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Conserved domains on  [gi|1124158116|gb|APQ44493|]
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polyprotein [Basavirus sp.]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
ps-ssRNAv-Picornavirales cd23169
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of ...
1653-1945 3.15e-69

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: 236.34  E-value: 3.15e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1653 FVAYLKDELVSEKKIKQKRCRIIYGGDMIANTAFRMIFGSFVIAYNHSYDKLSHAVGLNQYSYDMDIIHSYLLEVGNNFV 1732
Cdd:cd23169      3 FVDCLKDELRPIEKVKAGKTRLFSASPLDYTIAFRKYFGDFIAAFQKNRIKLEHAVGINPDSVEWTRLYRRLLKKGPNIF 82
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1733 AGDFKGWDKNMNAYLQKKVY---YGIMQTCSSLINSRNYESFYEHQVKAPVIVEKHLLTFANTQFSGCFFTTILNCLVHD 1809
Cdd:cd23169     83 AGDYSNFDGSLPPDVMEAAFdiiNDWYDEYVDDEDERVRKVLFEELINTIHLVGNLVYQVHGGNPSGNPLTTIINSIVNL 162
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1810 AMLRYIFelnCEKFGRNLI--FEEHVRAKILGDDHIYSFSDEAAKFMNPKNIQEAYKELGAEYTDDQKEAEVsEEFRKFE 1887
Cdd:cd23169    163 LYIRYAW---LRITGLTSLsdFKKNVRLVTYGDDVIISVSDEVKDEFNFVTISEFLKELGITYTDADKSGDI-VPYRPLE 238
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1124158116 1888 DLTFLGAHPRL--IKGRWVGALKKDTITEMVLWTRDFNEDLLARCQTSIEMSSL---WGEEYY 1945
Cdd:cd23169    239 EVTFLKRGFRPhpTPGLVLAPLDLESIEEQLNWTRKEDDLLEATIENARAALLLafgHGPEYY 301
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
2337-2510 5.30e-20

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: 89.76  E-value: 5.30e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 2337 CMRNCLMTTIPLNTSmPTNTALVELSLDSRLNIAVGNNIPVNvAVLNQFHFWRGDIEFTFVLVRTQYHSCRLQgvVAY-- 2414
Cdd:cd00205      5 ADRPTTVGTNNWNSS-ASGTQLFQWKLSPALGFLLLQNTPLG-ALLSYFTYWRGDLEVTVQFNGSKFHTGRLL--VAYvp 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 2415 -----GVDAIEEGSRSVAYSNIMDFsGENSVCSMTIQFNAQTEFLRTYEGskvvDPTQNHSLGTFGLYIANQLVAPDTVP 2489
Cdd:cd00205     81 pgapaPTTGDTRWQATLNPHVIWDL-GTNSSVTFVVPYVSPTPYRSTRYD----GYGPLNSFGTLVVRVLTPLTVPSGAP 155
                          170       180
                   ....*....|....*....|.
gi 1124158116 2490 QTIDVLMYVRFLNVKVAVPRA 2510
Cdd:cd00205    156 TTVDITVYVRAGDFELYGPRP 176
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
2045-2202 2.91e-16

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: 78.98  E-value: 2.91e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 2045 SFEWSTSDiPGKAIKTIPIPFGLLELGDSDNVQNMPFDRFLFWNGDVKLTFQVNGTPFMCGLLAVYFMPLASYE----CE 2120
Cdd:cd00205     13 TNNWNSSA-SGTQLFQWKLSPALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPPGAPApttgDT 91
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 2121 LANISTTNHVYLQPDKNNTVEITIPFLY---FRTVMNTVARTTESLGTIFVTPISPLSSVGGEP--VSISLYSSFHNSSF 2195
Cdd:cd00205     92 RWQATLNPHVIWDLGTNSSVTFVVPYVSptpYRSTRYDGYGPLNSFGTLVVRVLTPLTVPSGAPttVDITVYVRAGDFEL 171

                   ....*..
gi 1124158116 2196 SIPRPLP 2202
Cdd:cd00205    172 YGPRPPR 178
RNA_helicase pfam00910
RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...
705-805 9.28e-14

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: 69.56  E-value: 9.28e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116  705 PGFGKSLLAPVLINR---AFDYSPADVYTRNQTEEYWSGYIAQPVVFIDEFLVNKDPQVVNraadEYLKLISPSKFTPEF 781
Cdd:pfam00910    7 PGCGKSTLAKYLARAllkKLGLPKDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEA----ELIRLVSSTPYPPPM 82
                           90       100
                   ....*....|....*....|....*
gi 1124158116  782 ASTDNivmglKGTTVSPTIVI-TAN 805
Cdd:pfam00910   83 AALEE-----KGTPFTSKFVIvTSN 102
ps-ssRNAv_RdRp-like super family cl40470
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
1488-1718 1.10e-03

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 cd23227:

Pssm-ID: 477363  Cd Length: 466  Bit Score: 44.17  E-value: 1.10e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1488 LPPRERVILSRVSKIRPSVIAPEMpeTPKKHLPLLSPNDPRAeneDPLVNMINDTLSKLSP----------RCDESRADR 1557
Cdd:cd23227      6 LPDGPRIHVPRKTKLRKSPAYPIF--KPDAGPAVLSKNDPRL---AEGVDFDKQVFSKHSAnqkeypkafrRMARWYADR 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1558 AVLgtmyHMRKNltwifpKRRLTFEEAVGGVPgLLTSMNRFTSAGYPLCKitKGRGKREYFWFDDNgklcydPLYKTLVM 1637
Cdd:cd23227     81 VFT----YLGKD------NGPLSVKDAIKGID-NLDAMDPTTSPGLPYSA--AGIKRTDLLDFDTG------EIISPALR 141
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1638 NFIEKFDRGECEKGRFVAYLKDELVSEKKIKQKRCRIIYGGDMIANTAFRMIFGSFVIAYNHS----------------Y 1701
Cdd:cd23227    142 AEYNKYVSGDYSDHVFQTFLKDEIRSEEKIKAGKTRIVDVPSLAHVIIGRVLLGKFCSKFQASpgtelgsaigcnpdwdW 221
                          250
                   ....*....|....*..
gi 1124158116 1702 DKLSHAVGLNQYSYDMD 1718
Cdd:cd23227    222 TYFAHQLMERQWCYDID 238
 
Name Accession Description Interval E-value
ps-ssRNAv-Picornavirales cd23169
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of ...
1653-1945 3.15e-69

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: 236.34  E-value: 3.15e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1653 FVAYLKDELVSEKKIKQKRCRIIYGGDMIANTAFRMIFGSFVIAYNHSYDKLSHAVGLNQYSYDMDIIHSYLLEVGNNFV 1732
Cdd:cd23169      3 FVDCLKDELRPIEKVKAGKTRLFSASPLDYTIAFRKYFGDFIAAFQKNRIKLEHAVGINPDSVEWTRLYRRLLKKGPNIF 82
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1733 AGDFKGWDKNMNAYLQKKVY---YGIMQTCSSLINSRNYESFYEHQVKAPVIVEKHLLTFANTQFSGCFFTTILNCLVHD 1809
Cdd:cd23169     83 AGDYSNFDGSLPPDVMEAAFdiiNDWYDEYVDDEDERVRKVLFEELINTIHLVGNLVYQVHGGNPSGNPLTTIINSIVNL 162
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1810 AMLRYIFelnCEKFGRNLI--FEEHVRAKILGDDHIYSFSDEAAKFMNPKNIQEAYKELGAEYTDDQKEAEVsEEFRKFE 1887
Cdd:cd23169    163 LYIRYAW---LRITGLTSLsdFKKNVRLVTYGDDVIISVSDEVKDEFNFVTISEFLKELGITYTDADKSGDI-VPYRPLE 238
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1124158116 1888 DLTFLGAHPRL--IKGRWVGALKKDTITEMVLWTRDFNEDLLARCQTSIEMSSL---WGEEYY 1945
Cdd:cd23169    239 EVTFLKRGFRPhpTPGLVLAPLDLESIEEQLNWTRKEDDLLEATIENARAALLLafgHGPEYY 301
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
1505-1945 1.67e-29

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: 124.83  E-value: 1.67e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1505 SVIAPEMPETPKKHLPLLSPNDPRA----ENEDPLVNMIndtlSKLS-PRCDESRADRAVLG---TMYHMRKNLTWIFPK 1576
Cdd:pfam00680    1 SPTERHLVAIPAYVPASLGPEDPRWarsyLNTDPYVDDI----KKYSrPKLPGPADERDKLLnrsAAKMVLSELRGVPKK 76
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1577 --RRLTFEEAVGGVPGLlTSMNRFTSAGYPLcKITKGRGKREYFWFDDNGKlcYDPLYKTLVMNFiEKFDRGECEKGRFV 1654
Cdd:pfam00680   77 anSTLIVYRAIDGVEQI-DPLNWDTSAGYPY-VGLGGKKGDLIEHLKDGTE--ARELAERLAADW-EVLQNGTPLKLVYQ 151
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1655 AYLKDELVSEKKIKQKRCRIIYGGDMIANTAFRMIFGSFVIAY--NHSydKLSHAVGLNQYSYDMDIIHSYLLEVGNNFV 1732
Cdd:pfam00680  152 TCLKDELRPLEKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFmlNNG--FHPIQVGINPFDRGWPRLLRRLARFGDYVY 229
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1733 AGDFKGWDKNMNAYLqkkvyygiMQTCSSLINS--------RNYESFYEHQVKAPVIVEKH--LLTFANTQfSGCFFTTI 1802
Cdd:pfam00680  230 ELDYSGFDSSVPPWL--------IRFAFEILREllgfpsnvKEWRAILELLIYTPIALPNGtvFKKTGGLP-SGSPFTSI 300
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1803 LNCLVHDAMLRY-IFELNCEKFGRNLIFEEHVRAKILGDDHIYSFSDEAAKFMnpKNIQEAYKELGAEYTDDQKEAEVse 1881
Cdd:pfam00680  301 INSIVNYLLILYaLLKSLENDGPRVCNLDKYFDFFTYGDDSLVAVSPDFDPVL--DRLSPHLKELGLTITPAKKTFPV-- 376
                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1124158116 1882 eFRKFEDLTFLGAHPRLIKGRWVGALKKDTITEMVLWTR--DFNEDLLARCQTsieMSSLWGEEYY 1945
Cdd:pfam00680  377 -SRELEEVSFLKRTFRKTPGGYRPPLDRKRILAQLEYIRskPVPSGQLENIRA---YASHHGYEFY 438
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
2337-2510 5.30e-20

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: 89.76  E-value: 5.30e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 2337 CMRNCLMTTIPLNTSmPTNTALVELSLDSRLNIAVGNNIPVNvAVLNQFHFWRGDIEFTFVLVRTQYHSCRLQgvVAY-- 2414
Cdd:cd00205      5 ADRPTTVGTNNWNSS-ASGTQLFQWKLSPALGFLLLQNTPLG-ALLSYFTYWRGDLEVTVQFNGSKFHTGRLL--VAYvp 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 2415 -----GVDAIEEGSRSVAYSNIMDFsGENSVCSMTIQFNAQTEFLRTYEGskvvDPTQNHSLGTFGLYIANQLVAPDTVP 2489
Cdd:cd00205     81 pgapaPTTGDTRWQATLNPHVIWDL-GTNSSVTFVVPYVSPTPYRSTRYD----GYGPLNSFGTLVVRVLTPLTVPSGAP 155
                          170       180
                   ....*....|....*....|.
gi 1124158116 2490 QTIDVLMYVRFLNVKVAVPRA 2510
Cdd:cd00205    156 TTVDITVYVRAGDFELYGPRP 176
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
2045-2202 2.91e-16

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: 78.98  E-value: 2.91e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 2045 SFEWSTSDiPGKAIKTIPIPFGLLELGDSDNVQNMPFDRFLFWNGDVKLTFQVNGTPFMCGLLAVYFMPLASYE----CE 2120
Cdd:cd00205     13 TNNWNSSA-SGTQLFQWKLSPALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPPGAPApttgDT 91
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 2121 LANISTTNHVYLQPDKNNTVEITIPFLY---FRTVMNTVARTTESLGTIFVTPISPLSSVGGEP--VSISLYSSFHNSSF 2195
Cdd:cd00205     92 RWQATLNPHVIWDLGTNSSVTFVVPYVSptpYRSTRYDGYGPLNSFGTLVVRVLTPLTVPSGAPttVDITVYVRAGDFEL 171

                   ....*..
gi 1124158116 2196 SIPRPLP 2202
Cdd:cd00205    172 YGPRPPR 178
RNA_helicase pfam00910
RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...
705-805 9.28e-14

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: 69.56  E-value: 9.28e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116  705 PGFGKSLLAPVLINR---AFDYSPADVYTRNQTEEYWSGYIAQPVVFIDEFLVNKDPQVVNraadEYLKLISPSKFTPEF 781
Cdd:pfam00910    7 PGCGKSTLAKYLARAllkKLGLPKDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEA----ELIRLVSSTPYPPPM 82
                           90       100
                   ....*....|....*....|....*
gi 1124158116  782 ASTDNivmglKGTTVSPTIVI-TAN 805
Cdd:pfam00910   83 AALEE-----KGTPFTSKFVIvTSN 102
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
2044-2148 1.56e-05

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: 47.69  E-value: 1.56e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 2044 ESFEWSTSDipgKAIKTIPIPFGLLELGDSDnvQNMpfDRFLFWNGDVKLTFQVNGTPFMCG-LLAVY---FMPLASYEC 2119
Cdd:pfam00073   44 DSTDWTSLS---KGFFWWKLPLALLSMGLLG--RLL--RYHTYYRGGLEVTVQFNGSKFHQGkLLVAYvppGAPPPGSRD 116
                           90       100
                   ....*....|....*....|....*....
gi 1124158116 2120 ELANISTTNHVYLQPDKNNTVEITIPFLY 2148
Cdd:pfam00073  117 YLWQATLNPHQFWNLGLNSSARLSVPYIS 145
Mischivirus_RdRp cd23227
RNA-dependent RNA polymerase (RdRp) in the genus Mischivirus of positive-sense single-stranded ...
1488-1718 1.10e-03

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: 44.17  E-value: 1.10e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1488 LPPRERVILSRVSKIRPSVIAPEMpeTPKKHLPLLSPNDPRAeneDPLVNMINDTLSKLSP----------RCDESRADR 1557
Cdd:cd23227      6 LPDGPRIHVPRKTKLRKSPAYPIF--KPDAGPAVLSKNDPRL---AEGVDFDKQVFSKHSAnqkeypkafrRMARWYADR 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1558 AVLgtmyHMRKNltwifpKRRLTFEEAVGGVPgLLTSMNRFTSAGYPLCKitKGRGKREYFWFDDNgklcydPLYKTLVM 1637
Cdd:cd23227     81 VFT----YLGKD------NGPLSVKDAIKGID-NLDAMDPTTSPGLPYSA--AGIKRTDLLDFDTG------EIISPALR 141
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1638 NFIEKFDRGECEKGRFVAYLKDELVSEKKIKQKRCRIIYGGDMIANTAFRMIFGSFVIAYNHS----------------Y 1701
Cdd:cd23227    142 AEYNKYVSGDYSDHVFQTFLKDEIRSEEKIKAGKTRIVDVPSLAHVIIGRVLLGKFCSKFQASpgtelgsaigcnpdwdW 221
                          250
                   ....*....|....*..
gi 1124158116 1702 DKLSHAVGLNQYSYDMD 1718
Cdd:cd23227    222 TYFAHQLMERQWCYDID 238
 
Name Accession Description Interval E-value
ps-ssRNAv-Picornavirales cd23169
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of ...
1653-1945 3.15e-69

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: 236.34  E-value: 3.15e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1653 FVAYLKDELVSEKKIKQKRCRIIYGGDMIANTAFRMIFGSFVIAYNHSYDKLSHAVGLNQYSYDMDIIHSYLLEVGNNFV 1732
Cdd:cd23169      3 FVDCLKDELRPIEKVKAGKTRLFSASPLDYTIAFRKYFGDFIAAFQKNRIKLEHAVGINPDSVEWTRLYRRLLKKGPNIF 82
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1733 AGDFKGWDKNMNAYLQKKVY---YGIMQTCSSLINSRNYESFYEHQVKAPVIVEKHLLTFANTQFSGCFFTTILNCLVHD 1809
Cdd:cd23169     83 AGDYSNFDGSLPPDVMEAAFdiiNDWYDEYVDDEDERVRKVLFEELINTIHLVGNLVYQVHGGNPSGNPLTTIINSIVNL 162
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1810 AMLRYIFelnCEKFGRNLI--FEEHVRAKILGDDHIYSFSDEAAKFMNPKNIQEAYKELGAEYTDDQKEAEVsEEFRKFE 1887
Cdd:cd23169    163 LYIRYAW---LRITGLTSLsdFKKNVRLVTYGDDVIISVSDEVKDEFNFVTISEFLKELGITYTDADKSGDI-VPYRPLE 238
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1124158116 1888 DLTFLGAHPRL--IKGRWVGALKKDTITEMVLWTRDFNEDLLARCQTSIEMSSL---WGEEYY 1945
Cdd:cd23169    239 EVTFLKRGFRPhpTPGLVLAPLDLESIEEQLNWTRKEDDLLEATIENARAALLLafgHGPEYY 301
Dicistroviridae_RdRp cd23194
RNA-dependent RNA polymerase (RdRp) in the family Dicistroviridae of positive-sense ...
1653-1952 5.54e-52

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: 186.94  E-value: 5.54e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1653 FVAYLKDELVSEKKIKQKRCRIIYGGDMIANTAFRMIFGSFVIA------YNHSydklshAVGLNQYSYDMDIIHSYLLE 1726
Cdd:cd23194      8 FVDTLKDERRPIEKVDAGKTRVFSAGPMDYTIAFRMYFLGFVAHlmrnriDNEI------AVGTNVYSLDWDKLARKLLS 81
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1727 VGNNFVAGDFKGWDknmnAYLQKKVYYGIMQtcssLINSrnyesFY--------------EHQVKAPVIVEKHLLTFANT 1792
Cdd:cd23194     82 KGDKVIAGDFSNFD----GSLNPQILWAILD----IINE-----WYddgeenalirrvlwEDIVNSVHICGGYVYQWTHS 148
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1793 QFSGCFFTTILNCLVHDAMLRYIFELNCEKFGRNLI--FEEHVRAKILGDDHIYSFSDEAAKFMNPKNIQEAYKELGAEY 1870
Cdd:cd23194    149 QPSGNPLTAIINSIYNSIIMRYVYLLLTKEAGLMTMsdFNKHVSMVSYGDDNVINVSDEVSEWFNQLTITEAMAEIGMTY 228
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1871 TDDQKEAEVsEEFRKFEDLTFLGAHPRLIK--GRWVGALKKDTITEMVLWTR---DFNEDLLARCQTSIEMSSLWGEEYY 1945
Cdd:cd23194    229 TDETKTGEI-VPYRSLEEVSFLKRGFRYDDdlGRWVAPLDLDTILEMPNWVRkgkDPEEITKQNVENALRELSLHGEEVF 307

                   ....*..
gi 1124158116 1946 LERAASI 1952
Cdd:cd23194    308 DKWAPKI 314
RNA_dep_RNAP cd01699
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
1653-1919 1.49e-40

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: 152.44  E-value: 1.49e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1653 FVAYLKDELVSEKKIKQKRCRIIYGGDMIANTAFRMIFGSFVIAYNHSYDKLSHAVGLNQYSYDMDIIHSYLLEVGNNFV 1732
Cdd:cd01699     20 FTTFLKDELRPLEKVEAGKTRLIQPRPLDYNIALRMYLGPFEAKLMKNRGGLPIAVGINPYSRDWTILANKLRSFSPVAI 99
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1733 AGDFKGWDKNMNAYLQKKVYYgIMQTCSSLINSRNYESFYEHQVKAPVIvekhllTFANTQF-------SGCFFTTILNC 1805
Cdd:cd01699    100 ALDYSRFDSSLSPQLLEAEHS-IYNALYDDDDELERRNLLRSLTNNSLH------IGFNEVYkvrggrpSGDPLTSIGNS 172
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1806 LVHDAMLRYIFelnCEKFGRNliFEEHVRAKILGDDHIYSFSDEAAKFmNPKNIQEAYKELGAEYTDdqkEAEVSEEFRK 1885
Cdd:cd01699    173 IINCILVRYAF---RKLGGKS--FFKNVRLLNYGDDCLLSVEKADDKF-NLETLAEWLKEYGLTMTD---EDKVESPFRP 243
                          250       260       270
                   ....*....|....*....|....*....|....*
gi 1124158116 1886 FEDLTFLGAHPRLIKG-RWVGALKKDTITEMVLWT 1919
Cdd:cd01699    244 LEEVEFLKRRFVLDEGgGWRAPLDPSSILSKLSWS 278
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
1505-1945 1.67e-29

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: 124.83  E-value: 1.67e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1505 SVIAPEMPETPKKHLPLLSPNDPRA----ENEDPLVNMIndtlSKLS-PRCDESRADRAVLG---TMYHMRKNLTWIFPK 1576
Cdd:pfam00680    1 SPTERHLVAIPAYVPASLGPEDPRWarsyLNTDPYVDDI----KKYSrPKLPGPADERDKLLnrsAAKMVLSELRGVPKK 76
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1577 --RRLTFEEAVGGVPGLlTSMNRFTSAGYPLcKITKGRGKREYFWFDDNGKlcYDPLYKTLVMNFiEKFDRGECEKGRFV 1654
Cdd:pfam00680   77 anSTLIVYRAIDGVEQI-DPLNWDTSAGYPY-VGLGGKKGDLIEHLKDGTE--ARELAERLAADW-EVLQNGTPLKLVYQ 151
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1655 AYLKDELVSEKKIKQKRCRIIYGGDMIANTAFRMIFGSFVIAY--NHSydKLSHAVGLNQYSYDMDIIHSYLLEVGNNFV 1732
Cdd:pfam00680  152 TCLKDELRPLEKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFmlNNG--FHPIQVGINPFDRGWPRLLRRLARFGDYVY 229
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1733 AGDFKGWDKNMNAYLqkkvyygiMQTCSSLINS--------RNYESFYEHQVKAPVIVEKH--LLTFANTQfSGCFFTTI 1802
Cdd:pfam00680  230 ELDYSGFDSSVPPWL--------IRFAFEILREllgfpsnvKEWRAILELLIYTPIALPNGtvFKKTGGLP-SGSPFTSI 300
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1803 LNCLVHDAMLRY-IFELNCEKFGRNLIFEEHVRAKILGDDHIYSFSDEAAKFMnpKNIQEAYKELGAEYTDDQKEAEVse 1881
Cdd:pfam00680  301 INSIVNYLLILYaLLKSLENDGPRVCNLDKYFDFFTYGDDSLVAVSPDFDPVL--DRLSPHLKELGLTITPAKKTFPV-- 376
                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1124158116 1882 eFRKFEDLTFLGAHPRLIKGRWVGALKKDTITEMVLWTR--DFNEDLLARCQTsieMSSLWGEEYY 1945
Cdd:pfam00680  377 -SRELEEVSFLKRTFRKTPGGYRPPLDRKRILAQLEYIRskPVPSGQLENIRA---YASHHGYEFY 438
Marnaviridae_RdRp cd23195
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Marnaviridae of ...
1653-1948 7.49e-28

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: 116.78  E-value: 7.49e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1653 FVAYLKDElvsEKKIKQKRCRIIYGGDMIANTAFRMIFGSFV--IAYNHsydKLS-HAVGLNQYSYDMDIIHSYLLEVG- 1728
Cdd:cd23195      3 FKACLKDE---PTKLTKDKVRVFQAAPVALQLLVRKYFLPIArfLQMNP---LLSeCAVGINAQSPEWEELYEHLTKFGe 76
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1729 NNFVAGDFKGWDKNMNAYL---------------------QKKVYYGIMQ-TCSSLINsrnyesfyehqvkapviVEKHL 1786
Cdd:cd23195     77 DRIIAGDYSKYDKRMSAQLilaafkilidiaaksggyseeDLKIMRGIATdIAYPLVD-----------------FNGDL 139
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1787 LTFANTQFSGCFFTTILNCLVHDAMLRYIFELNCEKFGRNLiFEEHVRAKILGDDHIYSFSDEAAKFmNPKNIQEAYKEL 1866
Cdd:cd23195    140 IQFFGSNPSGHPLTVIINSIVNSLYMRYAYYSLYPEKEVPP-FRDVVALMTYGDDNIMSVSPGYPWF-NHTSIAEFLAKI 217
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1867 GAEYTDDQKEAEvSEEFRKFEDLTFLGAHPRLIK--GRWVGALKKDTITEMVLW-TRDFNEDLLARCQTSIEmSSL---- 1939
Cdd:cd23195    218 GIKYTMADKEAE-SVPFIHISEADFLKRKFVFDPelGVYVGPLDEDSIFKSLHCyLKSKVLTPEEQAAQNID-GALrewf 295
                          330
                   ....*....|
gi 1124158116 1940 -WGEEYYLER 1948
Cdd:cd23195    296 fHGREVYEKR 305
ps-ssRNA_Picornaviridae cd23193
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Picornaviridae of ...
1584-1947 4.97e-27

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: 115.34  E-value: 4.97e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1584 AVGGVPGLlTSMNRFTSAGYPLCkiTKGRGKREYFWFDDNGklcydplYKTLVMNFIEKFDRGECEKGRFVAYLKDELVS 1663
Cdd:cd23193      1 AINGIDGL-DPIDLNTSPGYPYT--TQGLRRRDLIDNDKGG-------VSPLLEEEEQVLLDLDGPDVVFTTFLKDELRP 70
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1664 EKKIKQKRCRIIYGGDMIANTAFRMIFGSFVIAYNHSYDKLSH-AVGLNQYsYDMD-IIHSylLEVGNNFvAGDFKGWDk 1741
Cdd:cd23193     71 KEKVKAGKTRVIEAAPLDYVIAGRMVFGRLFAQFHSNPGILTGsAVGCNPD-TDWTrLFAS--LKQDNVY-DLDYSGFD- 145
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1742 nmnAYLQKkvyyGIMQTCSSLINSRNYesfYEHQVK---APVIVEKHLltFANTQF-------SGCFFTTILNCLVHDAM 1811
Cdd:cd23193    146 ---ASLSS----QLFEAAVEVLAECHG---DPELVLrylEPIINSKHV--VGDERYtveggmpSGCPCTSILNSICNNLV 213
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1812 LRYIFELNCEKFGRNLifeehvraKIL--GDDHIYSFSDEaakfMNPKNIQEAYKE-LGAEYTDDQKEAEVSEEFRkfED 1888
Cdd:cd23193    214 VRYALLETGKFDPDEY--------YILayGDDVLVSTDEP----IDPSDLAEFYKKyFGMTVTPADKSSDFPESSP--IE 279
                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1124158116 1889 LTFLGAHPRLIKGRW--VGALKKDTITEMVLWTRD--FNEDLLarcQTSIEMSSLWGEEYYLE 1947
Cdd:cd23193    280 DVFLKRRFFVPDGTFliHPVMDLETLEQSLMWCGRggFFQQLL---SSLCELALHHGPEEYER 339
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
2337-2510 5.30e-20

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: 89.76  E-value: 5.30e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 2337 CMRNCLMTTIPLNTSmPTNTALVELSLDSRLNIAVGNNIPVNvAVLNQFHFWRGDIEFTFVLVRTQYHSCRLQgvVAY-- 2414
Cdd:cd00205      5 ADRPTTVGTNNWNSS-ASGTQLFQWKLSPALGFLLLQNTPLG-ALLSYFTYWRGDLEVTVQFNGSKFHTGRLL--VAYvp 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 2415 -----GVDAIEEGSRSVAYSNIMDFsGENSVCSMTIQFNAQTEFLRTYEGskvvDPTQNHSLGTFGLYIANQLVAPDTVP 2489
Cdd:cd00205     81 pgapaPTTGDTRWQATLNPHVIWDL-GTNSSVTFVVPYVSPTPYRSTRYD----GYGPLNSFGTLVVRVLTPLTVPSGAP 155
                          170       180
                   ....*....|....*....|.
gi 1124158116 2490 QTIDVLMYVRFLNVKVAVPRA 2510
Cdd:cd00205    156 TTVDITVYVRAGDFELYGPRP 176
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
2045-2202 2.91e-16

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: 78.98  E-value: 2.91e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 2045 SFEWSTSDiPGKAIKTIPIPFGLLELGDSDNVQNMPFDRFLFWNGDVKLTFQVNGTPFMCGLLAVYFMPLASYE----CE 2120
Cdd:cd00205     13 TNNWNSSA-SGTQLFQWKLSPALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPPGAPApttgDT 91
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 2121 LANISTTNHVYLQPDKNNTVEITIPFLY---FRTVMNTVARTTESLGTIFVTPISPLSSVGGEP--VSISLYSSFHNSSF 2195
Cdd:cd00205     92 RWQATLNPHVIWDLGTNSSVTFVVPYVSptpYRSTRYDGYGPLNSFGTLVVRVLTPLTVPSGAPttVDITVYVRAGDFEL 171

                   ....*..
gi 1124158116 2196 SIPRPLP 2202
Cdd:cd00205    172 YGPRPPR 178
Secoviridae_RdRp cd23196
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Secoviridae of ...
1657-1920 3.08e-16

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: 82.43  E-value: 3.08e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1657 LKDELVSEKKIKQK-RCRIIYGGDMIANTAFRMIFGSFVIAYNHSYDKLSHAVGLNQYSYDMDIIHSYLLEVGNNFVAGD 1735
Cdd:cd23196      7 PKDERLKKRKVLEKpKTRLFDVLPMEYNLLLRKYFLNFVRFIQANRHRLPCQVGINPYSREWTTLYDRLAEKSDTALNCD 86
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1736 FKGWDknmnAYLQKKVYYGIMQTCSSLINSrnyesfyEHQVKApviVEKHLLTFANTQF--------------SGCFFTT 1801
Cdd:cd23196     87 YSRFD----GLLSHQVYVWIADMINRLYGD-------GDEAKA---RRNLLMMFCGRRSicgrqvymvrggmpSGCALTV 152
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1802 ILNCLVHDAMLRYIFELNCEKFGRNLiFEEHVRAKILGDDHIYSFSDEAAKFMNPKNIQEAYKELGAEYTDDQKEAEVSE 1881
Cdd:cd23196    153 IINSIFNEILIRYVYRKVVPRPARNN-FNKYVRLVVYGDDNLISVKEEIIPYFDGPVIKKEMAKVGVTITDGTDKTSPTL 231
                          250       260       270       280
                   ....*....|....*....|....*....|....*....|
gi 1124158116 1882 EFRKFEDLTFLGAHPRLIK-GRWVGALKKDTitemvLWTR 1920
Cdd:cd23196    232 ERKPLESLDFLKRGFRVQSdGLVVAPLDKTS-----LYSR 266
Nora-virus_RdRp cd23200
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in a novel picorna-like ...
1657-1947 1.37e-15

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: 80.35  E-value: 1.37e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1657 LKDELVSEKKIKQKRCRI---IYGGDMIANTAfrmIFGSFVIAYNHSYDKLSHAVGLNQYSYDMDIIHSYLLEvGNNFVA 1733
Cdd:cd23200      7 LKDQPIKIAQAKSGRTRVfhcIPVDLILFSGA---LYGPYKEAYTKAGLKCYHAVGIDPKSVGWQQLATYMTK-HPNYFD 82
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1734 GDFKGWDKnmnaYLQKKVYYGIMQTCSSLI---------NSRNYESfyEHQVKAPVIVEKHLLTFANTQFSGCFFTTILN 1804
Cdd:cd23200     83 ADYKNYDK----YLHRQVFKAVRKIQRSVIqqvcpdkwdKARAVEE--LDAIDTYVVDYQTVYKTNRGNKSGSYTTTIDN 156
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1805 CLVHDAMLRYIFELNCEkfGRNLI-FEEHVRAKILGDDHIYSFSDEAAKFMNPKNIQEAYKELGAEYTDDQKEAEvSEEF 1883
Cdd:cd23200    157 CLANDIYGLYAWVKTTG--LRSLWdYRQNVSSVAFGDDIIKSVSDEYKDKYNYCTYRDVLNATGHIMTPGSKDGE-EKPF 233
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1124158116 1884 RKFEDLTFLGAHPRLIKGRWVGALKKDTITEMVLWTrDFNEDLLAR----CQTSIEMSSLWGEEYYLE 1947
Cdd:cd23200    234 TSFENLQFLKRGFKLENGMVLAPLLQRSIEGPFVWT-DIREDQITVwvnlVQEQLIEAALWGEEYYNE 300
Caliciviridae_RdRp cd23192
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Caliciviridae of ...
1657-1920 7.81e-14

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: 74.99  E-value: 7.81e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1657 LKDELVSEKKIKQKRCRIIYGGDMIANTAFRMIFGSFviaynhsYDKLSH-------AVGLNQYSYDMDIIHSYLLEVGN 1729
Cdd:cd23192      7 LKDELRPVEKIAEGKRRLLWGCDVGVTLVAAAAFGPV-------ADALKAvcptgpiAVGINMDSEDVEVIFERLSGFRY 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1730 NFVAgDFKGWDKNMNAYLQKKVyYGIMQTCSSlinSRNYESFYEHQVKAP--VIVEKHLLTFANTQFSGCFFTTILNCLV 1807
Cdd:cd23192     80 HYCL-DYSKWDSTQSPAVTAAA-IDILADLSE---ETPLRDSVVETLSSPpmGIFDDVIFVTKRGLPSGMPFTSVINSLN 154
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1808 HDAMLRYIFELNCEKFG---RNLIFEEHVRAkiLGDDHIYSFSDEAAKFMNpkNIQEAYKELGAEYTDDQKEAEVseEFR 1884
Cdd:cd23192    155 HWLLFSAAVLKAYELVGiytGNVFDEADFFT--YGDDGVYAMPPATASVMD--EIIENLKSYGLKPTAADKTENP--DIP 228
                          250       260       270
                   ....*....|....*....|....*....|....*.
gi 1124158116 1885 KFEDLTFLGAHPRLIKGRWVGALKKDTITEMVLWTR 1920
Cdd:cd23192    229 PLQGPVFLKRTFVRTPGGWRALLDRSSILRQLYWVK 264
RNA_helicase pfam00910
RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...
705-805 9.28e-14

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: 69.56  E-value: 9.28e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116  705 PGFGKSLLAPVLINR---AFDYSPADVYTRNQTEEYWSGYIAQPVVFIDEFLVNKDPQVVNraadEYLKLISPSKFTPEF 781
Cdd:pfam00910    7 PGCGKSTLAKYLARAllkKLGLPKDSVYSRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEA----ELIRLVSSTPYPPPM 82
                           90       100
                   ....*....|....*....|....*
gi 1124158116  782 ASTDNivmglKGTTVSPTIVI-TAN 805
Cdd:pfam00910   83 AALEE-----KGTPFTSKFVIvTSN 102
Fipivirus_RdRp cd23229
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Fipivirus of ...
1585-1945 1.83e-13

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: 75.23  E-value: 1.83e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1585 VGGVPGLlTSMNRFTSAGYPLCKITKGRGKREYfwfDDNGKLCYDPLYKTLVMNFIE---KFDRGECEKGRFVAYLKDEL 1661
Cdd:cd23229      2 VEGIPGM-EGLDMKTSAGYPWCEQNQKKKDKIK---LLAGKNFLVRPLREVVHIVVDwyiMPPDMPKPEIKYVVYLKDEL 77
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1662 VSEKKIKQKRCRIIYGGDMIANTAFRMIFGSFVIAYNHSYDKLSH----AVGLNQYSYDMDIihsYLLEVGNNFVAGDFK 1737
Cdd:cd23229     78 LSSDKVKMGRTRWICAAPVQLVCAWKKVFGRAIAAIHLESVTDGKstgcAVGMDPETAWTDI---ALARPGWPVIALDYS 154
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1738 GWDKNmnayLQKKVYYGIMQTCSSLINSRNYESFYEHQVKAPV--IVEKHLLTFANTQFSGCFFTTILNCLVHDAMLRYI 1815
Cdd:cd23229    155 NFDGS----LQSFVITGAVRILGYIAGLPDGQSYRLAEFVYDVkqIVGKYLYTTVGPLPSGCPSTSIIGSLCNVLMLLYT 230
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1816 FelnCEKFGRNLifeEHVRAKIlgddHIYSFSDEAAKFMNPKNIQ-------EAYKELGAEYTDDQKEaEVSEEFRKFED 1888
Cdd:cd23229    231 L---SHATGQRY---SAFRDWM----HVVTYGDDVLVFVHPEVVVvldtlahEMYLVFGVTATDATDK-RAPPQLRELSN 299
                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1124158116 1889 LTFLGAHPR---LIKGRWVGALKKDTITEMVLWTR-DFNEDLLARCQTSIEMSSlwGEEYY 1945
Cdd:cd23229    300 VTFLKRGFRqcsSVPFLVHPTMDKSTIYQMLAWKRkGTTLAENVKCAAEFMMHH--GEEEY 358
Limnipivirus_RdRp cd23228
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Limnipivirus of ...
1599-1971 3.72e-13

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: 74.14  E-value: 3.72e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1599 TSAGYplcKITK-GRGKREYFWFDDNGKLCYDPLYKTLVMNFIEKFDRGECEKGRFVAYLKDELVSEKKIKQKRCRIIYG 1677
Cdd:cd23228     14 TSPGL---KYTRdGLKKSDLYTIDEDGNVVVSDMLRADVEAWEELIQSGGYPTTLFTACLKDELRSDEKVALGKTRVIEA 90
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1678 GDMIANTAFRMIFGSFviaYNHSYDKLSHAVGLNQYSYDMDIIHSYLLEVG--NNFVAGDFKGWDKNMNAYLqkkvyygi 1755
Cdd:cd23228     91 AELDYVVAYRMYMSSI---YSDLYNAYAGDTGIAAGINPPADGHRLREELSqyDSFLALDYSRFDGSLPEML-------- 159
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1756 MQTCSSLINSRNYESFYEHQVKAPVIVEKHLL-----TFANTQFSGCFFTTILNCLVHDAMLRY----IFELNCEKFGRN 1826
Cdd:cd23228    160 MRAAVEILADLHEDPDLVRRLHETVIISKHLVvdedwTVKGGMPSGSPCTTVLNCICNLLVLEYaflvHFGVYEDDDGVG 239
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1827 LIFEEHVRAkILGDDHIYSFSDEAakfMNPKNIQEAYKELGAEYTDDQK-----EAEVSE-EFRKFEDLTFLGAHPRLIK 1900
Cdd:cd23228    240 LPQCDYLSV-VYGDDCIVAYNGME---MGLAFAETIEDTFGMEVTPASKvgdhfNVELHEvEFLKRKFFAFETEEYDRIA 315
                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1124158116 1901 GRwvgaLKKDTITEMVLWTRdfNEDLLARCQTSIEMS-SLWGEEYYLERAASINRALRRVNYpQIEVKPWEL 1971
Cdd:cd23228    316 LR----LSENTIVQSLMWMR--NLKTFPDQVQSLMMElSAWGKEKYDKLRDTCKRRLAKQNL-QVTVPGYDI 380
Hepatovirus_RdRp cd23215
RNA-dependent RNA polymerase (RdRp) in the genus Hepatovirus of positive-sense single-stranded ...
1579-1945 7.01e-13

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: 73.73  E-value: 7.01e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1579 LTFEEAVGGVPGLlTSMNRFTSAGYPLckITKGRGKREYFWFDDNGKLC-YDPLYKTLVMNFIEKFDRGECEKGRFVAYL 1657
Cdd:cd23215     65 FDLEQAITGVPGM-DAINMDSSPGYPY--VQEKLTKSDLIWLDDNGELLgMHPRLAQRILFNLTMMDNGNDLDVVYTTCP 141
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1658 KDELVSEKKIKQKRCRIIYGGDMIANTAFRMIFGSfVIAYNHSYDKLSH--AVGLNQySYDMDIIHSYLLEVGNNFVAGD 1735
Cdd:cd23215    142 KDELRPLEKVLESKTRAIDACPLDFTIICRMFWGP-AISYFQLNPGFHTgvAVGIDP-DRDWDALFKTMIRFGDYGIDLD 219
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1736 FKGWDKNMNAYLqkkvyygIMQTCSSLINSRNYESFYEHQVKAPVIVEKHLL-----TFANTQFSGCFFTTILNCLVHDA 1810
Cdd:cd23215    220 FSSFDASLSPFM-------IREACRVLSELSGVPDHQGQALINTIIYSKHLLynlcyHVCGSMPSGSPCTSLLNSIVNNV 292
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1811 MLRYIFELNCEKfgRNLIFEEHVRAKILGDDHIYSFS-DEAAKFMNP--KNIQEAYKELGAEYTDDQKEAEvseEFRKFE 1887
Cdd:cd23215    293 NLYYVFSKIFKK--SPVFFYDAVKFLCYGDDVLIVFSrDLEIKNLDKlgQRIQDEFKLLGMTATSADKGEP---QVVPVS 367
                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1124158116 1888 DLTFLGAHPRLIKGRWVGALKKDTITEMVLWTRDfNEDLLARCQTSIEMSSLWGEEYY 1945
Cdd:cd23215    368 ELTFLKRSFNLIEDRFRPAISEKTIWSLVAWQRS-NAEFEQNLDTACWFAFMHGYDFY 424
Avisivirus_RdRp cd23231
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Avisivirus of ...
1610-1955 1.36e-10

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: 66.07  E-value: 1.36e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1610 KGRGKREyfwfddngkLCYDPLYKTLVMNFIEKFDRGECE--KGRFVAYLKDELVSEKKIKQKRCRIIYGGDMIANTAFR 1687
Cdd:cd23231     22 KGKTKAQ---------LVDDKKFKADVMNLVRFNGDPNREppDVYFTTYLKDELRPKEKAKAGKTRVISAASFDYTIACR 92
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1688 MIFGSFVIAYNHSYDKLSHAVGLNQYS-YD--MDIIHSYLLEVgnnfvagDFKGWDKNMNAYLqkkvyygiMQTCSSLIn 1764
Cdd:cd23231     93 MVFGPILRQLFAWGREFGFGPGLNPYThFDelYDKILPFVICL-------DYSGFDGSLSSEL--------MFHAAQVI- 156
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1765 srnyESFYEhqvKAPVIVEKHLLTFANTQF-------------SGCFFTTILNCLVHDAMLR-YIFEL--NCEKfgrnli 1828
Cdd:cd23231    157 ----ACFSE---KPEAIMASAELTIGSTERvsdevwyvyggmpSGSPWTTTLNTICNLLMCYtYLLDMghCWSE------ 223
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1829 feehVRAKILGDDHIYSfsdeAAKFMNPKNIQEAYKE-LGAEYTDDQKEAEVSEEFRkfEDLTFLGAHPRLIK--GRWVG 1905
Cdd:cd23231    224 ----TFVVAYGDDVVIS----ANIKHNLEGIEQWFKTkFGATVTPSDKQGKITWTTK--NNMEFLKRRPKQLDflPKIVG 293
                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1124158116 1906 ALKKDTITEMVLWTR-DFNEDLLArcqTSIEMsSLWGEEYYLERAASI-NRA 1955
Cdd:cd23231    294 ALDLDNMLDRIQWTKgHFQDQLNS---FYLEL-ALHGRETYNEIRAKLaPRA 341
Megrivirus_RdRp cd23223
RNA-dependent RNA polymerase (RdRp) in the genus Megrivirus of positive-sense single-stranded ...
1515-1931 2.32e-10

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: 65.63  E-value: 2.32e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1515 PKKHLP-LLSPNDPRAEnedPLVNMINDTLSKLSPrcDES---RADRAVLGTMYHMRKNLTWIF--PKRRLTFEEAVGGV 1588
Cdd:cd23223      6 PVTHGPaALTNKDKRLE---EGVDLDDVMFSKHVP--DHPgwpTLEPAMSYVVEDLMHKLGFSKdePVPMWTLEQAINGE 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1589 pGLLTSMNRFTSAGYPLCkiTKGRGKREYFWFDDNGKLCYDPLYKtLVMNFIEkfdrgECEKGRFVAYLKDELVSEKKIK 1668
Cdd:cd23223     81 -GVMDGIDMGQSPGYPYN--AQGRSRRSFFEWNGEKWQPTEELKK-EVDHALK-----DPDDFYFSTFLKDELRPLEKVK 151
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1669 QKRCRIIYGGDMIANTAFRMIFGSF---VIAYNHSydKLSHAVGLNQYSYDMDIIHSYLLEVGNNFVAGDFKGWDKNmna 1745
Cdd:cd23223    152 AGKTRLVDGDSLPRILAMRMVFGPLfeaMLRKNGP--EIHSAVGCNPDTDWTRYYHEMGPDSFPYCFDLDYSCFDST--- 226
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1746 ylQKKVYYGIMqtcsslinSRNYESFYEHQVK---APVIVEKHLltFANTQF-------SGCFFTTILNCLVHDA-MLRY 1814
Cdd:cd23223    227 --EPKIAFRLM--------AKYLKPYFSVDVTpffEALATSKHV--YGDKAYemeggmpSGCVGTSMFNCINNSAfIVSA 294
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1815 IFELNcekfgrnlIFEEHVRAKILGDDHIYSfSDEAAKfmnPKNIQEAY-KELGAEYTDDQKEAEVSEEfRKFEDLTFL- 1892
Cdd:cd23223    295 LIALK--------ISPEDCAWICYGDDVIIS-TDEKAL---SKRIADFYhKNTNLVVTPASKSGDFPET-STIYDVTFLk 361
                          410       420       430       440
                   ....*....|....*....|....*....|....*....|....*..
gi 1124158116 1893 ------GAHPRLIKgrwvGALKKDTITEMVLWTRD--FNEDLLARCQ 1931
Cdd:cd23223    362 rffqpdSHYPHLIH----PYMPLEHLEQSVMWQTDgpFQQKLDSLCL 404
Parechovirus_RdRp cd23217
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Parechovirus of ...
1592-1976 5.15e-10

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: 64.12  E-value: 5.15e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1592 LTSMNRFTSAGYPLCKitKGRGKR-----EYFWFDdngklcydPLYKTLVMNFIEKFDRGECEKGRFVAYLKDELVSEKK 1666
Cdd:cd23217      8 LNSLDLSTSPGYKYVK--SGYKKRdllslEPFSVS--------PQLEKDVKDKLHAVYKGNQPTTIFNACLKDELRKLDK 77
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1667 IKQKRCRIIYGGDMIANTAFRMIFGSFVIA-YNHSYDKLSHAVGLNQYSyDMDIIHSYLLEVGNNFvagDFKGWDKNMNA 1745
Cdd:cd23217     78 IAQGKTRCIEACSIDYVIAYRVVMSSLYEAiYQTPCQELGLAVGMNPWT-DWDFMINALNPYNYGL---DYSSYDGSLSE 153
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1746 YLqkkVYYG--IMQTCSSlinsrnyESFYEHQVKAPVIVEKHLLT-----FANTQFSGCFFTTILNCLVHDAMLRYIfel 1818
Cdd:cd23217    154 ML---MWEAveVLAYCHE-------SPDLVMQLHKPVINSDHVVMderwlVHGGMPSGSPCTTVLNSICNLLVCIYL--- 220
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1819 nceKFGRNLIFEehVRAKILGDDHIYSFSDEaakfMNPKNIQE-AYKELGAEYTDDQKEAEVSeeFRKFEDLTFLGAHPR 1897
Cdd:cd23217    221 ---AYLQSPGIE--CLPIVYGDDVIFSVSSE----IDPEYLVSsAADSFGMEVTGSDKDEPPS--LLPRMEVEFLKRTTG 289
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1898 LIKGRW--VGALKKDTITEMVLWTRD---FNEDLlarcqTSIEMS-SLWGEEYYLERAASINRALrrvnypqievKPWEL 1971
Cdd:cd23217    290 YFPGSTykVGALDLETMEQHIMWMKNlstFPQQL-----QSFENElCLHGKDIYDDYKKIFNPYL----------KEWNI 354

                   ....*..
gi 1124158116 1972 MV--YEV 1976
Cdd:cd23217    355 TMddYDV 361
Dicipivirus_RdRp cd23222
RNA-dependent RNA polymerase (RdRp) in the genus Dicipivirus of positive-sense single-stranded ...
1503-1969 8.38e-10

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: 63.84  E-value: 8.38e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1503 RPSVIAPEMPETpkKHLPLLSPNDPRAENED----PLVNMINDTLSKLSPRCDESRadRAVLGtmyHMRKnltwIFPKRR 1578
Cdd:cd23222      1 KPSPVYGVYPVT--KEPAPLKPTDRRIDEGVdfnePVFGKYGADMKEPFRNLDVGR--DVVIA---RLKK----VLPNKK 69
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1579 L---TFEEAVGGVPGLlTSMNRFTSAGYPLCkiTKGRGKREYFWFDDNGKLCYDPlykTLVMNFIEKfdRGECEKGRFVA 1655
Cdd:cd23222     70 FapcTVSEALNGKDGL-PKLDLKQASGYPYN--LSAIKRKHLIESDKDGFLTATP---KLLADIEES--KKHPEKFPYTS 141
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1656 YLKDELVSEKKIKQKRCRIIYGGDMIANTAFRMIFGSFVIAYN-HSYDKLSHAVGLNQYSYDMDIIHSyLLEVGNNFvAG 1734
Cdd:cd23222    142 FLKDELRSVKKVKAGKTRVVEAGSLPVIVEGRMIFGNLFAYFNtHPGFETMAAVGCDPEVCWTDWYYK-MREKAHTW-DY 219
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1735 DFKGWDKNMNAyLQKKVYYGIMqtCSSLINSRNYESFYEHQVKAPVIVEKHLLTFANTQFSGCFFTTILNCLVHDAMLRY 1814
Cdd:cd23222    220 DYTGFDGSIPS-CSFDALADLL--CEFVENEDDVRRYISNIKNSYHAYDGNLYLIEGAMPSGCAGTSVFNCLINAMLCFS 296
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1815 IFELNCEKFGRnliFEEHVRAkiLGDDHIYS-----FSDEAAKFMNPKN---IQEAYKelGAEYTDDQKEAEVSEEFRKF 1886
Cdd:cd23222    297 CFMDLEPEMDP---FEPLLIA--YGDDILVSsdhdlFPSRVSEWMKANTtfkITPADK--GEIFNDDSDVSDVRFLKRLF 369
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1887 -EDLTFLGAHPrlikgrwvgALKKDTITEMVLWTrdfNEDLLARCQTSIEMSSL-WGEEYYLERAASINRALRRVNYPQI 1964
Cdd:cd23222    370 vEDPVCELIHP---------VIETETLEPSLNWC---HEGEFETKVDAISMLAFhHGPEYYRDWCKKLTDICEERNISPP 437

                   ....*
gi 1124158116 1965 EVKPW 1969
Cdd:cd23222    438 GLKPY 442
Aalivirus_RdRp cd23216
RNA-dependent RNA polymerase (RdRp) in the genus Aalivirus of positive-sense single-stranded ...
1653-1946 1.37e-09

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: 62.38  E-value: 1.37e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1653 FVAYLKDELVSEKKIKQKRCRIIYGGDMIANTAFRMIFGSFVIAYNHSYDKLS-HAVGLNQYSYdmdiIHSYLLEVGNNF 1731
Cdd:cd23216     51 FTTYLKDELRSIEKIANGNTRAIEAANFDHVVAWRQVMGNIVKQLFSDHDRVTgFAPGMNPYTH----FDSLMDQVKWNV 126
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1732 VAGDFKGWDKNMNAYLqkkvyygiMQTCSSLINSRNYE-----SFYEHQVKAPVIVEKHLLTFANTQFSGCFFTTILNCL 1806
Cdd:cd23216    127 LALDFKKFDGSLSPQV--------MEEAVDILASFHDMpqmvvDIHKHTIYSTNVVSDETWFVEGGMCSGSPCTTVLNTI 198
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1807 VHdamlryiFELNCEKFGRNLIFEEHVRAKILGDDHIYSFSDEAAKFMNPKNIQEAYKE-LGAEYTDDQKEAEVSEEFRK 1885
Cdd:cd23216    199 CN-------LLVNTTILLSEGIQPDNFYIAAYGDDTIISVDGLSSSLPDPKIMQQKYKEwFGMTVTSADKGSEITWDTRN 271
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1124158116 1886 feDLTFLGAHPRLIKG--RWVGALKKDTITEMVLWTR-DFNEDLLARCQTSIemssLWGEEYYL 1946
Cdd:cd23216    272 --HVQFLKRRPGFFPGtqKVVGVLDLESMMEHIAWTKgSFQDQLNSFYQELV----LHGEQVYM 329
Cosavirus_RdRp cd23226
RNA-dependent RNA polymerase (RdRp) in the genus Cosavirus of positive-sense single-stranded ...
1493-1979 3.59e-09

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: 61.96  E-value: 3.59e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1493 RVILSRVSKIRPSviAPEMPETPKKHLPLLSPNDPRAeneDPLVNMINDTLSKLSPRcDESRADRAVLGTMYHMRKNLTW 1572
Cdd:cd23226     11 RVHVPRQSKLKRT--NATYPATGKYGPAVLSKNDPRL---DPDVDFDKVIFSKHVAN-VVIDEDTSFWNALKMSAQIYAE 84
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1573 IFPKRR---LTFEEAVGGVPGLlTSMNRFTSAGYPLCKItkgrgKREYFWFDDnGKLcYDPLYKTLvmnfIEKFDRGECE 1649
Cdd:cd23226     85 KFKGVDfspLTVEEAILGIPGL-DRMDPNTASGLPYTKT-----RRQMIDFQE-GKI-LDPELQER----LDTWLSGKQP 152
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1650 KGRFVAYLKDELVSEKKIKQKRCRIIYGGDMIANTAFRMIFGSFVIAYNHSYD-KLSHAVG-------------LNQ--Y 1713
Cdd:cd23226    153 EMLYQTFLKDEIRPIEKVKAGKTRIIDVTPLDHVLAFRIVLGRFMAHFHNNYGfELGSAVGcdpdvawanfgfaLSSkkY 232
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1714 SYDMDI-----IHSY-LLEVGNNFVAGDFKGWDKNmnaylqkkvyygimqtCSSLINSRNYESF-YEHQvkapvivEKHL 1786
Cdd:cd23226    233 QYDFDYsnfdaSHSEsIFELLKQFVFTKDNGFDHR----------------CSLMIDSLVTSTHcYEDQ-------RMTI 289
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1787 LTFANTQFSG-CFFTTILNCLVHDAMLRYIFElncekfgrnlIFE-EHVRAKILGDDhIYSFSDEaakFMNPKNIQEAYK 1864
Cdd:cd23226    290 RGGLPSGTSGtSVINTIINNIIFKAALYHTYS----------NFEwDDVQMLAYGDD-IVAASDC---LLDLDRVKYFMA 355
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1865 ELGAEYTddqkEAEVSEEF--RKFEDLTFLGAHPRLIKGRWVGALKKDTITEMVLWTRDFNedLLARCQTSIEMSSLWGE 1942
Cdd:cd23226    356 LIGYKIT----PADKGEKFipKDMQNIQFLKRSFRKVAGVWAPIMDLENLQAMLSWYKPGT--LQEKLDSVARLAHFCGE 429
                          490       500       510
                   ....*....|....*....|....*....|....*..
gi 1124158116 1943 EYYleraasiNRALRRVNYPQIEVKPWELMVYEVSNR 1979
Cdd:cd23226    430 KVY-------DHLFTTFVKDGFQIKPWKQLHFEWLNR 459
Polycipiviridae_RdRp cd23198
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Polycipiviridae of ...
1725-1920 4.49e-09

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: 60.89  E-value: 4.49e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1725 LEVGNNFVAGDFKGWDKNMNA---YLQKKVYYGIMQTCSS-----LINSRNYESFYEHQVKAPVIVEKHlltfaNTQFSG 1796
Cdd:cd23198     80 LNRHPNAVDFDVSNWDGHLPAelfYAVLDIIKTVLGLKPNspnakVIYSILTEVMNCHIQFEDIIYQKL-----RGLISG 154
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1797 CFFTTILNCLVHDAMLRYIFELNCEKFGRNLIFE---EHVRAKILGDDHIYSFSDEAAKFMNPKNIQEAYKELGAEYTDD 1873
Cdd:cd23198    155 FPGTAEVNTLAHWLLIYYIYLYLAQNTIYDMTITaflRNVSAIFYGDDIIITISDEILHWFNGKTIQRMYEEHGYPVTSA 234
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*...
gi 1124158116 1874 QKEAEVsEEFRKFEDLTFLGAHPR-LIKGRWVGALKKDTITEMVLWTR 1920
Cdd:cd23198    235 AKDTEI-PESKPLSDCQFLKSSWNpILPGYYIRKMDIEVVYDLVYWVR 281
Mosavirus_RdRp cd23225
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Mosavirus of ...
1590-1900 2.88e-07

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: 55.69  E-value: 2.88e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1590 GLLTSMNRFTSAGYPLCKITKGRGKREYFWFDDNGKLcYDPLyKTLVMNfIEKFDRGEcEKGRFVAYLKDELVSEKKIKQ 1669
Cdd:cd23225      7 GISDAMDMTKAVGYPYCLDSIKRLDLVEIKETENGKV-YLPT-ERLVEE-TEKFFTGE-EKPKFVTFLKDEVRSNEKIKQ 82
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1670 KRCRIIYGGDMIANTAFRMIFGSFVI-AYNHSYDKLSHAVGLNQysyDMDIIHsYLLEVGNNFVAG-DFKGWDKN----M 1743
Cdd:cd23225     83 GKTRIVDASPFPYAIAGRMVMQNFMSnMMRCNGTEVGSAVGCDP---DTEWTR-YFFELCDRYVFDlDYKAFDSThptaM 158
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1744 NAYLQKKVY---YGIMQTCSSLInsRNYESFYEHqvkapVIVEKHLLTFANTQfSGCFFTTILNCLVHDAMLRY----IF 1816
Cdd:cd23225    159 FNLLAERFFterNGFDQQAVRIF--LNGLSDSDH-----VYEGKHFRIRGGLP-SGCPCTSILNTVINNIIVRAailgAY 230
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1817 ELNCEKFgrnlifeEHVRAKILGDDHIYSfsdeAAKFMNPKNIQE-AYKELGAEYTDDQKEAEVSEEFRkFEDLTFLGA- 1894
Cdd:cd23225    231 QIDTVDF-------QKFRMLAYGDDVVYA----TPQPIKPQDLADwLHANTNYKVTPASKAGTFPEEST-IWDVTFLKRs 298
                          330
                   ....*....|..
gi 1124158116 1895 ------HPRLIK 1900
Cdd:cd23225    299 fkpdedHGHLIR 310
Enterovirus_RdRp cd23213
RNA-dependent RNA polymerase (RdRp) in the Enterovirus genus of positive-sense single-stranded ...
1579-1961 3.05e-07

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: 55.61  E-value: 3.05e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1579 LTFEEAVGGVPGLlTSMNRFTSAGYPLckITKGRGKREYFwfdDNG-------KLCYDPLYKTLVMnfiekfdrgecekg 1651
Cdd:cd23213     87 MSLEDAMYGTDGL-EALDLHTSAGYPY--VALGIKKRDIL---NKKtrdtskmKKYLDKYGLDLPM-------------- 146
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1652 rfVAYLKDELVSEKKIKQKRCRIIYGGDMIANTAFRMIFGSFVIAYNHSYDKLS-HAVGLnqysyDMDIIHSYL-LEVGN 1729
Cdd:cd23213    147 --VTYVKDELRSKDKVEKGKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVVTgSAVGC-----DPDTFWSKIpILLDG 219
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1730 NFVAGDFKGWDKNMNAylqkkVYYGIMQTCSSLINSRNYESFYEHQVKApviveKHLltFANTQF-------SGCFFTTI 1802
Cdd:cd23213    220 SLFAFDYTGYDASLSP-----VWFRALKMVLEKGYSEEAVSLIDYLNHS-----HHL--YKNKTYcvlggmpSGCSGTSI 287
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1803 LNCLVHDAMLRYIFeLNCEKfGRNLifeEHVRAKILGDDHIYSFSDEaakfMNPKNIQEAYKELGAEYTDDQKEAEVSEe 1882
Cdd:cd23213    288 FNSMINNIIIRTLL-LKTYK-GIDL---DELKMIAYGDDVIASYPHP----IDCSLLARTGKEYGLTMTPADKSPCFNE- 357
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1883 fRKFEDLTFLG-------AHPRLIKGrwVGALKKdtITEMVLWTRDfnedllARcQTSIEMSSL----W--GEEYYLE-- 1947
Cdd:cd23213    358 -VNWENVTFLKrgfradeQYPFLIHP--VMPMKE--IHESIRWTKD------PR-NTQDHVRSLcllaWhnGEEEYEKfv 425
                          410
                   ....*....|....*..
gi 1124158116 1948 ---RAASINRALRRVNY 1961
Cdd:cd23213    426 skiRSVPVGRALALPNY 442
Solinviviridae_RdRp cd23199
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Solinviviridae of ...
1707-1945 4.73e-07

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


Pssm-ID: 438049  Cd Length: 323  Bit Score: 54.67  E-value: 4.73e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1707 AVGLNQYSYDMDIIHSylLEVGNNFVAGDFKGWDKNMNAYLQKKVYYGIMQTCSSLINS-RNYESFYEHQVKapvIVEKH 1785
Cdd:cd23199     72 AVGCNPYATFHKFATK--FFKFKNFFSCDYKNFDRTIPKCVFEDFRDMLIQANPHMKNEiYACFQTIIDRIQ---VSGNS 146
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1786 LLTFANTQFSGCFFT----TILNCLVHDAMLRYIFELNCEKFGRNLIFEEHVRAKIL-GDDHIYSFSDEAAKFMNPKNIQ 1860
Cdd:cd23199    147 ILLVHGGMPSGCVPTaplnSKVNDIMIYTAYVNILRRADRGDITSYRYYRDLVCRLFyGDDVIIAVDDSIADIFNCQTLS 226
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1861 EAYKEL-GAEYTDDQKEAEVsEEFRKFEDLTFLGAHPRLIKGRW---VGALKKDTITEMVLWTRDFN-EDLLARCQTSIE 1935
Cdd:cd23199    227 EEMKILfGMNMTDGSKSDII-PKFETIETLSFISRFFRPLKHQEnfiVGALKKISIQTHFYYATDDTpEHFGQVFKTIQE 305
                          250
                   ....*....|
gi 1124158116 1936 MSSLWGEEYY 1945
Cdd:cd23199    306 EAALWEEEYF 315
Aphthovirus_RdRp cd23210
RNA-dependent RNA polymerase (RdRp) in the Aphthovirus genus of positive-sense single-stranded ...
1492-1895 1.64e-06

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: 53.41  E-value: 1.64e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1492 ERVILSRVSKIRPS----VIAPEMPETPkkhlplLSPNDPRAENEDPLVNMIndtLSKLSPRCDESRADRAVL---GTMY 1564
Cdd:cd23210      4 ERVHVMRKTKLAPTvahgVFNPEFGPAA------LSNKDPRLNEGVVLDEVI---FSKHKGDTKMSAEDKALFrrcAADY 74
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1565 HMRKNLTWIFPKRRLTFEEAVGGVPGLlTSMNRFTSAGYPLCKITKGRGKREYFwfdDNGKLcydplyKTLVMNFIEKFD 1644
Cdd:cd23210     75 ASRLHSVLGTANAPLSIYEAIKGVDGL-DAMEPDTAPGLPWALQGKRRGALIDF---ENGTV------GPEVEAALKLME 144
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1645 RGEcEKGRFVAYLKDELVSEKKIKQKRCRIIYGGDMIANTAFRMIFGSFViAYNHSYD--KLSHAVGLNQysyDMDIIHS 1722
Cdd:cd23210    145 KRE-YKFACQTFLKDEIRPMEKVRAGKTRIVDVLPVEHILYTRMMIGRFC-AQMHSNNgpQIGSAVGCNP---DVDWQRF 219
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1723 YL-LEVGNNFVAGDFKGWDKNMNAYLQKKVYYGIMQTCSSLinSRNYESFYEHQVKAPVIVEKHLLTFANTQFSGCFFTT 1801
Cdd:cd23210    220 GThFAQYRNVWDVDYSAFDANHCSDAMNIMFEEVFRTEFGF--HPNAEWILKTLVNTEHAYENKRITVEGGMPSGCSATS 297
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1802 ILNCLVHDAMLRYIFELNCEKFGRNLIfeehvRAKILGDDHIYSfSDEAAKFmnpKNIQEAYKELGAEYTDDQKEAEVSE 1881
Cdd:cd23210    298 IINTILNNIYVLYALRRHYEGVELDTY-----TMISYGDDIVVA-SDYDLDF---EALKPHFKSLGQTITPADKSDKGFV 368
                          410
                   ....*....|....
gi 1124158116 1882 EFRKFEDLTFLGAH 1895
Cdd:cd23210    369 LGHSITDVTFLKRH 382
Rabovirus_RdRp cd23230
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Rabovirus of ...
1599-1921 1.91e-06

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: 52.96  E-value: 1.91e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1599 TSAGYPLckITKGRGKREYFwfddngklcyDPLYK--TLVMNFIEKFDRGEcekgRFVAYLKDELVSEKKIKQKRCRIIY 1676
Cdd:cd23230     15 TSAGYPY--VLNGIKKRDIL----------DPETRdtTKLQECLDKYGVDL----PFVTYLKDELRPLEKIKKGKTRLIE 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1677 GGDMIANTAFRMIFGSFVIAYNHSYDKLS-HAVGLNQysyDMDIIhSYLLEVGNNFVAGDFKGWDKNMNAY-------LQ 1748
Cdd:cd23230     79 CSSMNDTIRMKMMFGRLFATYHRNPGPITgSAVGCNP---DIHWT-KFRAEMHGEIIAFDYSNYDASLNKVwfeclkmVL 154
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1749 KKVYYGIMQTCSSLINSRNYESFYEHQVKAPVIvekhlltfantqfSGCFFTTILNCLVHDAMLRYIFeLNCEKfGRNLi 1828
Cdd:cd23230    155 KNFGFKDLRPIDHIIRSRHIYKGIEYDVEGGMP-------------SGCSGTSIFNSIINNIIIMTLV-LDAYK-GIDL- 218
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1829 feEHVRAKILGDDHIYSFSDEaakfMNPKNIQEAYKELGAEYTDDQKEAevseEFRK--FEDLTFL-------GAHPRLI 1899
Cdd:cd23230    219 --EQLKIIAYGDDVIVTYPYP----LDAALLADCGKKYGLKMTPPDKSA----EFKNvtWEDVTFLkrrfkpaKHYPFLI 288
                          330       340
                   ....*....|....*....|..
gi 1124158116 1900 KgrwvGALKKDTITEMVLWTRD 1921
Cdd:cd23230    289 H----PVFDQQEILESLRWTRN 306
Sapelovirus_RdRp cd23218
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Sapelovirus of ...
1653-1964 5.57e-06

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: 51.44  E-value: 5.57e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1653 FVAYLKDELVSEKKIKQKRCRIIYGGDMiaNTAFRM--IFGSFVIAYNHSYDKLS-HAVGLNQysydmDIIHSYLLEVG- 1728
Cdd:cd23218     56 FTTYLKDELRPKEKVKMGKTRLIECSSL--NDTIRMkrIFGRLFQTFHKNPGTYTgSAVGCNP-----DVHWSKFAEEGg 128
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1729 -NNFVAGDFKGWDKNMNAYL--QKKVYYgimqtcSSLINSRNYESFYEHQVKAPVIVEKHLLTFANTQFSGCFFTTILNC 1805
Cdd:cd23218    129 mDNVCAFDYTNWDASLSPFWfdALKLFL------SKLGYSERDIVLIDHLCYSNHIFKNEGYKVAGGMPSGCSGTSIFNS 202
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1806 LVHDAMLRYIFeLNCEKfGRNLifeEHVRAKILGDDHIYSFSDEaakfMNPKNIQEAYKELGAEYTDDQKeAEVSEEFRK 1885
Cdd:cd23218    203 IINNIVVRTLV-LLVYK-GINL---DELRILCYGDDLLVAYPYP----LDPNVLADLGKSLGLTMTPADK-SDTFQGCTK 272
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1886 FEDLTFLG------------AHPrlikgrwvgALKKDTITEMVLWTRD---FNEDLLARCQTSiemsslW--GEEYYLE- 1947
Cdd:cd23218    273 LTEVTFLKrsfvfdeefpflCHP---------VFPMEEVHESIRWTRNastTQEHVTSLCLLA------WhnGEEVYEEf 337
                          330       340
                   ....*....|....*....|.
gi 1124158116 1948 ----RAASINRALRRVNYPQI 1964
Cdd:cd23218    338 cekiRSVPVGRALILPPYSQL 358
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
2044-2148 1.56e-05

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: 47.69  E-value: 1.56e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 2044 ESFEWSTSDipgKAIKTIPIPFGLLELGDSDnvQNMpfDRFLFWNGDVKLTFQVNGTPFMCG-LLAVY---FMPLASYEC 2119
Cdd:pfam00073   44 DSTDWTSLS---KGFFWWKLPLALLSMGLLG--RLL--RYHTYYRGGLEVTVQFNGSKFHQGkLLVAYvppGAPPPGSRD 116
                           90       100
                   ....*....|....*....|....*....
gi 1124158116 2120 ELANISTTNHVYLQPDKNNTVEITIPFLY 2148
Cdd:pfam00073  117 YLWQATLNPHQFWNLGLNSSARLSVPYIS 145
Iflaviridae_RdRp cd23197
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Iflaviridae of ...
1653-1945 1.78e-05

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: 49.48  E-value: 1.78e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1653 FVAYLKDELVSEKKIKQkrcriiYGGDMIANTA-------FRMIFGSFVIAYNHSYDKLSHAVGLNQYSYDMDIIHSYLL 1725
Cdd:cd23197      8 YWAHLKDELRPSEKLRR------FGGTRVFSVPplelvlnSRRFLLPFMDAFQSFPIEAHHAIGLNPNSGDWRRLRDTLL 81
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1726 EVGNNFVAGDFKG------WDKNMNAYLQKKVYYGiMQTCSSLINSRNYESFYEHQVKAPVIVEKHLLTFANTQFSGCFF 1799
Cdd:cd23197     82 EKGPCLLQMDYKNysdaipKECVAKAFHIIVDYYR-KWHCLTVEIENALKTLFLDTADAELLVYGDVFKVNNGVLAGHPM 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1800 TTILNCLVHDAMLRYIFELNCEKFGRNliFEEHVRAKILGDDHIYSFSDEAAKFMNPKNIQEAYKELGAEYTDDQKE-AE 1878
Cdd:cd23197    161 TSVVNSVVNLILMNYMWIKITRRRASE--FFKLTYIIVMGDDVVISLPKQLTEEFDCRKICAEFAKYDIKVTDSEKNlTG 238
                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1124158116 1879 VSEEFRKFEDLTFLGAHPRLIKGR---WVGALKKDTITEMVLWTR---DFNEDLLARCQTSIEMSSLWGEEYY 1945
Cdd:cd23197    239 EPKPYDSFDKFEFLSRGFSDCDAYpdiTFAPVKTIALFDCPLWISkgqDEEEQTIQAIQAGLLLAFDHGPEFF 311
Crohivirus_RdRp cd23232
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Crohivirus of ...
1653-1971 1.53e-04

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: 47.02  E-value: 1.53e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1653 FVAYLKDELVSEKKIKQKRCRIIYGGDMIANTAFRMIFGS-FVIAYNHSYDKLSHAVGLNQYSyDMDIIHSYLLEVGNNF 1731
Cdd:cd23232     67 FTAHLKDELRKLEKIRSGKTRCIEACDFDYTVAHKMMFGTlYKAIYDTPGIITGLAVGMNPWK-DWELIQQSLFKYNYDF 145
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1732 vagDFKGWDKNMNAYLQKKVyYGIMQTCSS---LINSRNYESFYEHQvkapvIVEKHLLTFANTQFSGCFFTTILNCLVh 1808
Cdd:cd23232    146 ---DYKTFDGSLSRELMLHA-VDILSACVEndeMAKLMLSVVVESVH-----LVLDQKWNVSGGMPSGSPCTTVLNSVC- 215
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1809 DAMLRYIFELNCEKfgrnlifeEHVRAKILGDDHIYSFSDEaakfMNPKNIQEAYKE-LGAEYTDDQKeaevSEEFRKFE 1887
Cdd:cd23232    216 NLIVSSTIADMCTE--------GDFKILVYGDDLIISSTAP----LDCDRFKTLVELhYGMEVTPGDK----GDEFKVKD 279
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1888 D--LTFLGAHPRLIKGR--WVGALKKDTITEMVLWTR---DFNEDLLARCQTSIemssLWGEEYYLERAASINRALR--R 1958
Cdd:cd23232    280 ReqVSFLKRVTRKFPGTnyRVGALDLDTVKQHLMWCKsysSFKQQLDSALMEVA----MHGEETYNGFLTEIKTKLDkfK 355
                          330
                   ....*....|...
gi 1124158116 1959 VNYPQIEVKPWEL 1971
Cdd:cd23232    356 IYPPKFKHIISRL 368
ps-ssRNAv_RdRp-like cd23167
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
1730-1847 2.28e-04

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: 41.94  E-value: 2.28e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1730 NFVAGDFKGWDKNMNAYLQKkvyygimqtcsslinsrnyesfyehqvkapvivekhlltfaNTQFSGCFFTTILNCLVHD 1809
Cdd:cd23167      1 HVVESDYSGFDSSISPDLLK-----------------------------------------AGQPSGSPNTSADNSLINL 39
                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1124158116 1810 AMLRYIfelnCEKFGRNLIFEEHVRAKILGDDHIYSFS 1847
Cdd:cd23167     40 LLARLA----LRKACGRAEFLNSVGILVYGDDSLVSVP 73
Kunsagivirus_RdRp cd23219
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Kunsagivirus of ...
1592-1814 2.40e-04

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: 46.01  E-value: 2.40e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1592 LTSMNRFTSAGYPLckitKGRGKREYFWFDDngKLCYDPLyKTLVMNFIEKFDRGECEKGRFVAYLKDELVSEKKIKQKR 1671
Cdd:cd23219      9 VTPMDHTASAGPKY----PGTKRSELIDFQN--RIISDRL-RNDVLELQFRGTSGGAGEVKFSSFLKDELRPLSKIRSGD 81
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1672 CRIIYGGDMIANTAFRMIFGSFV-IAYNHSYDKLSHAVGLNQYSyDMDIIHSYLLEvgNNFVAgDFKGWDKNMNAylqkk 1750
Cdd:cd23219     82 TRVVECSSLDYTVAFRMQFLRVLqMCYGSDPTLTGLAPGMNVYT-DMLPLCTSLYD--YNLCL-DFSKYDSRLPL----- 152
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1124158116 1751 vyyGIMQTCSSLINSRNYESFYEHQVKAPVIVEKHLLTFANTQF-----SGCFFTTILNCLVHDAMLRY 1814
Cdd:cd23219    153 ---QVMHRVAQLISNLTPDPQVSMRLFQPIIISTHIVGSYEVVVeggmpSGCPITTIMNSVCNVVMTSY 218
Mischivirus_RdRp cd23227
RNA-dependent RNA polymerase (RdRp) in the genus Mischivirus of positive-sense single-stranded ...
1488-1718 1.10e-03

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: 44.17  E-value: 1.10e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1488 LPPRERVILSRVSKIRPSVIAPEMpeTPKKHLPLLSPNDPRAeneDPLVNMINDTLSKLSP----------RCDESRADR 1557
Cdd:cd23227      6 LPDGPRIHVPRKTKLRKSPAYPIF--KPDAGPAVLSKNDPRL---AEGVDFDKQVFSKHSAnqkeypkafrRMARWYADR 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1558 AVLgtmyHMRKNltwifpKRRLTFEEAVGGVPgLLTSMNRFTSAGYPLCKitKGRGKREYFWFDDNgklcydPLYKTLVM 1637
Cdd:cd23227     81 VFT----YLGKD------NGPLSVKDAIKGID-NLDAMDPTTSPGLPYSA--AGIKRTDLLDFDTG------EIISPALR 141
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1638 NFIEKFDRGECEKGRFVAYLKDELVSEKKIKQKRCRIIYGGDMIANTAFRMIFGSFVIAYNHS----------------Y 1701
Cdd:cd23227    142 AEYNKYVSGDYSDHVFQTFLKDEIRSEEKIKAGKTRIVDVPSLAHVIIGRVLLGKFCSKFQASpgtelgsaigcnpdwdW 221
                          250
                   ....*....|....*..
gi 1124158116 1702 DKLSHAVGLNQYSYDMD 1718
Cdd:cd23227    222 TYFAHQLMERQWCYDID 238
Kobuvirus_RdRp cd23214
RNA-dependent RNA polymerase (RdRp) in the Kobuvirus genus of positive-sense single-stranded ...
1494-1711 2.41e-03

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: 43.30  E-value: 2.41e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1494 VILSRVSKIRPSviaPEMPETPKKHLP-LLSPNDPRAEnedPLVNMINDTLSKLSP-------RCDESRADravlgtMYH 1565
Cdd:cd23214      3 VNVNRKSRLGPS---PAYGAFPVKKQPaPLTQKDDRLE---DGIRLDDQLFLKHNKgdmdepwPGLEAAAD------LYF 70
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1566 MRknltwiFPK--RRLTFEEAVGGVPGLlTSMNRFTSAGYPLCkiTKGRGKREYFWFDDNGKLCYDPLYKTLVMNFIEKF 1643
Cdd:cd23214     71 SK------FPTmiRTLTQEEAINGTPNL-EGLDMNQAAGYPWN--TMGRSRRSLFVEVQPGIYVPKPELQAEIDKTLEDP 141
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1124158116 1644 DRgecekgRFVAYLKDELVSEKKIKQKRCRIIYGGDMIANTAFRMIFGSFVIAYNHSYDKLSHAVGLN 1711
Cdd:cd23214    142 DY------FYSTFLKDELRPTAKVTLGLTRVVEAAPIHAIVAGRMLLGGLIEYMQARPGKHGSAVGCN 203
Cardiovirus_RdRp cd23211
RNA-dependent RNA polymerase (RdRp) in the Cardiovirus genus of positive-sense single-stranded ...
1486-1722 7.36e-03

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: 41.75  E-value: 7.36e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1486 EILPPRERVILSRVSKIRPSVIAPEMpeTPKKHLPLLSPNDPRAENEDPLVNMINDT--LSKLSPRCDesradraVLGTM 1563
Cdd:cd23211      4 VRIGTGPVVHVPRKTKLRRTVAHPVF--QPKFEPAVLSKYDPRTDKDVDEVAFSKHTtnQESLPPVFR-------MVAKE 74
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1564 YHMRKNLTWIFPKRRLTFEEAVGGVPGlLTSMNRFTSAGYPLckITKGRGKREYFWFDDngklcydplyKTLVMNFIE-- 1641
Cdd:cd23211     75 YANRVFTLLGKDNGRLTVEQAVLGLEG-MDPMEKDTSPGLPY--TQQGLRRTDVVDFET----------ATMIPFLAEah 141
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1124158116 1642 -KFDRGECEKGRFVAYLKDELVSEKKIKQKRCRI---------IYGGDMIANTAFR------MIFGSfVIAYNHSYDKLS 1705
Cdd:cd23211    142 rKMVEGDYSDVVYQSFLKDEIRPIEKVQAAKTRIvdvppfehcILGRQLLGRFASKfqtnpgLELGS-AIGCDPDVDWTA 220
                          250
                   ....*....|....*..
gi 1124158116 1706 HAVGLNQYSYDMDIIHS 1722
Cdd:cd23211    221 FAVALSGFKYVYDVDYS 237
 
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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