANTAKVYGLTITPADKSATFKPITWENVTFLKRGFR 2073
Cdd:pfam02123  408 PADATSLLDKYARLGFKVNPSKQSVGHTIAEFLRVAFCSHEVR 450
ps-ssRNAv_Astroviridae_RdRp cd23172
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Astroviridae of ...
 1850-2050 7.69e-06

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


Pssm-ID: 438022  Cd Length: 243  Bit Score: 49.39  E-value: 7.69e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1850 YVtYLKDELRAPEKIRSGktriieaasvndtvNFRMIY---------GNLF-----SMFHANPGiQTGSAVGCNPdtFWS 1915
Cdd:cd23172      5 YL-FLKKEILKKEKIEDG--------------DIRQILcpdpifariGARFeqdqnNLMKERTL-TNEGQVGWSP--FYG 66

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1916 QLYSTM------GGHLLAFDYTNYDGSIhPIW---------FDALGKVLDQLGFpghlmKRLNSTRH--IYKNAF----- 1973
Cdd:cd23172     67 GFDARVrrlgskGNYFVEFDWTRFDGTI-PAElfrhirklrWSFLDPEKTEENR-----KVYDWYVHnlLNRYVLlptge 140

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1974 -YITEGGMPSGICGTSIFNTMINNIIirtlviQTY--------KHIDLDKLR----IVAYGDDVIASYPELLDP---QEI 2037
Cdd:cd23172    141 vTRVTKGNPSGQISTTMDNCMVNTFL------TAFefayvygpKTGTLKELWdnydTIVYGDDRLSGYPSLPDPyveRVV 214

                          250
                   ....*....|...
gi 1737293894 2038 ANTAKVYGLTITP 2050
Cdd:cd23172    215 DMYKDVFGMWVKP 227
AAA_16 pfam13191
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 1195-1242 2.35e-03

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


Pssm-ID: 433025 [Multi-domain]  Cd Length: 167  Bit Score: 40.95  E-value: 2.35e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1737293894 1195 KELKQLQ-CYKRTKRTEPVCLMIHGPPGCGKSLVTTVIARGLATEGDIY 1242
Cdd:pfam13191    7 EELEQLLdALDRVRSGRPPSVLLTGEAGTGKTTLLRELLRALERDGGYF 55
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 1194-1329 4.13e-03

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


Pssm-ID: 99707 [Multi-domain]  Cd Length: 151  Bit Score: 39.82  E-value: 4.13e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1194 HKELKQLQcyKRTKRTEPVCLMIHGPPGCGKSLVTTVIARGLA--------------TEGDIYSLPPNPKHFDG------ 1253
Cdd:cd00009      4 EEAIEALR--EALELPPPKNLLLYGPPGTGKTTLARAIANELFrpgapflylnasdlLEGLVVAELFGHFLVRLlfelae 81

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1737293894 1254 YNQQKVVIMDDVGQNPDGedlstfcqmVSTADFHVpMAALEDKGRSFTSDFVLASTNLASLvpqtVQTPEALLRRF 1329
Cdd:cd00009     82 KAKPGVLFIDEIDSLSRG---------AQNALLRV-LETLNDLRIDRENVRVIGATNRPLL----GDLDRALYDRL 143
ps-ssRNAv_Potyviridae_RdRp cd23175
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Potyviridae of ...
 1854-2030 4.87e-03

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


Pssm-ID: 438025  Cd Length: 236  Bit Score: 40.90  E-value: 4.87e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1854 LKDELRAPEKIRSGKTRIIEAASVnDTV--------NFRmiygNLFSMFHanpgIQTGSAVGCNpdTF---WSQLYSTMG 1922
Cdd:cd23175     10 LKAELRPIEKVEANKTRTFTAAPI-DTLlggkvcvdDFN----NQFYSLH----LKAPWTVGIT--KFyggWDKLLRKLP 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737293894 1923 GHLLafdYTNYDG-----SIHPIWFDAlgkVLD-QLgfpgHLM-------KRLnstRHIYknafyiTE------------ 1977
Cdd:cd23175     79 DGWV---YCDADGsqfdsSLTPYLINA---VLRiRL----HFMedwdigeQML---RNLY------TEivytpiltpdgt 139

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1737293894 1978 -----GGMPSGICGTSIFNTMINNI-----IIRTLViqTYKHIDlDKLRIVAYGDD-VIASYPE 2030
Cdd:cd23175    140 ivkkfKGNNSGQPSTVVDNTLMVMIamyyaLLKLGI--DFEEID-ERCVFFCNGDDlLIAVSPE 200
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 1197-1238 8.70e-03

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


Pssm-ID: 440232 [Multi-domain]  Cd Length: 397  Bit Score: 41.05  E-value: 8.70e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1737293894 1197 LKQLQCYKRTKRTEPVCLMIHGPPGCGKSLVttviARGLATE 1238
Cdd:COG0464    177 LKRPELREEYGLPPPRGLLLYGPPGTGKTLL----ARALAGE 214
 
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

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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