NCBI Conserved Domain Search

Conserved domains on [gi|403044785|gb|AFR11851|]

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polyprotein [Kobuvirus sewage Kathmandu]

Protein Classification

Graphical summary

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List of domain hits

Name

Accession

Description

Interval

E-value

ps-ssRNAv_RdRp-like super family

cl40470

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

1706-2141

0e+00

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

The actual alignment was detected with superfamily member cd23214:

Pssm-ID: 477363 Cd Length: 459 Bit Score: 911.15 E-value: 0e+00

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1706 PGVNINRMSRLHPSPAYGAFPLKKQPAPLRRNDKRLQEGIDLDSQL*LKHGKGDMAEPWPGLEAAADLYFSTFPPSLPVF 1785
Cdd:cd23214     1 PGVNVNRKSRLGPSPAYGAFPVKKQPAPLTQKDDRLEDGIRLDDQLFLKHNKGDMDEPWPGLEAAADLYFSKFPTMIRTL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1786 SQEQAIMGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDEPEPGLFVPKPELQIEIDRTLENPDYVYSTFLKDELRPTAKVE 1865
Cdd:cd23214    81 TQEEAINGTPNLEGLDMNQAAGYPWNTMGRSRRSLFVEVQPGIYVPKPELQAEIDKTLEDPDYFYSTFLKDELRPTAKVT 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1866 QGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPGQHGCAVGCNPDVHWTEFFYKFSEFSQVYDLDYKCFDATLPSAAFSL 1945
Cdd:cd23214   161 LGLTRVVEAAPIHAIVAGRMLLGGLIEYMQARPGKHGSAVGCNPDLHWTKFFYKFCHYPQVFDLDYKCFDATLPSCAFRI 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1946 VATHLERLTGDPRVSRYINSIRHSHHIYGNQTYDMIGGNPSGCVATSILNTIINNICVLSALIQHPDFSPAKFQILAYGD 2025
Cdd:cd23214   241 VEDHLERLTGDERVTRYIESIRHSHHVYGNETYEMIGGNPSGCVGTSIINTIINNICVLSALIQHPDFSPESFRILAYGD 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 2026 DVIYATEPPIHPSYIREFYQRCTPLVVTPANKGQDFPETSTIYEVTFLKRWFVPDDRRPFYIHPVMDPDTYEQS*MWLRD 2105
Cdd:cd23214   321 DVIYGCDPPIHPSFIKEFYDKHTPLVVTPANKGSDFPETSTIYDVTFLKRWFVPDDIRPFYIHPVMDPDTYEQSVMWLRD 400

                         410       420       430
                  ....*....|....*....|....*....|....*.
gi 403044785 2106 GDFQDVVTSLCHLAFHSGPRTYERWCMKVREQCLKS 2141
Cdd:cd23214   401 GDFQDLVTSLCYLAFHSGPKTYDRWCTRVRDQVMKT 436

RNA_helicase

pfam00910

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

1175-1277

2.45e-40

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

Pssm-ID: 459992 Cd Length: 102 Bit Score: 145.05 E-value: 2.45e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  1175 VYFYGPPGTGKSLLASLLAQTLAQRISGNPDDVYSPTAAScEYFDGYTGQAVHFIDDIGQDPEGRDWANFPNLVSSAPYI 1254
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKKLGLPKDSVYSRNPDD-DFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYP 79

                           90       100
                   ....*....|....*....|...
gi 403044785  1255 LPMASLEEKGTHYTSRVIVITSN 1277
Cdd:pfam00910   80 PPMAALEEKGTPFTSKFVIVTSN 102

rhv_like

cd00205

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

318-490

3.48e-33

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

Pssm-ID: 119412 Cd Length: 178 Bit Score: 127.51 E-value: 3.48e-33

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  318 EFAHRPGLMASLNWTmADQPGERLAIIPVSPSA--IAGTGAPISYVLSLFSQWRGELAAHLLFTGSAQHYCRLVVCYTP- 394
Cdd:cd00205     3 SFADRPTTVGTNNWN-SSASGTQLFQWKLSPALgfLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPp 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  395 --AAPSPPSTMQQAMRGTYTVWDINAASTLEFTIPFISQSYWKTVDINNPDAlLSTTGYLSVWVQNPLTGPNTAPAGATI 472
Cdd:cd00205    82 gaPAPTTGDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDGYGP-LNSFGTLVVRVLTPLTVPSGAPTTVDI 160

                         170
                  ....*....|....*...
gi 403044785  473 QGFLSASDsFNVRLMQNP 490
Cdd:cd00205   161 TVYVRAGD-FELYGPRPP 177

rhv_like

cd00205

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

130-268

7.83e-33

Pssm-ID: 119412 Cd Length: 178 Bit Score: 126.36 E-value: 7.83e-33

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  130 PFSFVRAYPDSPWAAMYDTHSMWNCGWRVQVTVNGSQFHAGALVLYMIPEGTTKAVETARLNSGFVYPYVILNLYESNTA 209
Cdd:cd00205    32 PALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPPGAPAPTTGDTRWQATLNPHVIWDLGTNSSV 111

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 403044785  210 TVEVPYISPTP------NTTSGLHAPWTFYLQVLTPLSPPTGLPTSLSCSIYVTPVDTTFHGLRY 268
Cdd:cd00205   112 TFVVPYVSPTPyrstryDGYGPLNSFGTLVVRVLTPLTVPSGAPTTVDITVYVRAGDFELYGPRP 176

rhv_like

cd00205

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

538-723

1.16e-21

Pssm-ID: 119412 Cd Length: 178 Bit Score: 94.39 E-value: 1.16e-21

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  538 LENFFSFYRLLPLSTTGPtlPLPLTDAAQVPLDPIHWLQNADVSGLAAMLSCFTYIAADLRFTLRVANPNGLPVSLIVAF 617
Cdd:cd00205     1 VESFADRPTTVGTNNWNS--SASGTQLFQWKLSPALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAY 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  618 APPGATIPSK-PDRQALSNFFMSEVPISASSStlVSFSIPYTSPLSAIPTSYFGWedWSGTNFGRLHAGSWGTLLFLPSL 696
Cdd:cd00205    79 VPPGAPAPTTgDTRWQATLNPHVIWDLGTNSS--VTFVVPYVSPTPYRSTRYDGY--GPLNSFGTLVVRVLTPLTVPSGA 154

                         170       180
                  ....*....|....*....|....*..
gi 403044785  697 PSQgaalldLSLTCWLAFGNFKAWVPR 723
Cdd:cd00205   155 PTT------VDITVYVRAGDFELYGPR 175

Peptidase_C3 super family

cl02893

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

1514-1669

4.81e-08

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

The actual alignment was detected with superfamily member pfam00548:

Pssm-ID: 278947 Cd Length: 174 Bit Score: 54.76 E-value: 4.81e-08

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  1514 ISNNVVHVESGNGleKNVMSGFYLFSRILIVPTHLrEPHHTRLLVG---TDSyDWATLQCQEFG---ELMAIHTSTSRQY 1587
Cdd:pfam00548   11 LKQNAVPVTTSKG--VFTCCATGVYDNVILLPRHA-EPGLTIVLDGkvvTIS-DPEVELVDQEGmplDAAIVKLKRNEKF 86

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  1588 KDMRRFI--GAHPYPTG-LLVSQFKAAPLYVRISD----NRIVNLD---FPGVVVcpqaygYRAATF*SLCGSPLVTDDP 1657
Cdd:pfam00548   87 KDIRKHLpnRITKGNPVvLLINNNEQGRIYVPVGAvthsGGIKTLDgttTPRTIS------YNAPTKAGMCGGVVIAKVE 160

                          170
                   ....*....|..
gi 403044785  1658 SGVKILGLHVAG 1669
Cdd:pfam00548  161 GNGKILGMHIAG 172

SpoVK super family

cl33891

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

1149-1196

1.75e-04

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

The actual alignment was detected with superfamily member COG0464:

Pssm-ID: 440232 [Multi-domain] Cd Length: 397 Bit Score: 46.44 E-value: 1.75e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 403044785 1149 QALRNYTLALSKH-RKRQVGPRPEPVVVYFYGPPGTGKSLLASLLAQTL 1196
Cdd:COG0464   167 EELRELVALPLKRpELREEYGLPPPRGLLLYGPPGTGKTLLARALAGEL 215

Name

Accession

Description

Interval

E-value

Kobuvirus_RdRp

cd23214

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

1706-2141

0e+00

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: 911.15 E-value: 0e+00

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1706 PGVNINRMSRLHPSPAYGAFPLKKQPAPLRRNDKRLQEGIDLDSQL*LKHGKGDMAEPWPGLEAAADLYFSTFPPSLPVF 1785
Cdd:cd23214     1 PGVNVNRKSRLGPSPAYGAFPVKKQPAPLTQKDDRLEDGIRLDDQLFLKHNKGDMDEPWPGLEAAADLYFSKFPTMIRTL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1786 SQEQAIMGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDEPEPGLFVPKPELQIEIDRTLENPDYVYSTFLKDELRPTAKVE 1865
Cdd:cd23214    81 TQEEAINGTPNLEGLDMNQAAGYPWNTMGRSRRSLFVEVQPGIYVPKPELQAEIDKTLEDPDYFYSTFLKDELRPTAKVT 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1866 QGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPGQHGCAVGCNPDVHWTEFFYKFSEFSQVYDLDYKCFDATLPSAAFSL 1945
Cdd:cd23214   161 LGLTRVVEAAPIHAIVAGRMLLGGLIEYMQARPGKHGSAVGCNPDLHWTKFFYKFCHYPQVFDLDYKCFDATLPSCAFRI 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1946 VATHLERLTGDPRVSRYINSIRHSHHIYGNQTYDMIGGNPSGCVATSILNTIINNICVLSALIQHPDFSPAKFQILAYGD 2025
Cdd:cd23214   241 VEDHLERLTGDERVTRYIESIRHSHHVYGNETYEMIGGNPSGCVGTSIINTIINNICVLSALIQHPDFSPESFRILAYGD 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 2026 DVIYATEPPIHPSYIREFYQRCTPLVVTPANKGQDFPETSTIYEVTFLKRWFVPDDRRPFYIHPVMDPDTYEQS*MWLRD 2105
Cdd:cd23214   321 DVIYGCDPPIHPSFIKEFYDKHTPLVVTPANKGSDFPETSTIYDVTFLKRWFVPDDIRPFYIHPVMDPDTYEQSVMWLRD 400

                         410       420       430
                  ....*....|....*....|....*....|....*.
gi 403044785 2106 GDFQDVVTSLCHLAFHSGPRTYERWCMKVREQCLKS 2141
Cdd:cd23214   401 GDFQDLVTSLCYLAFHSGPKTYDRWCTRVRDQVMKT 436

RdRP_1

pfam00680

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

1717-2129

1.61e-53

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: 195.32 E-value: 1.61e-53

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  1717 HPSPAYGAFPLKKQPAPLRRNDKRLQE-----GIDLDSQL*LKHGKGDMAEPWPG---LEAAADLYFSTF----PPSLPV 1784
Cdd:pfam00680    1 SPTERHLVAIPAYVPASLGPEDPRWARsylntDPYVDDIKKYSRPKLPGPADERDkllNRSAAKMVLSELrgvpKKANST 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  1785 FSQEQAIMGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDEPEPGLFVPKPELQIEIDRTLENP----DYVYSTFLKDELRP 1860
Cdd:pfam00680   81 LIVYRAIDGVEQIDPLNWDTSAGYPYVGLGGKKGDLIEHLKDGTEARELAERLAADWEVLQNgtplKLVYQTCLKDELRP 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  1861 TAKVEQGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPGQHGCAVGCNP-DVHWTEFFYKFSEFSQ-VYDLDYKCFDATL 1938
Cdd:pfam00680  161 LEKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHPIQVGINPfDRGWPRLLRRLARFGDyVYELDYSGFDSSV 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  1939 PSAAFSLVATHLERLTG-DPRVSRYINS----IRHSHHIYGNQTYDMIGGNPSGCVATSILNTIINNICVLSALI----- 2008
Cdd:pfam00680  241 PPWLIRFAFEILRELLGfPSNVKEWRAIlellIYTPIALPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYALLkslen 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  2009 QHPD--FSPAKFQILAYGDDVIYATEPPIHPSYIReFYQ--RCTPLVVTPANKgqDFPETSTIYEVTFLKRWFVpddRRP 2084
Cdd:pfam00680  321 DGPRvcNLDKYFDFFTYGDDSLVAVSPDFDPVLDR-LSPhlKELGLTITPAKK--TFPVSRELEEVSFLKRTFR---KTP 394

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|....*.
gi 403044785  2085 FYIHPVMDPDTYEQS*MWLRDGD-FQDVVTSLCHLAFHSGPRTYER 2129
Cdd:pfam00680  395 GGYRPPLDRKRILAQLEYIRSKPvPSGQLENIRAYASHHGYEFYRD 440

RNA_helicase

pfam00910

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

1175-1277

2.45e-40

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

Pssm-ID: 459992 Cd Length: 102 Bit Score: 145.05 E-value: 2.45e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  1175 VYFYGPPGTGKSLLASLLAQTLAQRISGNPDDVYSPTAAScEYFDGYTGQAVHFIDDIGQDPEGRDWANFPNLVSSAPYI 1254
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKKLGLPKDSVYSRNPDD-DFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYP 79

                           90       100
                   ....*....|....*....|...
gi 403044785  1255 LPMASLEEKGTHYTSRVIVITSN 1277
Cdd:pfam00910   80 PPMAALEEKGTPFTSKFVIVTSN 102

rhv_like

cd00205

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

318-490

3.48e-33

Pssm-ID: 119412 Cd Length: 178 Bit Score: 127.51 E-value: 3.48e-33

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  318 EFAHRPGLMASLNWTmADQPGERLAIIPVSPSA--IAGTGAPISYVLSLFSQWRGELAAHLLFTGSAQHYCRLVVCYTP- 394
Cdd:cd00205     3 SFADRPTTVGTNNWN-SSASGTQLFQWKLSPALgfLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPp 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  395 --AAPSPPSTMQQAMRGTYTVWDINAASTLEFTIPFISQSYWKTVDINNPDAlLSTTGYLSVWVQNPLTGPNTAPAGATI 472
Cdd:cd00205    82 gaPAPTTGDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDGYGP-LNSFGTLVVRVLTPLTVPSGAPTTVDI 160

                         170
                  ....*....|....*...
gi 403044785  473 QGFLSASDsFNVRLMQNP 490
Cdd:cd00205   161 TVYVRAGD-FELYGPRPP 177

rhv_like

cd00205

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

130-268

7.83e-33

Pssm-ID: 119412 Cd Length: 178 Bit Score: 126.36 E-value: 7.83e-33

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  130 PFSFVRAYPDSPWAAMYDTHSMWNCGWRVQVTVNGSQFHAGALVLYMIPEGTTKAVETARLNSGFVYPYVILNLYESNTA 209
Cdd:cd00205    32 PALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPPGAPAPTTGDTRWQATLNPHVIWDLGTNSSV 111

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 403044785  210 TVEVPYISPTP------NTTSGLHAPWTFYLQVLTPLSPPTGLPTSLSCSIYVTPVDTTFHGLRY 268
Cdd:cd00205   112 TFVVPYVSPTPyrstryDGYGPLNSFGTLVVRVLTPLTVPSGAPTTVDITVYVRAGDFELYGPRP 176

rhv_like

cd00205

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

538-723

1.16e-21

Pssm-ID: 119412 Cd Length: 178 Bit Score: 94.39 E-value: 1.16e-21

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  538 LENFFSFYRLLPLSTTGPtlPLPLTDAAQVPLDPIHWLQNADVSGLAAMLSCFTYIAADLRFTLRVANPNGLPVSLIVAF 617
Cdd:cd00205     1 VESFADRPTTVGTNNWNS--SASGTQLFQWKLSPALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAY 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  618 APPGATIPSK-PDRQALSNFFMSEVPISASSStlVSFSIPYTSPLSAIPTSYFGWedWSGTNFGRLHAGSWGTLLFLPSL 696
Cdd:cd00205    79 VPPGAPAPTTgDTRWQATLNPHVIWDLGTNSS--VTFVVPYVSPTPYRSTRYDGY--GPLNSFGTLVVRVLTPLTVPSGA 154

                         170       180
                  ....*....|....*....|....*..
gi 403044785  697 PSQgaalldLSLTCWLAFGNFKAWVPR 723
Cdd:cd00205   155 PTT------VDITVYVRAGDFELYGPR 175

Rhv

pfam00073

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

149-240

2.07e-13

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: 70.42 E-value: 2.07e-13

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785   149 HSMWNCGWRVQVTVNGSQFHAGALVLYMIPEGTTKAVETARLNSGFVYPYVILNLYESNTATVEVPYISPTP--NTTSgl 226
Cdd:pfam00073   77 HTYYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRDYLWQATLNPHQFWNLGLNSSARLSVPYISIAHyySTFY-- 154

                           90
                   ....*....|....
gi 403044785   227 HAPWTFYLQVLTPL 240
Cdd:pfam00073  155 DGNWTLVVAGWVPL 168

Rhv

pfam00073

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

362-456

1.24e-08

Pssm-ID: 395026 Cd Length: 170 Bit Score: 56.55 E-value: 1.24e-08

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785   362 LSLFSQWRGELAAHLLFTGSAQHYCRLVVCYTPAAPSPPSTMQ---QAMRGTYTVWDINAASTLEFTIPFISQ-SYWKTV 437
Cdd:pfam00073   74 LRYHTYYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRDylwQATLNPHQFWNLGLNSSARLSVPYISIaHYYSTF 153

                           90
                   ....*....|....*....
gi 403044785   438 DINNPDalLSTTGYLSVWV 456
Cdd:pfam00073  154 YDGNWT--LVVAGWVPLNY 170

Peptidase_C3

pfam00548

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

1514-1669

4.81e-08

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

Pssm-ID: 278947 Cd Length: 174 Bit Score: 54.76 E-value: 4.81e-08

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  1514 ISNNVVHVESGNGleKNVMSGFYLFSRILIVPTHLrEPHHTRLLVG---TDSyDWATLQCQEFG---ELMAIHTSTSRQY 1587
Cdd:pfam00548   11 LKQNAVPVTTSKG--VFTCCATGVYDNVILLPRHA-EPGLTIVLDGkvvTIS-DPEVELVDQEGmplDAAIVKLKRNEKF 86

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  1588 KDMRRFI--GAHPYPTG-LLVSQFKAAPLYVRISD----NRIVNLD---FPGVVVcpqaygYRAATF*SLCGSPLVTDDP 1657
Cdd:pfam00548   87 KDIRKHLpnRITKGNPVvLLINNNEQGRIYVPVGAvthsGGIKTLDgttTPRTIS------YNAPTKAGMCGGVVIAKVE 160

                          170
                   ....*....|..
gi 403044785  1658 SGVKILGLHVAG 1669
Cdd:pfam00548  161 GNGKILGMHIAG 172

AAA

cd00009

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

1160-1299

1.47e-06

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

Pssm-ID: 99707 [Multi-domain] Cd Length: 151 Bit Score: 49.84 E-value: 1.47e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1160 KHRKRQVGPRPEPVVVYFYGPPGTGKSLLASLLAQTLAQR----ISGNPDDVYSPTAASCEYFDGYTGQAVH-------- 1227
Cdd:cd00009     7 IEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPgapfLYLNASDLLEGLVVAELFGHFLVRLLFElaekakpg 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 403044785 1228 --FIDDIGQDPEGRDWANFPNlvssapyilpMASLEEKGTHYTSRVIVITSNFHEPNERAARSMGALKRRVHLR 1299
Cdd:cd00009    87 vlFIDEIDSLSRGAQNALLRV----------LETLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRIVIP 150

SpoVK

COG0464

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

1149-1196

1.75e-04

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

Pssm-ID: 440232 [Multi-domain] Cd Length: 397 Bit Score: 46.44 E-value: 1.75e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 403044785 1149 QALRNYTLALSKH-RKRQVGPRPEPVVVYFYGPPGTGKSLLASLLAQTL 1196
Cdd:COG0464   167 EELRELVALPLKRpELREEYGLPPPRGLLLYGPPGTGKTLLARALAGEL 215

RecA-like_protease

cd19481

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

1151-1196

4.47e-04

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

Pssm-ID: 410889 [Multi-domain] Cd Length: 158 Bit Score: 43.04 E-value: 4.47e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 403044785 1151 LRNYTLALSKHRKRQVGPRPEPVVVYFYGPPGTGKSLLASLLAQTL 1196
Cdd:cd19481     5 LREAVEAPRRGSRLRRYGLGLPKGILLYGPPGTGKTLLAKALAGEL 50

AAA

smart00382

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...

1174-1299

1.72e-03

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.

Pssm-ID: 214640 [Multi-domain] Cd Length: 148 Bit Score: 41.20 E-value: 1.72e-03

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785   1174 VVYFYGPPGTGKSLLASLLAQTLAQR----ISGNPDDVYSPTAASCEYFDGYTGQAVH---------------------F 1228
Cdd:smart00382    4 VILIVGPPGSGKTTLARALARELGPPgggvIYIDGEDILEEVLDQLLLIIVGGKKASGsgelrlrlalalarklkpdvlI 83

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 403044785   1229 IDDIG--QDPEGRDWANFpnlvssapyILPMASLEEKGTHYTSRVIVITSNFHEPNERAARSMgaLKRRVHLR 1299
Cdd:smart00382   84 LDEITslLDAEQEALLLL---------LEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRRR--FDRRIVLL 145

Rhv

pfam00073

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

529-668

5.71e-03

Pssm-ID: 395026 Cd Length: 170 Bit Score: 39.99 E-value: 5.71e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785   529 ENPTPPDTRLENFFsfyrLLPLSTTGPT--------LPLPLTDAAQvpldpihwlqnadvsgLAAMLSCFTYIAADLRFT 600
Cdd:pfam00073   28 DAPVQPDVQGERFY----TLDSTDWTSLskgffwwkLPLALLSMGL----------------LGRLLRYHTYYRGGLEVT 87

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 403044785   601 LrVANPNGLPV-SLIVAFAPPGATIPSKPDRQALSNFFMSeVPISASSSTLVSFSIPYTSPLSAIPTSY 668
Cdd:pfam00073   88 V-QFNGSKFHQgKLLVAYVPPGAPPPGSRDYLWQATLNPH-QFWNLGLNSSARLSVPYISIAHYYSTFY 154

PRK13342

recombination factor protein RarA; Reviewed

1177-1196

7.80e-03

recombination factor protein RarA; Reviewed

Pssm-ID: 237355 [Multi-domain] Cd Length: 413 Bit Score: 41.22 E-value: 7.80e-03

                          10        20
                  ....*....|....*....|
gi 403044785 1177 FYGPPGTGKSLLASLLAQTL 1196
Cdd:PRK13342   41 LWGPPGTGKTTLARIIAGAT 60

RarA

COG2256

Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...

1177-1196

9.22e-03

Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, recombination and repair];

Pssm-ID: 441857 [Multi-domain] Cd Length: 439 Bit Score: 40.81 E-value: 9.22e-03

                          10        20
                  ....*....|....*....|
gi 403044785 1177 FYGPPGTGKSLLASLLAQTL 1196
Cdd:COG2256    54 LWGPPGTGKTTLARLIANAT 73

Name

Accession

Description

Interval

E-value

Kobuvirus_RdRp

cd23214

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

1706-2141

0e+00

Pssm-ID: 438064 Cd Length: 459 Bit Score: 911.15 E-value: 0e+00

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1706 PGVNINRMSRLHPSPAYGAFPLKKQPAPLRRNDKRLQEGIDLDSQL*LKHGKGDMAEPWPGLEAAADLYFSTFPPSLPVF 1785
Cdd:cd23214     1 PGVNVNRKSRLGPSPAYGAFPVKKQPAPLTQKDDRLEDGIRLDDQLFLKHNKGDMDEPWPGLEAAADLYFSKFPTMIRTL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1786 SQEQAIMGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDEPEPGLFVPKPELQIEIDRTLENPDYVYSTFLKDELRPTAKVE 1865
Cdd:cd23214    81 TQEEAINGTPNLEGLDMNQAAGYPWNTMGRSRRSLFVEVQPGIYVPKPELQAEIDKTLEDPDYFYSTFLKDELRPTAKVT 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1866 QGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPGQHGCAVGCNPDVHWTEFFYKFSEFSQVYDLDYKCFDATLPSAAFSL 1945
Cdd:cd23214   161 LGLTRVVEAAPIHAIVAGRMLLGGLIEYMQARPGKHGSAVGCNPDLHWTKFFYKFCHYPQVFDLDYKCFDATLPSCAFRI 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1946 VATHLERLTGDPRVSRYINSIRHSHHIYGNQTYDMIGGNPSGCVATSILNTIINNICVLSALIQHPDFSPAKFQILAYGD 2025
Cdd:cd23214   241 VEDHLERLTGDERVTRYIESIRHSHHVYGNETYEMIGGNPSGCVGTSIINTIINNICVLSALIQHPDFSPESFRILAYGD 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 2026 DVIYATEPPIHPSYIREFYQRCTPLVVTPANKGQDFPETSTIYEVTFLKRWFVPDDRRPFYIHPVMDPDTYEQS*MWLRD 2105
Cdd:cd23214   321 DVIYGCDPPIHPSFIKEFYDKHTPLVVTPANKGSDFPETSTIYDVTFLKRWFVPDDIRPFYIHPVMDPDTYEQSVMWLRD 400

                         410       420       430
                  ....*....|....*....|....*....|....*.
gi 403044785 2106 GDFQDVVTSLCHLAFHSGPRTYERWCMKVREQCLKS 2141
Cdd:cd23214   401 GDFQDLVTSLCYLAFHSGPKTYDRWCTRVRDQVMKT 436

ps-ssRNA_Picornaviridae

cd23193

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

1790-2135

4.61e-158

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: 490.52 E-value: 4.61e-158

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1790 AIMGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDePEPGLFVPKPELQIEIDRTLENPDYVYSTFLKDELRPTAKVEQGLT 1869
Cdd:cd23193     1 AINGIDGLDPIDLNTSPGYPYTTQGLRRRDLID-NDKGGVSPLLEEEEQVLLDLDGPDVVFTTFLKDELRPKEKVKAGKT 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1870 RIVEAAPIHAIVAGRMLLGGLIDYMQGRPG-QHGCAVGCNPDVHWTEFFYKFsEFSQVYDLDYKCFDATLPSAAFSLVAT 1948
Cdd:cd23193    80 RVIEAAPLDYVIAGRMVFGRLFAQFHSNPGiLTGSAVGCNPDTDWTRLFASL-KQDNVYDLDYSGFDASLSSQLFEAAVE 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1949 HLERLTGDP-RVSRYINSIRHSHHIYGNQTYDMIGGNPSGCVATSILNTIINNICVLSALIQHPDFSPAKFQILAYGDDV 2027
Cdd:cd23193   159 VLAECHGDPeLVLRYLEPIINSKHVVGDERYTVEGGMPSGCPCTSILNSICNNLVVRYALLETGKFDPDEYYILAYGDDV 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 2028 IYATEPPIHPSYIREFYQRCTPLVVTPANKGQDFPETSTIYEVTFLKRWFVPDDRrpFYIHPVMDPDTYEQS*MWL-RDG 2106
Cdd:cd23193   239 LVSTDEPIDPSDLAEFYKKYFGMTVTPADKSSDFPESSPIEDVFLKRRFFVPDGT--FLIHPVMDLETLEQSLMWCgRGG 316

                         330       340
                  ....*....|....*....|....*....
gi 403044785 2107 DFQDVVTSLCHLAFHSGPRTYERWCMKVR 2135
Cdd:cd23193   317 FFQQLLSSLCELALHHGPEEYERLVSKVR 345

Passerivirus_RdRp

cd23224

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

1789-2143

8.66e-143

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Passerivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Passerivirus genus within the family Picornaviridae, order Picornavirales. The Passerivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. There are two species in this genus: Passerivirus A and a second, novel passerivirus (Passerivirus B) that was discovered in 2018 in a population of Hungarian home-reared finches, where it achieved an over 50 percent mortality rate. Birds serve as natural hosts. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438074 Cd Length: 380 Bit Score: 449.54 E-value: 8.66e-143

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1789 QAIMGTPNMEGLDMGQAAGFPWNTQgRSRRSLFDEPEPGLFVPKPELQIEIDRTLENPDYVYSTFLKDELRPTAKVEQGL 1868
Cdd:cd23224     1 EAINGTPLLDGLDMKQSPGYPWSLT-TNRRSLFTQDETGKYYPVPELEEAVLACLENPDYFYTTHLKDELRPVEKALAGK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1869 TRIVEAAPIHAIVAGRMLLGGLIDYMQGRPGQHGCAVGCNPDVHWTEFFYKFSEFSQVYDLDYKCFDATLPSAAFSLVAT 1948
Cdd:cd23224    80 TRLIEAAPIHAIIAGRMLLGGLFEYMHARPGEHGSAVGCDPDYHWTPFFHSFDEFSQVWALDYSCFDSTLPSCCFDLIAQ 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1949 HLERLT------GDPRVSRYINSIRHSHHIYGNQTYDMIGGNPSGCVATSILNTIINNICVLSALIQHPDFSPAKFQILA 2022
Cdd:cd23224   160 KLAKIItpgegiAPDAIVKYIRSISISKHVFGNEAYLMVGGNPSGCVGTSILNSMINNCVLISAFLTQKDFNPNQMRILT 239

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 2023 YGDDVIYATEPPIHPSYIREFYQRCTPLVVTPANKGQDFPETSTIYEVTFLKRWFVPDDRRPFYIHPVMDPDTYEQS*MW 2102
Cdd:cd23224   240 YGDDVLYATNPPIHPRVVKKFFDENTTLIVTPATKAGDFPDESTIWDVTFLKRYFVPDEIRPWYVHPVIEPATYEQSVMW 319

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|.
gi 403044785 2103 LRDGDFQDVVTSLCHLAFHSGPRTYERWCMKVREQCLKSGV 2143
Cdd:cd23224   320 TRGGDFQDVVTSLSFLAHHAGPTNYMIWEEKVRKAAAAKGV 360

Megrivirus_RdRp

cd23223

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

1721-2144

4.98e-137

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: 435.43 E-value: 4.98e-137

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1721 AYGAFPLKKQPAPLRRNDKRLQEGIDLDSQL*LKHGKGDmaEPWPGLEAAA---------DLYFSTFPPsLPVFSQEQAI 1791
Cdd:cd23223     1 AYGAFPVTHGPAALTNKDKRLEEGVDLDDVMFSKHVPDH--PGWPTLEPAMsyvvedlmhKLGFSKDEP-VPMWTLEQAI 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1792 MGTPNMEGLDMGQAAGFPWNTQGRSRRSLFdEPEPGLFVPKPELQIEIDRTLENP-DYVYSTFLKDELRPTAKVEQGLTR 1870
Cdd:cd23223    78 NGEGVMDGIDMGQSPGYPYNAQGRSRRSFF-EWNGEKWQPTEELKKEVDHALKDPdDFYFSTFLKDELRPLEKVKAGKTR 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1871 IVEAAPIHAIVAGRMLLGGLIDYMQGRPGQ--HGcAVGCNPDVHWTEFFYKFS--EFSQVYDLDYKCFDATLPSAAFSLV 1946
Cdd:cd23223   157 LVDGDSLPRILAMRMVFGPLFEAMLRKNGPeiHS-AVGCNPDTDWTRYYHEMGpdSFPYCFDLDYSCFDSTEPKIAFRLM 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1947 ATHLERLTGDPrVSRYINSIRHSHHIYGNQTYDMIGGNPSGCVATSILNTIINNICVLSALIQHpDFSPAKFQILAYGDD 2026
Cdd:cd23223   236 AKYLKPYFSVD-VTPFFEALATSKHVYGDKAYEMEGGMPSGCVGTSMFNCINNSAFIVSALIAL-KISPEDCAWICYGDD 313

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 2027 VIYATEPPIHPSYIREFYQRCTPLVVTPANKGQDFPETSTIYEVTFLKRWFVPDDRRPFYIHPVMDPDTYEQS*MWLRDG 2106
Cdd:cd23223   314 VIISTDEKALSKRIADFYHKNTNLVVTPASKSGDFPETSTIYDVTFLKRFFQPDSHYPHLIHPYMPLEHLEQSVMWQTDG 393

                         410       420       430
                  ....*....|....*....|....*....|....*...
gi 403044785 2107 DFQDVVTSLCHLAFHSGPRTYERWCMKVREQCLKSGVR 2144
Cdd:cd23223   394 PFQQKLDSLCLLAFHAGGPDYREFVDAIDKKCRSRGEE 431

Dicipivirus_RdRp

cd23222

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

1718-2143

5.14e-117

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: 379.32 E-value: 5.14e-117

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1718 PSPAYGAFPLKKQPAPLRRNDKRLQEGIDLDSQL*LKHGkGDMAEPWPGLEAAADLYFS---------TFPPSLPvfsqE 1788
Cdd:cd23222     2 PSPVYGVYPVTKEPAPLKPTDRRIDEGVDFNEPVFGKYG-ADMKEPFRNLDVGRDVVIArlkkvlpnkKFAPCTV----S 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1789 QAIMGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDEPEPGLFVPKPELQIEIDRTLENPD-YVYSTFLKDELRPTAKVEQG 1867
Cdd:cd23222    77 EALNGKDGLPKLDLKQASGYPYNLSAIKRKHLIESDKDGFLTATPKLLADIEESKKHPEkFPYTSFLKDELRSVKKVKAG 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1868 LTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPG-QHGCAVGCNPDVHWTEFFYKFSEFSQVYDLDYKCFDATLPSAAFSLV 1946
Cdd:cd23222   157 KTRVVEAGSLPVIVEGRMIFGNLFAYFNTHPGfETMAAVGCDPEVCWTDWYYKMREKAHTWDYDYTGFDGSIPSCSFDAL 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1947 ATHL-ERLTGDPRVSRYINSIRHSHHIYGNQTYDMIGGNPSGCVATSILNTIINNICVLSALIQ-HPDFSPAKFQILAYG 2024
Cdd:cd23222   237 ADLLcEFVENEDDVRRYISNIKNSYHAYDGNLYLIEGAMPSGCAGTSVFNCLINAMLCFSCFMDlEPEMDPFEPLLIAYG 316

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 2025 DDVIYATEPPIHPSYIREFYQRCTPLVVTPANKGQDFPETSTIYEVTFLKRWFVPDDRRPFyIHPVMDPDTYEQS*MWLR 2104
Cdd:cd23222   317 DDILVSSDHDLFPSRVSEWMKANTTFKITPADKGEIFNDDSDVSDVRFLKRLFVEDPVCEL-IHPVIETETLEPSLNWCH 395

                         410       420       430
                  ....*....|....*....|....*....|....*....
gi 403044785 2105 DGDFQDVVTSLCHLAFHSGPRTYERWCMKVREQCLKSGV 2143
Cdd:cd23222   396 EGEFETKVDAISMLAFHHGPEYYRDWCKKLTDICEERNI 434

Rosavirus_RdRp

cd23221

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

1790-2148

4.61e-103

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Rosavirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Rosavirus genus within the family Picornaviridae, order Picornavirales. The Rosavirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. This genus contains three species Rosavirus A, Rosavirus B and Rosavirus C found in rats. The name rosavirus is derived from rodent stool-associated picornavirus. Viral RNA was detected in fecal samples of humans and rodents [canyon mouse (Peromyscus crinitus), brown rat (Rattus norvegicus), black rat (R. rattus), Sikkim rat (R. andamanensis), chestnut white-bellied rat (Niviventer fulvescens)]. Eight genetic types are distinguished by means of phylogenetic analysis (Rosavirus A: 2 types; Rosavirus B: 2 types; Rosavirus C: 4 types). RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438071 Cd Length: 381 Bit Score: 336.12 E-value: 4.61e-103

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1790 AIMGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDEPEpGLFVPKPELQIEIDRTLENPDY-VYSTFLKDELRPTAKVEQGL 1868
Cdd:cd23221     1 AINGIDNMDGLDMNQSPGVPYVSEGVSRRSLFDCVD-GQWVPRERLASDIAQVSGDPSLgHFATFLKDELRSTEKVAAGK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1869 TRIVEAAPIHAIVAGRMLLGGLIDYMQGRPG-QHGCAVGCNPDVHWTEFFYKFSEFSQVYDLDYKCFDATLPSAAFSLVA 1947
Cdd:cd23221    80 TRVVEAGSLPHIIVGRKIFGNLFALFNSNPGfQTMCAVGCDPDVTWTELYHPLSAKTYVFDYDYSGFDGSVPSCCFDALA 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1948 THL-ERLTGDPRVSRYINSIRHSHHIYGNQTYDMIGGNPSGCVATSILNTIINNICVLSALIQ-HPDFSPAKFQILAYGD 2025
Cdd:cd23221   160 DLLaDFVEGEEDVRKYISSLKTSFHHYKGKLWRLDGAMPSGCCGTSVFNSLINAMLLFSAFSQiCPDFRASEPLLVAYGD 239

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 2026 DVIYATEPPIHPSYIREFYQRCTPLVVTPANKGQDFPETSTIYEVTFLKRWFVPDDRRPFYIHPVMDPDTYEQS*MWLRD 2105
Cdd:cd23221   240 DVLVGTDQPLFPSKVAEWVNSHTTFRITPADKGSVFNDESDIHSVQFLKRHFTPDPDFPALIHPTIDPDTYEQSVMWQRT 319

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|...
gi 403044785 2106 GDFQDVVTSLCHLAFHSGPRTYERWCMKVREQCLKSGVRSKFF 2148
Cdd:cd23221   320 GDFQETVNSLALLVFHRGPKSYSRWCESVTRKCVDGGYPPPFF 362

Mosavirus_RdRp

cd23225

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

1789-2128

2.30e-85

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: 285.27 E-value: 2.30e-85

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1789 QAIMGTPNMEGLDMGQAAGFPWNTQGRSRRSLFD---EPEPGLFVPKPELQIEIDRTL---ENPDYVysTFLKDELRPTA 1862
Cdd:cd23225     1 RAMNGDGISDAMDMTKAVGYPYCLDSIKRLDLVEikeTENGKVYLPTERLVEETEKFFtgeEKPKFV--TFLKDEVRSNE 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1863 KVEQGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPG-QHGCAVGCNPDVHWTEFFYKFSEfSQVYDLDYKCFDATLPSA 1941
Cdd:cd23225    79 KIKQGKTRIVDASPFPYAIAGRMVMQNFMSNMMRCNGtEVGSAVGCDPDTEWTRYFFELCD-RYVFDLDYKAFDSTHPTA 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1942 AFSLVATH--LERLTGDPRVSR-YINSIRHSHHIYGNQTYDMIGGNPSGCVATSILNTIINNICVLSALIQHPDFSPA-- 2016
Cdd:cd23225   158 MFNLLAERffTERNGFDQQAVRiFLNGLSDSDHVYEGKHFRIRGGLPSGCPCTSILNTVINNIIVRAAILGAYQIDTVdf 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 2017 -KFQILAYGDDVIYATEPPIHPSYIREFYQRCTPLVVTPANKGQDFPETSTIYEVTFLKRWFVPDDRRPFYIHPVMDPDT 2095
Cdd:cd23225   238 qKFRMLAYGDDVVYATPQPIKPQDLADWLHANTNYKVTPASKAGTFPEESTIWDVTFLKRSFKPDEDHGHLIRPVMAVGN 317

                         330       340       350
                  ....*....|....*....|....*....|...
gi 403044785 2096 YEQS*MWLRDGDFQDVVTSLCHLAFHSGPRTYE 2128
Cdd:cd23225   318 LKQMLSFMRPGTFPDKVRSVAGLAVHCGEEDYN 350

Aphthovirus_RdRp

cd23210

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

1708-2129

2.59e-84

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: 285.30 E-value: 2.59e-84

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1708 VNINRMSRLHPSPAYGAFPLKKQPAPLRRNDKRLQEGIDLDSQL*LKH-GKGDM-AEPWPGLEAAADLY----FSTFPPS 1781
Cdd:cd23210     6 VHVMRKTKLAPTVAHGVFNPEFGPAALSNKDPRLNEGVVLDEVIFSKHkGDTKMsAEDKALFRRCAADYasrlHSVLGTA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1782 LPVFSQEQAIMGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDEPEPGLfvpKPELQIEIDRTLE-NPDYVYSTFLKDELRP 1860
Cdd:cd23210    86 NAPLSIYEAIKGVDGLDAMEPDTAPGLPWALQGKRRGALIDFENGTV---GPEVEAALKLMEKrEYKFACQTFLKDEIRP 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1861 TAKVEQGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPG-QHGCAVGCNPDVHWTEFFYKFSEFSQVYDLDYKCFDATLP 1939
Cdd:cd23210   163 MEKVRAGKTRIVDVLPVEHILYTRMMIGRFCAQMHSNNGpQIGSAVGCNPDVDWQRFGTHFAQYRNVWDVDYSAFDANHC 242

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1940 SAAFSLVATHL--ERLTGDPRVSRYINSIRHSHHIYGNQTYDMIGGNPSGCVATSILNTIINNICVLSALIQH-PDFSPA 2016
Cdd:cd23210   243 SDAMNIMFEEVfrTEFGFHPNAEWILKTLVNTEHAYENKRITVEGGMPSGCSATSIINTILNNIYVLYALRRHyEGVELD 322

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 2017 KFQILAYGDDVIYATEPPIHpsyirefYQRCTPL------VVTPANKGQDFPETS-TIYEVTFLKRWFVPDDRRPFYiHP 2089
Cdd:cd23210   323 TYTMISYGDDIVVASDYDLD-------FEALKPHfkslgqTITPADKSDKGFVLGhSITDVTFLKRHFHMDYGTGFY-KP 394

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|
gi 403044785 2090 VMDPDTYEQS*MWLRDGDFQDVVTSLCHLAFHSGPRTYER 2129
Cdd:cd23210   395 VMASKTLEAILSFARRGTIQEKLISVAGLAVHSGPDEYRR 434

Enterovirus_RdRp

cd23213

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

1706-2135

1.63e-82

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: 279.80 E-value: 1.63e-82

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1706 PGVNINRMSRLHPSPAYGAFPLKKQPAPLRRNDKRLQegIDLDSQL*LKHGKGDMAEPWPGLEAAADLY---FSTFPPSL 1782
Cdd:cd23213     7 PNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLK--VDFEEAIFSKYVGNTITEVDEYMKEAVDHYagqLATLDIDT 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1783 PVFSQEQAIMGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDEPEPGLfvpkPELQIEIDRTleNPDYVYSTFLKDELRPTA 1862
Cdd:cd23213    85 EQMSLEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDT----SKMKKYLDKY--GLDLPMVTYVKDELRSKD 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1863 KVEQGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPGQ-HGCAVGCNPDVHWTEFFYKFSEfsQVYDLDYKCFDATLPSA 1941
Cdd:cd23213   159 KVEKGKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVvTGSAVGCDPDTFWSKIPILLDG--SLFAFDYTGYDASLSPV 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1942 AFSLVATHLERLTGDPRVSrYINSIRHSHHIYGNQTYDMIGGNPSGCVATSILNTIINNICVLSALI---QHPDFSpaKF 2018
Cdd:cd23213   237 WFRALKMVLEKGYSEEAVS-LIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLktyKGIDLD--EL 313

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 2019 QILAYGDDVIYATEPPIHPSYIREFYQRcTPLVVTPANKGQDFPETsTIYEVTFLKRWFVPDDRRPFYIHPVMDPDTYEQ 2098
Cdd:cd23213   314 KMIAYGDDVIASYPHPIDCSLLARTGKE-YGLTMTPADKSPCFNEV-NWENVTFLKRGFRADEQYPFLIHPVMPMKEIHE 391

                         410       420       430
                  ....*....|....*....|....*....|....*...
gi 403044785 2099 S*MWLRDG-DFQDVVTSLCHLAFHSGPRTYERWCMKVR 2135
Cdd:cd23213   392 SIRWTKDPrNTQDHVRSLCLLAWHNGEEEYEKFVSKIR 429

Mischivirus_RdRp

cd23227

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

1706-2128

2.32e-82

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: 279.91 E-value: 2.32e-82

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1706 PGVNINRMSRLHPSPAYGAFPLKKQPAPLRRNDKRLQEGIDLDSQL*LKHGKGDMAEPWPGLEAA---ADLYFSTFPPSL 1782
Cdd:cd23227    10 PRIHVPRKTKLRKSPAYPIFKPDAGPAVLSKNDPRLAEGVDFDKQVFSKHSANQKEYPKAFRRMArwyADRVFTYLGKDN 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1783 PVFSQEQAIMGTPNMEGLDMGQAAGFPWNTQGRSRRSL--FDEPEpglfVPKPELQIEIDRTLEN--PDYVYSTFLKDEL 1858
Cdd:cd23227    90 GPLSVKDAIKGIDNLDAMDPTTSPGLPYSAAGIKRTDLldFDTGE----IISPALRAEYNKYVSGdySDHVFQTFLKDEI 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1859 RPTAKVEQGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPG-QHGCAVGCNPDVHWTEFFYKFSEFSQVYDLDYKCFDAT 1937
Cdd:cd23227   166 RSEEKIKAGKTRIVDVPSLAHVIIGRVLLGKFCSKFQASPGtELGSAIGCNPDWDWTYFAHQLMERQWCYDIDYSNFDST 245

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1938 LPSAAFSLVATHL--ERLTGDPRVSRYINSIRHSHHIYGNQTYDMIGGNPSGCVATSILNTIINNICVLSAL-IQHPDFS 2014
Cdd:cd23227   246 HGTGMFELLIDCFftPENGFSPAVAPYLRSLAFSKHAWMDKRYKIEGGLPSGCSATSVLNTVMNNIIIRALLsLTYKNFH 325

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 2015 PAKFQILAYGDDVIYATEPPIHPSYIREFYQRCTPLVVTPANKGQDFPETSTIYEVTFLKRWFVPDDRRPFYIHPVMDPD 2094
Cdd:cd23227   326 PEDVLVLAYGDDLLVASDYQLDFNRVREKAAEHTLYKLTTANKAPDFPETSTLLDCQFLKRKFVLHSTRNFIWRPVMDVT 405

                         410       420       430
                  ....*....|....*....|....*....|....
gi 403044785 2095 TYEQS*MWLRDGDFQDVVTSLCHLAFHSGPRTYE 2128
Cdd:cd23227   406 NLKTMLSFYKPNTLSEKLLSVAQLAFHSGYTVYE 439

Cardiovirus_RdRp

cd23211

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

1699-2136

1.01e-77

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: 266.32 E-value: 1.01e-77

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1699 VPTGEVkpgVNINRMSRLHPSPAYGAFPLKKQPAPLRRNDKRLQEgiDLDSQL*LKHgKGDMAEPWPGLEAAADLY---- 1774
Cdd:cd23211     6 IGTGPV---VHVPRKTKLRRTVAHPVFQPKFEPAVLSKYDPRTDK--DVDEVAFSKH-TTNQESLPPVFRMVAKEYanrv 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1775 FSTFPPSLPVFSQEQAIMGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDEpEPGLFVPKPElqiEIDRTLENPDY---VYS 1851
Cdd:cd23211    80 FTLLGKDNGRLTVEQAVLGLEGMDPMEKDTSPGLPYTQQGLRRTDVVDF-ETATMIPFLA---EAHRKMVEGDYsdvVYQ 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1852 TFLKDELRPTAKVEQGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPG-QHGCAVGCNPDVHWTEFFYKFSEFSQVYDLD 1930
Cdd:cd23211   156 SFLKDEIRPIEKVQAAKTRIVDVPPFEHCILGRQLLGRFASKFQTNPGlELGSAIGCDPDVDWTAFAVALSGFKYVYDVD 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1931 YKCFDATLPSAAFSLVATHL--ERLTGDPRVSRYINSIRHSHHIYGNQTYDMIGGNPSGCVATSILNTIINNICVLSAL- 2007
Cdd:cd23211   236 YSNFDSTHSTAMFELLIENFftEENGFDPRIGEYLRSLAVSRHAYEERRVLIRGGLPSGCAATSMLNTIMNNIIIRAGLy 315

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 2008 IQHPDFSPAKFQILAYGDDVIYATEPPIHPSYIREFYQRcTPLVVTPANKGQDFPETSTIYEVTFLKRWFVPDDrrPFYI 2087
Cdd:cd23211   316 LTYKNFEFDDIKVLSYGDDLLVATNYQIDFNLVKARLAK-FGYKITPANKTSTFPLTSTLEDVVFLKRKFVKEN--SYLY 392

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....*....
gi 403044785 2088 HPVMDPDTYEQS*MWLRDGDFQDVVTSLCHLAFHSGPRTYERWCMKVRE 2136
Cdd:cd23211   393 RPVMDRENLKAMLSYYRPGTLKEKLTSIALLAVHSGKQVYDEIFAPFRE 441

Cosavirus_RdRp

cd23226

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

1706-2146

1.64e-70

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: 245.31 E-value: 1.64e-70

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1706 PGVNINRMSRLHPSPA-YGAFPlKKQPAPLRRNDKRLQEGIDLDSQL*LKHGKGDMAEP----WPGLEAAADLYFSTFP- 1779
Cdd:cd23226    10 PRVHVPRQSKLKRTNAtYPATG-KYGPAVLSKNDPRLDPDVDFDKVIFSKHVANVVIDEdtsfWNALKMSAQIYAEKFKg 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1780 PSLPVFSQEQAIMGTPNMEGLDMGQAAGFPWNtqgRSRRSLFDEPEPGLFvpKPELQIEIDRTLEN--PDYVYSTFLKDE 1857
Cdd:cd23226    89 VDFSPLTVEEAILGIPGLDRMDPNTASGLPYT---KTRRQMIDFQEGKIL--DPELQERLDTWLSGkqPEMLYQTFLKDE 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1858 LRPTAKVEQGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPG-QHGCAVGCNPDVHWTEFFYKFSEFSQVYDLDYKCFDA 1936
Cdd:cd23226   164 IRPIEKVKAGKTRIIDVTPLDHVLAFRIVLGRFMAHFHNNYGfELGSAVGCDPDVAWANFGFALSSKKYQYDFDYSNFDA 243

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1937 TLPSAAFSLVATHL--ERLTGDPRVSRYINSIRHSHHIYGNQTYDMIGGNPSGCVATSILNTIINNICVLSALIQ-HPDF 2013
Cdd:cd23226   244 SHSESIFELLKQFVftKDNGFDHRCSLMIDSLVTSTHCYEDQRMTIRGGLPSGTSGTSVINTIINNIIFKAALYHtYSNF 323

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 2014 SPAKFQILAYGDDVIYATEPPIHPSYIREFYQRCTpLVVTPANKGQDF-PEtsTIYEVTFLKRWFVpddRRPFYIHPVMD 2092
Cdd:cd23226   324 EWDDVQMLAYGDDIVAASDCLLDLDRVKYFMALIG-YKITPADKGEKFiPK--DMQNIQFLKRSFR---KVAGVWAPIMD 397

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....
gi 403044785 2093 PDTYEQS*MWLRDGDFQDVVTSLCHLAFHSGPRTYErwcmKVREQCLKSGVRSK 2146
Cdd:cd23226   398 LENLQAMLSWYKPGTLQEKLDSVARLAHFCGEKVYD----HLFTTFVKDGFQIK 447

Sapelovirus_RdRp

cd23218

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

1791-2135

3.10e-70

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: 240.96 E-value: 3.10e-70

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1791 IMGTPNMEGLDMGQAAGFPWNTQGRSRRSLFdePEPGlfVPKPELQIEIDrtLENPDYVYSTFLKDELRPTAKVEQGLTR 1870
Cdd:cd23218     3 VYGIDNLEGLDLNTSAGYPYNTMGIRKKDLI--PPRG--EPLSPLLKALD--LHGYDLPFTTYLKDELRPKEKVKMGKTR 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1871 IVEAAPIHAIVAGRMLLGGLIDYMQGRPGQH-GCAVGCNPDVHWTEFFYKFSeFSQVYDLDYKCFDATLPSAAFSLVATH 1949
Cdd:cd23218    77 LIECSSLNDTIRMKRIFGRLFQTFHKNPGTYtGSAVGCNPDVHWSKFAEEGG-MDNVCAFDYTNWDASLSPFWFDALKLF 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1950 LERLTGDPRVSRYINSIRHSHHIYGNQTYDMIGGNPSGCVATSILNTIINNICVLSALIQ-HPDFSPAKFQILAYGDDVI 2028
Cdd:cd23218   156 LSKLGYSERDIVLIDHLCYSNHIFKNEGYKVAGGMPSGCSGTSIFNSIINNIVVRTLVLLvYKGINLDELRILCYGDDLL 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 2029 YATEPPIHPSYIREFYQRCTpLVVTPANKGQDFPETSTIYEVTFLKRWFVPDDRRPFYIHPVMDPDTYEQS*MWLRDGDF 2108
Cdd:cd23218   236 VAYPYPLDPNVLADLGKSLG-LTMTPADKSDTFQGCTKLTEVTFLKRSFVFDEEFPFLCHPVFPMEEVHESIRWTRNAST 314

                         330       340
                  ....*....|....*....|....*...
gi 403044785 2109 -QDVVTSLCHLAFHSGPRTYERWCMKVR 2135
Cdd:cd23218   315 tQEHVTSLCLLAWHNGEEVYEEFCEKIR 342

Rabovirus_RdRp

cd23230

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

1790-2135

3.14e-67

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: 232.08 E-value: 3.14e-67

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1790 AIMGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDepepglfvPKPELQIEIDRTLE--NPDYVYSTFLKDELRPTAKVEQG 1867
Cdd:cd23230     1 AAYGIENLEGLDLNTSAGYPYVLNGIKKRDILD--------PETRDTTKLQECLDkyGVDLPFVTYLKDELRPLEKIKKG 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1868 LTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPGQH-GCAVGCNPDVHWTEFFYKFSefSQVYDLDYKCFDATLPSAAFSLV 1946
Cdd:cd23230    73 KTRLIECSSMNDTIRMKMMFGRLFATYHRNPGPItGSAVGCNPDIHWTKFRAEMH--GEIIAFDYSNYDASLNKVWFECL 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1947 ATHLERLTGDPRvsRYINSIRHSHHIYGNQTYDMIGGNPSGCVATSILNTIINNICVLSALIQ-HPDFSPAKFQILAYGD 2025
Cdd:cd23230   151 KMVLKNFGFKDL--RPIDHIIRSRHIYKGIEYDVEGGMPSGCSGTSIFNSIINNIIIMTLVLDaYKGIDLEQLKIIAYGD 228

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 2026 DVIYATEPPIHPSYIREFYQRcTPLVVTPANKGQDFpETSTIYEVTFLKRWFVPDDRRPFYIHPVMDPDTYEQS*MWLRD 2105
Cdd:cd23230   229 DVIVTYPYPLDAALLADCGKK-YGLKMTPPDKSAEF-KNVTWEDVTFLKRRFKPAKHYPFLIHPVFDQQEILESLRWTRN 306

                         330       340       350
                  ....*....|....*....|....*....|.
gi 403044785 2106 -GDFQDVVTSLCHLAFHSGPRTYERWCMKVR 2135
Cdd:cd23230   307 pAHTQEHVRSLAELAWHSGRKSYEEFCNLVK 337

RNA_dep_RNAP

cd01699

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

1835-2103

7.19e-67

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: 227.94 E-value: 7.19e-67

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1835 LQIEIDRTLENPDYVYSTFLKDELRPTAKVEQGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPGQHGCAVGCNPDV-HW 1913
Cdd:cd01699     5 VESLEDLPLIRPDLVFTTFLKDELRPLEKVEAGKTRLIQPRPLDYNIALRMYLGPFEAKLMKNRGGLPIAVGINPYSrDW 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1914 TEFFYKFSEFSQV-YDLDYKCFDATLPSAAFSLVATHLERLTGDPRVSR---YINSIRHS-HHIYGNQTYDMIGGNPSGC 1988
Cdd:cd01699    85 TILANKLRSFSPVaIALDYSRFDSSLSPQLLEAEHSIYNALYDDDDELErrnLLRSLTNNsLHIGFNEVYKVRGGRPSGD 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1989 VATSILNTIINNICVLSALIQH-PDFSPAKFQILAYGDDVIYATEP---PIHPSYIREFYQRCTpLVVTPANKgqDFPET 2064
Cdd:cd01699   165 PLTSIGNSIINCILVRYAFRKLgGKSFFKNVRLLNYGDDCLLSVEKaddKFNLETLAEWLKEYG-LTMTDEDK--VESPF 241

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 403044785 2065 STIYEVTFLKRWFVPDDrrPFYIHPVMDPDTYEQS*MWL 2103
Cdd:cd01699   242 RPLEEVEFLKRRFVLDE--GGGWRAPLDPSSILSKLSWS 278

ps-ssRNAv-Picornavirales

cd23169

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

1849-2135

4.82e-59

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: 206.68 E-value: 4.82e-59

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1849 VYSTFLKDELRPTAKVEQGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPGQHGCAVGCNPDVH-WTEFFYKFSEFS-QV 1926
Cdd:cd23169     2 IFVDCLKDELRPIEKVKAGKTRLFSASPLDYTIAFRKYFGDFIAAFQKNRIKLEHAVGINPDSVeWTRLYRRLLKKGpNI 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1927 YDLDYKCFDATLPSAAFSLVATHLERLT------GDPRV-SRYINSIRHSHHIYGNQTYDMIGGNPSGCVATSILNTIIN 1999
Cdd:cd23169    82 FAGDYSNFDGSLPPDVMEAAFDIINDWYdeyvddEDERVrKVLFEELINTIHLVGNLVYQVHGGNPSGNPLTTIINSIVN 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 2000 NI---CVLSALIQHPDFSPAK--FQILAYGDDVIYAteppIHPSYIREFYQR-------CTPLVVTPANKGQDFPETSTI 2067
Cdd:cd23169   162 LLyirYAWLRITGLTSLSDFKknVRLVTYGDDVIIS----VSDEVKDEFNFVtiseflkELGITYTDADKSGDIVPYRPL 237

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 403044785 2068 YEVTFLKRWFVPDDrRPFYIHPVMDPDTYEQS*MWLRDGdfQDVVTSLCH-------LAFHSGPRTYERWCMKVR 2135
Cdd:cd23169   238 EEVTFLKRGFRPHP-TPGLVLAPLDLESIEEQLNWTRKE--DDLLEATIEnaraallLAFGHGPEYYNKFRQKLN 309

Teschovirus_RdRp

cd23212

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

1779-2136

1.59e-55

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

Pssm-ID: 438062 Cd Length: 354 Bit Score: 198.30 E-value: 1.59e-55

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1779 PPSLPVFSQEQAIMGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDePEPGlfvPKPELQIEIDRTLE-NPD-YVYSTFLKD 1856
Cdd:cd23212     5 PDFLEPLSVREAVEGIDGLDPMDMDKSPGLPYVKKGLRRTDLWN-PKTG---PSIELMAEINRYLDyNYDkHVFLTFLKD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1857 ELRPTAKVEQGLTRIVEAAPI-HAIVaGRMLLGGLIDYMQGRPGQH-GCAVGCNPDVHWTEFFYKfSEFSQVYDLDYKCF 1934
Cdd:cd23212    81 ELRPKEKVQAGKTRVIDVAGFgHAIV-GRMLFGRLFAFFHKNPGWNtGSAVGVNPDLAWTQIFYT-APSRNVLAMDYSGF 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1935 DATLPSAAFSLVATHLERLTGDPRVSRYINSIRHSHHIYGNQTYDMIGGNPSGCVATSILNTIINNICVLSALIQHPDfs 2014
Cdd:cd23212   159 DASHTSGMFCILKHFLTTLGYGTLQLSYIDSLCYSKHHWDDETYRLDGGLPSGCSGTTIFNTIMNNIVARAAASYAAE-- 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 2015 pAKFQILAYGDDVIYATEPPIHPSYIREFYQRcTPLVVTPANKGQDFpETSTIYEVTFLKRWFVPDDRrpfYIHPVMDPD 2094
Cdd:cd23212   237 -GPVGILCYGDDILVSSPEKFPVSDWLEFYSK-TPYKVTAADKSEQI-DWRDITQCTFLKRGFVLDGS---LVRPVMEEQ 310

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|..
gi 403044785 2095 TYEQS*MWLRDGDFQDVVTSLCHLAFHSGPRTYERWCMKVRE 2136
Cdd:cd23212   311 HLAELLKWARPGTLQAKLLSIAQLAFHLPRQAYDRLMLPFEE 352

RdRP_1

pfam00680

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

1717-2129

1.61e-53

Pssm-ID: 425815 Cd Length: 450 Bit Score: 195.32 E-value: 1.61e-53

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  1717 HPSPAYGAFPLKKQPAPLRRNDKRLQE-----GIDLDSQL*LKHGKGDMAEPWPG---LEAAADLYFSTF----PPSLPV 1784
Cdd:pfam00680    1 SPTERHLVAIPAYVPASLGPEDPRWARsylntDPYVDDIKKYSRPKLPGPADERDkllNRSAAKMVLSELrgvpKKANST 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  1785 FSQEQAIMGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDEPEPGLFVPKPELQIEIDRTLENP----DYVYSTFLKDELRP 1860
Cdd:pfam00680   81 LIVYRAIDGVEQIDPLNWDTSAGYPYVGLGGKKGDLIEHLKDGTEARELAERLAADWEVLQNgtplKLVYQTCLKDELRP 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  1861 TAKVEQGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPGQHGCAVGCNP-DVHWTEFFYKFSEFSQ-VYDLDYKCFDATL 1938
Cdd:pfam00680  161 LEKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHPIQVGINPfDRGWPRLLRRLARFGDyVYELDYSGFDSSV 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  1939 PSAAFSLVATHLERLTG-DPRVSRYINS----IRHSHHIYGNQTYDMIGGNPSGCVATSILNTIINNICVLSALI----- 2008
Cdd:pfam00680  241 PPWLIRFAFEILRELLGfPSNVKEWRAIlellIYTPIALPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYALLkslen 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  2009 QHPD--FSPAKFQILAYGDDVIYATEPPIHPSYIReFYQ--RCTPLVVTPANKgqDFPETSTIYEVTFLKRWFVpddRRP 2084
Cdd:pfam00680  321 DGPRvcNLDKYFDFFTYGDDSLVAVSPDFDPVLDR-LSPhlKELGLTITPAKK--TFPVSRELEEVSFLKRTFR---KTP 394

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|....*.
gi 403044785  2085 FYIHPVMDPDTYEQS*MWLRDGD-FQDVVTSLCHLAFHSGPRTYER 2129
Cdd:pfam00680  395 GGYRPPLDRKRILAQLEYIRSKPvPSGQLENIRAYASHHGYEFYRD 440

Fipivirus_RdRp

cd23229

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

1791-2146

4.71e-52

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: 189.25 E-value: 4.71e-52

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1791 IMGTPNMEGLDMGQAAGFPWNTQGRSRR---SLFDEPEPGLFVPKPELQIEIDRTLE-----NPDYVYSTFLKDELRPTA 1862
Cdd:cd23229     2 VEGIPGMEGLDMKTSAGYPWCEQNQKKKdkiKLLAGKNFLVRPLREVVHIVVDWYIMppdmpKPEIKYVVYLKDELLSSD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1863 KVEQGLTRIVEAAPIHAIVAGRMLLGGLIDYMQ------GRPgqHGCAVGCNPDVHWTEFFYKFSEFsQVYDLDYKCFDA 1936
Cdd:cd23229    82 KVKMGRTRWICAAPVQLVCAWKKVFGRAIAAIHlesvtdGKS--TGCAVGMDPETAWTDIALARPGW-PVIALDYSNFDG 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1937 TLPS----AAFSLVAtHLERLTgDPRVSRYINSIRHSHHIYGNQTYDMIGGNPSGCVATSILNTIINNICVLSALIQHPD 2012
Cdd:cd23229   159 SLQSfvitGAVRILG-YIAGLP-DGQSYRLAEFVYDVKQIVGKYLYTTVGPLPSGCPSTSIIGSLCNVLMLLYTLSHATG 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 2013 FSPAKFQ----ILAYGDDVIYATEPPIhpSYIREFYQRCTPLV----VTPANKGQDFPETSTIYEVTFLKRWFVPDDRRP 2084
Cdd:cd23229   237 QRYSAFRdwmhVVTYGDDVLVFVHPEV--VVVLDTLAHEMYLVfgvtATDATDKRAPPQLRELSNVTFLKRGFRQCSSVP 314

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 403044785 2085 FYIHPVMDPDTYEQS*MWLRDG-DFQDVVTSLCHLAFHSGPRTYERWCMKVREQCLKSGVRSK 2146
Cdd:cd23229   315 FLVHPTMDKSTIYQMLAWKRKGtTLAENVKCAAEFMMHHGEEEYEDFVGVVKECSTLIGVDQR 377

Hepatovirus_RdRp

cd23215

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

1785-2140

3.17e-45

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

Pssm-ID: 438065 Cd Length: 464 Bit Score: 171.57 E-value: 3.17e-45

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1785 FSQEQAIMGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDEPEPGLFV---PKPELQIEIDRTL-ENP---DYVYSTFLKDE 1857
Cdd:cd23215    65 FDLEQAITGVPGMDAINMDSSPGYPYVQEKLTKSDLIWLDDNGELLgmhPRLAQRILFNLTMmDNGndlDVVYTTCPKDE 144

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1858 LRPTAKVEQGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPGQH-GCAVGCNPDVHWTEFFYKFSEFSQV-YDLDYKCFD 1935
Cdd:cd23215   145 LRPLEKVLESKTRAIDACPLDFTIICRMFWGPAISYFQLNPGFHtGVAVGIDPDRDWDALFKTMIRFGDYgIDLDFSSFD 224

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1936 ATLPSAAFSLVATHLERLTGDP--RVSRYINSIRHSHHIYGNQTYDMIGGNPSGCVATSILNTIINNI---CVLSALI-Q 2009
Cdd:cd23215   225 ASLSPFMIREACRVLSELSGVPdhQGQALINTIIYSKHLLYNLCYHVCGSMPSGSPCTSLLNSIVNNVnlyYVFSKIFkK 304

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 2010 HPDFSPAKFQILAYGDDVIYATEPPIHPSYIREFYQRCTP------LVVTPANKGQdfPETSTIYEVTFLKRWF-VPDDR 2082
Cdd:cd23215   305 SPVFFYDAVKFLCYGDDVLIVFSRDLEIKNLDKLGQRIQDefkllgMTATSADKGE--PQVVPVSELTFLKRSFnLIEDR 382

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 403044785 2083 rpfyIHPVMDPDTYEQS*MWLRDG-DFQDVVTSLCHLAFHSGPRTYERWCMKVrEQCLK 2140
Cdd:cd23215   383 ----FRPAISEKTIWSLVAWQRSNaEFEQNLDTACWFAFMHGYDFYQNFYLQL-QSCLE 436

Dicistroviridae_RdRp

cd23194

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

1846-2135

7.20e-44

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: 163.05 E-value: 7.20e-44

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1846 PDYVYSTFLKDELRPTAKVEQGLTRIVEAAPIHAIVAGRMLLGGLIDY-MQGRPgQHGCAVGCNP---DvhWTEFFYKFS 1921
Cdd:cd23194     4 LPHVFVDTLKDERRPIEKVDAGKTRVFSAGPMDYTIAFRMYFLGFVAHlMRNRI-DNEIAVGTNVyslD--WDKLARKLL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1922 EFSQ-VYDLDYKCFDATLPSAAFSLVATHLERLTGDP----RVsRYI--NSIRHSHHIYGNQTYDMIGGNPSGCVATSIL 1994
Cdd:cd23194    81 SKGDkVIAGDFSNFDGSLNPQILWAILDIINEWYDDGeenaLI-RRVlwEDIVNSVHICGGYVYQWTHSQPSGNPLTAII 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1995 NTIINNI-CVLSALIQHPDFSPA-------KFQILAYGDDVIYAteppIHPSYIREFYQRCTP-------LVVTPANKGQ 2059
Cdd:cd23194   160 NSIYNSIiMRYVYLLLTKEAGLMtmsdfnkHVSMVSYGDDNVIN----VSDEVSEWFNQLTITeamaeigMTYTDETKTG 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 2060 DFPETSTIYEVTFLKRWFVPDDRRPFYIHPvMDPDTYEQS*MWLR-----DGDFQDVV-TSLCHLAFHsGPRTYERWCMK 2133
Cdd:cd23194   236 EIVPYRSLEEVSFLKRGFRYDDDLGRWVAP-LDLDTILEMPNWVRkgkdpEEITKQNVeNALRELSLH-GEEVFDKWAPK 313


                  ..
gi 403044785 2134 VR 2135
Cdd:cd23194   314 IR 315

RNA_helicase

pfam00910

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

1175-1277

2.45e-40

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

Pssm-ID: 459992 Cd Length: 102 Bit Score: 145.05 E-value: 2.45e-40

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  1175 VYFYGPPGTGKSLLASLLAQTLAQRISGNPDDVYSPTAAScEYFDGYTGQAVHFIDDIGQDPEGRDWANFPNLVSSAPYI 1254
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKKLGLPKDSVYSRNPDD-DFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYP 79

                           90       100
                   ....*....|....*....|...
gi 403044785  1255 LPMASLEEKGTHYTSRVIVITSN 1277
Cdd:pfam00910   80 PPMAALEEKGTPFTSKFVIVTSN 102

Kunsagivirus_RdRp

cd23219

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

1834-2129

2.39e-34

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: 136.15 E-value: 2.39e-34

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1834 ELQIEIDRTlENPDYVYSTFLKDELRPTAKVEQGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGR-PGQHGCAVGCNPdvh 1912
Cdd:cd23219    48 ELQFRGTSG-GAGEVKFSSFLKDELRPLSKIRSGDTRVVECSSLDYTVAFRMQFLRVLQMCYGSdPTLTGLAPGMNV--- 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1913 WTEFFYKFSE-FSQVYDLDYKCFDATLPSAAFSLVATHLERLTGDPRVS-RYINSIRHSHHIYGNQTYDMIGGNPSGCVA 1990
Cdd:cd23219   124 YTDMLPLCTSlYDYNLCLDFSKYDSRLPLQVMHRVAQLISNLTPDPQVSmRLFQPIIISTHIVGSYEVVVEGGMPSGCPI 203

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1991 TSILNTIINNI-CVLSALIQHPDfspAKFQILAYGDDVIYATEPPIHPSYIREFYQRCTPLVVTPANKGQDFPETSTIyE 2069
Cdd:cd23219   204 TTIMNSVCNVVmTSYAMLLLDPD---SDFWPVAYGDDNIVSTRKPIDTELFCSILNEEFGMILTGADKTTTVQAVPPM-S 279

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 403044785 2070 VTFLKR--WFVPDDRRPFyihPVMDPDTYEQS*MWLR-DGDFQDVVTSLCH-LAFHsGPRTYER 2129
Cdd:cd23219   280 VDFLKRrlRYTPEFPLPV---PVLPLDSMLSRICWCKgETEFKDQLESFSYeLALY-GQEVYER 339

rhv_like

cd00205

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

318-490

3.48e-33

Pssm-ID: 119412 Cd Length: 178 Bit Score: 127.51 E-value: 3.48e-33

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  318 EFAHRPGLMASLNWTmADQPGERLAIIPVSPSA--IAGTGAPISYVLSLFSQWRGELAAHLLFTGSAQHYCRLVVCYTP- 394
Cdd:cd00205     3 SFADRPTTVGTNNWN-SSASGTQLFQWKLSPALgfLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPp 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  395 --AAPSPPSTMQQAMRGTYTVWDINAASTLEFTIPFISQSYWKTVDINNPDAlLSTTGYLSVWVQNPLTGPNTAPAGATI 472
Cdd:cd00205    82 gaPAPTTGDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDGYGP-LNSFGTLVVRVLTPLTVPSGAPTTVDI 160

                         170
                  ....*....|....*...
gi 403044785  473 QGFLSASDsFNVRLMQNP 490
Cdd:cd00205   161 TVYVRAGD-FELYGPRPP 177

Parechovirus_RdRp

cd23217

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

1790-2130

6.74e-33

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: 132.68 E-value: 6.74e-33

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1790 AIMGTPNMEGLDMGQAAGFPWNTQGRSRRSLFD-EPepglFVPKPELQIEIDRTL------ENPDYVYSTFLKDELRPTA 1862
Cdd:cd23217     1 AVLGTSHLNSLDLSTSPGYKYVKSGYKKRDLLSlEP----FSVSPQLEKDVKDKLhavykgNQPTTIFNACLKDELRKLD 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1863 KVEQGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPGQH-GCAVGCNPDVHWTEFFYKFSEFSqvYDLDYKCFDATLPSA 1941
Cdd:cd23217    77 KIAQGKTRCIEACSIDYVIAYRVVMSSLYEAIYQTPCQElGLAVGMNPWTDWDFMINALNPYN--YGLDYSSYDGSLSEM 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1942 AFSLVATHLERLTGDPRVSRYINS-IRHSHHIYGNQTYDMIGGNPSGCVATSILNTIIN-NICVLSALIQHPDFspaKFQ 2019
Cdd:cd23217   155 LMWEAVEVLAYCHESPDLVMQLHKpVINSDHVVMDERWLVHGGMPSGSPCTTVLNSICNlLVCIYLAYLQSPGI---ECL 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 2020 ILAYGDDVIYATEPPIHPSYIREFYQRCTPLVVTPANKGQDfPETSTIYEVTFLKRW--FVPDDRrpfYIHPVMDPDTYE 2097
Cdd:cd23217   232 PIVYGDDVIFSVSSEIDPEYLVSSAADSFGMEVTGSDKDEP-PSLLPRMEVEFLKRTtgYFPGST---YKVGALDLETME 307

                         330       340       350
                  ....*....|....*....|....*....|....*
gi 403044785 2098 QS*MWLRD-GDF-QDVVTSLCHLAFHsGPRTYERW 2130
Cdd:cd23217   308 QHIMWMKNlSTFpQQLQSFENELCLH-GKDIYDDY 341

rhv_like

cd00205

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

130-268

7.83e-33

Pssm-ID: 119412 Cd Length: 178 Bit Score: 126.36 E-value: 7.83e-33

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  130 PFSFVRAYPDSPWAAMYDTHSMWNCGWRVQVTVNGSQFHAGALVLYMIPEGTTKAVETARLNSGFVYPYVILNLYESNTA 209
Cdd:cd00205    32 PALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPPGAPAPTTGDTRWQATLNPHVIWDLGTNSSV 111

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 403044785  210 TVEVPYISPTP------NTTSGLHAPWTFYLQVLTPLSPPTGLPTSLSCSIYVTPVDTTFHGLRY 268
Cdd:cd00205   112 TFVVPYVSPTPyrstryDGYGPLNSFGTLVVRVLTPLTVPSGAPTTVDITVYVRAGDFELYGPRP 176

Crohivirus_RdRp

cd23232

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

1788-2154

1.16e-30

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: 126.37 E-value: 1.16e-30

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1788 EQAIMGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDEPEPGL--FVPKPELQIEID-RTLENPDYVYSTFLKDELRPTAKV 1864
Cdd:cd23232     2 EEACFEEGDEHALDLKTSPGFKYVQMGLKKTDLVNRPNKFIhpILRNDVRLIFDEmAKGQMPVVTFTAHLKDELRKLEKI 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1865 EQGLTRIVEAAPIHAIVAGRMLLGGLIDYM-QGRPGQHGCAVGCNPDVHWTEFFYKFSEFSqvYDLDYKCFDATLPSAAF 1943
Cdd:cd23232    82 RSGKTRCIEACDFDYTVAHKMMFGTLYKAIyDTPGIITGLAVGMNPWKDWELIQQSLFKYN--YDFDYKTFDGSLSRELM 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1944 SLVATHLERLTGDPRVSRYI--NSIrHSHHIYGNQTYDMIGGNPSGCVATSILNTIINNICVLSALIQHPDfspAKFQIL 2021
Cdd:cd23232   160 LHAVDILSACVENDEMAKLMlsVVV-ESVHLVLDQKWNVSGGMPSGSPCTTVLNSVCNLIVSSTIADMCTE---GDFKIL 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 2022 AYGDDVIYATEPPIHPSYIREFYQRCTPLVVTPANKGQDFpETSTIYEVTFLKRwfvpdDRRPF----YIHPVMDPDTYE 2097
Cdd:cd23232   236 VYGDDLIISSTAPLDCDRFKTLVELHYGMEVTPGDKGDEF-KVKDREQVSFLKR-----VTRKFpgtnYRVGALDLDTVK 309

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 403044785 2098 QS*MWLRD-GDFQDVVTSLCHLAFHSGPRTYERWCMKVREqclksgVRSKFFFHIPTF 2154
Cdd:cd23232   310 QHLMWCKSySSFKQQLDSALMEVAMHGEETYNGFLTEIKT------KLDKFKIYPPKF 361

Caliciviridae_RdRp

cd23192

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

1849-2131

6.47e-30

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

Pssm-ID: 438042 Cd Length: 310 Bit Score: 122.37 E-value: 6.47e-30

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1849 VYSTFLKDELRPTAKVEQGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPGQHGCAVGCNPD-VHWTEFFYKFSEFSQVY 1927
Cdd:cd23192     2 AYALALKDELRPVEKIAEGKRRLLWGCDVGVTLVAAAAFGPVADALKAVCPTGPIAVGINMDsEDVEVIFERLSGFRYHY 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1928 DLDYKCFDATLPSAAFSLVATHLERLTGDPRVSRYINSIRHSHHI--YGNQTYDMIGGNPSGCVATSILNTIINNICVLS 2005
Cdd:cd23192    82 CLDYSKWDSTQSPAVTAAAIDILADLSEETPLRDSVVETLSSPPMgiFDDVIFVTKRGLPSGMPFTSVINSLNHWLLFSA 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 2006 ALIQHPD---------FSPAKFqiLAYGDDVIYATEPPIH---PSYI---REFyqrctPLVVTPANKGQ--DFPETSTIy 2068
Cdd:cd23192   162 AVLKAYElvgiytgnvFDEADF--FTYGDDGVYAMPPATAsvmDEIIenlKSY-----GLKPTAADKTEnpDIPPLQGP- 233

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 403044785 2069 evTFLKRWFVPDDRRpfyIHPVMDPDTYEQS*MWLRDGDFQDVVTS---------------LCHLAFHSGPRTYERWC 2131
Cdd:cd23192   234 --VFLKRTFVRTPGG---WRALLDRSSILRQLYWVKGPNTHDWTEPpteidheartvqlenVLLEAAQHGPEFYEKVL 306

Limnipivirus_RdRp

cd23228

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

1834-2137

5.67e-29

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Limnipivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Limnipivirus genus within the family Picornaviridae, order Picornavirales. The Limnipivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. This genus contains three species, Limnipivirus A (bluegill picornavirus 1), Limnipivirus B (carp picornavirus 1) and Limnipivirus C (fathead minnow picornavirus 1). Limnipiviruses infect freshwater fishes. The virus can be grown in various fish cell lines. Experimental infection of bluegills with bluegill picornavirus induces morbidity (inflammation and redness at the base of fins, exophthalmia, abdomen distension, internal hemorrhaging and ascites) and mortality. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438078 Cd Length: 390 Bit Score: 121.52 E-value: 5.67e-29

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1834 ELQIEIDRTLENPDYVYSTFLKDELRPTAKVEQGLTRIVEAAPIHAIVAGRMLLGGLI-DYMQGRPGQHGCAVGCNPDVH 1912
Cdd:cd23228    50 EAWEELIQSGGYPTTLFTACLKDELRSDEKVALGKTRVIEAAELDYVVAYRMYMSSIYsDLYNAYAGDTGIAAGINPPAD 129

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1913 WTEFFYKFSEFSQVYDLDYKCFDATLPSAAFSLVATHLERLTGDP-RVSRYINSIRHSHHIYGNQTYDMIGGNPSGCVAT 1991
Cdd:cd23228   130 GHRLREELSQYDSFLALDYSRFDGSLPEMLMRAAVEILADLHEDPdLVRRLHETVIISKHLVVDEDWTVKGGMPSGSPCT 209

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1992 SILNTIINNICVLSALIQHPDFSPAKFQ---------ILAYGDDVIYATEPPIHPSYIREFYQRCTPLVVTPANKGQDFP 2062
Cdd:cd23228   210 TVLNCICNLLVLEYAFLVHFGVYEDDDGvglpqcdylSVVYGDDCIVAYNGMEMGLAFAETIEDTFGMEVTPASKVGDHF 289

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 2063 ETStIYEVTFLKRWF-----VPDDRrpfyIHPVMDPDTYEQS*MWLRD-GDFQDVVTSLCHLAFHSGPRTYERWCMKVRE 2136
Cdd:cd23228   290 NVE-LHEVEFLKRKFfafetEEYDR----IALRLSENTIVQSLMWMRNlKTFPDQVQSLMMELSAWGKEKYDKLRDTCKR 364


                  .
gi 403044785 2137 Q 2137
Cdd:cd23228   365 R 365

Avisivirus_RdRp

cd23231

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

1800-2128

4.41e-24

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: 106.51 E-value: 4.41e-24

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1800 LDMGQAAGFPWntQGRSRRSLFDEPEPGLFVPKPeLQIEIDRTLENPDYVYSTFLKDELRPTAKVEQGLTRIVEAAPIHA 1879
Cdd:cd23231    11 IDWGTSPGDKY--KGKTKAQLVDDKKFKADVMNL-VRFNGDPNREPPDVYFTTYLKDELRPKEKAKAGKTRVISAASFDY 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1880 IVAGRMLLGGLIDYMQGRPGQHGCAVGCNPDVHWTEFFYKFSEFsqVYDLDYKCFDATLPSAAFSLVATHLERLTGDPR- 1958
Cdd:cd23231    88 TIACRMVFGPILRQLFAWGREFGFGPGLNPYTHFDELYDKILPF--VICLDYSGFDGSLSSELMFHAAQVIACFSEKPEa 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1959 VSRYINSIRHSHHIYGNQTYDMIGGNPSGCVATSILNTIINNI-CVLSALIQHPDFSpaKFQILAYGDDVIYATEPPIHP 2037
Cdd:cd23231   166 IMASAELTIGSTERVSDEVWYVYGGMPSGSPWTTTLNTICNLLmCYTYLLDMGHCWS--ETFVVAYGDDVVISANIKHNL 243

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 2038 SYIREFYQRCTPLVVTPANKGQDFPETsTIYEVTFLKRWFVPDDRRPfYIHPVMDPDTYEQS*MWLRdGDFQDVVTSL-C 2116
Cdd:cd23231   244 EGIEQWFKTKFGATVTPSDKQGKITWT-TKNNMEFLKRRPKQLDFLP-KIVGALDLDNMLDRIQWTK-GHFQDQLNSFyL 320

                         330
                  ....*....|..
gi 403044785 2117 HLAFHsGPRTYE 2128
Cdd:cd23231   321 ELALH-GRETYN 331

Aalivirus_RdRp

cd23216

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

1829-2141

2.75e-23

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: 103.59 E-value: 2.75e-23

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1829 FVPKPELQIEIDRTLENPDYVYSTFLKDELRPTAKVEQGLTRIVEAAPIHAIVAGRMLLGGLIDYM-QGRPGQHGCAVGC 1907
Cdd:cd23216    30 LVQDPKFKEDVKEILAGKPTFFTTYLKDELRSIEKIANGNTRAIEAANFDHVVAWRQVMGNIVKQLfSDHDRVTGFAPGM 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1908 NPDVHWTEFFYKFSefSQVYDLDYKCFDATLPSAAFSLVATHLERLTGDPRVSRYINS-IRHSHHIYGNQTYDMIGGNPS 1986
Cdd:cd23216   110 NPYTHFDSLMDQVK--WNVLALDFKKFDGSLSPQVMEEAVDILASFHDMPQMVVDIHKhTIYSTNVVSDETWFVEGGMCS 187

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1987 GCVATSILNTIInNICVLSALIQHPDFSPAKFQILAYGDDVI-----YATEPPiHPSYIREFYQRCTPLVVTPANKGqDF 2061
Cdd:cd23216   188 GSPCTTVLNTIC-NLLVNTTILLSEGIQPDNFYIAAYGDDTIisvdgLSSSLP-DPKIMQQKYKEWFGMTVTSADKG-SE 264

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 2062 PETSTIYEVTFLKR--WFVPDDRRpfyIHPVMDPDTYEQS*MWLRdGDFQDVVTSLCHLAFHSGPRTYerwcMKVReQCL 2139
Cdd:cd23216   265 ITWDTRNHVQFLKRrpGFFPGTQK---VVGVLDLESMMEHIAWTK-GSFQDQLNSFYQELVLHGEQVY----MTVR-QTL 335


                  ..
gi 403044785 2140 KS 2141
Cdd:cd23216   336 KS 337

rhv_like

cd00205

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

538-723

1.16e-21

Pssm-ID: 119412 Cd Length: 178 Bit Score: 94.39 E-value: 1.16e-21

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  538 LENFFSFYRLLPLSTTGPtlPLPLTDAAQVPLDPIHWLQNADVSGLAAMLSCFTYIAADLRFTLRVANPNGLPVSLIVAF 617
Cdd:cd00205     1 VESFADRPTTVGTNNWNS--SASGTQLFQWKLSPALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAY 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  618 APPGATIPSK-PDRQALSNFFMSEVPISASSStlVSFSIPYTSPLSAIPTSYFGWedWSGTNFGRLHAGSWGTLLFLPSL 696
Cdd:cd00205    79 VPPGAPAPTTgDTRWQATLNPHVIWDLGTNSS--VTFVVPYVSPTPYRSTRYDGY--GPLNSFGTLVVRVLTPLTVPSGA 154

                         170       180
                  ....*....|....*....|....*..
gi 403044785  697 PSQgaalldLSLTCWLAFGNFKAWVPR 723
Cdd:cd00205   155 PTT------VDITVYVRAGDFELYGPR 175

Marnaviridae_RdRp

cd23195

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

1849-2135

3.63e-21

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: 96.75 E-value: 3.63e-21

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1849 VYSTFLKDElrPTaKVEQGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPGQHGCAVGCN---PDvhWTEFFYKFSEFS- 1924
Cdd:cd23195     2 IFKACLKDE--PT-KLTKDKVRVFQAAPVALQLLVRKYFLPIARFLQMNPLLSECAVGINaqsPE--WEELYEHLTKFGe 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1925 -QVYDLDYKCFDATLPS----AAFSLVATHLERLTG----DPRVSRYI-NSIRHSHHIYGNQTYDMIGGNPSGCVATSIL 1994
Cdd:cd23195    77 dRIIAGDYSKYDKRMSAqlilAAFKILIDIAAKSGGyseeDLKIMRGIaTDIAYPLVDFNGDLIQFFGSNPSGHPLTVII 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1995 NTIINNICVLSA-LIQHPDFSPAKFQ----ILAYGDDVIYATEPPIHP---SYIREFYQRCTpLVVTPANKGQDFPETST 2066
Cdd:cd23195   157 NSIVNSLYMRYAyYSLYPEKEVPPFRdvvaLMTYGDDNIMSVSPGYPWfnhTSIAEFLAKIG-IKYTMADKEAESVPFIH 235

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 403044785 2067 IYEVTFLKRWFVPDDRRPFYIHPVmDPDTYEQS-*MWLRDGD------FQDVVTSLCHLAFHSGPRTYERWCMKVR 2135
Cdd:cd23195   236 ISEADFLKRKFVFDPELGVYVGPL-DEDSIFKSlHCYLKSKVltpeeqAAQNIDGALREWFFHGREVYEKRREQLK 310

Aquamavirus_RdRp

cd23220

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

1814-2090

2.61e-20

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Aquamavirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Aquamavirus genus within the family Picornaviridae, order Picornavirales. The Aquamavirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. Aquamavirus is a genus containing a single species, Aquamavirus A. This species consists of the previously named seal picornavirus 1, now to be called seal aquamavirus A1. Recently other aquamaviruses have been discovered in bears and seals (unassigned aquamaviruses). RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438070 Cd Length: 338 Bit Score: 94.77 E-value: 2.61e-20

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1814 GRSRRSLFDEPEPGLFVPKPELQIEIDRTLENpdYVYSTFLKDELRPTAKVEQGLTRIVEAAPIHAIVAGRM-LLGGLID 1892
Cdd:cd23220    24 GMNRRQLLLPLNPQVRDDVVKLAGDVGNGTAT--VVFETFMKDELRPKEKIESGKTRIVESCPLDYLLLYRMvMLKSMIW 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1893 YMQGRPGQHGCAVGCNPDVHWTEFFYKFSEFSqvYDLDYKCFDATLPSaafSLVATHLERLTGDPRVSRYINSIRH---- 1968
Cdd:cd23220   102 WYNSDCIKTGVAPGMNVYTDFVPMVKQFKKIK--YCLDFSAYDSTLSD---EILAAGVEVLACTSAVPSYVRKLHApiic 176

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1969 SHHIYGNQTYDMIGGNPSGCVATSILNTIINNICV--LSAL--IQHPdfspakfQILAYGDDVIYATEPPIHPSYIREFY 2044
Cdd:cd23220   177 SHHWHNNVVDLVLGGMPSGAPCTSVLNSIVNVLMAryICALmdIDYP-------VMVAYGDDNVVSFDEEIDIERMVSLY 249

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 403044785 2045 QrcTPLVVTPANKGQDfPETSTIYEVTFLKRW--FVPDDRRPFYIHPV 2090
Cdd:cd23220   250 K--TEFGVTATNHDKT-PVPRPMANPVFLKRRlrFNPDLNIQFPVLPL 294

Rhv

pfam00073

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

149-240

2.07e-13

Pssm-ID: 395026 Cd Length: 170 Bit Score: 70.42 E-value: 2.07e-13

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785   149 HSMWNCGWRVQVTVNGSQFHAGALVLYMIPEGTTKAVETARLNSGFVYPYVILNLYESNTATVEVPYISPTP--NTTSgl 226
Cdd:pfam00073   77 HTYYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRDYLWQATLNPHQFWNLGLNSSARLSVPYISIAHyySTFY-- 154

                           90
                   ....*....|....
gi 403044785   227 HAPWTFYLQVLTPL 240
Cdd:pfam00073  155 DGNWTLVVAGWVPL 168

Nora-virus_RdRp

cd23200

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

1851-2081

2.09e-13

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

Pssm-ID: 438050 Cd Length: 306 Bit Score: 73.42 E-value: 2.09e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1851 STFLKDELRPTAKVEQGLTRIVEAAPIHAIVAGRMLLGGLID--YMQGRPGQHgcAVGCNP-DVHWTEFFYKFSEFSQVY 1927
Cdd:cd23200     4 SSKLKDQPIKIAQAKSGRTRVFHCIPVDLILFSGALYGPYKEayTKAGLKCYH--AVGIDPkSVGWQQLATYMTKHPNYF 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1928 DLDYKCFDATLPSAAFSLVATHLERLTGDPRVSRYINSiRH-------SHHIYGNQT-YDMIGGNPSGCVATSILNTIIN 1999
Cdd:cd23200    82 DADYKNYDKYLHRQVFKAVRKIQRSVIQQVCPDKWDKA-RAveeldaiDTYVVDYQTvYKTNRGNKSGSYTTTIDNCLAN 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 2000 NICVLSA------LIQHPDFSpAKFQILAYGDDVIYATEPPIHPSYIREFYQRC---TPLVVTPANKGQDFPETSTIYEV 2070
Cdd:cd23200   161 DIYGLYAwvkttgLRSLWDYR-QNVSSVAFGDDIIKSVSDEYKDKYNYCTYRDVlnaTGHIMTPGSKDGEEKPFTSFENL 239

                         250
                  ....*....|.
gi 403044785 2071 TFLKRWFVPDD 2081
Cdd:cd23200   240 QFLKRGFKLEN 250

Iflaviridae_RdRp

cd23197

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

1846-2130

2.44e-13

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: 73.36 E-value: 2.44e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1846 PDYVYSTFLKDELRPTAKVEQ-GLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPGQHGCAVGCNPD-VHWTEFFYKFSEF 1923
Cdd:cd23197     4 PPCVYWAHLKDELRPSEKLRRfGGTRVFSVPPLELVLNSRRFLLPFMDAFQSFPIEAHHAIGLNPNsGDWRRLRDTLLEK 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1924 SQ-VYDLDYKCFDATLP----SAAFSLVATHLER---LTgdPRVSRYINSIRH-----SHHIYGnQTYDMIGGNPSGCVA 1990
Cdd:cd23197    84 GPcLLQMDYKNYSDAIPkecvAKAFHIIVDYYRKwhcLT--VEIENALKTLFLdtadaELLVYG-DVFKVNNGVLAGHPM 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1991 TSILNTIINNICVLSALIQHPDFSPAKF----QILAYGDDVIYATEPPIHPSY-----IREFYQrcTPLVVTPANK---G 2058
Cdd:cd23197   161 TSVVNSVVNLILMNYMWIKITRRRASEFfkltYIIVMGDDVVISLPKQLTEEFdcrkiCAEFAK--YDIKVTDSEKnltG 238

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 403044785 2059 QDFPETStIYEVTFLKRWFVPDDRRPF-YIHPVmDPDTYEQS*MWL-RDGDF-----QDVVTSLcHLAFHSGPRTYERW 2130
Cdd:cd23197   239 EPKPYDS-FDKFEFLSRGFSDCDAYPDiTFAPV-KTIALFDCPLWIsKGQDEeeqtiQAIQAGL-LLAFDHGPEFFGKY 314

Secoviridae_RdRp

cd23196

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

1854-2078

4.36e-13

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

Pssm-ID: 438046 Cd Length: 309 Bit Score: 72.42 E-value: 4.36e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1854 LKDELRPTAKV-EQGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPGQHGCAVGCNP-DVHWTEFFYKFSEFSQV-YDLD 1930
Cdd:cd23196     7 PKDERLKKRKVlEKPKTRLFDVLPMEYNLLLRKYFLNFVRFIQANRHRLPCQVGINPySREWTTLYDRLAEKSDTaLNCD 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1931 YKCFDATLPSAAFSLVATHLERLTGDPRVSRYINSI------RHShhIYGNQTYDMIGGNPSGCVATSILNTIINNI--- 2001
Cdd:cd23196    87 YSRFDGLLSHQVYVWIADMINRLYGDGDEAKARRNLlmmfcgRRS--ICGRQVYMVRGGMPSGCALTVIINSIFNEIlir 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 2002 -----CVLSALIQHPDfspAKFQILAYGDDVIYATEPPIHPSY----IREFYQRCTPLVVTPANKGQDFPETSTIYEVTF 2072
Cdd:cd23196   165 yvyrkVVPRPARNNFN---KYVRLVVYGDDNLISVKEEIIPYFdgpvIKKEMAKVGVTITDGTDKTSPTLERKPLESLDF 241


                  ....*.
gi 403044785 2073 LKRWFV 2078
Cdd:cd23196   242 LKRGFR 247

Solinviviridae_RdRp

cd23199

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

1903-2077

1.33e-12

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: 71.23 E-value: 1.33e-12

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1903 CAVGCNPDVHWTEFFYKFSEFSQVYDLDYKCFDATLPSAAFSLVATHLERLTG--DPRVSRYINSIRHSHHIYGNQTYDM 1980
Cdd:cd23199    71 CAVGCNPYATFHKFATKFFKFKNFFSCDYKNFDRTIPKCVFEDFRDMLIQANPhmKNEIYACFQTIIDRIQVSGNSILLV 150

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1981 IGGNPSGCVATSILNTIINNICVLSALI-----------QHPDFSPAKFQILAYGDDVIYATEppihpSYIREFYQRCT- 2048
Cdd:cd23199   151 HGGMPSGCVPTAPLNSKVNDIMIYTAYVnilrradrgdiTSYRYYRDLVCRLFYGDDVIIAVD-----DSIADIFNCQTl 225

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 403044785 2049 --------PLVVTPANKGQDFPETSTIYEVTFLKRWF 2077
Cdd:cd23199   226 seemkilfGMNMTDGSKSDIIPKFETIETLSFISRFF 262

Polycipiviridae_RdRp

cd23198

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

1853-2137

4.40e-10

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

Pssm-ID: 438048 Cd Length: 317 Bit Score: 63.59 E-value: 4.40e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1853 FLKDELRPTAKV---EQG--LTRIVEAAPIHAIVAGRMLLGGLIDYM-QGRPGQHGCAVGCNPD-VHWTEFFYKFSEFSQ 1925
Cdd:cd23198     6 FPKDELRPIYKAlgdPQTppKTRSVTCMNVYYILAWRRVTLDFWASMhRAADGNFPFCPGINPEgPDWNRLYHYLNRHPN 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1926 VYDLDYKCFDATLPSAAFSLVATHLERLTG-DP--RVSRYINSIR----HSHHIYGNQTYDMIGGNPSGCVATSILNT-- 1996
Cdd:cd23198    86 AVDFDVSNWDGHLPAELFYAVLDIIKTVLGlKPnsPNAKVIYSILtevmNCHIQFEDIIYQKLRGLISGFPGTAEVNTla 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1997 ---IINNICVLSALIQHPDFSPAKF----QILAYGDDVIYATEPPIHPSY----IREFYQRcTPLVVTPANKGQDFPETS 2065
Cdd:cd23198   166 hwlLIYYIYLYLAQNTIYDMTITAFlrnvSAIFYGDDIIITISDEILHWFngktIQRMYEE-HGYPVTSAAKDTEIPESK 244

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 403044785 2066 TIYEVTFLKRWFVPddRRPFYIHPVMDPDTYEQS*MWLRDGD------FQDVVTSLcHLAFHSGPRTYErwcmKVREQ 2137
Cdd:cd23198   245 PLSDCQFLKSSWNP--ILPGYYIRKMDIEVVYDLVYWVRAKEhprdqfYSNYHDAL-RILFGHGEQVFE----AFREQ 315

ps-ssRNAv_Astroviridae_RdRp

cd23172

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

1847-2044

1.19e-08

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

Pssm-ID: 438022 Cd Length: 243 Bit Score: 57.87 E-value: 1.19e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1847 DYVYSTFLKDELRPTAKVEQGLTR-IVEAAPIHAIVAGRmllgglIDY-----MQGRPGQHGCAVGcnpdvhWTEFFYKF 1920
Cdd:cd23172     1 RPLWYLFLKKEILKKEKIEDGDIRqILCPDPIFARIGAR------FEQdqnnlMKERTLTNEGQVG------WSPFYGGF 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1921 --------SEFSQVYDLDYKCFDATLPSAAFSLVathlerltgdpRVSRYIN-SIRHSH---HIYGNQTYDMI------- 1981
Cdd:cd23172    69 darvrrlgSKGNYFVEFDWTRFDGTIPAELFRHI-----------RKLRWSFlDPEKTEenrKVYDWYVHNLLnryvllp 137

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1982 --------GGNPSGCVATSILNTIINNIcvLSALIQ---HPDFSP------AKFQILAYGDDVI--YATEPPIHPSYIRE 2042
Cdd:cd23172   138 tgevtrvtKGNPSGQISTTMDNCMVNTF--LTAFEFayvYGPKTGtlkelwDNYDTIVYGDDRLsgYPSLPDPYVERVVD 215


                  ..
gi 403044785 2043 FY 2044
Cdd:cd23172   216 MY 217

Rhv

pfam00073

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

362-456

1.24e-08

Pssm-ID: 395026 Cd Length: 170 Bit Score: 56.55 E-value: 1.24e-08

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785   362 LSLFSQWRGELAAHLLFTGSAQHYCRLVVCYTPAAPSPPSTMQ---QAMRGTYTVWDINAASTLEFTIPFISQ-SYWKTV 437
Cdd:pfam00073   74 LRYHTYYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRDylwQATLNPHQFWNLGLNSSARLSVPYISIaHYYSTF 153

                           90
                   ....*....|....*....
gi 403044785   438 DINNPDalLSTTGYLSVWV 456
Cdd:pfam00073  154 YDGNWT--LVVAGWVPLNY 170

Peptidase_C3

pfam00548

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

1514-1669

4.81e-08

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

Pssm-ID: 278947 Cd Length: 174 Bit Score: 54.76 E-value: 4.81e-08

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  1514 ISNNVVHVESGNGleKNVMSGFYLFSRILIVPTHLrEPHHTRLLVG---TDSyDWATLQCQEFG---ELMAIHTSTSRQY 1587
Cdd:pfam00548   11 LKQNAVPVTTSKG--VFTCCATGVYDNVILLPRHA-EPGLTIVLDGkvvTIS-DPEVELVDQEGmplDAAIVKLKRNEKF 86

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  1588 KDMRRFI--GAHPYPTG-LLVSQFKAAPLYVRISD----NRIVNLD---FPGVVVcpqaygYRAATF*SLCGSPLVTDDP 1657
Cdd:pfam00548   87 KDIRKHLpnRITKGNPVvLLINNNEQGRIYVPVGAvthsGGIKTLDgttTPRTIS------YNAPTKAGMCGGVVIAKVE 160

                          170
                   ....*....|..
gi 403044785  1658 SGVKILGLHVAG 1669
Cdd:pfam00548  161 GNGKILGMHIAG 172

ps-ssRNAv_EoPV-like_RdRp

cd23171

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

1846-2081

6.32e-08

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

Pssm-ID: 438021 Cd Length: 239 Bit Score: 55.68 E-value: 6.32e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1846 PDYVYSTFLKDELRPTAKVeqglTRIVEAAPIHAIVAGRMLLGGLIDYMQGRpgQHGCAVGCnpDVHWTEFFYKFSEFSQ 1925
Cdd:cd23171    12 PPTTFMDFPKDELLKPGKD----TRLINGAPLHHTLDMRRYLMEFFAAITTI--NNKIAVGI--DVHSGDWALIHGGADD 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1926 VYDLDYKCFDATLPSAAFSLVA------THLERlTGDPR----VSRYINSIRHSHHIYGNQTYDMIGGNPSGCVATSILN 1995
Cdd:cd23171    84 VVDEDYSGFGPGFHSQWLDVIRriavawCKHHK-TVDPEyenvVRCLIRELQNAYHVAGDLVYQVLCGSPSGAFATDRIN 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1996 TIIN----NICVLSALIQHPDFspAKFQILAYGDDVIYAteppiHPSYIREFYQRCTP---LVVTPANKGQDfpetstiy 2068
Cdd:cd23171   163 SLANlcyhCLCYLRKYGTLTGF--WSHYLLVYGDDTRRR-----ETAYTGDEFQDCMAsigITVNRDKSGVT-------- 227

                         250
                  ....*....|...
gi 403044785 2069 evTFLKRWFVPDD 2081
Cdd:cd23171   228 --SFLKRQFIPYD 238

AAA

cd00009

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

1160-1299

1.47e-06

Pssm-ID: 99707 [Multi-domain] Cd Length: 151 Bit Score: 49.84 E-value: 1.47e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1160 KHRKRQVGPRPEPVVVYFYGPPGTGKSLLASLLAQTLAQR----ISGNPDDVYSPTAASCEYFDGYTGQAVH-------- 1227
Cdd:cd00009     7 IEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPgapfLYLNASDLLEGLVVAELFGHFLVRLLFElaekakpg 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 403044785 1228 --FIDDIGQDPEGRDWANFPNlvssapyilpMASLEEKGTHYTSRVIVITSNFHEPNERAARSMGALKRRVHLR 1299
Cdd:cd00009    87 vlFIDEIDSLSRGAQNALLRV----------LETLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRIVIP 150

ps-ssRNAv_RdRp-like

cd23167

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

1926-2032

4.07e-06

Pssm-ID: 438017 [Multi-domain] Cd Length: 73 Bit Score: 46.56 E-value: 4.07e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785 1926 VYDLDYKCFDATLPSAAFSLvathlerltgdprvsryinsirhshhiygnqtydmigGNPSGCVATSILNTIINNICVLS 2005
Cdd:cd23167     2 VVESDYSGFDSSISPDLLKA-------------------------------------GQPSGSPNTSADNSLINLLLARL 44

                          90       100
                  ....*....|....*....|....*....
gi 403044785 2006 ALIQHPDFSPAK--FQILAYGDDVIYATE 2032
Cdd:cd23167    45 ALRKACGRAEFLnsVGILVYGDDSLVSVP 73

SpoVK

COG0464

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

1149-1196

1.75e-04

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

Pssm-ID: 440232 [Multi-domain] Cd Length: 397 Bit Score: 46.44 E-value: 1.75e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 403044785 1149 QALRNYTLALSKH-RKRQVGPRPEPVVVYFYGPPGTGKSLLASLLAQTL 1196
Cdd:COG0464   167 EELRELVALPLKRpELREEYGLPPPRGLLLYGPPGTGKTLLARALAGEL 215

AAA

pfam00004

ATPase family associated with various cellular activities (AAA); AAA family proteins often ...

1175-1196

2.43e-04

ATPase family associated with various cellular activities (AAA); AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes.

Pssm-ID: 459627 [Multi-domain] Cd Length: 130 Bit Score: 42.97 E-value: 2.43e-04

                           10        20
                   ....*....|....*....|..
gi 403044785  1175 VYFYGPPGTGKSLLASLLAQTL 1196
Cdd:pfam00004    1 LLLYGPPGTGKTTLAKAVAKEL 22

RecA-like_protease

cd19481

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

1151-1196

4.47e-04

Pssm-ID: 410889 [Multi-domain] Cd Length: 158 Bit Score: 43.04 E-value: 4.47e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 403044785 1151 LRNYTLALSKHRKRQVGPRPEPVVVYFYGPPGTGKSLLASLLAQTL 1196
Cdd:cd19481     5 LREAVEAPRRGSRLRRYGLGLPKGILLYGPPGTGKTLLAKALAGEL 50

AAA

smart00382

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...

1174-1299

1.72e-03

Pssm-ID: 214640 [Multi-domain] Cd Length: 148 Bit Score: 41.20 E-value: 1.72e-03

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785   1174 VVYFYGPPGTGKSLLASLLAQTLAQR----ISGNPDDVYSPTAASCEYFDGYTGQAVH---------------------F 1228
Cdd:smart00382    4 VILIVGPPGSGKTTLARALARELGPPgggvIYIDGEDILEEVLDQLLLIIVGGKKASGsgelrlrlalalarklkpdvlI 83

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 403044785   1229 IDDIG--QDPEGRDWANFpnlvssapyILPMASLEEKGTHYTSRVIVITSNFHEPNERAARSMgaLKRRVHLR 1299
Cdd:smart00382   84 LDEITslLDAEQEALLLL---------LEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRRR--FDRRIVLL 145

Rhv

pfam00073

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

529-668

5.71e-03

Pssm-ID: 395026 Cd Length: 170 Bit Score: 39.99 E-value: 5.71e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785   529 ENPTPPDTRLENFFsfyrLLPLSTTGPT--------LPLPLTDAAQvpldpihwlqnadvsgLAAMLSCFTYIAADLRFT 600
Cdd:pfam00073   28 DAPVQPDVQGERFY----TLDSTDWTSLskgffwwkLPLALLSMGL----------------LGRLLRYHTYYRGGLEVT 87

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 403044785   601 LrVANPNGLPV-SLIVAFAPPGATIPSKPDRQALSNFFMSeVPISASSSTLVSFSIPYTSPLSAIPTSY 668
Cdd:pfam00073   88 V-QFNGSKFHQgKLLVAYVPPGAPPPGSRDYLWQATLNPH-QFWNLGLNSSARLSVPYISIAHYYSTFY 154

RecA-like_CDC48_NLV2_r1-like

cd19503

first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...

1164-1209

6.41e-03

first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and p97 or VCP metazoans is an ATP-dependent molecular chaperone which plays an essential role in many cellular processes, by segregating polyubiquitinated proteins from complexes or membranes. Cdc48/p97 consists of an N-terminal domain and two ATPase domains; this subfamily represents the first of the two ATPase domains. This subfamily also includes the first of the two ATPase domains of NVL (nuclear VCP-like protein) 2, an isoform of NVL mainly present in the nucleolus, which is involved in ribosome biogenesis, in telomerase assembly and the regulation of telomerase activity, and in pre-rRNA processing. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

Pssm-ID: 410911 [Multi-domain] Cd Length: 165 Bit Score: 39.58 E-value: 6.41e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 403044785 1164 RQVGPRPePVVVYFYGPPGTGKSLLASLLAQTL-AQRISGNPDDVYS 1209
Cdd:cd19503    27 RALGLKP-PRGVLLHGPPGTGKTLLARAVANEAgANFLSISGPSIVS 72

AAA_16

pfam13191

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

1169-1245

6.73e-03

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

Pssm-ID: 433025 [Multi-domain] Cd Length: 167 Bit Score: 39.79 E-value: 6.73e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403044785  1169 RPEPVVVYFYGPPGTGKSLLASLLAQTLAQR----ISGNPDDvYSPTAASCEYFDgytgqAVHFIDDIGQDPEGRDWANF 1244
Cdd:pfam13191   21 SGRPPSVLLTGEAGTGKTTLLRELLRALERDggyfLRGKCDE-NLPYSPLLEALT-----REGLLRQLLDELESSLLEAW 94


                   .
gi 403044785  1245 P 1245
Cdd:pfam13191   95 R 95

PRK13342

recombination factor protein RarA; Reviewed

1177-1196

7.80e-03

recombination factor protein RarA; Reviewed

Pssm-ID: 237355 [Multi-domain] Cd Length: 413 Bit Score: 41.22 E-value: 7.80e-03

                          10        20
                  ....*....|....*....|
gi 403044785 1177 FYGPPGTGKSLLASLLAQTL 1196
Cdd:PRK13342   41 LWGPPGTGKTTLARIIAGAT 60

ps-ssRNAv_Potyviridae_RdRp

cd23175

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

1849-1886

8.63e-03

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

Pssm-ID: 438025 Cd Length: 236 Bit Score: 40.12 E-value: 8.63e-03

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 403044785 1849 VYSTFLKDELRPTAKVEQGLTRIVEAAPIHAIVAGRML 1886
Cdd:cd23175     5 VWNGSLKAELRPIEKVEANKTRTFTAAPIDTLLGGKVC 42

RarA

COG2256

Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...

1177-1196

9.22e-03

Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, recombination and repair];

Pssm-ID: 441857 [Multi-domain] Cd Length: 439 Bit Score: 40.81 E-value: 9.22e-03

                          10        20
                  ....*....|....*....|
gi 403044785 1177 FYGPPGTGKSLLASLLAQTL 1196
Cdd:COG2256    54 LWGPPGTGKTTLARLIANAT 73

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