NCBI Conserved Domain Search

Conserved domains on [gi|2347425630|gb|UZV41926|]

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MAG: polyprotein [Feline kobuvirus]

Protein Classification

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List of domain hits

Name

Accession

Description

Interval

E-value

Kobuvirus_RdRp

cd23214

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

1980-2437

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: 969.31 E-value: 0e+00

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 1980 PGVNINRQSRLKPSPAYGAFPIKKEPAPLKRNDRRLNDGVDLDTQLFLKHGKGDQSEPWPGLEAAADLYFSTFPSSLPVL 2059
Cdd:cd23214      1 PGVNVNRKSRLGPSPAYGAFPVKKQPAPLTQKDDRLEDGIRLDDQLFLKHNKGDMDEPWPGLEAAADLYFSKFPTMIRTL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2060 TQEQAIHGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDEPEPGVYTPKPELQALIDQTLENPDYVYSTFLKDELRPTAKVQ 2139
Cdd:cd23214     81 TQEEAINGTPNLEGLDMNQAAGYPWNTMGRSRRSLFVEVQPGIYVPKPELQAEIDKTLEDPDYFYSTFLKDELRPTAKVT 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2140 DGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPGEHGCAVGCNPDIHWTEFFYKFADFSQVYDLDYKCFDATLPSAAFTL 2219
Cdd:cd23214    161 LGLTRVVEAAPIHAIVAGRMLLGGLIEYMQARPGKHGSAVGCNPDLHWTKFFYKFCHYPQVFDLDYKCFDATLPSCAFRI 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2220 VAERLERLTGDPRVSKYIHSIRHSHHVYGNKMYDMIGGNPSGCVATSILNTIINNICVLSALIQHPDFSPSQFQILAYGD 2299
Cdd:cd23214    241 VEDHLERLTGDERVTRYIESIRHSHHVYGNETYEMIGGNPSGCVGTSIINTIINNICVLSALIQHPDFSPESFRILAYGD 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2300 DVIYATEPPIHPSFLRDFYQKYTPLVVTPANKGSDFPDTSTIYEVTFLKRWFVPDDIRPFYIHPVMDPDTYEQSVMWLRD 2379
Cdd:cd23214    321 DVIYGCDPPIHPSFIKEFYDKHTPLVVTPANKGSDFPETSTIYDVTFLKRWFVPDDIRPFYIHPVMDPDTYEQSVMWLRD 400

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2347425630 2380 GDFQDVVTSLCHLAFHSGPKTYERWCMKVREQCLKT-GFTPTFLPYSYLQLRWLNLLAA 2437
Cdd:cd23214    401 GDFQDLVTSLCYLAFHSGPKTYDRWCTRVRDQVMKTtGFPPTFLPYSYLQTRWLNLLAA 459

RNA_helicase

pfam00910

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

1450-1552

1.03e-39

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

Pssm-ID: 459992 Cd Length: 102 Bit Score: 143.13 E-value: 1.03e-39

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 1450 VYFYGPPGTGKSLLASLLAQTLAQRLSGDPDDVYSPTAAScEYFDGYNGQSVHFIDDIGQDPEGRDWANFPNLVSSAPYI 1529
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKKLGLPKDSVYSRNPDD-DFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYP 79

                           90       100
                   ....*....|....*....|...
gi 2347425630 1530 LPMASLEEKGIHYTSRVIVVTSN 1552
Cdd:pfam00910   80 PPMAALEEKGTPFTSKFVIVTSN 102

rhv_like

cd00205

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

390-541

3.98e-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: 3.98e-33

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630  390 GVQDQQPPTAYPL-PASFARAYPDSPWTAMYNTHSMWNCGWRVQVTVNGSQFHAGALTLYMVPEGATESVEAARLNAGFV 468
Cdd:cd00205     18 SSASGTQLFQWKLsPALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPPGAPAPTTGDTRWQATL 97

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2347425630  469 FPYVILNLYESNTATLEVPFISPTPNTSSGLH------HPWTFYLQVLSPLNPPTGVPTSLSCSIYVTPVDSTFHGLRY 541
Cdd:cd00205     98 NPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDgygplnSFGTLVVRVLTPLTVPSGAPTTVDITVYVRAGDFELYGPRP 176

rhv_like

cd00205

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

591-763

7.27e-31

Pssm-ID: 119412 Cd Length: 178 Bit Score: 120.96 E-value: 7.27e-31

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630  591 EFAQRPGLMAPFAWTmAEEPGQRLGIFPVSPSA--IAGTGAPISYVLSLFSQWRGELAAHLLFTGSAQHYGRLVVCYTP- 667
Cdd:cd00205      3 SFADRPTTVGTNNWN-SSASGTQLFQWKLSPALgfLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPp 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630  668 --SAPAPPSSMHEAMRGTYTVWDVNAASTLEFTIPFISQSYWKTVDIfNPDALLSTTGYVSVWVLNPLTGPSSAPASALV 745
Cdd:cd00205     82 gaPAPTTGDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRY-DGYGPLNSFGTLVVRVLTPLTVPSGAPTTVDI 160

                          170
                   ....*....|....*...
gi 2347425630  746 QGFLSAGEsFNVRFMQNP 763
Cdd:cd00205    161 TVYVRAGD-FELYGPRPP 177

rhv_like

cd00205

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

843-995

1.51e-19

Pssm-ID: 119412 Cd Length: 178 Bit Score: 88.22 E-value: 1.51e-19

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630  843 LSPLNWQTTANYTGLTAMLSCFTYIAADLRFTLRLSNPNGVPATVLIAYAPPGATLPRT-PDRQMLSNFFMSEIPISASN 921
Cdd:cd00205     30 LSPALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPPGAPAPTTgDTRWQATLNPHVIWDLGTNS 109

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2347425630  922 AtlISFSIPYTSPLSAIPTTYYGWedWSGTNFGVLQAGSWGTLLLMPTFPTEVPhasplsATMWMAFGNFKAWV 995
Cdd:cd00205    110 S--VTFVVPYVSPTPYRSTRYDGY--GPLNSFGTLVVRVLTPLTVPSGAPTTVD------ITVYVRAGDFELYG 173

Peptidase_C3 super family

cl02893

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

1788-1943

6.66e-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: 6.66e-08

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 1788 ISQNVVHVESGNGseKVVMSGFYIFSRYLLVPTHLREPHHTTL--LVGTDTYDWATLPTL--TLGELTLVHTPTSRQYKD 1863
Cdd:pfam00548   11 LKQNAVPVTTSKG--VFTCCATGVYDNVILLPRHAEPGLTIVLdgKVVTISDPEVELVDQegMPLDAAIVKLKRNEKFKD 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 1864 MRRFIGAHPHPTG---ILVSQYKAAPLY-----VRFSDNRV-LDMD-FPGAIVckqaygYRAATFEGLCGSPLVTDDPAG 1933
Cdd:pfam00548   89 IRKHLPNRITKGNpvvLLINNNEQGRIYvpvgaVTHSGGIKtLDGTtTPRTIS------YNAPTKAGMCGGVVIAKVEGN 162

                          170
                   ....*....|
gi 2347425630 1934 IKILGLHVAG 1943
Cdd:pfam00548  163 GKILGMHIAG 172

P-loop_NTPase super family

cl38936

P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...

1424-1471

4.03e-04

P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.

The actual alignment was detected with superfamily member cd19481:

Pssm-ID: 476819 [Multi-domain] Cd Length: 158 Bit Score: 43.04 E-value: 4.03e-04

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 2347425630 1424 QSLKNYTLALSQHRKRQVGPRPEPVVVYFYGPPGTGKSLLASLLAQTL 1471
Cdd:cd19481      3 ASLREAVEAPRRGSRLRRYGLGLPKGILLYGPPGTGKTLLAKALAGEL 50

Name

Accession

Description

Interval

E-value

Kobuvirus_RdRp

cd23214

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

1980-2437

0e+00

Pssm-ID: 438064 Cd Length: 459 Bit Score: 969.31 E-value: 0e+00

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 1980 PGVNINRQSRLKPSPAYGAFPIKKEPAPLKRNDRRLNDGVDLDTQLFLKHGKGDQSEPWPGLEAAADLYFSTFPSSLPVL 2059
Cdd:cd23214      1 PGVNVNRKSRLGPSPAYGAFPVKKQPAPLTQKDDRLEDGIRLDDQLFLKHNKGDMDEPWPGLEAAADLYFSKFPTMIRTL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2060 TQEQAIHGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDEPEPGVYTPKPELQALIDQTLENPDYVYSTFLKDELRPTAKVQ 2139
Cdd:cd23214     81 TQEEAINGTPNLEGLDMNQAAGYPWNTMGRSRRSLFVEVQPGIYVPKPELQAEIDKTLEDPDYFYSTFLKDELRPTAKVT 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2140 DGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPGEHGCAVGCNPDIHWTEFFYKFADFSQVYDLDYKCFDATLPSAAFTL 2219
Cdd:cd23214    161 LGLTRVVEAAPIHAIVAGRMLLGGLIEYMQARPGKHGSAVGCNPDLHWTKFFYKFCHYPQVFDLDYKCFDATLPSCAFRI 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2220 VAERLERLTGDPRVSKYIHSIRHSHHVYGNKMYDMIGGNPSGCVATSILNTIINNICVLSALIQHPDFSPSQFQILAYGD 2299
Cdd:cd23214    241 VEDHLERLTGDERVTRYIESIRHSHHVYGNETYEMIGGNPSGCVGTSIINTIINNICVLSALIQHPDFSPESFRILAYGD 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2300 DVIYATEPPIHPSFLRDFYQKYTPLVVTPANKGSDFPDTSTIYEVTFLKRWFVPDDIRPFYIHPVMDPDTYEQSVMWLRD 2379
Cdd:cd23214    321 DVIYGCDPPIHPSFIKEFYDKHTPLVVTPANKGSDFPETSTIYDVTFLKRWFVPDDIRPFYIHPVMDPDTYEQSVMWLRD 400

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2347425630 2380 GDFQDVVTSLCHLAFHSGPKTYERWCMKVREQCLKT-GFTPTFLPYSYLQLRWLNLLAA 2437
Cdd:cd23214    401 GDFQDLVTSLCYLAFHSGPKTYDRWCTRVRDQVMKTtGFPPTFLPYSYLQTRWLNLLAA 459

RdRP_1

pfam00680

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

1992-2403

2.07e-55

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: 201.10 E-value: 2.07e-55

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 1992 PSPAYGAFPIKKEPAPLKRND-----RRLNDGVDLDTQLFLKHGKGDQSEPWPG---LEAAADLYFSTF----PSSLPVL 2059
Cdd:pfam00680    2 PTERHLVAIPAYVPASLGPEDprwarSYLNTDPYVDDIKKYSRPKLPGPADERDkllNRSAAKMVLSELrgvpKKANSTL 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2060 TQEQAIHGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDE----PEPGVYTPKPELQALIDQTLENPDYVYSTFLKDELRPT 2135
Cdd:pfam00680   82 IVYRAIDGVEQIDPLNWDTSAGYPYVGLGGKKGDLIEHlkdgTEARELAERLAADWEVLQNGTPLKLVYQTCLKDELRPL 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2136 AKVQDGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPGEHGCAVGCNPDI-HWTEFFYKFADFSQ-VYDLDYKCFDATLP 2213
Cdd:pfam00680  162 EKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHPIQVGINPFDrGWPRLLRRLARFGDyVYELDYSGFDSSVP 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2214 SAAFTLVAERLERLTGDP-------RVSKYIhsIRHSHHVYGNKMYDMIGGNPSGCVATSILNTIINNICVLSALI---- 2282
Cdd:pfam00680  242 PWLIRFAFEILRELLGFPsnvkewrAILELL--IYTPIALPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYALLksle 319

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2283 -QHPD--FSPSQFQILAYGDDVIYATEPPIHPSF------LRDFYQKYtplvvTPANKgsDFPDTSTIYEVTFLKRWFVP 2353
Cdd:pfam00680  320 nDGPRvcNLDKYFDFFTYGDDSLVAVSPDFDPVLdrlsphLKELGLTI-----TPAKK--TFPVSRELEEVSFLKRTFRK 392

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2347425630 2354 DdirPFYIHPVMDPDTYEQSVMWLRDGD-FQDVVTSLCHLAFHSGPKTYER 2403
Cdd:pfam00680  393 T---PGGYRPPLDRKRILAQLEYIRSKPvPSGQLENIRAYASHHGYEFYRD 440

RNA_helicase

pfam00910

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

1450-1552

1.03e-39

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

Pssm-ID: 459992 Cd Length: 102 Bit Score: 143.13 E-value: 1.03e-39

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 1450 VYFYGPPGTGKSLLASLLAQTLAQRLSGDPDDVYSPTAAScEYFDGYNGQSVHFIDDIGQDPEGRDWANFPNLVSSAPYI 1529
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKKLGLPKDSVYSRNPDD-DFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYP 79

                           90       100
                   ....*....|....*....|...
gi 2347425630 1530 LPMASLEEKGIHYTSRVIVVTSN 1552
Cdd:pfam00910   80 PPMAALEEKGTPFTSKFVIVTSN 102

rhv_like

cd00205

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

390-541

3.98e-33

Pssm-ID: 119412 Cd Length: 178 Bit Score: 127.51 E-value: 3.98e-33

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630  390 GVQDQQPPTAYPL-PASFARAYPDSPWTAMYNTHSMWNCGWRVQVTVNGSQFHAGALTLYMVPEGATESVEAARLNAGFV 468
Cdd:cd00205     18 SSASGTQLFQWKLsPALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPPGAPAPTTGDTRWQATL 97

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2347425630  469 FPYVILNLYESNTATLEVPFISPTPNTSSGLH------HPWTFYLQVLSPLNPPTGVPTSLSCSIYVTPVDSTFHGLRY 541
Cdd:cd00205     98 NPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDgygplnSFGTLVVRVLTPLTVPSGAPTTVDITVYVRAGDFELYGPRP 176

rhv_like

cd00205

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

591-763

7.27e-31

Pssm-ID: 119412 Cd Length: 178 Bit Score: 120.96 E-value: 7.27e-31

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630  591 EFAQRPGLMAPFAWTmAEEPGQRLGIFPVSPSA--IAGTGAPISYVLSLFSQWRGELAAHLLFTGSAQHYGRLVVCYTP- 667
Cdd:cd00205      3 SFADRPTTVGTNNWN-SSASGTQLFQWKLSPALgfLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPp 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630  668 --SAPAPPSSMHEAMRGTYTVWDVNAASTLEFTIPFISQSYWKTVDIfNPDALLSTTGYVSVWVLNPLTGPSSAPASALV 745
Cdd:cd00205     82 gaPAPTTGDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRY-DGYGPLNSFGTLVVRVLTPLTVPSGAPTTVDI 160

                          170
                   ....*....|....*...
gi 2347425630  746 QGFLSAGEsFNVRFMQNP 763
Cdd:cd00205    161 TVYVRAGD-FELYGPRPP 177

rhv_like

cd00205

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

843-995

1.51e-19

Pssm-ID: 119412 Cd Length: 178 Bit Score: 88.22 E-value: 1.51e-19

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630  843 LSPLNWQTTANYTGLTAMLSCFTYIAADLRFTLRLSNPNGVPATVLIAYAPPGATLPRT-PDRQMLSNFFMSEIPISASN 921
Cdd:cd00205     30 LSPALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPPGAPAPTTgDTRWQATLNPHVIWDLGTNS 109

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2347425630  922 AtlISFSIPYTSPLSAIPTTYYGWedWSGTNFGVLQAGSWGTLLLMPTFPTEVPhasplsATMWMAFGNFKAWV 995
Cdd:cd00205    110 S--VTFVVPYVSPTPYRSTRYDGY--GPLNSFGTLVVRVLTPLTVPSGAPTTVD------ITVYVRAGDFELYG 173

Rhv

pfam00073

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

422-514

1.93e-14

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: 73.50 E-value: 1.93e-14

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630  422 HSMWNCGWRVQVTVNGSQFHAGALTLYMVPEGATESVEAARLNAGFVFPYVILNLYESNTATLEVPFISPTPNTSSGLHH 501
Cdd:pfam00073   77 HTYYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRDYLWQATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDG 156

                           90
                   ....*....|...
gi 2347425630  502 PWTFYLQVLSPLN 514
Cdd:pfam00073  157 NWTLVVAGWVPLN 169

Rhv

pfam00073

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

635-729

3.26e-09

Pssm-ID: 395026 Cd Length: 170 Bit Score: 58.09 E-value: 3.26e-09

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630  635 LSLFSQWRGELAAHLLFTGSAQHYGRLVVCYTPSAPAPPSSMH---EAMRGTYTVWDVNAASTLEFTIPFISQS---YWK 708
Cdd:pfam00073   74 LRYHTYYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRDylwQATLNPHQFWNLGLNSSARLSVPYISIAhyySTF 153

                           90       100
                   ....*....|....*....|.
gi 2347425630  709 TVDIFNpdalLSTTGYVSVWV 729
Cdd:pfam00073  154 YDGNWT----LVVAGWVPLNY 170

Peptidase_C3

pfam00548

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

1788-1943

6.66e-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: 6.66e-08

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 1788 ISQNVVHVESGNGseKVVMSGFYIFSRYLLVPTHLREPHHTTL--LVGTDTYDWATLPTL--TLGELTLVHTPTSRQYKD 1863
Cdd:pfam00548   11 LKQNAVPVTTSKG--VFTCCATGVYDNVILLPRHAEPGLTIVLdgKVVTISDPEVELVDQegMPLDAAIVKLKRNEKFKD 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 1864 MRRFIGAHPHPTG---ILVSQYKAAPLY-----VRFSDNRV-LDMD-FPGAIVckqaygYRAATFEGLCGSPLVTDDPAG 1933
Cdd:pfam00548   89 IRKHLPNRITKGNpvvLLINNNEQGRIYvpvgaVTHSGGIKtLDGTtTPRTIS------YNAPTKAGMCGGVVIAKVEGN 162

                          170
                   ....*....|
gi 2347425630 1934 IKILGLHVAG 1943
Cdd:pfam00548  163 GKILGMHIAG 172

AAA

cd00009

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

1436-1574

2.48e-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: 49.45 E-value: 2.48e-06

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 1436 HRKRQVGPRPEPVVVYFYGPPGTGKSLLASLLAQTLAQR----LSGDPDDVYSPTAASCEYFDGYNGQ----------SV 1501
Cdd:cd00009      8 EALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPgapfLYLNASDLLEGLVVAELFGHFLVRLlfelaekakpGV 87

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2347425630 1502 HFIDDIGQDPEGRDWANFPNlvssapyilpMASLEEKGIHYTSRVIVVTSNFHEPNERAARSMGALRRRVHLR 1574
Cdd:cd00009     88 LFIDEIDSLSRGAQNALLRV----------LETLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRIVIP 150

SpoVK

COG0464

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

1431-1471

2.77e-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: 45.67 E-value: 2.77e-04

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 2347425630 1431 LALSQHRKRQVGPRPEPVVVYFYGPPGTGKSLLASLLAQTL 1471
Cdd:COG0464    175 LPLKRPELREEYGLPPPRGLLLYGPPGTGKTLLARALAGEL 215

RecA-like_protease

cd19481

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

1424-1471

4.03e-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: 4.03e-04

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 2347425630 1424 QSLKNYTLALSQHRKRQVGPRPEPVVVYFYGPPGTGKSLLASLLAQTL 1471
Cdd:cd19481      3 ASLREAVEAPRRGSRLRRYGLGLPKGILLYGPPGTGKTLLAKALAGEL 50

AAA

smart00382

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

1449-1574

9.53e-04

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: 41.98 E-value: 9.53e-04

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630  1449 VVYFYGPPGTGKSLLASLLAQTLAQR------LSGDPDDVYSPTAASCEYFDGYNGQSVH-------------------F 1503
Cdd:smart00382    4 VILIVGPPGSGKTTLARALARELGPPgggviyIDGEDILEEVLDQLLLIIVGGKKASGSGelrlrlalalarklkpdvlI 83

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2347425630  1504 IDDIG--QDPEGRDWANFpnlvssapyILPMASLEEKGIHYTSRVIVVTSNFHEPNERAARSMgaLRRRVHLR 1574
Cdd:smart00382   84 LDEITslLDAEQEALLLL---------LEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRRR--FDRRIVLL 145

Rhv

pfam00073

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

864-944

6.17e-03

Pssm-ID: 395026 Cd Length: 170 Bit Score: 39.99 E-value: 6.17e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630  864 FTYIAADLRFTLRLsNPNGVPA-TVLIAYAPPGATLPRTPDRQMLSNFFMSEIPISASNATlISFSIPYTSPLSAIPTTY 942
Cdd:pfam00073   77 HTYYRGGLEVTVQF-NGSKFHQgKLLVAYVPPGAPPPGSRDYLWQATLNPHQFWNLGLNSS-ARLSVPYISIAHYYSTFY 154


                   ..
gi 2347425630  943 YG 944
Cdd:pfam00073  155 DG 156

PRK13342

recombination factor protein RarA; Reviewed

1452-1471

8.86e-03

recombination factor protein RarA; Reviewed

Pssm-ID: 237355 [Multi-domain] Cd Length: 413 Bit Score: 41.22 E-value: 8.86e-03

                           10        20
                   ....*....|....*....|
gi 2347425630 1452 FYGPPGTGKSLLASLLAQTL 1471
Cdd:PRK13342    41 LWGPPGTGKTTLARIIAGAT 60

Name

Accession

Description

Interval

E-value

Kobuvirus_RdRp

cd23214

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

1980-2437

0e+00

Pssm-ID: 438064 Cd Length: 459 Bit Score: 969.31 E-value: 0e+00

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 1980 PGVNINRQSRLKPSPAYGAFPIKKEPAPLKRNDRRLNDGVDLDTQLFLKHGKGDQSEPWPGLEAAADLYFSTFPSSLPVL 2059
Cdd:cd23214      1 PGVNVNRKSRLGPSPAYGAFPVKKQPAPLTQKDDRLEDGIRLDDQLFLKHNKGDMDEPWPGLEAAADLYFSKFPTMIRTL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2060 TQEQAIHGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDEPEPGVYTPKPELQALIDQTLENPDYVYSTFLKDELRPTAKVQ 2139
Cdd:cd23214     81 TQEEAINGTPNLEGLDMNQAAGYPWNTMGRSRRSLFVEVQPGIYVPKPELQAEIDKTLEDPDYFYSTFLKDELRPTAKVT 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2140 DGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPGEHGCAVGCNPDIHWTEFFYKFADFSQVYDLDYKCFDATLPSAAFTL 2219
Cdd:cd23214    161 LGLTRVVEAAPIHAIVAGRMLLGGLIEYMQARPGKHGSAVGCNPDLHWTKFFYKFCHYPQVFDLDYKCFDATLPSCAFRI 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2220 VAERLERLTGDPRVSKYIHSIRHSHHVYGNKMYDMIGGNPSGCVATSILNTIINNICVLSALIQHPDFSPSQFQILAYGD 2299
Cdd:cd23214    241 VEDHLERLTGDERVTRYIESIRHSHHVYGNETYEMIGGNPSGCVGTSIINTIINNICVLSALIQHPDFSPESFRILAYGD 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2300 DVIYATEPPIHPSFLRDFYQKYTPLVVTPANKGSDFPDTSTIYEVTFLKRWFVPDDIRPFYIHPVMDPDTYEQSVMWLRD 2379
Cdd:cd23214    321 DVIYGCDPPIHPSFIKEFYDKHTPLVVTPANKGSDFPETSTIYDVTFLKRWFVPDDIRPFYIHPVMDPDTYEQSVMWLRD 400

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2347425630 2380 GDFQDVVTSLCHLAFHSGPKTYERWCMKVREQCLKT-GFTPTFLPYSYLQLRWLNLLAA 2437
Cdd:cd23214    401 GDFQDLVTSLCYLAFHSGPKTYDRWCTRVRDQVMKTtGFPPTFLPYSYLQTRWLNLLAA 459

ps-ssRNA_Picornaviridae

cd23193

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

2064-2409

1.97e-162

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: 504.39 E-value: 1.97e-162

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2064 AIHGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDePEPGVYTPKPELQALIDQTLENPDYVYSTFLKDELRPTAKVQDGLT 2143
Cdd:cd23193      1 AINGIDGLDPIDLNTSPGYPYTTQGLRRRDLID-NDKGGVSPLLEEEEQVLLDLDGPDVVFTTFLKDELRPKEKVKAGKT 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2144 RIVEAAPIHAIVAGRMLLGGLIDYMQGRPG-EHGCAVGCNPDIHWTEFFYKFaDFSQVYDLDYKCFDATLPSAAFTLVAE 2222
Cdd:cd23193     80 RVIEAAPLDYVIAGRMVFGRLFAQFHSNPGiLTGSAVGCNPDTDWTRLFASL-KQDNVYDLDYSGFDASLSSQLFEAAVE 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2223 RLERLTGDP-RVSKYIHSIRHSHHVYGNKMYDMIGGNPSGCVATSILNTIINNICVLSALIQHPDFSPSQFQILAYGDDV 2301
Cdd:cd23193    159 VLAECHGDPeLVLRYLEPIINSKHVVGDERYTVEGGMPSGCPCTSILNSICNNLVVRYALLETGKFDPDEYYILAYGDDV 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2302 IYATEPPIHPSFLRDFYQKYTPLVVTPANKGSDFPDTSTIYEVTFLKRWFVPDDIrpFYIHPVMDPDTYEQSVMWL-RDG 2380
Cdd:cd23193    239 LVSTDEPIDPSDLAEFYKKYFGMTVTPADKSSDFPESSPIEDVFLKRRFFVPDGT--FLIHPVMDLETLEQSLMWCgRGG 316

                          330       340
                   ....*....|....*....|....*....
gi 2347425630 2381 DFQDVVTSLCHLAFHSGPKTYERWCMKVR 2409
Cdd:cd23193    317 FFQQLLSSLCELALHHGPEEYERLVSKVR 345

Passerivirus_RdRp

cd23224

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

2063-2437

5.36e-153

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: 479.58 E-value: 5.36e-153

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2063 QAIHGTPNMEGLDMGQAAGFPWNTQgRSRRSLFDEPEPGVYTPKPELQALIDQTLENPDYVYSTFLKDELRPTAKVQDGL 2142
Cdd:cd23224      1 EAINGTPLLDGLDMKQSPGYPWSLT-TNRRSLFTQDETGKYYPVPELEEAVLACLENPDYFYTTHLKDELRPVEKALAGK 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2143 TRIVEAAPIHAIVAGRMLLGGLIDYMQGRPGEHGCAVGCNPDIHWTEFFYKFADFSQVYDLDYKCFDATLPSAAFTLVAE 2222
Cdd:cd23224     80 TRLIEAAPIHAIIAGRMLLGGLFEYMHARPGEHGSAVGCDPDYHWTPFFHSFDEFSQVWALDYSCFDSTLPSCCFDLIAQ 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2223 RLERLT------GDPRVSKYIHSIRHSHHVYGNKMYDMIGGNPSGCVATSILNTIINNICVLSALIQHPDFSPSQFQILA 2296
Cdd:cd23224    160 KLAKIItpgegiAPDAIVKYIRSISISKHVFGNEAYLMVGGNPSGCVGTSILNSMINNCVLISAFLTQKDFNPNQMRILT 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2297 YGDDVIYATEPPIHPSFLRDFYQKYTPLVVTPANKGSDFPDTSTIYEVTFLKRWFVPDDIRPFYIHPVMDPDTYEQSVMW 2376
Cdd:cd23224    240 YGDDVLYATNPPIHPRVVKKFFDENTTLIVTPATKAGDFPDESTIWDVTFLKRYFVPDEIRPWYVHPVIEPATYEQSVMW 319

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2347425630 2377 LRDGDFQDVVTSLCHLAFHSGPKTYERWCMKVREQCLKTGFTPTFLPYSYLQLRWLNLLAA 2437
Cdd:cd23224    320 TRGGDFQDVVTSLSFLAHHAGPTNYMIWEEKVRKAAAAKGVSLNILPYSYLQHRWMLLVTS 380

Megrivirus_RdRp

cd23223

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

1995-2416

1.98e-141

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: 448.91 E-value: 1.98e-141

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 1995 AYGAFPIKKEPAPLKRNDRRLNDGVDLDTQLFLKHgKGDQsEPWPGLEAAA---------DLYFSTFpSSLPVLTQEQAI 2065
Cdd:cd23223      1 AYGAFPVTHGPAALTNKDKRLEEGVDLDDVMFSKH-VPDH-PGWPTLEPAMsyvvedlmhKLGFSKD-EPVPMWTLEQAI 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2066 HGTPNMEGLDMGQAAGFPWNTQGRSRRSLFdEPEPGVYTPKPELQALIDQTLENP-DYVYSTFLKDELRPTAKVQDGLTR 2144
Cdd:cd23223     78 NGEGVMDGIDMGQSPGYPYNAQGRSRRSFF-EWNGEKWQPTEELKKEVDHALKDPdDFYFSTFLKDELRPLEKVKAGKTR 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2145 IVEAAPIHAIVAGRMLLGGLIDYMQGRPG-EHGCAVGCNPDIHWTEFFYKF--ADFSQVYDLDYKCFDATLPSAAFTLVA 2221
Cdd:cd23223    157 LVDGDSLPRILAMRMVFGPLFEAMLRKNGpEIHSAVGCNPDTDWTRYYHEMgpDSFPYCFDLDYSCFDSTEPKIAFRLMA 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2222 ERLERLTGDPrVSKYIHSIRHSHHVYGNKMYDMIGGNPSGCVATSILNTIINNICVLSALIQHpDFSPSQFQILAYGDDV 2301
Cdd:cd23223    237 KYLKPYFSVD-VTPFFEALATSKHVYGDKAYEMEGGMPSGCVGTSMFNCINNSAFIVSALIAL-KISPEDCAWICYGDDV 314

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2302 IYATEPPIHPSFLRDFYQKYTPLVVTPANKGSDFPDTSTIYEVTFLKRWFVPDDIRPFYIHPVMDPDTYEQSVMWLRDGD 2381
Cdd:cd23223    315 IISTDEKALSKRIADFYHKNTNLVVTPASKSGDFPETSTIYDVTFLKRFFQPDSHYPHLIHPYMPLEHLEQSVMWQTDGP 394

                          410       420       430
                   ....*....|....*....|....*....|....*
gi 2347425630 2382 FQDVVTSLCHLAFHSGPKTYERWCMKVREQCLKTG 2416
Cdd:cd23223    395 FQQKLDSLCLLAFHAGGPDYREFVDAIDKKCRSRG 429

Dicipivirus_RdRp

cd23222

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

1991-2432

7.94e-125

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: 402.04 E-value: 7.94e-125

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 1991 KPSPAYGAFPIKKEPAPLKRNDRRLNDGVDLDTQLFLKHGkGDQSEPWPGLEAAADLYFS----TFPSSL-PVLTQEQAI 2065
Cdd:cd23222      1 KPSPVYGVYPVTKEPAPLKPTDRRIDEGVDFNEPVFGKYG-ADMKEPFRNLDVGRDVVIArlkkVLPNKKfAPCTVSEAL 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2066 HGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDEPEPGVYTPKPELQALIDQTLENPD-YVYSTFLKDELRPTAKVQDGLTR 2144
Cdd:cd23222     80 NGKDGLPKLDLKQASGYPYNLSAIKRKHLIESDKDGFLTATPKLLADIEESKKHPEkFPYTSFLKDELRSVKKVKAGKTR 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2145 IVEAAPIHAIVAGRMLLGGLIDYMQGRPG-EHGCAVGCNPDIHWTEFFYKFADFSQVYDLDYKCFDATLPSAAFTLVAER 2223
Cdd:cd23222    160 VVEAGSLPVIVEGRMIFGNLFAYFNTHPGfETMAAVGCDPEVCWTDWYYKMREKAHTWDYDYTGFDGSIPSCSFDALADL 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2224 L-ERLTGDPRVSKYIHSIRHSHHVYGNKMYDMIGGNPSGCVATSILNTIINNICVLSALIQ-HPDFSPSQFQILAYGDDV 2301
Cdd:cd23222    240 LcEFVENEDDVRRYISNIKNSYHAYDGNLYLIEGAMPSGCAGTSVFNCLINAMLCFSCFMDlEPEMDPFEPLLIAYGDDI 319

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2302 IYATEPPIHPSFLRDFYQKYTPLVVTPANKGSDFPDTSTIYEVTFLKRWFVPDDIRPFyIHPVMDPDTYEQSVMWLRDGD 2381
Cdd:cd23222    320 LVSSDHDLFPSRVSEWMKANTTFKITPADKGEIFNDDSDVSDVRFLKRLFVEDPVCEL-IHPVIETETLEPSLNWCHEGE 398

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2347425630 2382 FQDVVTSLCHLAFHSGPKTYERWCMKVREQCLKTGFT-PTFLPYSYLQLRWL 2432
Cdd:cd23222    399 FETKVDAISMLAFHHGPEYYRDWCKKLTDICEERNISpPGLKPYSVHRNRWL 450

Rosavirus_RdRp

cd23221

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

2064-2432

5.85e-110

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: 356.15 E-value: 5.85e-110

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2064 AIHGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDEPEpGVYTPKPELQALIDQTLENPDY-VYSTFLKDELRPTAKVQDGL 2142
Cdd:cd23221      1 AINGIDNMDGLDMNQSPGVPYVSEGVSRRSLFDCVD-GQWVPRERLASDIAQVSGDPSLgHFATFLKDELRSTEKVAAGK 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2143 TRIVEAAPIHAIVAGRMLLGGLIDYMQGRPG-EHGCAVGCNPDIHWTEFFYKFADFSQVYDLDYKCFDATLPSAAFTLVA 2221
Cdd:cd23221     80 TRVVEAGSLPHIIVGRKIFGNLFALFNSNPGfQTMCAVGCDPDVTWTELYHPLSAKTYVFDYDYSGFDGSVPSCCFDALA 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2222 ERL-ERLTGDPRVSKYIHSIRHSHHVYGNKMYDMIGGNPSGCVATSILNTIINNICVLSALIQ-HPDFSPSQFQILAYGD 2299
Cdd:cd23221    160 DLLaDFVEGEEDVRKYISSLKTSFHHYKGKLWRLDGAMPSGCCGTSVFNSLINAMLLFSAFSQiCPDFRASEPLLVAYGD 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2300 DVIYATEPPIHPSFLRDFYQKYTPLVVTPANKGSDFPDTSTIYEVTFLKRWFVPDDIRPFYIHPVMDPDTYEQSVMWLRD 2379
Cdd:cd23221    240 DVLVGTDQPLFPSKVAEWVNSHTTFRITPADKGSVFNDESDIHSVQFLKRHFTPDPDFPALIHPTIDPDTYEQSVMWQRT 319

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2347425630 2380 GDFQDVVTSLCHLAFHSGPKTYERWCMKVREQCLKTGFTPTFL-PYSYLQLRWL 2432
Cdd:cd23221    320 GDFQETVNSLALLVFHRGPKSYSRWCESVTRKCVDGGYPPPFFpPFSLLRHQWL 373

Aphthovirus_RdRp

cd23210

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

1982-2433

5.07e-90

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: 301.87 E-value: 5.07e-90

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 1982 VNINRQSRLKPSPAYGAFPIKKEPAPLKRNDRRLNDGVDLDTQLFLKHgKGDQ---SEPWPGLEAAADLY----FSTFPS 2054
Cdd:cd23210      6 VHVMRKTKLAPTVAHGVFNPEFGPAALSNKDPRLNEGVVLDEVIFSKH-KGDTkmsAEDKALFRRCAADYasrlHSVLGT 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2055 SLPVLTQEQAIHGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDEpEPGvyTPKPELQALIDQTLE-NPDYVYSTFLKDELR 2133
Cdd:cd23210     85 ANAPLSIYEAIKGVDGLDAMEPDTAPGLPWALQGKRRGALIDF-ENG--TVGPEVEAALKLMEKrEYKFACQTFLKDEIR 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2134 PTAKVQDGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPG-EHGCAVGCNPDIHWTEFFYKFADFSQVYDLDYKCFDATL 2212
Cdd:cd23210    162 PMEKVRAGKTRIVDVLPVEHILYTRMMIGRFCAQMHSNNGpQIGSAVGCNPDVDWQRFGTHFAQYRNVWDVDYSAFDANH 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2213 PSAAFTLVAERL--ERLTGDPRVSKYIHSIRHSHHVYGNKMYDMIGGNPSGCVATSILNTIINNICVLSALIQH-PDFSP 2289
Cdd:cd23210    242 CSDAMNIMFEEVfrTEFGFHPNAEWILKTLVNTEHAYENKRITVEGGMPSGCSATSIINTILNNIYVLYALRRHyEGVEL 321

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2290 SQFQILAYGDDVIYATEPPIhpsflrDFyQKYTPL------VVTPANKGSDFPDTS-TIYEVTFLKRWFVPDDIRPFYiH 2362
Cdd:cd23210    322 DTYTMISYGDDIVVASDYDL------DF-EALKPHfkslgqTITPADKSDKGFVLGhSITDVTFLKRHFHMDYGTGFY-K 393

                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2347425630 2363 PVMDPDTYEQSVMWLRDGDFQDVVTSLCHLAFHSGPKTYERwcmkVREQCLKTGFTPTflpYSYLQLRWLN 2433
Cdd:cd23210    394 PVMASKTLEAILSFARRGTIQEKLISVAGLAVHSGPDEYRR----LFEPFQGLFEIPS---YRSLYLRWVN 457

Mosavirus_RdRp

cd23225

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

2063-2434

7.32e-89

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: 295.28 E-value: 7.32e-89

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2063 QAIHGTPNMEGLDMGQAAGFPWNTQGRSRRSLFD---EPEPGVYTPKPELQALIDQTL---ENPDYVysTFLKDELRPTA 2136
Cdd:cd23225      1 RAMNGDGISDAMDMTKAVGYPYCLDSIKRLDLVEikeTENGKVYLPTERLVEETEKFFtgeEKPKFV--TFLKDEVRSNE 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2137 KVQDGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPG-EHGCAVGCNPDIHWTEFFYKFADfSQVYDLDYKCFDATLPSA 2215
Cdd:cd23225     79 KIKQGKTRIVDASPFPYAIAGRMVMQNFMSNMMRCNGtEVGSAVGCDPDTEWTRYFFELCD-RYVFDLDYKAFDSTHPTA 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2216 AFTLVAER--LERLTGDPRVSK-YIHSIRHSHHVYGNKMYDMIGGNPSGCVATSILNTIINNICVLSALIQHPDFSPSQF 2292
Cdd:cd23225    158 MFNLLAERffTERNGFDQQAVRiFLNGLSDSDHVYEGKHFRIRGGLPSGCPCTSILNTVINNIIVRAAILGAYQIDTVDF 237

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2293 Q---ILAYGDDVIYATEPPIHPSFLRDFYQKYTPLVVTPANKGSDFPDTSTIYEVTFLKRWFVPDDIRPFYIHPVMDPDT 2369
Cdd:cd23225    238 QkfrMLAYGDDVVYATPQPIKPQDLADWLHANTNYKVTPASKAGTFPEESTIWDVTFLKRSFKPDEDHGHLIRPVMAVGN 317

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2347425630 2370 YEQSVMWLRDGDFQDVVTSLCHLAFHSGPKTYErwcmKVREQCLKTGFTPTFLPYSYLQLRWLNL 2434
Cdd:cd23225    318 LKQMLSFMRPGTFPDKVRSVAGLAVHCGEEDYN----QLADAVALYVPGVSMPAYKYMKACWYAK 378

Enterovirus_RdRp

cd23213

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

1980-2434

2.43e-87

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: 294.05 E-value: 2.43e-87

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 1980 PGVNINRQSRLKPSPAYGAFPIKKEPAPLKRNDRRLNdgVDLDTQLFLKHGKGDQSEPWPGLEAAADLYFSTFpSSLPVL 2059
Cdd:cd23213      7 PNINAPTKTKLEPSVFHDVFEGNKEPAVLTSKDPRLK--VDFEEAIFSKYVGNTITEVDEYMKEAVDHYAGQL-ATLDID 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2060 TQ----EQAIHGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDEPEPGVytpkPELQALIDQTleNPDYVYSTFLKDELRPT 2135
Cdd:cd23213     84 TEqmslEDAMYGTDGLEALDLHTSAGYPYVALGIKKRDILNKKTRDT----SKMKKYLDKY--GLDLPMVTYVKDELRSK 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2136 AKVQDGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPGE-HGCAVGCNPDIHWTEFFYKFADfsQVYDLDYKCFDATLPS 2214
Cdd:cd23213    158 DKVEKGKSRLIEASSLNDSVAMRMTFGNLYATFHLNPGVvTGSAVGCDPDTFWSKIPILLDG--SLFAFDYTGYDASLSP 235

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2215 AAFTLVAERLERLTGDPRVSkYIHSIRHSHHVYGNKMYDMIGGNPSGCVATSILNTIINNICVLSALI---QHPDFspSQ 2291
Cdd:cd23213    236 VWFRALKMVLEKGYSEEAVS-LIDYLNHSHHLYKNKTYCVLGGMPSGCSGTSIFNSMINNIIIRTLLLktyKGIDL--DE 312

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2292 FQILAYGDDVIYATEPPIHPSFLRDFYQKYTpLVVTPANKGSDFPDTsTIYEVTFLKRWFVPDDIRPFYIHPVMDPDTYE 2371
Cdd:cd23213    313 LKMIAYGDDVIASYPHPIDCSLLARTGKEYG-LTMTPADKSPCFNEV-NWENVTFLKRGFRADEQYPFLIHPVMPMKEIH 390

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2347425630 2372 QSVMWLRDG-DFQDVVTSLCHLAFHSGPKTYERWCMKVREqcLKTGFTPTFLPYSYLQLRWLNL 2434
Cdd:cd23213    391 ESIRWTKDPrNTQDHVRSLCLLAWHNGEEEYEKFVSKIRS--VPVGRALALPNYSTLRRNWLDS 452

Mischivirus_RdRp

cd23227

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

1973-2431

3.81e-87

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: 293.78 E-value: 3.81e-87

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 1973 IPTGeikPGVNINRQSRLKPSPAYGAFPIKKEPAPLKRNDRRLNDGVDLDTQLFLKHgKGDQSEpWPG-----LEAAADL 2047
Cdd:cd23227      6 LPDG---PRIHVPRKTKLRKSPAYPIFKPDAGPAVLSKNDPRLAEGVDFDKQVFSKH-SANQKE-YPKafrrmARWYADR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2048 YFSTFPSSLPVLTQEQAIHGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDEPEPGVYTP--KPELQALIDQTLEnpDYVYS 2125
Cdd:cd23227     81 VFTYLGKDNGPLSVKDAIKGIDNLDAMDPTTSPGLPYSAAGIKRTDLLDFDTGEIISPalRAEYNKYVSGDYS--DHVFQ 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2126 TFLKDELRPTAKVQDGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPG-EHGCAVGCNPDIHWTEFFYKFADFSQVYDLD 2204
Cdd:cd23227    159 TFLKDEIRSEEKIKAGKTRIVDVPSLAHVIIGRVLLGKFCSKFQASPGtELGSAIGCNPDWDWTYFAHQLMERQWCYDID 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2205 YKCFDATLPSAAFTLVAERL--ERLTGDPRVSKYIHSIRHSHHVYGNKMYDMIGGNPSGCVATSILNTIINNICVLSAL- 2281
Cdd:cd23227    239 YSNFDSTHGTGMFELLIDCFftPENGFSPAVAPYLRSLAFSKHAWMDKRYKIEGGLPSGCSATSVLNTVMNNIIIRALLs 318

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2282 IQHPDFSPSQFQILAYGDDVIYATEPPIHPSFLRDFYQKYTPLVVTPANKGSDFPDTSTIYEVTFLKRWFVPDDIRPFYI 2361
Cdd:cd23227    319 LTYKNFHPEDVLVLAYGDDLLVASDYQLDFNRVREKAAEHTLYKLTTANKAPDFPETSTLLDCQFLKRKFVLHSTRNFIW 398

                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2362 HPVMDPDTYEQSVMWLRDGDFQDVVTSLCHLAFHSGPKTYERWCMKVREQCLKtgfTPTFLpysYLQLRW 2431
Cdd:cd23227    399 RPVMDVTNLKTMLSFYKPNTLSEKLLSVAQLAFHSGYTVYEELFAPFKELQMT---VPSWW---YLEHEW 462

Cardiovirus_RdRp

cd23211

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

1973-2434

1.78e-84

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: 285.97 E-value: 1.78e-84

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 1973 IPTGEIkpgVNINRQSRLKPSPAYGAFPIKKEPAPLKRNDRRLNDgvDLDTQLFLKHGKGDQSEPwPGLEAAADLY---- 2048
Cdd:cd23211      6 IGTGPV---VHVPRKTKLRRTVAHPVFQPKFEPAVLSKYDPRTDK--DVDEVAFSKHTTNQESLP-PVFRMVAKEYanrv 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2049 FSTFPSSLPVLTQEQAIHGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDEPEPgvyTPKPELQALIDQtLENPDY---VYS 2125
Cdd:cd23211     80 FTLLGKDNGRLTVEQAVLGLEGMDPMEKDTSPGLPYTQQGLRRTDVVDFETA---TMIPFLAEAHRK-MVEGDYsdvVYQ 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2126 TFLKDELRPTAKVQDGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPG-EHGCAVGCNPDIHWTEFFYKFADFSQVYDLD 2204
Cdd:cd23211    156 SFLKDEIRPIEKVQAAKTRIVDVPPFEHCILGRQLLGRFASKFQTNPGlELGSAIGCDPDVDWTAFAVALSGFKYVYDVD 235

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2205 YKCFDATLPSAAFTLVAERL--ERLTGDPRVSKYIHSIRHSHHVYGNKMYDMIGGNPSGCVATSILNTIINNICVLSAL- 2281
Cdd:cd23211    236 YSNFDSTHSTAMFELLIENFftEENGFDPRIGEYLRSLAVSRHAYEERRVLIRGGLPSGCAATSMLNTIMNNIIIRAGLy 315

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2282 IQHPDFSPSQFQILAYGDDVIYATEPPIHPSFLRDFYQKyTPLVVTPANKGSDFPDTSTIYEVTFLKRWFVPDDirPFYI 2361
Cdd:cd23211    316 LTYKNFEFDDIKVLSYGDDLLVATNYQIDFNLVKARLAK-FGYKITPANKTSTFPLTSTLEDVVFLKRKFVKEN--SYLY 392

                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2347425630 2362 HPVMDPDTYEQSVMWLRDGDFQDVVTSLCHLAFHSGPKTYERWCMKVREQCLktgFTPTflpYSYLQLRWLNL 2434
Cdd:cd23211    393 RPVMDRENLKAMLSYYRPGTLKEKLTSIALLAVHSGKQVYDEIFAPFREVGI---VVPT---YESVLYRWLSL 459

Cosavirus_RdRp

cd23226

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

1980-2435

1.13e-79

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: 271.89 E-value: 1.13e-79

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 1980 PGVNINRQSRLKPSPA-YGAFPiKKEPAPLKRNDRRLNDGVDLDTQLFLKHGKG----DQSEPWPGLEAAADLYFSTFPS 2054
Cdd:cd23226     10 PRVHVPRQSKLKRTNAtYPATG-KYGPAVLSKNDPRLDPDVDFDKVIFSKHVANvvidEDTSFWNALKMSAQIYAEKFKG 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2055 -SLPVLTQEQAIHGTPNMEGLDMGQAAGFPWNtqgRSRRSLFDEPEPGVYtpKPELQALIDQTLEN--PDYVYSTFLKDE 2131
Cdd:cd23226     89 vDFSPLTVEEAILGIPGLDRMDPNTASGLPYT---KTRRQMIDFQEGKIL--DPELQERLDTWLSGkqPEMLYQTFLKDE 163

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2132 LRPTAKVQDGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPG-EHGCAVGCNPDIHWTEFFYKFADFSQVYDLDYKCFDA 2210
Cdd:cd23226    164 IRPIEKVKAGKTRIIDVTPLDHVLAFRIVLGRFMAHFHNNYGfELGSAVGCDPDVAWANFGFALSSKKYQYDFDYSNFDA 243

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2211 TLPSAAFTLVAERL--ERLTGDPRVSKYIHSIRHSHHVYGNKMYDMIGGNPSGCVATSILNTIINNICVLSALIQ-HPDF 2287
Cdd:cd23226    244 SHSESIFELLKQFVftKDNGFDHRCSLMIDSLVTSTHCYEDQRMTIRGGLPSGTSGTSVINTIINNIIFKAALYHtYSNF 323

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2288 SPSQFQILAYGDDVIYATEPPIHPSFLRDFyQKYTPLVVTPANKGSDFPdTSTIYEVTFLKRWFVpdDIRPFYIhPVMDP 2367
Cdd:cd23226    324 EWDDVQMLAYGDDIVAASDCLLDLDRVKYF-MALIGYKITPADKGEKFI-PKDMQNIQFLKRSFR--KVAGVWA-PIMDL 398

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2347425630 2368 DTYEQSVMWLRDGDFQDVVTSLCHLAFHSGPKTYErwcmKVREQCLKTGFtpTFLPYSYLQLRWLNLL 2435
Cdd:cd23226    399 ENLQAMLSWYKPGTLQEKLDSVARLAHFCGEKVYD----HLFTTFVKDGF--QIKPWKQLHFEWLNRF 460

Sapelovirus_RdRp

cd23218

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

2065-2435

5.37e-76

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: 257.91 E-value: 5.37e-76

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2065 IHGTPNMEGLDMGQAAGFPWNTQGRSRRSLFdePEPGvyTPKPELQALIDqtLENPDYVYSTFLKDELRPTAKVQDGLTR 2144
Cdd:cd23218      3 VYGIDNLEGLDLNTSAGYPYNTMGIRKKDLI--PPRG--EPLSPLLKALD--LHGYDLPFTTYLKDELRPKEKVKMGKTR 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2145 IVEAAPIHAIVAGRMLLGGLIDYMQGRPGEH-GCAVGCNPDIHWTEFfYKFADFSQVYDLDYKCFDATLPSAAFTLVAER 2223
Cdd:cd23218     77 LIECSSLNDTIRMKRIFGRLFQTFHKNPGTYtGSAVGCNPDVHWSKF-AEEGGMDNVCAFDYTNWDASLSPFWFDALKLF 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2224 LERLTGDPRVSKYIHSIRHSHHVYGNKMYDMIGGNPSGCVATSILNTIINNICVLSALIQ-HPDFSPSQFQILAYGDDVI 2302
Cdd:cd23218    156 LSKLGYSERDIVLIDHLCYSNHIFKNEGYKVAGGMPSGCSGTSIFNSIINNIVVRTLVLLvYKGINLDELRILCYGDDLL 235

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2303 YATEPPIHPSFLRDFYQKYTpLVVTPANKGSDFPDTSTIYEVTFLKRWFVPDDIRPFYIHPVMDPDTYEQSVMWLRDGDF 2382
Cdd:cd23218    236 VAYPYPLDPNVLADLGKSLG-LTMTPADKSDTFQGCTKLTEVTFLKRSFVFDEEFPFLCHPVFPMEEVHESIRWTRNAST 314

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2347425630 2383 -QDVVTSLCHLAFHSGPKTYERWCMKVREqcLKTGFTPTFLPYSYLQLRWLNLL 2435
Cdd:cd23218    315 tQEHVTSLCLLAWHNGEEVYEEFCEKIRS--VPVGRALILPPYSQLRRSWLDMF 366

Rabovirus_RdRp

cd23230

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

2064-2433

3.09e-71

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: 244.02 E-value: 3.09e-71

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2064 AIHGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDePEPGVYTpkpELQALIDQTleNPDYVYSTFLKDELRPTAKVQDGLT 2143
Cdd:cd23230      1 AAYGIENLEGLDLNTSAGYPYVLNGIKKRDILD-PETRDTT---KLQECLDKY--GVDLPFVTYLKDELRPLEKIKKGKT 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2144 RIVEAAPIHAIVAGRMLLGGLIDYMQGRPGEH-GCAVGCNPDIHWTEFFYKFADfsQVYDLDYKCFDATLPSAAFTLVAE 2222
Cdd:cd23230     75 RLIECSSMNDTIRMKMMFGRLFATYHRNPGPItGSAVGCNPDIHWTKFRAEMHG--EIIAFDYSNYDASLNKVWFECLKM 152

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2223 RLERLtGDPRVSKYIHSIRhSHHVYGNKMYDMIGGNPSGCVATSILNTIINNICVLSALIQ-HPDFSPSQFQILAYGDDV 2301
Cdd:cd23230    153 VLKNF-GFKDLRPIDHIIR-SRHIYKGIEYDVEGGMPSGCSGTSIFNSIINNIIIMTLVLDaYKGIDLEQLKIIAYGDDV 230

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2302 IYATEPPIHPSFLRDFYQKYTpLVVTPANKGSDFpDTSTIYEVTFLKRWFVPDDIRPFYIHPVMDPDTYEQSVMWLRD-G 2380
Cdd:cd23230    231 IVTYPYPLDAALLADCGKKYG-LKMTPPDKSAEF-KNVTWEDVTFLKRRFKPAKHYPFLIHPVFDQQEILESLRWTRNpA 308

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2347425630 2381 DFQDVVTSLCHLAFHSGPKTYERWCMKVREQclKTGFTPTFLPYSYLQLRWLN 2433
Cdd:cd23230    309 HTQEHVRSLAELAWHSGRKSYEEFCNLVKST--NVGKACILPPYESFKRMWLD 359

RNA_dep_RNAP

cd01699

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

2109-2377

1.98e-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: 229.86 E-value: 1.98e-67

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2109 LQALIDQTLEN----PDYVYSTFLKDELRPTAKVQDGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPGEHGCAVGCNPD 2184
Cdd:cd01699      1 LEKAVESLEDLplirPDLVFTTFLKDELRPLEKVEAGKTRLIQPRPLDYNIALRMYLGPFEAKLMKNRGGLPIAVGINPY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2185 -IHWTEFFYKFADFSQV-YDLDYKCFDATLPSAAFTLVAERLERLTGDPR---VSKYIHSIRHS-HHVYGNKMYDMIGGN 2258
Cdd:cd01699     81 sRDWTILANKLRSFSPVaIALDYSRFDSSLSPQLLEAEHSIYNALYDDDDeleRRNLLRSLTNNsLHIGFNEVYKVRGGR 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2259 PSGCVATSILNTIINNICVLSALIQH-PDFSPSQFQILAYGDDVIYATEP---PIHPSFLRDFYQKYTpLVVTPANKgsD 2334
Cdd:cd01699    161 PSGDPLTSIGNSIINCILVRYAFRKLgGKSFFKNVRLLNYGDDCLLSVEKaddKFNLETLAEWLKEYG-LTMTDEDK--V 237

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|...
gi 2347425630 2335 FPDTSTIYEVTFLKRWFVPDDirPFYIHPVMDPDTYEQSVMWL 2377
Cdd:cd01699    238 ESPFRPLEEVEFLKRRFVLDE--GGGWRAPLDPSSILSKLSWS 278

ps-ssRNAv-Picornavirales

cd23169

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

2123-2409

9.64e-62

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: 214.38 E-value: 9.64e-62

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2123 VYSTFLKDELRPTAKVQDGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPGEHGCAVGCNPDIH-WTEFFYKFA-DFSQV 2200
Cdd:cd23169      2 IFVDCLKDELRPIEKVKAGKTRLFSASPLDYTIAFRKYFGDFIAAFQKNRIKLEHAVGINPDSVeWTRLYRRLLkKGPNI 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2201 YDLDYKCFDATLPSAAFTLVAERLERLT------GDPRVSK-YIHSIRHSHHVYGNKMYDMIGGNPSGCVATSILNTIIN 2273
Cdd:cd23169     82 FAGDYSNFDGSLPPDVMEAAFDIINDWYdeyvddEDERVRKvLFEELINTIHLVGNLVYQVHGGNPSGNPLTTIINSIVN 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2274 NI---CVLSALIQHPDFSP--SQFQILAYGDDVIYATEPPIHPSF----LRDFYQKYTpLVVTPANKGSDFPDTSTIYEV 2344
Cdd:cd23169    162 LLyirYAWLRITGLTSLSDfkKNVRLVTYGDDVIISVSDEVKDEFnfvtISEFLKELG-ITYTDADKSGDIVPYRPLEEV 240

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2347425630 2345 TFLKRWFVPDDIrPFYIHPVMDPDTYEQSVMWLRDGdfQDVVTSLCH-------LAFHSGPKTYERWCMKVR 2409
Cdd:cd23169    241 TFLKRGFRPHPT-PGLVLAPLDLESIEEQLNWTRKE--DDLLEATIEnaraallLAFGHGPEYYNKFRQKLN 309

RdRP_1

pfam00680

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

1992-2403

2.07e-55

Pssm-ID: 425815 Cd Length: 450 Bit Score: 201.10 E-value: 2.07e-55

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 1992 PSPAYGAFPIKKEPAPLKRND-----RRLNDGVDLDTQLFLKHGKGDQSEPWPG---LEAAADLYFSTF----PSSLPVL 2059
Cdd:pfam00680    2 PTERHLVAIPAYVPASLGPEDprwarSYLNTDPYVDDIKKYSRPKLPGPADERDkllNRSAAKMVLSELrgvpKKANSTL 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2060 TQEQAIHGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDE----PEPGVYTPKPELQALIDQTLENPDYVYSTFLKDELRPT 2135
Cdd:pfam00680   82 IVYRAIDGVEQIDPLNWDTSAGYPYVGLGGKKGDLIEHlkdgTEARELAERLAADWEVLQNGTPLKLVYQTCLKDELRPL 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2136 AKVQDGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPGEHGCAVGCNPDI-HWTEFFYKFADFSQ-VYDLDYKCFDATLP 2213
Cdd:pfam00680  162 EKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHPIQVGINPFDrGWPRLLRRLARFGDyVYELDYSGFDSSVP 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2214 SAAFTLVAERLERLTGDP-------RVSKYIhsIRHSHHVYGNKMYDMIGGNPSGCVATSILNTIINNICVLSALI---- 2282
Cdd:pfam00680  242 PWLIRFAFEILRELLGFPsnvkewrAILELL--IYTPIALPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYALLksle 319

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2283 -QHPD--FSPSQFQILAYGDDVIYATEPPIHPSF------LRDFYQKYtplvvTPANKgsDFPDTSTIYEVTFLKRWFVP 2353
Cdd:pfam00680  320 nDGPRvcNLDKYFDFFTYGDDSLVAVSPDFDPVLdrlsphLKELGLTI-----TPAKK--TFPVSRELEEVSFLKRTFRK 392

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2347425630 2354 DdirPFYIHPVMDPDTYEQSVMWLRDGD-FQDVVTSLCHLAFHSGPKTYER 2403
Cdd:pfam00680  393 T---PGGYRPPLDRKRILAQLEYIRSKPvPSGQLENIRAYASHHGYEFYRD 440

Teschovirus_RdRp

cd23212

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

2053-2410

8.01e-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: 196.38 E-value: 8.01e-55

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2053 PSSLPVLTQEQAIHGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDePEPGvytPKPELQALIDQTLE-NPD-YVYSTFLKD 2130
Cdd:cd23212      5 PDFLEPLSVREAVEGIDGLDPMDMDKSPGLPYVKKGLRRTDLWN-PKTG---PSIELMAEINRYLDyNYDkHVFLTFLKD 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2131 ELRPTAKVQDGLTRIVEAAPI-HAIVaGRMLLGGLIDYMQGRPGEH-GCAVGCNPDIHWTEFFYKfADFSQVYDLDYKCF 2208
Cdd:cd23212     81 ELRPKEKVQAGKTRVIDVAGFgHAIV-GRMLFGRLFAFFHKNPGWNtGSAVGVNPDLAWTQIFYT-APSRNVLAMDYSGF 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2209 DATLPSAAFTLVAERLERLTGDPRVSKYIHSIRHSHHVYGNKMYDMIGGNPSGCVATSILNTIINNICVLSALIQHPDfs 2288
Cdd:cd23212    159 DASHTSGMFCILKHFLTTLGYGTLQLSYIDSLCYSKHHWDDETYRLDGGLPSGCSGTTIFNTIMNNIVARAAASYAAE-- 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2289 pSQFQILAYGDDVIYATEPPIHPSFLRDFYQKyTPLVVTPANKGSDFpDTSTIYEVTFLKRWFVPDDIrpfYIHPVMDPD 2368
Cdd:cd23212    237 -GPVGILCYGDDILVSSPEKFPVSDWLEFYSK-TPYKVTAADKSEQI-DWRDITQCTFLKRGFVLDGS---LVRPVMEEQ 310

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|..
gi 2347425630 2369 TYEQSVMWLRDGDFQDVVTSLCHLAFHSGPKTYERWCMKVRE 2410
Cdd:cd23212    311 HLAELLKWARPGTLQAKLLSIAQLAFHLPRQAYDRLMLPFEE 352

Fipivirus_RdRp

cd23229

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

2065-2403

6.96e-53

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: 191.94 E-value: 6.96e-53

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2065 IHGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDEpEPGVYTPKPELQALIDQTLEN---------PDYVYSTFLKDELRPT 2135
Cdd:cd23229      2 VEGIPGMEGLDMKTSAGYPWCEQNQKKKDKIKL-LAGKNFLVRPLREVVHIVVDWyimppdmpkPEIKYVVYLKDELLSS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2136 AKVQDGLTRIVEAAPIHAIVAGRMLLGGLIDYMQ------GRPgeHGCAVGCNPDIHWTEfFYKFADFSQVYDLDYKCFD 2209
Cdd:cd23229     81 DKVKMGRTRWICAAPVQLVCAWKKVFGRAIAAIHlesvtdGKS--TGCAVGMDPETAWTD-IALARPGWPVIALDYSNFD 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2210 ATLPSAAFTLVAERLERLTG--DPRVSKYIHSIRHSHHVYGNKMYDMIGGNPSGCVATSILNTIINNICVLSALIQHPDF 2287
Cdd:cd23229    158 GSLQSFVITGAVRILGYIAGlpDGQSYRLAEFVYDVKQIVGKYLYTTVGPLPSGCPSTSIIGSLCNVLMLLYTLSHATGQ 237

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2288 SPSQFQ----ILAYGDDVIYAteppIHPSF------LRDFYQKYTPLVVTPANKGSDFPDTSTIYEVTFLKRWFVPDDIR 2357
Cdd:cd23229    238 RYSAFRdwmhVVTYGDDVLVF----VHPEVvvvldtLAHEMYLVFGVTATDATDKRAPPQLRELSNVTFLKRGFRQCSSV 313

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*..
gi 2347425630 2358 PFYIHPVMDPDTYEQSVMWLRDG-DFQDVVTSLCHLAFHSGPKTYER 2403
Cdd:cd23229    314 PFLVHPTMDKSTIYQMLAWKRKGtTLAENVKCAAEFMMHHGEEEYED 360

Hepatovirus_RdRp

cd23215

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

2059-2414

7.83e-44

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

Pssm-ID: 438065 Cd Length: 464 Bit Score: 167.72 E-value: 7.83e-44

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2059 LTQEQAIHGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDEPEPGVYTP-KPELQALIDQTL---ENP---DYVYSTFLKDE 2131
Cdd:cd23215     65 FDLEQAITGVPGMDAINMDSSPGYPYVQEKLTKSDLIWLDDNGELLGmHPRLAQRILFNLtmmDNGndlDVVYTTCPKDE 144

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2132 LRPTAKVQDGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPGEH-GCAVGCNPDIHWTEFFYKFADFSQV-YDLDYKCFD 2209
Cdd:cd23215    145 LRPLEKVLESKTRAIDACPLDFTIICRMFWGPAISYFQLNPGFHtGVAVGIDPDRDWDALFKTMIRFGDYgIDLDFSSFD 224

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2210 ATLPSAAFTLVAERLERLTGDP--RVSKYIHSIRHSHHVYGNKMYDMIGGNPSGCVATSILNTIINNI---CVLSALI-Q 2283
Cdd:cd23215    225 ASLSPFMIREACRVLSELSGVPdhQGQALINTIIYSKHLLYNLCYHVCGSMPSGSPCTSLLNSIVNNVnlyYVFSKIFkK 304

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2284 HPDFSPSQFQILAYGDDVIYATEPPIHPSFLRDFYQK----YTPLVVTPANKGSDFPDTSTIYEVTFLKRWF--VPDDIR 2357
Cdd:cd23215    305 SPVFFYDAVKFLCYGDDVLIVFSRDLEIKNLDKLGQRiqdeFKLLGMTATSADKGEPQVVPVSELTFLKRSFnlIEDRFR 384

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2347425630 2358 pfyihPVMDPDTYEQSVMWLRDG-DFQDVVTSLCHLAFHSGPKTYERWCMKVrEQCLK 2414
Cdd:cd23215    385 -----PAISEKTIWSLVAWQRSNaEFEQNLDTACWFAFMHGYDFYQNFYLQL-QSCLE 436

Dicistroviridae_RdRp

cd23194

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

2120-2409

7.08e-43

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: 160.36 E-value: 7.08e-43

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2120 PDYVYSTFLKDELRPTAKVQDGLTRIVEAAPIHAIVAGRMLLGGLIDY-MQGRPgEHGCAVGCNP---DihWTEFFYKFA 2195
Cdd:cd23194      4 LPHVFVDTLKDERRPIEKVDAGKTRVFSAGPMDYTIAFRMYFLGFVAHlMRNRI-DNEIAVGTNVyslD--WDKLARKLL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2196 DFSQ-VYDLDYKCFDATLPSAAFTLVAERLERLTGDPRVSKYI-----HSIRHSHHVYGNKMYDMIGGNPSGCVATSILN 2269
Cdd:cd23194     81 SKGDkVIAGDFSNFDGSLNPQILWAILDIINEWYDDGEENALIrrvlwEDIVNSVHICGGYVYQWTHSQPSGNPLTAIIN 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2270 TIINNI----CVLSALIQHPDFSPSQFQ----ILAYGDDVIYAteppIHPSFLRDFYQKYTP-------LVVTPANKGSD 2334
Cdd:cd23194    161 SIYNSIimryVYLLLTKEAGLMTMSDFNkhvsMVSYGDDNVIN----VSDEVSEWFNQLTITeamaeigMTYTDETKTGE 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2335 FPDTSTIYEVTFLKRWFVPDDIRPFYIHPvMDPDTYEQSVMWLR-----DGDFQDVV-TSLCHLAFHsGPKTYERWCMKV 2408
Cdd:cd23194    237 IVPYRSLEEVSFLKRGFRYDDDLGRWVAP-LDLDTILEMPNWVRkgkdpEEITKQNVeNALRELSLH-GEEVFDKWAPKI 314


                   .
gi 2347425630 2409 R 2409
Cdd:cd23194    315 R 315

RNA_helicase

pfam00910

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

1450-1552

1.03e-39

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

Pssm-ID: 459992 Cd Length: 102 Bit Score: 143.13 E-value: 1.03e-39

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 1450 VYFYGPPGTGKSLLASLLAQTLAQRLSGDPDDVYSPTAAScEYFDGYNGQSVHFIDDIGQDPEGRDWANFPNLVSSAPYI 1529
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKKLGLPKDSVYSRNPDD-DFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYP 79

                           90       100
                   ....*....|....*....|...
gi 2347425630 1530 LPMASLEEKGIHYTSRVIVVTSN 1552
Cdd:pfam00910   80 PPMAALEEKGTPFTSKFVIVTSN 102

Parechovirus_RdRp

cd23217

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

2064-2404

7.11e-36

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Parechovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the Parechovirus genus within the family Picornaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. The Parechovirus genus is comprised of six species, Parechovirus A (formerly named Human parechovirus), Parechovirus B (formerly named Ljungan virus), Parechovirus C (Sebokele virus) and Parechovirus D (ferret parechovirus), Parechovirus E (falcon parechovirus) and Parechovirus F (gecko parechovirus). Humans, ferrets, and various rodents serve as natural hosts. Human parechoviruses may cause gastrointestinal or respiratory illness in infants, and have been implicated in cases of myocarditis and encephalitis. Human parechoviruses replicate in the respiratory and gastrointestinal tract. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438067 Cd Length: 371 Bit Score: 141.54 E-value: 7.11e-36

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2064 AIHGTPNMEGLDMGQAAGFPWNTQGRSRRSLFD-EPepgvYTPKPELQALIDQTL------ENPDYVYSTFLKDELRPTA 2136
Cdd:cd23217      1 AVLGTSHLNSLDLSTSPGYKYVKSGYKKRDLLSlEP----FSVSPQLEKDVKDKLhavykgNQPTTIFNACLKDELRKLD 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2137 KVQDGLTRIVEAAPIHAIVAGRMLLGGLIDYM-QGRPGEHGCAVGCNPDIHWTEFFYKFADFSqvYDLDYKCFDATLPSA 2215
Cdd:cd23217     77 KIAQGKTRCIEACSIDYVIAYRVVMSSLYEAIyQTPCQELGLAVGMNPWTDWDFMINALNPYN--YGLDYSSYDGSLSEM 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2216 AFTLVAERLERLTGDPRVSKYIHS-IRHSHHVYGNKMYDMIGGNPSGCVATSILNTIIN-NICVLSALIQHPDFspsQFQ 2293
Cdd:cd23217    155 LMWEAVEVLAYCHESPDLVMQLHKpVINSDHVVMDERWLVHGGMPSGSPCTTVLNSICNlLVCIYLAYLQSPGI---ECL 231

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2294 ILAYGDDVIYATEPPIHPSFLRDFYQKYTPLVVTPANKgSDFPDTSTIYEVTFLKRW--FVPDDIrpfYIHPVMDPDTYE 2371
Cdd:cd23217    232 PIVYGDDVIFSVSSEIDPEYLVSSAADSFGMEVTGSDK-DEPPSLLPRMEVEFLKRTtgYFPGST---YKVGALDLETME 307

                          330       340       350
                   ....*....|....*....|....*....|....*
gi 2347425630 2372 QSVMWLRD-GDF-QDVVTSLCHLAFHsGPKTYERW 2404
Cdd:cd23217    308 QHIMWMKNlSTFpQQLQSFENELCLH-GKDIYDDY 341

Kunsagivirus_RdRp

cd23219

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

2108-2403

5.94e-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: 135.38 E-value: 5.94e-34

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2108 ELQALIDQTlENPDYVYSTFLKDELRPTAKVQDGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGR-PGEHGCAVGCNPdih 2186
Cdd:cd23219     48 ELQFRGTSG-GAGEVKFSSFLKDELRPLSKIRSGDTRVVECSSLDYTVAFRMQFLRVLQMCYGSdPTLTGLAPGMNV--- 123

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2187 WTEFFYKFAD-FSQVYDLDYKCFDATLPSAAFTLVAERLERLTGDPRVS-KYIHSIRHSHHVYGNKMYDMIGGNPSGCVA 2264
Cdd:cd23219    124 YTDMLPLCTSlYDYNLCLDFSKYDSRLPLQVMHRVAQLISNLTPDPQVSmRLFQPIIISTHIVGSYEVVVEGGMPSGCPI 203

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2265 TSILNTIINNI-CVLSALIQHPDfspSQFQILAYGDDVIYATEPPIHPSFLRDFYQKYTPLVVTPANKgsdfpdTSTIY- 2342
Cdd:cd23219    204 TTIMNSVCNVVmTSYAMLLLDPD---SDFWPVAYGDDNIVSTRKPIDTELFCSILNEEFGMILTGADK------TTTVQa 274

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2347425630 2343 ----EVTFLKR--WFVPDDIRPFyihPVMDPDTYEQSVMWLR-DGDFQDVVTSLCH-LAFHsGPKTYER 2403
Cdd:cd23219    275 vppmSVDFLKRrlRYTPEFPLPV---PVLPLDSMLSRICWCKgETEFKDQLESFSYeLALY-GQEVYER 339

rhv_like

cd00205

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

390-541

3.98e-33

Pssm-ID: 119412 Cd Length: 178 Bit Score: 127.51 E-value: 3.98e-33

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630  390 GVQDQQPPTAYPL-PASFARAYPDSPWTAMYNTHSMWNCGWRVQVTVNGSQFHAGALTLYMVPEGATESVEAARLNAGFV 468
Cdd:cd00205     18 SSASGTQLFQWKLsPALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPPGAPAPTTGDTRWQATL 97

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2347425630  469 FPYVILNLYESNTATLEVPFISPTPNTSSGLH------HPWTFYLQVLSPLNPPTGVPTSLSCSIYVTPVDSTFHGLRY 541
Cdd:cd00205     98 NPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDgygplnSFGTLVVRVLTPLTVPSGAPTTVDITVYVRAGDFELYGPRP 176

rhv_like

cd00205

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

591-763

7.27e-31

Pssm-ID: 119412 Cd Length: 178 Bit Score: 120.96 E-value: 7.27e-31

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630  591 EFAQRPGLMAPFAWTmAEEPGQRLGIFPVSPSA--IAGTGAPISYVLSLFSQWRGELAAHLLFTGSAQHYGRLVVCYTP- 667
Cdd:cd00205      3 SFADRPTTVGTNNWN-SSASGTQLFQWKLSPALgfLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPp 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630  668 --SAPAPPSSMHEAMRGTYTVWDVNAASTLEFTIPFISQSYWKTVDIfNPDALLSTTGYVSVWVLNPLTGPSSAPASALV 745
Cdd:cd00205     82 gaPAPTTGDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRY-DGYGPLNSFGTLVVRVLTPLTVPSGAPTTVDI 160

                          170
                   ....*....|....*...
gi 2347425630  746 QGFLSAGEsFNVRFMQNP 763
Cdd:cd00205    161 TVYVRAGD-FELYGPRPP 177

Caliciviridae_RdRp

cd23192

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

2123-2405

2.21e-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: 123.91 E-value: 2.21e-30

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2123 VYSTFLKDELRPTAKVQDGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPGEHGCAVGCNPDI-HWTEFFYKFADFSQVY 2201
Cdd:cd23192      2 AYALALKDELRPVEKIAEGKRRLLWGCDVGVTLVAAAAFGPVADALKAVCPTGPIAVGINMDSeDVEVIFERLSGFRYHY 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2202 DLDYKCFDATLPSAAFTLVAERLERLTGDPRVSKYIHSIRHSHHV--YGNKMYDMIGGNPSGCVATSILNTIINNICVLS 2279
Cdd:cd23192     82 CLDYSKWDSTQSPAVTAAAIDILADLSEETPLRDSVVETLSSPPMgiFDDVIFVTKRGLPSGMPFTSVINSLNHWLLFSA 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2280 ALIQHPD----FSPSQFQ---ILAYGDDVIYATEPPIHPSF------LRDFyqkytPLVVTPANKGS--DFPDTSTIyev 2344
Cdd:cd23192    162 AVLKAYElvgiYTGNVFDeadFFTYGDDGVYAMPPATASVMdeiienLKSY-----GLKPTAADKTEnpDIPPLQGP--- 233

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2347425630 2345 TFLKRWFVPDDIRpfyIHPVMDPDTYEQSVMWLRDGDFQDVVTS---------------LCHLAFHSGPKTYERWC 2405
Cdd:cd23192    234 VFLKRTFVRTPGG---WRALLDRSSILRQLYWVKGPNTHDWTEPpteidheartvqlenVLLEAAQHGPEFYEKVL 306

Crohivirus_RdRp

cd23232

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

2062-2421

2.68e-29

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: 122.52 E-value: 2.68e-29

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2062 EQAIHGTPNMEGLDMGQAAGFPWNTQGRSRRSLFDEPEPGVY-TPKPELQAL--IDQTLENPDYVYSTFLKDELRPTAKV 2138
Cdd:cd23232      2 EEACFEEGDEHALDLKTSPGFKYVQMGLKKTDLVNRPNKFIHpILRNDVRLIfdEMAKGQMPVVTFTAHLKDELRKLEKI 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2139 QDGLTRIVEAAPIHAIVAGRMLLGGLIDYM-QGRPGEHGCAVGCNPDIHWTEFFYKFADFSqvYDLDYKCFDATLPSAAF 2217
Cdd:cd23232     82 RSGKTRCIEACDFDYTVAHKMMFGTLYKAIyDTPGIITGLAVGMNPWKDWELIQQSLFKYN--YDFDYKTFDGSLSRELM 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2218 TLVAERLERLTGDPRVSKYI-HSIRHSHHVYGNKMYDMIGGNPSGCVATSILNTIINNICVLSALIQHPDfspSQFQILA 2296
Cdd:cd23232    160 LHAVDILSACVENDEMAKLMlSVVVESVHLVLDQKWNVSGGMPSGSPCTTVLNSVCNLIVSSTIADMCTE---GDFKILV 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2297 YGDDVIYATEPPIHPSFLRDFYQKYTPLVVTPANKGSDFpDTSTIYEVTFLKRwfVPDDIR-PFYIHPVMDPDTYEQSVM 2375
Cdd:cd23232    237 YGDDLIISSTAPLDCDRFKTLVELHYGMEVTPGDKGDEF-KVKDREQVSFLKR--VTRKFPgTNYRVGALDLDTVKQHLM 313

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2376 WLRD-GDFQDVVTSLCHLAFHSGPKTYERWCMKVreQCLKTGF---TPTF 2421
Cdd:cd23232    314 WCKSySSFKQQLDSALMEVAMHGEETYNGFLTEI--KTKLDKFkiyPPKF 361

Limnipivirus_RdRp

cd23228

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

2106-2411

2.68e-28

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: 119.60 E-value: 2.68e-28

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2106 KPELQALID--QTLENPDYVYSTFLKDELRPTAKVQDGLTRIVEAAPIHAIVAGRMLLGGLI-DYMQGRPGEHGCAVGCN 2182
Cdd:cd23228     46 RADVEAWEEliQSGGYPTTLFTACLKDELRSDEKVALGKTRVIEAAELDYVVAYRMYMSSIYsDLYNAYAGDTGIAAGIN 125

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2183 PDIHWTEFFYKFADFSQVYDLDYKCFDATLPSAAFTLVAERLERLTGDPRVSKYIH-SIRHSHHVYGNKMYDMIGGNPSG 2261
Cdd:cd23228    126 PPADGHRLREELSQYDSFLALDYSRFDGSLPEMLMRAAVEILADLHEDPDLVRRLHeTVIISKHLVVDEDWTVKGGMPSG 205

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2262 CVATSILNTIINNICVLSALIQHPDFSPSQFQ---------ILAYGDDVIYA-TEPPIHPSFLRDFYQKYTpLVVTPANK 2331
Cdd:cd23228    206 SPCTTVLNCICNLLVLEYAFLVHFGVYEDDDGvglpqcdylSVVYGDDCIVAyNGMEMGLAFAETIEDTFG-MEVTPASK 284

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2332 GSDFPDTStIYEVTFLKRWFVP-DDIRPFYIHPVMDPDTYEQSVMWLRD-GDFQDVVTSLCHLAFHSGPKTYERWCMKVR 2409
Cdd:cd23228    285 VGDHFNVE-LHEVEFLKRKFFAfETEEYDRIALRLSENTIVQSLMWMRNlKTFPDQVQSLMMELSAWGKEKYDKLRDTCK 363


                   ..
gi 2347425630 2410 EQ 2411
Cdd:cd23228    364 RR 365

Avisivirus_RdRp

cd23231

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

2074-2402

1.61e-25

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: 110.75 E-value: 1.61e-25

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2074 LDMGQAAGFPWntQGRSRRSLFDEP--EPGVYTPkpeLQALIDQTLENPDYVYSTFLKDELRPTAKVQDGLTRIVEAAPI 2151
Cdd:cd23231     11 IDWGTSPGDKY--KGKTKAQLVDDKkfKADVMNL---VRFNGDPNREPPDVYFTTYLKDELRPKEKAKAGKTRVISAASF 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2152 HAIVAGRMLLGGLIDYMQGRPGEHGCAVGCNPDIHWTEFFYKFADFsqVYDLDYKCFDATLPSAAFTLVAERLERLTGDP 2231
Cdd:cd23231     86 DYTIACRMVFGPILRQLFAWGREFGFGPGLNPYTHFDELYDKILPF--VICLDYSGFDGSLSSELMFHAAQVIACFSEKP 163

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2232 R-VSKYIHSIRHSHHVYGNKMYDMIGGNPSGCVATSILNTIINNI-CVLSALIQhpDFSPSQFQILAYGDDVIYATEPPI 2309
Cdd:cd23231    164 EaIMASAELTIGSTERVSDEVWYVYGGMPSGSPWTTTLNTICNLLmCYTYLLDM--GHCWSETFVVAYGDDVVISANIKH 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2310 HPSFLRDFYQKYTPLVVTPANKGSDFPDTsTIYEVTFLKRWFVPDDIRPfYIHPVMDPDTYEQSVMWLRdGDFQDVVTSL 2389
Cdd:cd23231    242 NLEGIEQWFKTKFGATVTPSDKQGKITWT-TKNNMEFLKRRPKQLDFLP-KIVGALDLDNMLDRIQWTK-GHFQDQLNSF 318

                          330
                   ....*....|....
gi 2347425630 2390 -CHLAFHsGPKTYE 2402
Cdd:cd23231    319 yLELALH-GRETYN 331

Aalivirus_RdRp

cd23216

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

2107-2415

1.72e-25

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: 110.14 E-value: 1.72e-25

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2107 PELQALIDQTLENPDYVYSTFLKDELRPTAKVQDGLTRIVEAAPIHAIVAGRMLLGGLIDYM-QGRPGEHGCAVGCNPDI 2185
Cdd:cd23216     34 PKFKEDVKEILAGKPTFFTTYLKDELRSIEKIANGNTRAIEAANFDHVVAWRQVMGNIVKQLfSDHDRVTGFAPGMNPYT 113

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2186 HWTEFFYKFAdfSQVYDLDYKCFDATLPSAAFTLVAERLERLTGDPRVSKYIHS-IRHSHHVYGNKMYDMIGGNPSGCVA 2264
Cdd:cd23216    114 HFDSLMDQVK--WNVLALDFKKFDGSLSPQVMEEAVDILASFHDMPQMVVDIHKhTIYSTNVVSDETWFVEGGMCSGSPC 191

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2265 TSILNTIInNICVLSALIQHPDFSPSQFQILAYGDDVI-----YATEPPiHPSFLRDFYQKYTPLVVTPANKGSDFP-DT 2338
Cdd:cd23216    192 TTVLNTIC-NLLVNTTILLSEGIQPDNFYIAAYGDDTIisvdgLSSSLP-DPKIMQQKYKEWFGMTVTSADKGSEITwDT 269

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2347425630 2339 STiyEVTFLKR--WFVPDDIRpfyIHPVMDPDTYEQSVMWLRdGDFQDVVTSLCHLAFHSGPKTYerwcMKVReQCLKT 2415
Cdd:cd23216    270 RN--HVQFLKRrpGFFPGTQK---VVGVLDLESMMEHIAWTK-GSFQDQLNSFYQELVLHGEQVY----MTVR-QTLKS 337

Marnaviridae_RdRp

cd23195

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

2123-2409

2.43e-22

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Marnaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Marnaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. They are mono- or dicistronic, have a polyadenylate tail and have conserved motifs for RNA helicase, RdRp, and structural protein domains. The first RNA virus isolated and characterized that infects a marine protist was Heterosigma akashiwo RNA virus (HaRNAV) in the genus Marnavirus, that infects the toxic bloom-forming Raphidophyte alga, Heterosigma akashiwo. Recently, it has undergone a major taxonomic revision and now includes 20 species within 7 genera, which include Bacillarnavirus, Kusarnavirus, Labyrnavirus, Locarnavirus, Marnavirus, Salisharnavirus, and Sogarnavirus. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

Pssm-ID: 438045 Cd Length: 310 Bit Score: 100.21 E-value: 2.43e-22

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2123 VYSTFLKDELRPTAKvqdGLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPGEHGCAVGCN---PDihWTEFF---YKFAD 2196
Cdd:cd23195      2 IFKACLKDEPTKLTK---DKVRVFQAAPVALQLLVRKYFLPIARFLQMNPLLSECAVGINaqsPE--WEELYehlTKFGE 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2197 fSQVYDLDYKCFDATLPS----AAFTLVAERLERLTG-DPRVSKYIHSIRHShhvYGNKMYDM-------IGGNPSGCVA 2264
Cdd:cd23195     77 -DRIIAGDYSKYDKRMSAqlilAAFKILIDIAAKSGGySEEDLKIMRGIATD---IAYPLVDFngdliqfFGSNPSGHPL 152

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2265 TSILNTIINNICVLSA-LIQHPDFSPSQFQ----ILAYGDDVIYATEPPI----HPS---FLRDFYQKYtplvvTPANKG 2332
Cdd:cd23195    153 TVIINSIVNSLYMRYAyYSLYPEKEVPPFRdvvaLMTYGDDNIMSVSPGYpwfnHTSiaeFLAKIGIKY-----TMADKE 227

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2333 SDFPDTSTIYEVTFLKRWFVPDDirpfyihpvmDPDTY-----EQSV-----MWLRDGD------FQDVVTSLCHLAFHS 2396
Cdd:cd23195    228 AESVPFIHISEADFLKRKFVFDP----------ELGVYvgpldEDSIfkslhCYLKSKVltpeeqAAQNIDGALREWFFH 297

                          330
                   ....*....|...
gi 2347425630 2397 GPKTYERWCMKVR 2409
Cdd:cd23195    298 GREVYEKRREQLK 310

rhv_like

cd00205

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

843-995

1.51e-19

Pssm-ID: 119412 Cd Length: 178 Bit Score: 88.22 E-value: 1.51e-19

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630  843 LSPLNWQTTANYTGLTAMLSCFTYIAADLRFTLRLSNPNGVPATVLIAYAPPGATLPRT-PDRQMLSNFFMSEIPISASN 921
Cdd:cd00205     30 LSPALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPPGAPAPTTgDTRWQATLNPHVIWDLGTNS 109

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2347425630  922 AtlISFSIPYTSPLSAIPTTYYGWedWSGTNFGVLQAGSWGTLLLMPTFPTEVPhasplsATMWMAFGNFKAWV 995
Cdd:cd00205    110 S--VTFVVPYVSPTPYRSTRYDGY--GPLNSFGTLVVRVLTPLTVPSGAPTTVD------ITVYVRAGDFELYG 173

Aquamavirus_RdRp

cd23220

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

2063-2364

3.14e-19

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

Pssm-ID: 438070 Cd Length: 338 Bit Score: 91.69 E-value: 3.14e-19

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2063 QAIHGTPNMEGLDMGQAAGFPwntqGRSRRSLFDEPEPGVYTPKPELQALIDQTLENpdYVYSTFLKDELRPTAKVQDGL 2142
Cdd:cd23220      3 EAINSSESPLNFNGTAGAKYP----GMNRRQLLLPLNPQVRDDVVKLAGDVGNGTAT--VVFETFMKDELRPKEKIESGK 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2143 TRIVEAAPIHAIVAGRM-LLGGLIDYMQGRPGEHGCAVGCNPDIHWTEFFYKFADFSqvYDLDYKCFDATLPSAAFTLVA 2221
Cdd:cd23220     77 TRIVESCPLDYLLLYRMvMLKSMIWWYNSDCIKTGVAPGMNVYTDFVPMVKQFKKIK--YCLDFSAYDSTLSDEILAAGV 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2222 ERLERLTGDPRVSKYIHS-IRHSHHVYGNKMYDMIGGNPSGCVATSILNTIINNICV--LSAL--IQHPdfspsqfQILA 2296
Cdd:cd23220    155 EVLACTSAVPSYVRKLHApIICSHHWHNNVVDLVLGGMPSGAPCTSVLNSIVNVLMAryICALmdIDYP-------VMVA 227

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2297 YGDDVIYATEPPIHPSFLRDFYQKYTPLVVTPANKGsdfPDTSTIYEVTFLKRW--FVPDDIRPFYIHPV 2364
Cdd:cd23220    228 YGDDNVVSFDEEIDIERMVSLYKTEFGVTATNHDKT---PVPRPMANPVFLKRRlrFNPDLNIQFPVLPL 294

Rhv

pfam00073

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

422-514

1.93e-14

Pssm-ID: 395026 Cd Length: 170 Bit Score: 73.50 E-value: 1.93e-14

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630  422 HSMWNCGWRVQVTVNGSQFHAGALTLYMVPEGATESVEAARLNAGFVFPYVILNLYESNTATLEVPFISPTPNTSSGLHH 501
Cdd:pfam00073   77 HTYYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRDYLWQATLNPHQFWNLGLNSSARLSVPYISIAHYYSTFYDG 156

                           90
                   ....*....|...
gi 2347425630  502 PWTFYLQVLSPLN 514
Cdd:pfam00073  157 NWTLVVAGWVPLN 169

Iflaviridae_RdRp

cd23197

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

2120-2404

3.26e-14

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: 76.06 E-value: 3.26e-14

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2120 PDYVYSTFLKDELRPTAKVQD-GLTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPGEHGCAVGCNPD-IHWTEFFYKFADF 2197
Cdd:cd23197      4 PPCVYWAHLKDELRPSEKLRRfGGTRVFSVPPLELVLNSRRFLLPFMDAFQSFPIEAHHAIGLNPNsGDWRRLRDTLLEK 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2198 SQ-VYDLDYKCFDATLP----SAAFTLVAERLER---LTgdPRVSKYIHSIRH-----SHHVYGNkMYDMIGGNPSGCVA 2264
Cdd:cd23197     84 GPcLLQMDYKNYSDAIPkecvAKAFHIIVDYYRKwhcLT--VEIENALKTLFLdtadaELLVYGD-VFKVNNGVLAGHPM 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2265 TSILNTIINNICVLSALIQHPDFSPSQF----QILAYGDDVIYATEPPIHPSF----LRDFYQKYTpLVVTPANK---GS 2333
Cdd:cd23197    161 TSVVNSVVNLILMNYMWIKITRRRASEFfkltYIIVMGDDVVISLPKQLTEEFdcrkICAEFAKYD-IKVTDSEKnltGE 239

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2347425630 2334 DFPDTStIYEVTFLKRWFVPDDIRPF-YIHPVmDPDTYEQSVMWL-RDGDF-----QDVVTSLcHLAFHSGPKTYERW 2404
Cdd:cd23197    240 PKPYDS-FDKFEFLSRGFSDCDAYPDiTFAPV-KTIALFDCPLWIsKGQDEeeqtiQAIQAGL-LLAFDHGPEFFGKY 314

Solinviviridae_RdRp

cd23199

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

2177-2351

8.80e-13

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: 72.00 E-value: 8.80e-13

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2177 CAVGCNPDIHWTEFFYKFADFSQVYDLDYKCFDATLPSAAFTLVAERLerLTGDPRVSKYIHSI----RHSHHVYGNKMY 2252
Cdd:cd23199     71 CAVGCNPYATFHKFATKFFKFKNFFSCDYKNFDRTIPKCVFEDFRDML--IQANPHMKNEIYACfqtiIDRIQVSGNSIL 148

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2253 DMIGGNPSGCVATSILNTIINNICVLSALI-----------QHPDFSPSQFQILAYGDDVIYATEPPIHPSFLRDFYQKY 2321
Cdd:cd23199    149 LVHGGMPSGCVPTAPLNSKVNDIMIYTAYVnilrradrgdiTSYRYYRDLVCRLFYGDDVIIAVDDSIADIFNCQTLSEE 228

                          170       180       190
                   ....*....|....*....|....*....|....
gi 2347425630 2322 TP----LVVTPANKGSDFPDTSTIYEVTFLKRWF 2351
Cdd:cd23199    229 MKilfgMNMTDGSKSDIIPKFETIETLSFISRFF 262

Polycipiviridae_RdRp

cd23198

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

2127-2411

1.18e-12

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: 71.29 E-value: 1.18e-12

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2127 FLKDELRPTAKV-----QDGLTRIVEAAPIHAIVAGRMLLGGLIDYM-QGRPGEHGCAVGCNPD-IHWTEFFYKFADFSQ 2199
Cdd:cd23198      6 FPKDELRPIYKAlgdpqTPPKTRSVTCMNVYYILAWRRVTLDFWASMhRAADGNFPFCPGINPEgPDWNRLYHYLNRHPN 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2200 VYDLDYKCFDATLPSAAFTLVAERLERLTG-DP--RVSKYIHSIR----HSHHVYGNKMYDMIGGNPSGCVATSILNTI- 2271
Cdd:cd23198     86 AVDFDVSNWDGHLPAELFYAVLDIIKTVLGlKPnsPNAKVIYSILtevmNCHIQFEDIIYQKLRGLISGFPGTAEVNTLa 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2272 ----INNICVLSALIQHPDFSPSQF----QILAYGDDVIYATEPPIHPSF----LRDFYQK--YTplvVTPANKGSDFPD 2337
Cdd:cd23198    166 hwllIYYIYLYLAQNTIYDMTITAFlrnvSAIFYGDDIIITISDEILHWFngktIQRMYEEhgYP---VTSAAKDTEIPE 242

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2338 TSTIYEVTFLKRWFVPddIRPFYIHPVMDPDTYEQSVMWLRDGD------FQDVVTSLcHLAFHSGPKTYErwcmKVREQ 2411
Cdd:cd23198    243 SKPLSDCQFLKSSWNP--ILPGYYIRKMDIEVVYDLVYWVRAKEhprdqfYSNYHDAL-RILFGHGEQVFE----AFREQ 315

Secoviridae_RdRp

cd23196

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

2128-2352

3.19e-12

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

Pssm-ID: 438046 Cd Length: 309 Bit Score: 70.11 E-value: 3.19e-12

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2128 LKDELRPTAKVQDG-LTRIVEAAPIHAIVAGRMLLGGLIDYMQGRPGEHGCAVGCNP-DIHWTEFFYKFADFSQV-YDLD 2204
Cdd:cd23196      7 PKDERLKKRKVLEKpKTRLFDVLPMEYNLLLRKYFLNFVRFIQANRHRLPCQVGINPySREWTTLYDRLAEKSDTaLNCD 86

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2205 YKCFDATLPSAAFTLVAERLERLTGDPRVSKYIHSI------RHShhVYGNKMYDMIGGNPSGCVATSILNTIINNI--- 2275
Cdd:cd23196     87 YSRFDGLLSHQVYVWIADMINRLYGDGDEAKARRNLlmmfcgRRS--ICGRQVYMVRGGMPSGCALTVIINSIFNEIlir 164

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2276 -----CVLSALIQHPDfspSQFQILAYGDDVIYATEPPIHPSF----LRDFYQKYTPLVVTPANKGSDFPDTSTIYEVTF 2346
Cdd:cd23196    165 yvyrkVVPRPARNNFN---KYVRLVVYGDDNLISVKEEIIPYFdgpvIKKEMAKVGVTITDGTDKTSPTLERKPLESLDF 241


                   ....*.
gi 2347425630 2347 LKRWFV 2352
Cdd:cd23196    242 LKRGFR 247

Nora-virus_RdRp

cd23200

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

2125-2355

3.27e-11

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: 66.87 E-value: 3.27e-11

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2125 STFLKDELRPTAKVQDGLTRIVEAAPIHAIVAGRMLLGGLID--YMQGRPGEHgcAVGCNP-DIHWTEFFYKFADFSQVY 2201
Cdd:cd23200      4 SSKLKDQPIKIAQAKSGRTRVFHCIPVDLILFSGALYGPYKEayTKAGLKCYH--AVGIDPkSVGWQQLATYMTKHPNYF 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2202 DLDYKCFDATLPSAAFTLVAERLERLTGDPRVSKYIHSiRH--------SHHVYGNKMYDMIGGNPSGCVATSILNTIIN 2273
Cdd:cd23200     82 DADYKNYDKYLHRQVFKAVRKIQRSVIQQVCPDKWDKA-RAveeldaidTYVVDYQTVYKTNRGNKSGSYTTTIDNCLAN 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2274 NICVLSA------LIQHPDFSpSQFQILAYGDDVIYateppihpSFLRDFYQKY-----------TPLVVTPANKGSDFP 2336
Cdd:cd23200    161 DIYGLYAwvkttgLRSLWDYR-QNVSSVAFGDDIIK--------SVSDEYKDKYnyctyrdvlnaTGHIMTPGSKDGEEK 231

                          250
                   ....*....|....*....
gi 2347425630 2337 DTSTIYEVTFLKRWFVPDD 2355
Cdd:cd23200    232 PFTSFENLQFLKRGFKLEN 250

ps-ssRNAv_Astroviridae_RdRp

cd23172

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

2121-2321

4.16e-10

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: 62.49 E-value: 4.16e-10

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2121 DYVYSTFLKDELRPTAKVQDGLTR-IVEAAPIHAIVAGRmllgglIDY-----MQGRPGEHGCAVGcnpdihWTEFFYKF 2194
Cdd:cd23172      1 RPLWYLFLKKEILKKEKIEDGDIRqILCPDPIFARIGAR------FEQdqnnlMKERTLTNEGQVG------WSPFYGGF 68

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2195 AD--------FSQVYDLDYKCFDATLPSAAFTLVAE-RLERLtgDPRVSK--------YIHSIRHSHHVYGN-KMYDMIG 2256
Cdd:cd23172     69 DArvrrlgskGNYFVEFDWTRFDGTIPAELFRHIRKlRWSFL--DPEKTEenrkvydwYVHNLLNRYVLLPTgEVTRVTK 146

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2347425630 2257 GNPSGCVATSILNTIINNI---CVLSALIQHPDFSPSQ----FQILAYGDDVI--YATEPPIHPSFLRDFYQKY 2321
Cdd:cd23172    147 GNPSGQISTTMDNCMVNTFltaFEFAYVYGPKTGTLKElwdnYDTIVYGDDRLsgYPSLPDPYVERVVDMYKDV 220

Rhv

pfam00073

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

635-729

3.26e-09

Pssm-ID: 395026 Cd Length: 170 Bit Score: 58.09 E-value: 3.26e-09

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630  635 LSLFSQWRGELAAHLLFTGSAQHYGRLVVCYTPSAPAPPSSMH---EAMRGTYTVWDVNAASTLEFTIPFISQS---YWK 708
Cdd:pfam00073   74 LRYHTYYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRDylwQATLNPHQFWNLGLNSSARLSVPYISIAhyySTF 153

                           90       100
                   ....*....|....*....|.
gi 2347425630  709 TVDIFNpdalLSTTGYVSVWV 729
Cdd:pfam00073  154 YDGNWT----LVVAGWVPLNY 170

Peptidase_C3

pfam00548

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

1788-1943

6.66e-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: 6.66e-08

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 1788 ISQNVVHVESGNGseKVVMSGFYIFSRYLLVPTHLREPHHTTL--LVGTDTYDWATLPTL--TLGELTLVHTPTSRQYKD 1863
Cdd:pfam00548   11 LKQNAVPVTTSKG--VFTCCATGVYDNVILLPRHAEPGLTIVLdgKVVTISDPEVELVDQegMPLDAAIVKLKRNEKFKD 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 1864 MRRFIGAHPHPTG---ILVSQYKAAPLY-----VRFSDNRV-LDMD-FPGAIVckqaygYRAATFEGLCGSPLVTDDPAG 1933
Cdd:pfam00548   89 IRKHLPNRITKGNpvvLLINNNEQGRIYvpvgaVTHSGGIKtLDGTtTPRTIS------YNAPTKAGMCGGVVIAKVEGN 162

                          170
                   ....*....|
gi 2347425630 1934 IKILGLHVAG 1943
Cdd:pfam00548  163 GKILGMHIAG 172

ps-ssRNAv_EoPV-like_RdRp

cd23171

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

2120-2355

3.88e-07

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: 53.75 E-value: 3.88e-07

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2120 PDYVYSTFLKDELRPTAKVqdglTRIVEAAPIHAIVAGRMLLGGLIDYMQGRpgEHGCAVGCnpDIHWTEFFYKFADFSQ 2199
Cdd:cd23171     12 PPTTFMDFPKDELLKPGKD----TRLINGAPLHHTLDMRRYLMEFFAAITTI--NNKIAVGI--DVHSGDWALIHGGADD 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2200 VYDLDYKCFDATLPSAAFTLVAERL-----ERLTGDPR----VSKYIHSIRHSHHVYGNKMYDMIGGNPSGCVATSILNT 2270
Cdd:cd23171     84 VVDEDYSGFGPGFHSQWLDVIRRIAvawckHHKTVDPEyenvVRCLIRELQNAYHVAGDLVYQVLCGSPSGAFATDRINS 163

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 2271 IIN----NICVLSALIQHPDFspSQFQILAYGDDVIYAteppiHPSFLRDFYQKYTP---LVVTPANKGSDfpdtstiye 2343
Cdd:cd23171    164 LANlcyhCLCYLRKYGTLTGF--WSHYLLVYGDDTRRR-----ETAYTGDEFQDCMAsigITVNRDKSGVT--------- 227

                          250
                   ....*....|..
gi 2347425630 2344 vTFLKRWFVPDD 2355
Cdd:cd23171    228 -SFLKRQFIPYD 238

AAA

cd00009

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

1436-1574

2.48e-06

Pssm-ID: 99707 [Multi-domain] Cd Length: 151 Bit Score: 49.45 E-value: 2.48e-06

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630 1436 HRKRQVGPRPEPVVVYFYGPPGTGKSLLASLLAQTLAQR----LSGDPDDVYSPTAASCEYFDGYNGQ----------SV 1501
Cdd:cd00009      8 EALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPgapfLYLNASDLLEGLVVAELFGHFLVRLlfelaekakpGV 87

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2347425630 1502 HFIDDIGQDPEGRDWANFPNlvssapyilpMASLEEKGIHYTSRVIVVTSNFHEPNERAARSMGALRRRVHLR 1574
Cdd:cd00009     88 LFIDEIDSLSRGAQNALLRV----------LETLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRIVIP 150

ps-ssRNAv_RdRp-like

cd23167

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

2252-2306

5.75e-06

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

Pssm-ID: 438017 [Multi-domain] Cd Length: 73 Bit Score: 46.18 E-value: 5.75e-06

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2347425630 2252 YDMIGGNPSGCVATSILNTIINNICVLSALIQHPDFSP--SQFQILAYGDDVIYATE 2306
Cdd:cd23167     17 DLLKAGQPSGSPNTSADNSLINLLLARLALRKACGRAEflNSVGILVYGDDSLVSVP 73

AAA

pfam00004

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

1450-1471

2.75e-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: 2.75e-04

                           10        20
                   ....*....|....*....|..
gi 2347425630 1450 VYFYGPPGTGKSLLASLLAQTL 1471
Cdd:pfam00004    1 LLLYGPPGTGKTTLAKAVAKEL 22

SpoVK

COG0464

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

1431-1471

2.77e-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: 45.67 E-value: 2.77e-04

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 2347425630 1431 LALSQHRKRQVGPRPEPVVVYFYGPPGTGKSLLASLLAQTL 1471
Cdd:COG0464    175 LPLKRPELREEYGLPPPRGLLLYGPPGTGKTLLARALAGEL 215

RecA-like_protease

cd19481

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

1424-1471

4.03e-04

Pssm-ID: 410889 [Multi-domain] Cd Length: 158 Bit Score: 43.04 E-value: 4.03e-04

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 2347425630 1424 QSLKNYTLALSQHRKRQVGPRPEPVVVYFYGPPGTGKSLLASLLAQTL 1471
Cdd:cd19481      3 ASLREAVEAPRRGSRLRRYGLGLPKGILLYGPPGTGKTLLAKALAGEL 50

AAA

smart00382

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

1449-1574

9.53e-04

Pssm-ID: 214640 [Multi-domain] Cd Length: 148 Bit Score: 41.98 E-value: 9.53e-04

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630  1449 VVYFYGPPGTGKSLLASLLAQTLAQR------LSGDPDDVYSPTAASCEYFDGYNGQSVH-------------------F 1503
Cdd:smart00382    4 VILIVGPPGSGKTTLARALARELGPPgggviyIDGEDILEEVLDQLLLIIVGGKKASGSGelrlrlalalarklkpdvlI 83

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2347425630  1504 IDDIG--QDPEGRDWANFpnlvssapyILPMASLEEKGIHYTSRVIVVTSNFHEPNERAARSMgaLRRRVHLR 1574
Cdd:smart00382   84 LDEITslLDAEQEALLLL---------LEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRRR--FDRRIVLL 145

Rhv

pfam00073

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

864-944

6.17e-03

Pssm-ID: 395026 Cd Length: 170 Bit Score: 39.99 E-value: 6.17e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2347425630  864 FTYIAADLRFTLRLsNPNGVPA-TVLIAYAPPGATLPRTPDRQMLSNFFMSEIPISASNATlISFSIPYTSPLSAIPTTY 942
Cdd:pfam00073   77 HTYYRGGLEVTVQF-NGSKFHQgKLLVAYVPPGAPPPGSRDYLWQATLNPHQFWNLGLNSS-ARLSVPYISIAHYYSTFY 154


                   ..
gi 2347425630  943 YG 944
Cdd:pfam00073  155 DG 156

PRK13342

recombination factor protein RarA; Reviewed

1452-1471

8.86e-03

recombination factor protein RarA; Reviewed

Pssm-ID: 237355 [Multi-domain] Cd Length: 413 Bit Score: 41.22 E-value: 8.86e-03

                           10        20
                   ....*....|....*....|
gi 2347425630 1452 FYGPPGTGKSLLASLLAQTL 1471
Cdd:PRK13342    41 LWGPPGTGKTTLARIIAGAT 60

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