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Conserved domains on  [gi|1934859774|emb|CAD7112394|]
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ORF 1 gene, partial [European brown hare syndrome virus]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Caliciviridae_RdRp cd23192
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Caliciviridae of ...
1407-1716 5.31e-165

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: 509.50  E-value: 5.31e-165
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1407 HVYACGLKDELRPLDKVKEGKKRLLWGCDVGVALCAAAVFHNLCFKLKTVARFGPIAVGIDMTSRDVDVMITQLtSKAGD 1486
Cdd:cd23192      1 HAYALALKDELRPVEKIAEGKRRLLWGCDVGVTLVAAAAFGPVADALKAVCPTGPIAVGINMDSEDVEVIFERL-SGFRY 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1487 FLCLDYSKWDSTMSPCVVRLAIDILADCCEQTELTKSVVLTLKSLPMTVLDAMIVPTKRGLPSGMPFTSVINSICHWLLW 1566
Cdd:cd23192     80 HYCLDYSKWDSTQSPAVTAAAIDILADLSEETPLRDSVVETLSSPPMGIFDDVIFVTKRGLPSGMPFTSVINSLNHWLLF 159
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1567 SAAVYKACDEIGLFCSNLYEDAPFFVYGDDGVYAMTPMMVSLLPAILDNLRDYGLSPTAADKTEFIDVCPLKNISFLKRK 1646
Cdd:cd23192    160 SAAVLKAYELVGIYTGNVFDEADFFTYGDDGVYAMPPATASVMDEIIENLKSYGLKPTAADKTENPDIPPLQGPVFLKRT 239
                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1647 FIMSELGWLSQLDKSSILRQLEWTKTTKRHMCIEECSELDKDERGVQLEELQVHAAAHGEEFFELVRKEL 1716
Cdd:cd23192    240 FVRTPGGWRALLDRSSILRQLYWVKGPNTHDWTEPPTEIDHEARTVQLENVLLEAAQHGPEFYEKVLKLV 309
Calici_coat pfam00915
Calicivirus coat protein;
1758-2050 3.64e-137

Calicivirus coat protein;


:

Pssm-ID: 459994  Cd Length: 291  Bit Score: 430.47  E-value: 3.64e-137
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1758 GKPRAD--APGTATTASVPGTTTDGMDPGVVAsTDVVTADNVAASVATAGIGGPPQQAspQESWRANFFYNDVFTWSVTD 1835
Cdd:pfam00915    1 MMASKDpqGAGTATSESDGASGTGILVPEVGA-SVPLAMAPVSGSSATAATAGQGKSV--DQEWITNFSYHTSQNWSTIE 77
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1836 APGSILYTVQHSPQNNPFTQVLSQMYAGWAGGMQFRFIVAGSGIFGGRLVCAIIPPGIQIQPGLEVRQFPHVVIDARSLE 1915
Cdd:pfam00915   78 PQGKVLFDQSLGPHLNPFLLHLSQMYNGWSGGMRVRFMVAGSGVFGGKLAASVIPPGVEPITSASMLQFPHVLFDARQLE 157
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1916 PVTITMPDLRPEMYHPTGNPGLVPTLVVSVYNNLINPFGGT-TSAIQVTVETRPSEDFEFVLIRAPSSKTVESVNPSwlL 1994
Cdd:pfam00915  158 PVIFTIPDLRNTLFHNMDRNTDTTRLVIMVYNPLINPGGTGdSSVCAVTVETRPSPDFNFLLLKPPGSTVEHGSRPS--D 235
                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1934859774 1995 TTPVLTGAGSDNRWGAPIVGLQPVPGGFSTCNRHWNMNGETYGWSSPRFDDIDHPS 2050
Cdd:pfam00915  236 TIPNLSLSWLGNRWWSPISGFGISPQVFQFQNRHFDLDGRTVGWSTPRFAPIRGTI 291
Peptidase_C24 pfam03510
2C endopeptidase (C24) cysteine protease family;
1110-1208 2.45e-36

2C endopeptidase (C24) cysteine protease family;


:

Pssm-ID: 281505  Cd Length: 105  Bit Score: 133.83  E-value: 2.45e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1110 GWMIHIGNGLYLSNTHTARSSC----SEIVTCSPTTDLCLVKAEPI-RSVAQIAEGTPVRDWKKASI-TTYGLKKTFSDS 1183
Cdd:pfam03510    1 GYMVHIGNGVYITVTHVASGSDeilgSEIVTIRTTGELCLVRGEKIlPSAAQIGEGKPVKDPTGSPVsTTFGIKNYTVTS 80
                           90       100
                   ....*....|....*....|....*
gi 1934859774 1184 TKIDVLAYDGPTQTTHGDCGLPLFD 1208
Cdd:pfam03510   81 GKIDGLAGDGCTETTHGDCGLPYVD 105
RNA_helicase pfam00910
RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...
510-605 2.24e-27

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: 108.08  E-value: 2.24e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774  510 IIFKGAPGIGKTYLVHRLAKDLGCPHPSN------INFGLDHFDSYTGEDVAIADEFNTSGDERWVELFIQMVNTNPCPL 583
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKKLGLPkdsvysRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80
                           90       100
                   ....*....|....*....|..
gi 1934859774  584 NCDKVENKNKVFNSKYLLCTTN 605
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102
 
Name Accession Description Interval E-value
Caliciviridae_RdRp cd23192
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Caliciviridae of ...
1407-1716 5.31e-165

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: 509.50  E-value: 5.31e-165
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1407 HVYACGLKDELRPLDKVKEGKKRLLWGCDVGVALCAAAVFHNLCFKLKTVARFGPIAVGIDMTSRDVDVMITQLtSKAGD 1486
Cdd:cd23192      1 HAYALALKDELRPVEKIAEGKRRLLWGCDVGVTLVAAAAFGPVADALKAVCPTGPIAVGINMDSEDVEVIFERL-SGFRY 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1487 FLCLDYSKWDSTMSPCVVRLAIDILADCCEQTELTKSVVLTLKSLPMTVLDAMIVPTKRGLPSGMPFTSVINSICHWLLW 1566
Cdd:cd23192     80 HYCLDYSKWDSTQSPAVTAAAIDILADLSEETPLRDSVVETLSSPPMGIFDDVIFVTKRGLPSGMPFTSVINSLNHWLLF 159
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1567 SAAVYKACDEIGLFCSNLYEDAPFFVYGDDGVYAMTPMMVSLLPAILDNLRDYGLSPTAADKTEFIDVCPLKNISFLKRK 1646
Cdd:cd23192    160 SAAVLKAYELVGIYTGNVFDEADFFTYGDDGVYAMPPATASVMDEIIENLKSYGLKPTAADKTENPDIPPLQGPVFLKRT 239
                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1647 FIMSELGWLSQLDKSSILRQLEWTKTTKRHMCIEECSELDKDERGVQLEELQVHAAAHGEEFFELVRKEL 1716
Cdd:cd23192    240 FVRTPGGWRALLDRSSILRQLYWVKGPNTHDWTEPPTEIDHEARTVQLENVLLEAAQHGPEFYEKVLKLV 309
Calici_coat pfam00915
Calicivirus coat protein;
1758-2050 3.64e-137

Calicivirus coat protein;


Pssm-ID: 459994  Cd Length: 291  Bit Score: 430.47  E-value: 3.64e-137
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1758 GKPRAD--APGTATTASVPGTTTDGMDPGVVAsTDVVTADNVAASVATAGIGGPPQQAspQESWRANFFYNDVFTWSVTD 1835
Cdd:pfam00915    1 MMASKDpqGAGTATSESDGASGTGILVPEVGA-SVPLAMAPVSGSSATAATAGQGKSV--DQEWITNFSYHTSQNWSTIE 77
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1836 APGSILYTVQHSPQNNPFTQVLSQMYAGWAGGMQFRFIVAGSGIFGGRLVCAIIPPGIQIQPGLEVRQFPHVVIDARSLE 1915
Cdd:pfam00915   78 PQGKVLFDQSLGPHLNPFLLHLSQMYNGWSGGMRVRFMVAGSGVFGGKLAASVIPPGVEPITSASMLQFPHVLFDARQLE 157
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1916 PVTITMPDLRPEMYHPTGNPGLVPTLVVSVYNNLINPFGGT-TSAIQVTVETRPSEDFEFVLIRAPSSKTVESVNPSwlL 1994
Cdd:pfam00915  158 PVIFTIPDLRNTLFHNMDRNTDTTRLVIMVYNPLINPGGTGdSSVCAVTVETRPSPDFNFLLLKPPGSTVEHGSRPS--D 235
                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1934859774 1995 TTPVLTGAGSDNRWGAPIVGLQPVPGGFSTCNRHWNMNGETYGWSSPRFDDIDHPS 2050
Cdd:pfam00915  236 TIPNLSLSWLGNRWWSPISGFGISPQVFQFQNRHFDLDGRTVGWSTPRFAPIRGTI 291
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
1278-1718 5.92e-119

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: 384.84  E-value: 5.92e-119
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1278 VPGVPEEYHTG-YRPANLGRGDPDS--HHTLMNIAVKNLQVYQQEPKLTKVD----TFIERAAADVLGFLRFLTKG---- 1346
Cdd:pfam00680    1 SPTERHLVAIPaYVPASLGPEDPRWarSYLNTDPYVDDIKKYSRPKLPGPADerdkLLNRSAAKMVLSELRGVPKKanst 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1347 -ERQMNLNFSAAFNVLDLSTSCG-PFV-----PGKKIDHVKDGKLDEILSKHLYKCWSVANSGKALHHVYACGLKDELRP 1419
Cdd:pfam00680   81 lIVYRAIDGVEQIDPLNWDTSAGyPYVglggkKGDLIEHLKDGTEARELAERLAADWEVLQNGTPLKLVYQTCLKDELRP 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1420 LDKVKEGKKRLLWGCDVGVALCAAAVFHNLCFKLKTVARFGPIAVGIDMTSRDVDVMITQLTSKAGDFLCLDYSKWDSTM 1499
Cdd:pfam00680  161 LEKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHPIQVGINPFDRGWPRLLRRLARFGDYVYELDYSGFDSSV 240
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1500 SPCVVRLAIDILADCCEQTELTKS---VVLTLKSLPMTVLDAMIVPTKRGLPSGMPFTSVINSICHWLLWSAAVYKACDE 1576
Cdd:pfam00680  241 PPWLIRFAFEILRELLGFPSNVKEwraILELLIYTPIALPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYALLKSLEN 320
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1577 IGLFCSNLYEDAPFFVYGDDGVYAMTPMMVSLLPAILDNLRDYGLSPTAADKTeFIDVCPLKNISFLKRKFIMSELGWLS 1656
Cdd:pfam00680  321 DGPRVCNLDKYFDFFTYGDDSLVAVSPDFDPVLDRLSPHLKELGLTITPAKKT-FPVSRELEEVSFLKRTFRKTPGGYRP 399
                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1934859774 1657 QLDKSSILRQLEWTKTtkrhmcieecseldKDERGVQLEELQVHAAAHGEEFFelvRKELCR 1718
Cdd:pfam00680  400 PLDRKRILAQLEYIRS--------------KPVPSGQLENIRAYASHHGYEFY---RDLLYR 444
Peptidase_C24 pfam03510
2C endopeptidase (C24) cysteine protease family;
1110-1208 2.45e-36

2C endopeptidase (C24) cysteine protease family;


Pssm-ID: 281505  Cd Length: 105  Bit Score: 133.83  E-value: 2.45e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1110 GWMIHIGNGLYLSNTHTARSSC----SEIVTCSPTTDLCLVKAEPI-RSVAQIAEGTPVRDWKKASI-TTYGLKKTFSDS 1183
Cdd:pfam03510    1 GYMVHIGNGVYITVTHVASGSDeilgSEIVTIRTTGELCLVRGEKIlPSAAQIGEGKPVKDPTGSPVsTTFGIKNYTVTS 80
                           90       100
                   ....*....|....*....|....*
gi 1934859774 1184 TKIDVLAYDGPTQTTHGDCGLPLFD 1208
Cdd:pfam03510   81 GKIDGLAGDGCTETTHGDCGLPYVD 105
RNA_helicase pfam00910
RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...
510-605 2.24e-27

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: 108.08  E-value: 2.24e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774  510 IIFKGAPGIGKTYLVHRLAKDLGCPHPSN------INFGLDHFDSYTGEDVAIADEFNTSGDERWVELFIQMVNTNPCPL 583
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKKLGLPkdsvysRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80
                           90       100
                   ....*....|....*....|..
gi 1934859774  584 NCDKVENKNKVFNSKYLLCTTN 605
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
1819-1981 5.62e-25

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: 104.02  E-value: 5.62e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1819 WRANFFYNDVFTWSVTDAPGSILYtvqhspQNNPFTQVLsQMYAGWAGGMQFRFIVAGSGIFGGRLVCAIIPPGIQIQPG 1898
Cdd:cd00205     16 WNSSASGTQLFQWKLSPALGFLLL------QNTPLGALL-SYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPPGAPAPTT 88
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1899 LEVRQ----FPHVVIDARSLEPVTITMPDLRPEMYHPTGNPGLVP-----TLVVSVYNNLINPFGGTTSaIQVTVETRPs 1969
Cdd:cd00205     89 GDTRWqatlNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDGYGPlnsfgTLVVRVLTPLTVPSGAPTT-VDITVYVRA- 166
                          170
                   ....*....|..
gi 1934859774 1970 EDFEFVLIRAPS 1981
Cdd:cd00205    167 GDFELYGPRPPR 178
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
494-589 2.77e-07

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: 52.15  E-value: 2.77e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774  494 VLGKINMTKQRPQPVAIIFKGAPGIGKTYLVHRLAKDLGcpHPSNINFGLDHFDSYTGEDVAIADEFntsgdERWVELFI 573
Cdd:cd00009      6 AIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELF--RPGAPFLYLNASDLLEGLVVAELFGH-----FLVRLLFE 78
                           90
                   ....*....|....*.
gi 1934859774  574 QMVNTNPCPLNCDKVE 589
Cdd:cd00009     79 LAEKAKPGVLFIDEID 94
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
509-538 3.16e-04

DNA polymerase III, delta prime subunit [Replication, recombination and repair];


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 44.97  E-value: 3.16e-04
                           10        20        30
                   ....*....|....*....|....*....|
gi 1934859774  509 AIIFKGAPGIGKTYLVHRLAKDLGCPHPSN 538
Cdd:COG0470     20 ALLLHGPPGIGKTTLALALARDLLCENPEG 49
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
504-630 9.28e-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: 9.28e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774   504 RPQPVAIIfkGAPGIGKTYLVHRLAKDLGCPHPSNINFGLDHFDSYTGED---VAIADEFNTSGDERWVELFIQMVNTNP 580
Cdd:smart00382    1 PGEVILIV--GPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQlllIIVGGKKASGSGELRLRLALALARKLK 78
                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1934859774   581 CPL---------------------NCDKVENKNKVFNSKYLLCTTNSSMVLNATHPRAtAFYRRVIIVDVR 630
Cdd:smart00382   79 PDVlildeitslldaeqealllllEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLIL 148
FN3 COG3401
Fibronectin type 3 domain [General function prediction only];
1929-2146 7.85e-03

Fibronectin type 3 domain [General function prediction only];


Pssm-ID: 442628 [Multi-domain]  Cd Length: 603  Bit Score: 41.53  E-value: 7.85e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1929 YHPTGNPGLVPTLVVSVYNNLINPFGGTTSAIQVTVETRPS-EDFEFVLIRAPSSKTVESVNPSWLLTTPVLTGAGSDNR 2007
Cdd:COG3401      5 YLTSLDAGIAASAAANTAVNALSKAGGSGKTILVYLAVVLSvTTKESPGTLLVAAGLSSGGGLGTGGRAGTTSGVAAVAV 84
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 2008 WGAPIVGLQPVPG-GFSTCNRHWNMNGETYGWSSPRFDDIDHPSGNVSYPTGSATNT---------IETWYANAGTATTN 2077
Cdd:COG3401     85 AAAPPTATGLTTLtGSGSVGGATNTGLTSSDEVPSPAVGTATTATAVAGGAATAGTYalgaglygvDGANASGTTASSVA 164
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1934859774 2078 PISNVAPDGFPDMGAIPFSGTTIPTGAWVGFGQVWNasNGTPYVGTVQAYELGfANGAPSNIRPVTTTT 2146
Cdd:COG3401    165 GAGVVVSPDTSATAAVATTSLTVTSTTLVDGGGDIE--PGTTYYYRVAATDTG-GESAPSNEVSVTTPT 230
 
Name Accession Description Interval E-value
Caliciviridae_RdRp cd23192
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Caliciviridae of ...
1407-1716 5.31e-165

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: 509.50  E-value: 5.31e-165
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1407 HVYACGLKDELRPLDKVKEGKKRLLWGCDVGVALCAAAVFHNLCFKLKTVARFGPIAVGIDMTSRDVDVMITQLtSKAGD 1486
Cdd:cd23192      1 HAYALALKDELRPVEKIAEGKRRLLWGCDVGVTLVAAAAFGPVADALKAVCPTGPIAVGINMDSEDVEVIFERL-SGFRY 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1487 FLCLDYSKWDSTMSPCVVRLAIDILADCCEQTELTKSVVLTLKSLPMTVLDAMIVPTKRGLPSGMPFTSVINSICHWLLW 1566
Cdd:cd23192     80 HYCLDYSKWDSTQSPAVTAAAIDILADLSEETPLRDSVVETLSSPPMGIFDDVIFVTKRGLPSGMPFTSVINSLNHWLLF 159
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1567 SAAVYKACDEIGLFCSNLYEDAPFFVYGDDGVYAMTPMMVSLLPAILDNLRDYGLSPTAADKTEFIDVCPLKNISFLKRK 1646
Cdd:cd23192    160 SAAVLKAYELVGIYTGNVFDEADFFTYGDDGVYAMPPATASVMDEIIENLKSYGLKPTAADKTENPDIPPLQGPVFLKRT 239
                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1647 FIMSELGWLSQLDKSSILRQLEWTKTTKRHMCIEECSELDKDERGVQLEELQVHAAAHGEEFFELVRKEL 1716
Cdd:cd23192    240 FVRTPGGWRALLDRSSILRQLYWVKGPNTHDWTEPPTEIDHEARTVQLENVLLEAAQHGPEFYEKVLKLV 309
Calici_coat pfam00915
Calicivirus coat protein;
1758-2050 3.64e-137

Calicivirus coat protein;


Pssm-ID: 459994  Cd Length: 291  Bit Score: 430.47  E-value: 3.64e-137
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1758 GKPRAD--APGTATTASVPGTTTDGMDPGVVAsTDVVTADNVAASVATAGIGGPPQQAspQESWRANFFYNDVFTWSVTD 1835
Cdd:pfam00915    1 MMASKDpqGAGTATSESDGASGTGILVPEVGA-SVPLAMAPVSGSSATAATAGQGKSV--DQEWITNFSYHTSQNWSTIE 77
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1836 APGSILYTVQHSPQNNPFTQVLSQMYAGWAGGMQFRFIVAGSGIFGGRLVCAIIPPGIQIQPGLEVRQFPHVVIDARSLE 1915
Cdd:pfam00915   78 PQGKVLFDQSLGPHLNPFLLHLSQMYNGWSGGMRVRFMVAGSGVFGGKLAASVIPPGVEPITSASMLQFPHVLFDARQLE 157
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1916 PVTITMPDLRPEMYHPTGNPGLVPTLVVSVYNNLINPFGGT-TSAIQVTVETRPSEDFEFVLIRAPSSKTVESVNPSwlL 1994
Cdd:pfam00915  158 PVIFTIPDLRNTLFHNMDRNTDTTRLVIMVYNPLINPGGTGdSSVCAVTVETRPSPDFNFLLLKPPGSTVEHGSRPS--D 235
                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1934859774 1995 TTPVLTGAGSDNRWGAPIVGLQPVPGGFSTCNRHWNMNGETYGWSSPRFDDIDHPS 2050
Cdd:pfam00915  236 TIPNLSLSWLGNRWWSPISGFGISPQVFQFQNRHFDLDGRTVGWSTPRFAPIRGTI 291
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
1278-1718 5.92e-119

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: 384.84  E-value: 5.92e-119
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1278 VPGVPEEYHTG-YRPANLGRGDPDS--HHTLMNIAVKNLQVYQQEPKLTKVD----TFIERAAADVLGFLRFLTKG---- 1346
Cdd:pfam00680    1 SPTERHLVAIPaYVPASLGPEDPRWarSYLNTDPYVDDIKKYSRPKLPGPADerdkLLNRSAAKMVLSELRGVPKKanst 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1347 -ERQMNLNFSAAFNVLDLSTSCG-PFV-----PGKKIDHVKDGKLDEILSKHLYKCWSVANSGKALHHVYACGLKDELRP 1419
Cdd:pfam00680   81 lIVYRAIDGVEQIDPLNWDTSAGyPYVglggkKGDLIEHLKDGTEARELAERLAADWEVLQNGTPLKLVYQTCLKDELRP 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1420 LDKVKEGKKRLLWGCDVGVALCAAAVFHNLCFKLKTVARFGPIAVGIDMTSRDVDVMITQLTSKAGDFLCLDYSKWDSTM 1499
Cdd:pfam00680  161 LEKVEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHPIQVGINPFDRGWPRLLRRLARFGDYVYELDYSGFDSSV 240
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1500 SPCVVRLAIDILADCCEQTELTKS---VVLTLKSLPMTVLDAMIVPTKRGLPSGMPFTSVINSICHWLLWSAAVYKACDE 1576
Cdd:pfam00680  241 PPWLIRFAFEILRELLGFPSNVKEwraILELLIYTPIALPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYALLKSLEN 320
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1577 IGLFCSNLYEDAPFFVYGDDGVYAMTPMMVSLLPAILDNLRDYGLSPTAADKTeFIDVCPLKNISFLKRKFIMSELGWLS 1656
Cdd:pfam00680  321 DGPRVCNLDKYFDFFTYGDDSLVAVSPDFDPVLDRLSPHLKELGLTITPAKKT-FPVSRELEEVSFLKRTFRKTPGGYRP 399
                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1934859774 1657 QLDKSSILRQLEWTKTtkrhmcieecseldKDERGVQLEELQVHAAAHGEEFFelvRKELCR 1718
Cdd:pfam00680  400 PLDRKRILAQLEYIRS--------------KPVPSGQLENIRAYASHHGYEFY---RDLLYR 444
RNA_dep_RNAP cd01699
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
1388-1670 2.51e-69

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: 235.26  E-value: 2.51e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1388 LSKHLYKCWSVANSGKalHHVYACGLKDELRPLDKVKEGKKRLLWGCDVGVALCAAAVFHNLCFKLKTVARFGPIAVGID 1467
Cdd:cd01699      1 LEKAVESLEDLPLIRP--DLVFTTFLKDELRPLEKVEAGKTRLIQPRPLDYNIALRMYLGPFEAKLMKNRGGLPIAVGIN 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1468 MTSRDVDVMITQLTSKAGDFLCLDYSKWDSTMSPCVVRLAIDILADCCEQ------TELTKSVVLTLKSlpmtVLDAMIV 1541
Cdd:cd01699     79 PYSRDWTILANKLRSFSPVAIALDYSRFDSSLSPQLLEAEHSIYNALYDDddelerRNLLRSLTNNSLH----IGFNEVY 154
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1542 PTKRGLPSGMPFTSVINSICHWLLWSAAVYKacdeigLFCSNLYEDAPFFVYGDDGVYAMTP-MMVSLLPAILDNLRDYG 1620
Cdd:cd01699    155 KVRGGRPSGDPLTSIGNSIINCILVRYAFRK------LGGKSFFKNVRLLNYGDDCLLSVEKaDDKFNLETLAEWLKEYG 228
                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1934859774 1621 LSPTAADKTEFIdVCPLKNISFLKRKFIM-SELGWLSQLDKSSILRQLEWT 1670
Cdd:cd01699    229 LTMTDEDKVESP-FRPLEEVEFLKRRFVLdEGGGWRAPLDPSSILSKLSWS 278
ps-ssRNAv-Picornavirales cd23169
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of ...
1413-1717 1.89e-51

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: 184.72  E-value: 1.89e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1413 LKDELRPLDKVKEGKKRLLWGCDVGVALCAAAVFHNLCFKLKTVARFGPIAVGIDMTSRDVDVMITQLTSKAGDFLCLDY 1492
Cdd:cd23169      7 LKDELRPIEKVKAGKTRLFSASPLDYTIAFRKYFGDFIAAFQKNRIKLEHAVGINPDSVEWTRLYRRLLKKGPNIFAGDY 86
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1493 SKWDSTMSPCVVRLAIDILADCCEQTELTKSVVLtLKSLPMTVLDAMIVP------TKRGLPSGMPFTSVINSICHWLLW 1566
Cdd:cd23169     87 SNFDGSLPPDVMEAAFDIINDWYDEYVDDEDERV-RKVLFEELINTIHLVgnlvyqVHGGNPSGNPLTTIINSIVNLLYI 165
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1567 SAAVYKACDEIGLfcSNLYEDAPFFVYGDDGVYAMTPMMVSLL--PAILDNLRDYGLSPTAADKTE-FIDVCPLKNISFL 1643
Cdd:cd23169    166 RYAWLRITGLTSL--SDFKKNVRLVTYGDDVIISVSDEVKDEFnfVTISEFLKELGITYTDADKSGdIVPYRPLEEVTFL 243
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1644 KRKFIMSELG--WLSQLDKSSILRQLEWTKTTKRHM------CIEECSeldkdergvqleelqvHAAAHGEEFFELVRKE 1715
Cdd:cd23169    244 KRGFRPHPTPglVLAPLDLESIEEQLNWTRKEDDLLeatienARAALL----------------LAFGHGPEYYNKFRQK 307

                   ..
gi 1934859774 1716 LC 1717
Cdd:cd23169    308 LN 309
ps-ssRNA_Picornaviridae cd23193
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Picornaviridae of ...
1361-1716 2.56e-41

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: 156.55  E-value: 2.56e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1361 LDLSTSCG-PFVP-GKK----IDHVKDGKLDEILSKhlykcWSVANSGKALHHVYACGLKDELRPLDKVKEGKKRLLWGC 1434
Cdd:cd23193     11 IDLNTSPGyPYTTqGLRrrdlIDNDKGGVSPLLEEE-----EQVLLDLDGPDVVFTTFLKDELRPKEKVKAGKTRVIEAA 85
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1435 DVGVALCAAAVFHNLC--FKLKTVARFGpIAVGIDmTSRDVDVMITQLTSKagDFLCLDYSKWDSTMSPCVVRLAIDILA 1512
Cdd:cd23193     86 PLDYVIAGRMVFGRLFaqFHSNPGILTG-SAVGCN-PDTDWTRLFASLKQD--NVYDLDYSGFDASLSSQLFEAAVEVLA 161
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1513 DCCEQTELtksVVLTLKSLPMT--VLDAMIVPTKRGLPSGMPFTSVINSICHWLLWSAAVYKACDEiglFCSNLYedapF 1590
Cdd:cd23193    162 ECHGDPEL---VLRYLEPIINSkhVVGDERYTVEGGMPSGCPCTSILNSICNNLVVRYALLETGKF---DPDEYY----I 231
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1591 FVYGDDGVYAMT-PMMVSLLPAILDNLrdYGLSPTAADKTEFIDVCPLKNISFLKRKFIMSELGWL--SQLDKSSILRQL 1667
Cdd:cd23193    232 LAYGDDVLVSTDePIDPSDLAEFYKKY--FGMTVTPADKSSDFPESSPIEDVFLKRRFFVPDGTFLihPVMDLETLEQSL 309
                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*....
gi 1934859774 1668 EWTKttkrhmcieecSELDKDERGVQLEELQVHaaaHGEEFFELVRKEL 1716
Cdd:cd23193    310 MWCG-----------RGGFFQQLLSSLCELALH---HGPEEYERLVSKV 344
Peptidase_C24 pfam03510
2C endopeptidase (C24) cysteine protease family;
1110-1208 2.45e-36

2C endopeptidase (C24) cysteine protease family;


Pssm-ID: 281505  Cd Length: 105  Bit Score: 133.83  E-value: 2.45e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1110 GWMIHIGNGLYLSNTHTARSSC----SEIVTCSPTTDLCLVKAEPI-RSVAQIAEGTPVRDWKKASI-TTYGLKKTFSDS 1183
Cdd:pfam03510    1 GYMVHIGNGVYITVTHVASGSDeilgSEIVTIRTTGELCLVRGEKIlPSAAQIGEGKPVKDPTGSPVsTTFGIKNYTVTS 80
                           90       100
                   ....*....|....*....|....*
gi 1934859774 1184 TKIDVLAYDGPTQTTHGDCGLPLFD 1208
Cdd:pfam03510   81 GKIDGLAGDGCTETTHGDCGLPYVD 105
Dicistroviridae_RdRp cd23194
RNA-dependent RNA polymerase (RdRp) in the family Dicistroviridae of positive-sense ...
1402-1716 8.38e-30

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: 122.22  E-value: 8.38e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1402 GKALHHVYACGLKDELRPLDKVKEGKKRLLWGCDVGVALC--------AAAVFHNlcfklktvaR-FGPIAVGIDMTSRD 1472
Cdd:cd23194      1 GIRLPHVFVDTLKDERRPIEKVDAGKTRVFSAGPMDYTIAfrmyflgfVAHLMRN---------RiDNEIAVGTNVYSLD 71
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1473 VDVMITQLTSK-----AGDFlcldySKWDSTMSPCVVRLAIDILADCCEQTELTKSVvltlkslpMTVLDAMIVP----- 1542
Cdd:cd23194     72 WDKLARKLLSKgdkviAGDF-----SNFDGSLNPQILWAILDIINEWYDDGEENALI--------RRVLWEDIVNsvhic 138
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1543 -------TKrGLPSGMPFTSVINSICHWLLWSAAVYKACDEIGLFC-SNLYEDAPFFVYGDDGVYAMTPMMVSLLP--AI 1612
Cdd:cd23194    139 ggyvyqwTH-SQPSGNPLTAIINSIYNSIIMRYVYLLLTKEAGLMTmSDFNKHVSMVSYGDDNVINVSDEVSEWFNqlTI 217
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1613 LDNLRDYGLSPTAADKTEFIDVC-PLKNISFLKRKFIMSEL--GWLSQLDKSSILRQLEWTKTTKrhmcieecselDKDE 1689
Cdd:cd23194    218 TEAMAEIGMTYTDETKTGEIVPYrSLEEVSFLKRGFRYDDDlgRWVAPLDLDTILEMPNWVRKGK-----------DPEE 286
                          330       340       350
                   ....*....|....*....|....*....|..
gi 1934859774 1690 RGVQ-----LEELqvhaAAHGEEFFELVRKEL 1716
Cdd:cd23194    287 ITKQnvenaLREL----SLHGEEVFDKWAPKI 314
RNA_helicase pfam00910
RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...
510-605 2.24e-27

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: 108.08  E-value: 2.24e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774  510 IIFKGAPGIGKTYLVHRLAKDLGCPHPSN------INFGLDHFDSYTGEDVAIADEFNTSGDERWVELFIQMVNTNPCPL 583
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKKLGLPkdsvysRNPDDDFWDGYTGQPVVIIDDFGQNPDGPDEAELIRLVSSTPYPP 80
                           90       100
                   ....*....|....*....|..
gi 1934859774  584 NCDKVENKNKVFNSKYLLCTTN 605
Cdd:pfam00910   81 PMAALEEKGTPFTSKFVIVTSN 102
Marnaviridae_RdRp cd23195
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Marnaviridae of ...
1408-1717 9.32e-26

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: 110.23  E-value: 9.32e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1408 VYACGLKDELRPLDKvkeGKKRLLWGCDVGVALcaaavfhnLCFK-LKTVARF---GPI----AVGIDMTSRDVDVMITQ 1479
Cdd:cd23195      2 IFKACLKDEPTKLTK---DKVRVFQAAPVALQL--------LVRKyFLPIARFlqmNPLlsecAVGINAQSPEWEELYEH 70
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1480 LTSKAGD-FLCLDYSKWDSTMSPCVVRLAIDILADCCEqteltksvvltlKSLPMTVLDAMIVptkRGL----------- 1547
Cdd:cd23195     71 LTKFGEDrIIAGDYSKYDKRMSAQLILAAFKILIDIAA------------KSGGYSEEDLKIM---RGIatdiayplvdf 135
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1548 -----------PSGMPFTSVINSICHWLLWSAAVYKACDEiglfcsnlYEDAPF------FVYGDD---GV------YAM 1601
Cdd:cd23195    136 ngdliqffgsnPSGHPLTVIINSIVNSLYMRYAYYSLYPE--------KEVPPFrdvvalMTYGDDnimSVspgypwFNH 207
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1602 TpmmvsllpAILDNLRDYGLSPTAADKT-EFIDVCPLKNISFLKRKFIMS-ELG-WLSQLDKSSILRQLEWTKTTKrhmc 1678
Cdd:cd23195    208 T--------SIAEFLAKIGIKYTMADKEaESVPFIHISEADFLKRKFVFDpELGvYVGPLDEDSIFKSLHCYLKSK---- 275
                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....
gi 1934859774 1679 ieecsELDKDERGVQ-----LEELqvhaAAHGEEFFELVRKELC 1717
Cdd:cd23195    276 -----VLTPEEQAAQnidgaLREW----FFHGREVYEKRREQLK 310
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
1819-1981 5.62e-25

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: 104.02  E-value: 5.62e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1819 WRANFFYNDVFTWSVTDAPGSILYtvqhspQNNPFTQVLsQMYAGWAGGMQFRFIVAGSGIFGGRLVCAIIPPGIQIQPG 1898
Cdd:cd00205     16 WNSSASGTQLFQWKLSPALGFLLL------QNTPLGALL-SYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPPGAPAPTT 88
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1899 LEVRQ----FPHVVIDARSLEPVTITMPDLRPEMYHPTGNPGLVP-----TLVVSVYNNLINPFGGTTSaIQVTVETRPs 1969
Cdd:cd00205     89 GDTRWqatlNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDGYGPlnsfgTLVVRVLTPLTVPSGAPTT-VDITVYVRA- 166
                          170
                   ....*....|..
gi 1934859774 1970 EDFEFVLIRAPS 1981
Cdd:cd00205    167 GDFELYGPRPPR 178
Fipivirus_RdRp cd23229
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Fipivirus of ...
1409-1713 3.71e-24

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: 107.59  E-value: 3.71e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1409 YACGLKDELRPLDKVKEGKKRLLWGCDVGVALCAAAVF-------HNL-CFKLKTVArfgpIAVGIDMTSRDVDVMitql 1480
Cdd:cd23229     69 YVVYLKDELLSSDKVKMGRTRWICAAPVQLVCAWKKVFgraiaaiHLEsVTDGKSTG----CAVGMDPETAWTDIA---- 140
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1481 TSKAG-DFLCLDYSKWDSTMSPCVVRLAIDILADCC----EQTELTKSVVLTLKSlpmtVLDAMIVPTKRGLPSGMPFTS 1555
Cdd:cd23229    141 LARPGwPVIALDYSNFDGSLQSFVITGAVRILGYIAglpdGQSYRLAEFVYDVKQ----IVGKYLYTTVGPLPSGCPSTS 216
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1556 VINSICHWLlwsAAVYKACDEIGLFCSNLYEDAPFFVYGDDGVYAMTPMMVSllpaILDNLRD-----YGLSPT-AADKT 1629
Cdd:cd23229    217 IIGSLCNVL---MLLYTLSHATGQRYSAFRDWMHVVTYGDDVLVFVHPEVVV----VLDTLAHemylvFGVTATdATDKR 289
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1630 EFIDVCPLKNISFLKRKF---IMSELGWLSQLDKSSILRQLEWTKttkrhmcieecseldkdeRGVQLEELqVHAAA--- 1703
Cdd:cd23229    290 APPQLRELSNVTFLKRGFrqcSSVPFLVHPTMDKSTIYQMLAWKR------------------KGTTLAEN-VKCAAefm 350
                          330
                   ....*....|..
gi 1934859774 1704 --HGEEFFELVR 1713
Cdd:cd23229    351 mhHGEEEYEDFV 362
Parechovirus_RdRp cd23217
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Parechovirus of ...
1359-1671 3.58e-23

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: 104.18  E-value: 3.58e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1359 NVLDLSTScgpfvPGKKidHVKDG--KLDEI----------LSKHLYKCWSVANSGKALHHVYACGLKDELRPLDKVKEG 1426
Cdd:cd23217      9 NSLDLSTS-----PGYK--YVKSGykKRDLLslepfsvspqLEKDVKDKLHAVYKGNQPTTIFNACLKDELRKLDKIAQG 81
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1427 KKRLLWGCDVGVALCAAAVFHNLCFKL-KTVARFGPIAVGIDmTSRDVDVMITQLTSKAGDflcLDYSKWDSTMSPCVVR 1505
Cdd:cd23217     82 KTRCIEACSIDYVIAYRVVMSSLYEAIyQTPCQELGLAVGMN-PWTDWDFMINALNPYNYG---LDYSSYDGSLSEMLMW 157
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1506 LAIDILADCCEQTELTKSVVLTLKSLPMTVLDAmIVPTKRGLPSGMPFTSVINSICHWLLWSAAVYKACDEIglfcsnly 1585
Cdd:cd23217    158 EAVEVLAYCHESPDLVMQLHKPVINSDHVVMDE-RWLVHGGMPSGSPCTTVLNSICNLLVCIYLAYLQSPGI-------- 228
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1586 EDAPfFVYGDDGVYAMT-PMMVSLLPAILdnLRDYGLSPTAADKTEFIDVCPLKNISFLKR--KFIMSELGWLSQLDKSS 1662
Cdd:cd23217    229 ECLP-IVYGDDVIFSVSsEIDPEYLVSSA--ADSFGMEVTGSDKDEPPSLLPRMEVEFLKRttGYFPGSTYKVGALDLET 305

                   ....*....
gi 1934859774 1663 ILRQLEWTK 1671
Cdd:cd23217    306 MEQHIMWMK 314
Limnipivirus_RdRp cd23228
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Limnipivirus of ...
1401-1727 7.95e-22

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: 100.34  E-value: 7.95e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1401 SGKALHHVYACGLKDELRPLDKVKEGKKRLLWGCD----VGVALCAAAVFHNLcfkLKTVARFGPIAVGIDmTSRDVDVM 1476
Cdd:cd23228     58 SGGYPTTLFTACLKDELRSDEKVALGKTRVIEAAEldyvVAYRMYMSSIYSDL---YNAYAGDTGIAAGIN-PPADGHRL 133
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1477 ITQLtSKAGDFLCLDYSKWDSTMSPCVVRLAIDILADCCEQTELTKSV---VLTLKSLpmtVLDAMIVpTKRGLPSGMPF 1553
Cdd:cd23228    134 REEL-SQYDSFLALDYSRFDGSLPEMLMRAAVEILADLHEDPDLVRRLhetVIISKHL---VVDEDWT-VKGGMPSGSPC 208
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1554 TSVINSICHWLLWSAA------VYKACDEIGLFCsnlyEDAPFFVYGDDGVYAMTPMMVSllPAILDNLRD-YGLSPTAA 1626
Cdd:cd23228    209 TTVLNCICNLLVLEYAflvhfgVYEDDDGVGLPQ----CDYLSVVYGDDCIVAYNGMEMG--LAFAETIEDtFGMEVTPA 282
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1627 DKTEFIDVCPLKNISFLKRKFIMSElgwlSQLDKSSILRqLEWTKTTKRHMCIEECSELDKdergvQLEELQVHAAAHGE 1706
Cdd:cd23228    283 SKVGDHFNVELHEVEFLKRKFFAFE----TEEYDRIALR-LSENTIVQSLMWMRNLKTFPD-----QVQSLMMELSAWGK 352
                          330       340
                   ....*....|....*....|.
gi 1934859774 1707 EFFELVRKELCRQQAFTRFSV 1727
Cdd:cd23228    353 EKYDKLRDTCKRRLAKQNLQV 373
Kunsagivirus_RdRp cd23219
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Kunsagivirus of ...
1355-1716 6.62e-21

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: 96.86  E-value: 6.62e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1355 SAAFNV---LDLSTSCGPFVPGKKIDHVKDGK---LDEILSKHLYKCWSVANSGKALHHVYACGLKDELRPLDKVKEGKK 1428
Cdd:cd23219      3 EAVFDTvtpMDHTASAGPKYPGTKRSELIDFQnriISDRLRNDVLELQFRGTSGGAGEVKFSSFLKDELRPLSKIRSGDT 82
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1429 RLLWGCDVGVALCAAAVF---HNLCFKLKTVaRFGpIAVGIDMTSrDVDVMITQLTSKAgdfLCLDYSKWDSTMSPCVVR 1505
Cdd:cd23219     83 RVVECSSLDYTVAFRMQFlrvLQMCYGSDPT-LTG-LAPGMNVYT-DMLPLCTSLYDYN---LCLDFSKYDSRLPLQVMH 156
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1506 LAIDILADcceqteLTKSVVLTLKSLPMTVLDAMIVPTKR-----GLPSGMPFTSVINSICHWLLWSAAVYKaCDeiglf 1580
Cdd:cd23219    157 RVAQLISN------LTPDPQVSMRLFQPIIISTHIVGSYEvvvegGMPSGCPITTIMNSVCNVVMTSYAMLL-LD----- 224
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1581 csnlyEDAPF--FVYGDDGVYAMT-PMMVSLLPAILDNlrDYGLSPTAADKTEFIDVCPLKNISFLKRKfimseLGWLSQ 1657
Cdd:cd23219    225 -----PDSDFwpVAYGDDNIVSTRkPIDTELFCSILNE--EFGMILTGADKTTTVQAVPPMSVDFLKRR-----LRYTPE 292
                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1934859774 1658 -------LDKSSILRQLEWTKttkrhmcieecselDKDERGVQLEELQVHAAAHGEEFFELVRKEL 1716
Cdd:cd23219    293 fplpvpvLPLDSMLSRICWCK--------------GETEFKDQLESFSYELALYGQEVYERVRVAL 344
Avisivirus_RdRp cd23231
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Avisivirus of ...
1361-1716 9.69e-21

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: 96.50  E-value: 9.69e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1361 LDLSTSCGPFVPGK-KIDHVKDGKLDEILSKhLYKCWSVANSgKALHHVYACGLKDELRPLDKVKEGKKRLLWGCDVGVA 1439
Cdd:cd23231     11 IDWGTSPGDKYKGKtKAQLVDDKKFKADVMN-LVRFNGDPNR-EPPDVYFTTYLKDELRPKEKAKAGKTRVISAASFDYT 88
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1440 LCAAAVFHNLCFKLKTVAR---FGPiavGIDMTSRdvdvmITQLTSKAGDF-LCLDYSKWDSTMSPCVVRLAIDILADCC 1515
Cdd:cd23231     89 IACRMVFGPILRQLFAWGRefgFGP---GLNPYTH-----FDELYDKILPFvICLDYSGFDGSLSSELMFHAAQVIACFS 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1516 EQTE-LTKSVVLTLKSLPmTVLDAmIVPTKRGLPSGMPFTSVINSICHWLLwsaaVYKACDEIGLFCSNLYEDApffvYG 1594
Cdd:cd23231    161 EKPEaIMASAELTIGSTE-RVSDE-VWYVYGGMPSGSPWTTTLNTICNLLM----CYTYLLDMGHCWSETFVVA----YG 230
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1595 DDGVyaMTPMMVSLLPAILDNLRD-YGLSPTAADKTEFIDVCPLKNISFLKRKfiMSELGWLSQ----LDKSSILRQLEW 1669
Cdd:cd23231    231 DDVV--ISANIKHNLEGIEQWFKTkFGATVTPSDKQGKITWTTKNNMEFLKRR--PKQLDFLPKivgaLDLDNMLDRIQW 306
                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*..
gi 1934859774 1670 TKTTkrhmcIEEcseldkdergvQLEELQVHAAAHGEEFFELVRKEL 1716
Cdd:cd23231    307 TKGH-----FQD-----------QLNSFYLELALHGRETYNEIRAKL 337
Secoviridae_RdRp cd23196
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Secoviridae of ...
1413-1714 3.55e-19

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: 90.91  E-value: 3.55e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1413 LKDELRPLDKV-KEGKKRLLWGCDVGVALCAAAVFHNLC-FKLKTVARFgPIAVGIDMTSRDVDVMITQLTSKAGDFLCL 1490
Cdd:cd23196      7 PKDERLKKRKVlEKPKTRLFDVLPMEYNLLLRKYFLNFVrFIQANRHRL-PCQVGINPYSREWTTLYDRLAEKSDTALNC 85
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1491 DYSKWDSTMSPCVVRLAIDILADCC--EQTELTKSVVLTLKSLPMTVLDAMIVPTKRGLPSGMPFTSVINSICHWLLWSa 1568
Cdd:cd23196     86 DYSRFDGLLSHQVYVWIADMINRLYgdGDEAKARRNLLMMFCGRRSICGRQVYMVRGGMPSGCALTVIINSIFNEILIR- 164
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1569 AVYKACDEiGLFCSNLYEDAPFFVYGDDGVYAMTPMMVSLL--PAILDNLRDYGLSPT-AADKTEF-IDVCPLKNISFLK 1644
Cdd:cd23196    165 YVYRKVVP-RPARNNFNKYVRLVVYGDDNLISVKEEIIPYFdgPVIKKEMAKVGVTITdGTDKTSPtLERKPLESLDFLK 243
                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1934859774 1645 RKFIMSELG-WLSQLDKSSILRQLEWTKTTKRHMCieecsELDKDERGVQLEELQVHAAAHGEEFFELVRK 1714
Cdd:cd23196    244 RGFRVQSDGlVVAPLDKTSLYSRLHYVTAGGDGMY-----SLYILNDNNKSFLEEHVDHPEFTEFRNRVVS 309
Crohivirus_RdRp cd23232
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Crohivirus of ...
1413-1710 2.98e-17

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: 86.31  E-value: 2.98e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1413 LKDELRPLDKVKEGKKRLLWGCDVGVALCAAAVFHNLCFKL-KTVARFGPIAVGIDMTSrDVDVMITQLTSKAGDFlclD 1491
Cdd:cd23232     71 LKDELRKLEKIRSGKTRCIEACDFDYTVAHKMMFGTLYKAIyDTPGIITGLAVGMNPWK-DWELIQQSLFKYNYDF---D 146
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1492 YSKWDSTMSPCVVRLAIDILADCCEQTELTKSVVLTLKSLPMTVLDAMIvPTKRGLPSGMPFTSVINSICHwLLWSAAVY 1571
Cdd:cd23232    147 YKTFDGSLSRELMLHAVDILSACVENDEMAKLMLSVVVESVHLVLDQKW-NVSGGMPSGSPCTTVLNSVCN-LIVSSTIA 224
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1572 KACDEIGLFCsnlyedapfFVYGDDGVYAMT-PMMVSLLPAILDnlRDYGLSPTAADKTEFIDVCPLKNISFLKR--KFI 1648
Cdd:cd23232    225 DMCTEGDFKI---------LVYGDDLIISSTaPLDCDRFKTLVE--LHYGMEVTPGDKGDEFKVKDREQVSFLKRvtRKF 293
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1934859774 1649 MSELGWLSQLDKSSILRQLEWtkttkrhmcieeCSELDKDERgvQLEELQVHAAAHGEEFFE 1710
Cdd:cd23232    294 PGTNYRVGALDLDTVKQHLMW------------CKSYSSFKQ--QLDSALMEVAMHGEETYN 341
Cosavirus_RdRp cd23226
RNA-dependent RNA polymerase (RdRp) in the genus Cosavirus of positive-sense single-stranded ...
1361-1671 5.04e-17

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: 86.61  E-value: 5.04e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1361 LDLSTSCG-PFVPGKKidHVKDGKLDEILSKHLYKCWSVANSGKALHHVYACGLKDELRPLDKVKEGKKRLLwgcDVgva 1439
Cdd:cd23226    109 MDPNTASGlPYTKTRR--QMIDFQEGKILDPELQERLDTWLSGKQPEMLYQTFLKDEIRPIEKVKAGKTRII---DV--- 180
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1440 lcaAAVFHNLCFKL---KTVARFGpIAVGIDMTSR---DVDVMITQ----LTSK--AGDFlclDYSKWDSTMSPCVVRLA 1507
Cdd:cd23226    181 ---TPLDHVLAFRIvlgRFMAHFH-NNYGFELGSAvgcDPDVAWANfgfaLSSKkyQYDF---DYSNFDASHSESIFELL 253
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1508 IDILADccEQTELTKSVVLTLKSLPMTV--LDAMIVPTKRGLPSGMPFTSVINSICHWLLWSAAVYKACdeiglfcSNL- 1584
Cdd:cd23226    254 KQFVFT--KDNGFDHRCSLMIDSLVTSThcYEDQRMTIRGGLPSGTSGTSVINTIINNIIFKAALYHTY-------SNFe 324
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1585 YEDAPFFVYGDDGVYAMTPMMvsllpaILDNLRDY----GLSPTAADKTE-FIDVCpLKNISFLKRKFIMSELGWLSQLD 1659
Cdd:cd23226    325 WDDVQMLAYGDDIVAASDCLL------DLDRVKYFmaliGYKITPADKGEkFIPKD-MQNIQFLKRSFRKVAGVWAPIMD 397
                          330
                   ....*....|..
gi 1934859774 1660 KSSILRQLEWTK 1671
Cdd:cd23226    398 LENLQAMLSWYK 409
Sapelovirus_RdRp cd23218
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Sapelovirus of ...
1409-1677 1.08e-16

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: 84.57  E-value: 1.08e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1409 YACGLKDELRPLDKVKEGKKRLLWGCDVGVALCAAAVFHnlcfKLKTVARFGPIAVGIDMTSRDVDVMITQLTSKAG-DF 1487
Cdd:cd23218     56 FTTYLKDELRPKEKVKMGKTRLIECSSLNDTIRMKRIFG----RLFQTFHKNPGTYTGSAVGCNPDVHWSKFAEEGGmDN 131
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1488 LC-LDYSKWDSTMSPC--------VVRL-----AIDILADCCEQTELTKSVVLTLKSlpmtvldamivptkrGLPSGMPF 1553
Cdd:cd23218    132 VCaFDYTNWDASLSPFwfdalklfLSKLgyserDIVLIDHLCYSNHIFKNEGYKVAG---------------GMPSGCSG 196
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1554 TSVINSICHWLLWSAAVYKACDEIGLfcsnlyEDAPFFVYGDDgvyamtpMMVS----LLPAILDNL-RDYGLSPTAADK 1628
Cdd:cd23218    197 TSIFNSIINNIVVRTLVLLVYKGINL------DELRILCYGDD-------LLVAypypLDPNVLADLgKSLGLTMTPADK 263
                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1934859774 1629 TEFIDVC-PLKNISFLKRKFIMSE-LGWLSQ--LDKSSILRQLEWTK---TTKRHM 1677
Cdd:cd23218    264 SDTFQGCtKLTEVTFLKRSFVFDEeFPFLCHpvFPMEEVHESIRWTRnasTTQEHV 319
Aalivirus_RdRp cd23216
RNA-dependent RNA polymerase (RdRp) in the genus Aalivirus of positive-sense single-stranded ...
1361-1716 5.55e-16

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: 81.64  E-value: 5.55e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1361 LDLSTSCGPFVPGK-KIDHVKDGKLDEILSKHLykcwsvanSGKALhhVYACGLKDELRPLDKVKEGKKRLLWGCDVGVA 1439
Cdd:cd23216     12 IDWQTSPGLKYKGRtKADLVQDPKFKEDVKEIL--------AGKPT--FFTTYLKDELRSIEKIANGNTRAIEAANFDHV 81
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1440 LCAAAVFHNLCFKL----KTVARFGPiavGIDMTSRdVDVMITQLTskaGDFLCLDYSKWDSTMSPCVVRLAIDILADCC 1515
Cdd:cd23216     82 VAWRQVMGNIVKQLfsdhDRVTGFAP---GMNPYTH-FDSLMDQVK---WNVLALDFKKFDGSLSPQVMEEAVDILASFH 154
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1516 EQTELTKSV-VLTLKSLPMTVLDAMIVptKRGLPSGMPFTSVINSICHWLLWSAAVYKAcdeiGLFCSNLYEDApffvYG 1594
Cdd:cd23216    155 DMPQMVVDIhKHTIYSTNVVSDETWFV--EGGMCSGSPCTTVLNTICNLLVNTTILLSE----GIQPDNFYIAA----YG 224
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1595 DDGVYAMTPMMVSLL-PAILDNLRD--YGLSPTAADKTEFIDVCPLKNISFLKRK--FIMSELGWLSQLDKSSILRQLEW 1669
Cdd:cd23216    225 DDTIISVDGLSSSLPdPKIMQQKYKewFGMTVTSADKGSEITWDTRNHVQFLKRRpgFFPGTQKVVGVLDLESMMEHIAW 304
                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*..
gi 1934859774 1670 TKTTKRHmcieecseldkdergvQLEELQVHAAAHGEEFFELVRKEL 1716
Cdd:cd23216    305 TKGSFQD----------------QLNSFYQELVLHGEQVYMTVRQTL 335
Hepatovirus_RdRp cd23215
RNA-dependent RNA polymerase (RdRp) in the genus Hepatovirus of positive-sense single-stranded ...
1400-1710 1.39e-15

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: 82.20  E-value: 1.39e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1400 NSGKALHHVYACGLKDELRPLDKVKEGKKRLLWGCDVG-VALC------AAAVFH-NLCFKLKtvarfgpIAVGIDmTSR 1471
Cdd:cd23215    128 DNGNDLDVVYTTCPKDELRPLEKVLESKTRAIDACPLDfTIICrmfwgpAISYFQlNPGFHTG-------VAVGID-PDR 199
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1472 DVDVMITQLTsKAGDF-LCLDYSKWDSTMSPCVVRLAIDILADCC-----EQTELTKSVVLT---LKSLPMTVLDAMivp 1542
Cdd:cd23215    200 DWDALFKTMI-RFGDYgIDLDFSSFDASLSPFMIREACRVLSELSgvpdhQGQALINTIIYSkhlLYNLCYHVCGSM--- 275
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1543 tkrglPSGMPFTSVINSICHWLLWSAAVYKACDEIGLFcsnLYEDAPFFVYGDDGVYAMT-----PMMVSLLPAILDNLR 1617
Cdd:cd23215    276 -----PSGSPCTSLLNSIVNNVNLYYVFSKIFKKSPVF---FYDAVKFLCYGDDVLIVFSrdleiKNLDKLGQRIQDEFK 347
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1618 DYGLSPTAADKTEfIDVCPLKNISFLKRKFIMSELGWLSQLDKSSILRQLEWTKTTKrhmcieecseldkdERGVQLEEL 1697
Cdd:cd23215    348 LLGMTATSADKGE-PQVVPVSELTFLKRSFNLIEDRFRPAISEKTIWSLVAWQRSNA--------------EFEQNLDTA 412
                          330
                   ....*....|...
gi 1934859774 1698 QVHAAAHGEEFFE 1710
Cdd:cd23215    413 CWFAFMHGYDFYQ 425
Teschovirus_RdRp cd23212
RNA-dependent RNA polymerase (RdRp) in the Teschovirus genus of positive-sense single-stranded ...
1406-1671 2.77e-14

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: 76.97  E-value: 2.77e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1406 HHVYACGLKDELRPLDKVKEGKKRLLWGCDVGVALCAAAVFHNL-CFKLKTVARFGPIAVGIdmtsrDVDVMITQL--TS 1482
Cdd:cd23212     71 KHVFLTFLKDELRPKEKVQAGKTRVIDVAGFGHAIVGRMLFGRLfAFFHKNPGWNTGSAVGV-----NPDLAWTQIfyTA 145
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1483 KAGDFLCLDYSKWDSTMSP---CVVRLAIDILADCCEQTELTKSVVLTLKSlpmtvLDAMIVPTKRGLPSGMPFTSVINS 1559
Cdd:cd23212    146 PSRNVLAMDYSGFDASHTSgmfCILKHFLTTLGYGTLQLSYIDSLCYSKHH-----WDDETYRLDGGLPSGCSGTTIFNT 220
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1560 ICHWLLWSAAVYKACDE-IGLFCsnlyedapffvYGDDgVYAMTPmmvSLLPaILDNLRDYGLSP---TAADKTEFIDVC 1635
Cdd:cd23212    221 IMNNIVARAAASYAAEGpVGILC-----------YGDD-ILVSSP---EKFP-VSDWLEFYSKTPykvTAADKSEQIDWR 284
                          250       260       270
                   ....*....|....*....|....*....|....*.
gi 1934859774 1636 PLKNISFLKRKFIMSELGWLSQLDKSSILRQLEWTK 1671
Cdd:cd23212    285 DITQCTFLKRGFVLDGSLVRPVMEEQHLAELLKWAR 320
Enterovirus_RdRp cd23213
RNA-dependent RNA polymerase (RdRp) in the Enterovirus genus of positive-sense single-stranded ...
1291-1651 2.70e-12

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: 71.40  E-value: 2.70e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1291 PANLGRGDP----DSHHTLMNIAVKNlqvyqqepKLTKVDTFIERAAADVLGFLRFLTKGERQMNLNfSAAFNV-----L 1361
Cdd:cd23213     32 PAVLTSKDPrlkvDFEEAIFSKYVGN--------TITEVDEYMKEAVDHYAGQLATLDIDTEQMSLE-DAMYGTdgleaL 102
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1362 DLSTSCG-PFVP--GKKID----HVKD-GKLDEILSKHlykcwsvansgkALHHVYACGLKDELRPLDKVKEGKKRLLWG 1433
Cdd:cd23213    103 DLHTSAGyPYVAlgIKKRDilnkKTRDtSKMKKYLDKY------------GLDLPMVTYVKDELRSKDKVEKGKSRLIEA 170
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1434 CDVGVALCAAAVFHNL--CFKLKTVARFGPiAVGIDMTS--RDVDVMITqltskaGDFLCLDYSKWDSTMSPCVVR---- 1505
Cdd:cd23213    171 SSLNDSVAMRMTFGNLyaTFHLNPGVVTGS-AVGCDPDTfwSKIPILLD------GSLFAFDYTGYDASLSPVWFRalkm 243
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1506 -LAIDILADCCEQTELTKSVVLTLKSLPMTVldamivptKRGLPSGMPFTSVINSICHWLLWSAAVYKACDEIGLfcsnl 1584
Cdd:cd23213    244 vLEKGYSEEAVSLIDYLNHSHHLYKNKTYCV--------LGGMPSGCSGTSIFNSMINNIIIRTLLLKTYKGIDL----- 310
                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1934859774 1585 yEDAPFFVYGDDgVYAMTPMMVSLLpAILDNLRDYGLSPTAADK-TEFIDVcPLKNISFLKRKFIMSE 1651
Cdd:cd23213    311 -DELKMIAYGDD-VIASYPHPIDCS-LLARTGKEYGLTMTPADKsPCFNEV-NWENVTFLKRGFRADE 374
Nora-virus_RdRp cd23200
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in a novel picorna-like ...
1413-1716 2.82e-12

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: 69.95  E-value: 2.82e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1413 LKDELRPLDKVKEGKKRLLWGCDVGVALCAAAVF--HNLCFKLKTVARFGpiAVGIDMTSRDVDVMITQLTsKAGDFLCL 1490
Cdd:cd23200      7 LKDQPIKIAQAKSGRTRVFHCIPVDLILFSGALYgpYKEAYTKAGLKCYH--AVGIDPKSVGWQQLATYMT-KHPNYFDA 83
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1491 DYSKWDSTMS----PCVVRLAIDILADCCEQTELTKSVVLTLKSLPMTVLDAMIV-PTKRGLPSGMPFTSVINSICHWLL 1565
Cdd:cd23200     84 DYKNYDKYLHrqvfKAVRKIQRSVIQQVCPDKWDKARAVEELDAIDTYVVDYQTVyKTNRGNKSGSYTTTIDNCLANDIY 163
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1566 WSAAVYKACDEIGLFCSNLYEDApfFVYGDDGVYAMTPMMVSL--LPAILDNLRDYGLSPTAADKT-EFIDVCPLKNISF 1642
Cdd:cd23200    164 GLYAWVKTTGLRSLWDYRQNVSS--VAFGDDIIKSVSDEYKDKynYCTYRDVLNATGHIMTPGSKDgEEKPFTSFENLQF 241
                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1934859774 1643 LKRKFIMSELGWLSQLDKSSILRQLEWTKttkrhmcIEEcselDKDERGVQL-EELQVHAAAHGEEFFELVRKEL 1716
Cdd:cd23200    242 LKRGFKLENGMVLAPLLQRSIEGPFVWTD-------IRE----DQITVWVNLvQEQLIEAALWGEEYYNELCQKL 305
Rosavirus_RdRp cd23221
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Rosavirus of ...
1409-1647 4.05e-12

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: 70.34  E-value: 4.05e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1409 YACGLKDELRPLDKVKEGKKRLLWGCDVGVALCAAAVFHNLCFKLKTVARFGPI-AVGIdmtsrDVDVMITQ----LTSK 1483
Cdd:cd23221     61 FATFLKDELRSTEKVAAGKTRVVEAGSLPHIIVGRKIFGNLFALFNSNPGFQTMcAVGC-----DPDVTWTElyhpLSAK 135
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1484 AGDFlCLDYSKWDSTMSPCVVRLAIDILADCCEQTELTKSVVLTLKSL------PMTVLDAmivptkrGLPSGMPFTSVI 1557
Cdd:cd23221    136 TYVF-DYDYSGFDGSVPSCCFDALADLLADFVEGEEDVRKYISSLKTSfhhykgKLWRLDG-------AMPSGCCGTSVF 207
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1558 NSICHWLLwsaaVYKACDEIglfCSNLYEDAPFFV-YGDDGVYAMT-PMMVSLLPAILDNLRDYGLSPtaADKTE-FIDV 1634
Cdd:cd23221    208 NSLINAML----LFSAFSQI---CPDFRASEPLLVaYGDDVLVGTDqPLFPSKVAEWVNSHTTFRITP--ADKGSvFNDE 278
                          250
                   ....*....|...
gi 1934859774 1635 CPLKNISFLKRKF 1647
Cdd:cd23221    279 SDIHSVQFLKRHF 291
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
1547-1647 1.03e-11

RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.


Pssm-ID: 238185 [Multi-domain]  Cd Length: 98  Bit Score: 63.14  E-value: 1.03e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1547 LPSGMPFTSVINSICHWLLWSAAVYKacdeiglfcsnlYEDAPFFVYGDDGVYAMT-PMMVSLLPAILDNLRDYGLSPTA 1625
Cdd:cd00304     12 LPQGSPLSPALANLYMEKLEAPILKQ------------LLDITLIRYVDDLVVIAKsEQQAVKKRELEEFLARLGLNLSD 79
                           90       100
                   ....*....|....*....|..
gi 1934859774 1626 ADKTEFidvCPLKNISFLKRKF 1647
Cdd:cd00304     80 EKTQFT---EKEKKFKFLGILV 98
Aquamavirus_RdRp cd23220
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Aquamavirus of ...
1408-1647 1.22e-11

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: 68.58  E-value: 1.22e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1408 VYACGLKDELRPLDKVKEGKKRLLWGCDVGVALCAAAVFhnlcfkLKTVARF---GPIAVGID---MTSRDVDVMITQLT 1481
Cdd:cd23220     57 VFETFMKDELRPKEKIESGKTRIVESCPLDYLLLYRMVM------LKSMIWWynsDCIKTGVApgmNVYTDFVPMVKQFK 130
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1482 SKAgdfLCLDYSKWDSTMSPCVVRLAIDILAdCCEQT-----ELTKSVVLTlKSLPMTVLDAMIvptkRGLPSGMPFTSV 1556
Cdd:cd23220    131 KIK---YCLDFSAYDSTLSDEILAAGVEVLA-CTSAVpsyvrKLHAPIICS-HHWHNNVVDLVL----GGMPSGAPCTSV 201
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1557 INSICHWLLwsaAVYkacdeiglFCSNLYEDAPFFV-YGDDGVYAM-----TPMMVSLLPAildnlrDYGLSPTAADKTE 1630
Cdd:cd23220    202 LNSIVNVLM---ARY--------ICALMDIDYPVMVaYGDDNVVSFdeeidIERMVSLYKT------EFGVTATNHDKTP 264
                          250
                   ....*....|....*..
gi 1934859774 1631 FIDvcPLKNISFLKRKF 1647
Cdd:cd23220    265 VPR--PMANPVFLKRRL 279
Dicipivirus_RdRp cd23222
RNA-dependent RNA polymerase (RdRp) in the genus Dicipivirus of positive-sense single-stranded ...
1409-1735 1.14e-10

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


Pssm-ID: 438072  Cd Length: 451  Bit Score: 66.53  E-value: 1.14e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1409 YACGLKDELRPLDKVKEGKKRLLWGCDVGVALCAAAVFHNLCFKLKTVARFGPI-AVGIdmtsrDVDVMITQ----LTSK 1483
Cdd:cd23222    139 YTSFLKDELRSVKKVKAGKTRVVEAGSLPVIVEGRMIFGNLFAYFNTHPGFETMaAVGC-----DPEVCWTDwyykMREK 213
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1484 AG--DFlclDYSKWDSTMSPCVVRLAIDILADCCEQTELTKSVVLTLKSlPMTVLDAMIVPTKRGLPSGMPFTSVINSIC 1561
Cdd:cd23222    214 AHtwDY---DYTGFDGSIPSCSFDALADLLCEFVENEDDVRRYISNIKN-SYHAYDGNLYLIEGAMPSGCAGTSVFNCLI 289
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1562 HWLLWSAAVYKACDEIGLFcsnlyeDAPFFVYGDDGV----YAMTPMMVSllpAILDNLRDYGLSPtaADK-TEFIDVCP 1636
Cdd:cd23222    290 NAMLCFSCFMDLEPEMDPF------EPLLIAYGDDILvssdHDLFPSRVS---EWMKANTTFKITP--ADKgEIFNDDSD 358
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1637 LKNISFLKRKFIMSELGWLSQ--LDKSSILRQLEWTkttkrhmcieecselDKDERGVQLEELQVHAAAHGEEFFE---L 1711
Cdd:cd23222    359 VSDVRFLKRLFVEDPVCELIHpvIETETLEPSLNWC---------------HEGEFETKVDAISMLAFHHGPEYYRdwcK 423
                          330       340
                   ....*....|....*....|....
gi 1934859774 1712 VRKELCRQQAFTRFSVFDYQTARK 1735
Cdd:cd23222    424 KLTDICEERNISPPGLKPYSVHRN 447
Mosavirus_RdRp cd23225
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Mosavirus of ...
1413-1651 1.15e-10

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: 66.09  E-value: 1.15e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1413 LKDELRPLDKVKEGKKRLLWGCDVGVALCAAAVFHNLcfkLKTVARFGPIAVGiDMTSRDVDVMITQLTSKAGD--FLCL 1490
Cdd:cd23225     70 LKDEVRSNEKIKQGKTRIVDASPFPYAIAGRMVMQNF---MSNMMRCNGTEVG-SAVGCDPDTEWTRYFFELCDryVFDL 145
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1491 DYSKWDSTMSPCVvrlaIDILAD--CCEQTEL-TKSVVLTLKSLPMT--VLDAMIVPTKRGLPSGMPFTSVINSICHWLL 1565
Cdd:cd23225    146 DYKAFDSTHPTAM----FNLLAErfFTERNGFdQQAVRIFLNGLSDSdhVYEGKHFRIRGGLPSGCPCTSILNTVINNII 221
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1566 WSAAVykacdeIGLFCSNLYEDAPF--FVYGDDGVYAM-TPMMVSLLPAILDNLRDYGLSPtAADKTEFIDVCPLKNISF 1642
Cdd:cd23225    222 VRAAI------LGAYQIDTVDFQKFrmLAYGDDVVYATpQPIKPQDLADWLHANTNYKVTP-ASKAGTFPEESTIWDVTF 294

                   ....*....
gi 1934859774 1643 LKRKFIMSE 1651
Cdd:cd23225    295 LKRSFKPDE 303
Mischivirus_RdRp cd23227
RNA-dependent RNA polymerase (RdRp) in the genus Mischivirus of positive-sense single-stranded ...
1401-1710 2.89e-10

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: 65.35  E-value: 2.89e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1401 SGKALHHVYACGLKDELRPLDKVKEGKKRLLWGCDVGVALCAAAVFHNLCFKLKtvARFGPI---AVGIDMTSrDVDVMI 1477
Cdd:cd23227    149 SGDYSDHVFQTFLKDEIRSEEKIKAGKTRIVDVPSLAHVIIGRVLLGKFCSKFQ--ASPGTElgsAIGCNPDW-DWTYFA 225
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1478 TQLTSKAgdfLC--LDYSKWDSTMSPCVVRLaidiLADC--CEQTELTKSVVLTLKSLPMTVLDAMivpTKR-----GLP 1548
Cdd:cd23227    226 HQLMERQ---WCydIDYSNFDSTHGTGMFEL----LIDCffTPENGFSPAVAPYLRSLAFSKHAWM---DKRykiegGLP 295
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1549 SGMPFTSVINSICHWLLWSAAvykacdeIGLFCSNLY-EDAPFFVYGDDGVYAMTPMM-VSLLPAILDNLRDYGLSpTAA 1626
Cdd:cd23227    296 SGCSATSVLNTVMNNIIIRAL-------LSLTYKNFHpEDVLVLAYGDDLLVASDYQLdFNRVREKAAEHTLYKLT-TAN 367
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1627 DKTEFIDVCPLKNISFLKRKFIM---SELGWLSQLDKSSILRQLEWTKTTkrHMcieecseldkDERGVQLEELQVHAAA 1703
Cdd:cd23227    368 KAPDFPETSTLLDCQFLKRKFVLhstRNFIWRPVMDVTNLKTMLSFYKPN--TL----------SEKLLSVAQLAFHSGY 435

                   ....*...
gi 1934859774 1704 HG-EEFFE 1710
Cdd:cd23227    436 TVyEELFA 443
Cardiovirus_RdRp cd23211
RNA-dependent RNA polymerase (RdRp) in the Cardiovirus genus of positive-sense single-stranded ...
1400-1653 3.47e-10

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: 64.86  E-value: 3.47e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1400 NSGKALHHVYACGLKDELRPLDKVKEGKKRLLwgcDVgvalcaaAVFHNLCFKLKTVARFGP---IAVGIDMTSR---DV 1473
Cdd:cd23211    145 VEGDYSDVVYQSFLKDEIRPIEKVQAAKTRIV---DV-------PPFEHCILGRQLLGRFASkfqTNPGLELGSAigcDP 214
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1474 DVMITQLTSKAGDF---LCLDYSKWDSTMSPCVVRLAIDILADccEQTELTKSVVLTLKSLPMTV--LDAMIVPTKRGLP 1548
Cdd:cd23211    215 DVDWTAFAVALSGFkyvYDVDYSNFDSTHSTAMFELLIENFFT--EENGFDPRIGEYLRSLAVSRhaYEERRVLIRGGLP 292
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1549 SGMPFTSVINSICHWLLWSAAVYkacdeigLFCSNL-YEDAPFFVYGDDGVYAMTPMMVSLLpaILDNLRDYGLSPTAAD 1627
Cdd:cd23211    293 SGCAATSMLNTIMNNIIIRAGLY-------LTYKNFeFDDIKVLSYGDDLLVATNYQIDFNL--VKARLAKFGYKITPAN 363
                          250       260
                   ....*....|....*....|....*..
gi 1934859774 1628 KT-EFIDVCPLKNISFLKRKFIMSELG 1653
Cdd:cd23211    364 KTsTFPLTSTLEDVVFLKRKFVKENSY 390
ps-ssRNAv_Potyviridae_RdRp cd23175
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Potyviridae of ...
1413-1620 1.00e-09

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


Pssm-ID: 438025  Cd Length: 236  Bit Score: 61.31  E-value: 1.00e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1413 LKDELRPLDKVKEGKKRLLWGCDVGVALCAAAV-------FHNLCFKlktvarfGPIAVGIDMTSRDVDVMITQLTSkaG 1485
Cdd:cd23175     10 LKAELRPIEKVEANKTRTFTAAPIDTLLGGKVCvddfnnqFYSLHLK-------APWTVGITKFYGGWDKLLRKLPD--G 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1486 DFLC-LDYSKWDSTMSP------CVVRLA----IDILADCCEQ--TELTKSVVLTlkslPmtvlDAMIVPTKRGLPSGMP 1552
Cdd:cd23175     81 WVYCdADGSQFDSSLTPylinavLRIRLHfmedWDIGEQMLRNlyTEIVYTPILT----P----DGTIVKKFKGNNSGQP 152
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1934859774 1553 FTSVINSICHWLlwsaAVYKACDEIGLFCSNLYEDAPFFVYGDDGVYAMTPMMVSllpaILDNLRDYG 1620
Cdd:cd23175    153 STVVDNTLMVMI----AMYYALLKLGIDFEEIDERCVFFCNGDDLLIAVSPEHEH----ILDTFSSSF 212
Rabovirus_RdRp cd23230
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Rabovirus of ...
1361-1713 7.01e-09

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: 60.28  E-value: 7.01e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1361 LDLSTSCG-PFV-PGKKIDHVKDGKLDEIlsKHLYKCWSVAnsgkALHHVYACGLKDELRPLDKVKEGKKRLLWGCDVGV 1438
Cdd:cd23230     11 LDLNTSAGyPYVlNGIKKRDILDPETRDT--TKLQECLDKY----GVDLPFVTYLKDELRPLEKIKKGKTRLIECSSMND 84
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1439 ALCAAAVFHNLCFKLKtvARFGPI---AVGIDmtsrdVDVMITQLTSKA-GDFLCLDYSKWDSTMSPCVVRlaidiladc 1514
Cdd:cd23230     85 TIRMKMMFGRLFATYH--RNPGPItgsAVGCN-----PDIHWTKFRAEMhGEIIAFDYSNYDASLNKVWFE--------- 148
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1515 CEQTELTKSVVLTLKSLPMTVLDAMIVP-----TKRGLPSGMPFTSVINSICHWLLWSAAVYKACDEIGLfcsnlyEDAP 1589
Cdd:cd23230    149 CLKMVLKNFGFKDLRPIDHIIRSRHIYKgieydVEGGMPSGCSGTSIFNSIINNIIIMTLVLDAYKGIDL------EQLK 222
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1590 FFVYGDDGVYAMT-PMMVSLLPailDNLRDYGLSPTAADKTEFIDVCPLKNISFLKRKFIMSE-LGWL--SQLDKSSILR 1665
Cdd:cd23230    223 IIAYGDDVIVTYPyPLDAALLA---DCGKKYGLKMTPPDKSAEFKNVTWEDVTFLKRRFKPAKhYPFLihPVFDQQEILE 299
                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1934859774 1666 QLEWTKT---TKRHMcieecseldkdergVQLEELQVHAAAHG-EEFFELVR 1713
Cdd:cd23230    300 SLRWTRNpahTQEHV--------------RSLAELAWHSGRKSyEEFCNLVK 337
Aphthovirus_RdRp cd23210
RNA-dependent RNA polymerase (RdRp) in the Aphthovirus genus of positive-sense single-stranded ...
1408-1653 1.84e-07

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: 56.11  E-value: 1.84e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1408 VYACGLKDELRPLDKVKEGKKRLLWGCDVGVALCAAAVFHNLCFKLKTVARFGP-IAVGIDmtsRDVD--VMITQLTSKA 1484
Cdd:cd23210    151 ACQTFLKDEIRPMEKVRAGKTRIVDVLPVEHILYTRMMIGRFCAQMHSNNGPQIgSAVGCN---PDVDwqRFGTHFAQYR 227
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1485 GDFLClDYSKWDSTMSPCVVRLAIDILADccEQTELTKSVVLTLKSLPMTV--LDAMIVPTKRGLPSGMPFTSVINSICH 1562
Cdd:cd23210    228 NVWDV-DYSAFDANHCSDAMNIMFEEVFR--TEFGFHPNAEWILKTLVNTEhaYENKRITVEGGMPSGCSATSIINTILN 304
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1563 WLLWSAAVYKACDEIGLfcsnlyEDAPFFVYGDDGVYAMTPMMVslLPAILDNLRDYGLSPTAADKTEFIDVCP--LKNI 1640
Cdd:cd23210    305 NIYVLYALRRHYEGVEL------DTYTMISYGDDIVVASDYDLD--FEALKPHFKSLGQTITPADKSDKGFVLGhsITDV 376
                          250
                   ....*....|...
gi 1934859774 1641 SFLKRKFIMSELG 1653
Cdd:cd23210    377 TFLKRHFHMDYGT 389
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
494-589 2.77e-07

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: 52.15  E-value: 2.77e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774  494 VLGKINMTKQRPQPVAIIFKGAPGIGKTYLVHRLAKDLGcpHPSNINFGLDHFDSYTGEDVAIADEFntsgdERWVELFI 573
Cdd:cd00009      6 AIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELF--RPGAPFLYLNASDLLEGLVVAELFGH-----FLVRLLFE 78
                           90
                   ....*....|....*.
gi 1934859774  574 QMVNTNPCPLNCDKVE 589
Cdd:cd00009     79 LAEKAKPGVLFIDEID 94
Megrivirus_RdRp cd23223
RNA-dependent RNA polymerase (RdRp) in the genus Megrivirus of positive-sense single-stranded ...
1403-1647 5.18e-06

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: 51.38  E-value: 5.18e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1403 KALHH----VYACGLKDELRPLDKVKEGKKRLLWGCDVGVALCAAAVFHNLcFKlKTVARFGP---IAVGIDmtsRDVdv 1475
Cdd:cd23223    126 HALKDpddfYFSTFLKDELRPLEKVKAGKTRLVDGDSLPRILAMRMVFGPL-FE-AMLRKNGPeihSAVGCN---PDT-- 198
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1476 mitqltskagdflclDYSKWDSTMSPCVVRLAIDILADCCEQTELTKSVVLTLKSL-------PMTVLDAMIVPT----- 1543
Cdd:cd23223    199 ---------------DWTRYYHEMGPDSFPYCFDLDYSCFDSTEPKIAFRLMAKYLkpyfsvdVTPFFEALATSKhvygd 263
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1544 -----KRGLPSGMPFTSVINSICHwllwSAAVYKACDEIGLFCsnlyEDAPFFVYGDDGVYAMTpmmVSLLPAILDNL-- 1616
Cdd:cd23223    264 kayemEGGMPSGCVGTSMFNCINN----SAFIVSALIALKISP----EDCAWICYGDDVIISTD---EKALSKRIADFyh 332
                          250       260       270
                   ....*....|....*....|....*....|..
gi 1934859774 1617 RDYGLSPTAADKT-EFIDVCPLKNISFLKRKF 1647
Cdd:cd23223    333 KNTNLVVTPASKSgDFPETSTIYDVTFLKRFF 364
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
1822-1922 5.55e-05

picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by clustalw. If a representative set is used for a seed, many so-called members are not recognized. The family should probably be split up into sub-families. Capsid proteins of picornaviruses. Picornaviruses are non-enveloped plus-strand ssRNA animal viruses with icosahedral capsids. They include rhinovirus (common cold) and poliovirus. Common structure is an 8-stranded beta sandwich. Variations (one or two extra strands) occur.


Pssm-ID: 395026  Cd Length: 170  Bit Score: 45.77  E-value: 5.55e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1822 NFFYNDVFTWSvTDAPGSILYTVQHSPQNNPFTQVLSQMYAGWAGGMQFRFIVAGSGIFGGRLVCAIIPPGiQIQPGLEV 1901
Cdd:pfam00073   39 RFYTLDSTDWT-SLSKGFFWWKLPLALLSMGLLGRLLRYHTYYRGGLEVTVQFNGSKFHQGKLLVAYVPPG-APPPGSRD 116
                           90       100
                   ....*....|....*....|....*.
gi 1934859774 1902 RQ-----FPHVVIDARSLEPVTITMP 1922
Cdd:pfam00073  117 YLwqatlNPHQFWNLGLNSSARLSVP 142
Polycipiviridae_RdRp cd23198
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Polycipiviridae of ...
1414-1647 6.30e-05

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: 47.41  E-value: 6.30e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1414 KDELRPLDKV-----KEGKKRLLWGCDVGVALCAAAVFHNLCFKLKTVAR----FGPiavGIDMTSRDVDVMITQLT--S 1482
Cdd:cd23198      8 KDELRPIYKAlgdpqTPPKTRSVTCMNVYYILAWRRVTLDFWASMHRAADgnfpFCP---GINPEGPDWNRLYHYLNrhP 84
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1483 KAGDFlclDYSKWDSTMSPCVVRLAIDILADCCeQTELTKSVVLTLKSLPMTVLDA------MIVPTKRGLPSGMPFTSV 1556
Cdd:cd23198     85 NAVDF---DVSNWDGHLPAELFYAVLDIIKTVL-GLKPNSPNAKVIYSILTEVMNChiqfedIIYQKLRGLISGFPGTAE 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1557 INSICHWL------LWSAAVYKACDEIGLFCSNLyedAPFFvYGDDgvyamtpmmvsLLPAILDNLRDY----------- 1619
Cdd:cd23198    161 VNTLAHWLliyyiyLYLAQNTIYDMTITAFLRNV---SAIF-YGDD-----------IIITISDEILHWfngktiqrmye 225
                          250       260       270
                   ....*....|....*....|....*....|...
gi 1934859774 1620 --GLSPTAADKTEfiDVCPLKNIS---FLKRKF 1647
Cdd:cd23198    226 ehGYPVTSAAKDT--EIPESKPLSdcqFLKSSW 256
Iflaviridae_RdRp cd23197
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Iflaviridae of ...
1408-1716 1.13e-04

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: 46.78  E-value: 1.13e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1408 VYACGLKDELRPLDKVKE-GKKRLLWGCDVGVALCAAAV-------FHNLCFKLKTvarfgpiAVGIDMTSRDVDVMITQ 1479
Cdd:cd23197      7 VYWAHLKDELRPSEKLRRfGGTRVFSVPPLELVLNSRRFllpfmdaFQSFPIEAHH-------AIGLNPNSGDWRRLRDT 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1480 LTSKAGDFLCLDYSKWDSTMSPCVVRLAIDILADCCEQTE-LTKSVVLTLKSLPMTVLDAMIV------PTKRGLPSGMP 1552
Cdd:cd23197     80 LLEKGPCLLQMDYKNYSDAIPKECVAKAFHIIVDYYRKWHcLTVEIENALKTLFLDTADAELLvygdvfKVNNGVLAGHP 159
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1553 FTSVINSICHWLLwsaAVYKACDEIGLFCSNLYEDAPFFVYGDDGVYAMTPMMVSLLPA--ILDNLRDYGLSPTAADKTE 1630
Cdd:cd23197    160 MTSVVNSVVNLIL---MNYMWIKITRRRASEFFKLTYIIVMGDDVVISLPKQLTEEFDCrkICAEFAKYDIKVTDSEKNL 236
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1631 FIDVCPLKNI---SFLKRKFIMSELG---WLSQLDKSSILRQLEWTKTtkrhmcieecselDKDERGVQLEELQ---VHA 1701
Cdd:cd23197    237 TGEPKPYDSFdkfEFLSRGFSDCDAYpdiTFAPVKTIALFDCPLWISK-------------GQDEEEQTIQAIQaglLLA 303
                          330
                   ....*....|....*
gi 1934859774 1702 AAHGEEFFELVRKEL 1716
Cdd:cd23197    304 FDHGPEFFGKYKQLL 318
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
509-538 3.16e-04

DNA polymerase III, delta prime subunit [Replication, recombination and repair];


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 44.97  E-value: 3.16e-04
                           10        20        30
                   ....*....|....*....|....*....|
gi 1934859774  509 AIIFKGAPGIGKTYLVHRLAKDLGCPHPSN 538
Cdd:COG0470     20 ALLLHGPPGIGKTTLALALARDLLCENPEG 49
ps-ssRNAv_Astroviridae_RdRp cd23172
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Astroviridae of ...
1413-1596 4.08e-04

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: 44.38  E-value: 4.08e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1413 LKDELRPLDKVKEGkkrllwgcDVGVALCAAAVFHNL--CF------KLKTVARFGPIAVGidMT--SRDVDVMITQLTS 1482
Cdd:cd23172      8 LKKEILKKEKIEDG--------DIRQILCPDPIFARIgaRFeqdqnnLMKERTLTNEGQVG--WSpfYGGFDARVRRLGS 77
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1483 KAGDFLCLDYSKWDSTMSPCVVRLAIDILADC--CEQTELTKSVvltLKSLPMTVLD-AMIVPT------KRGLPSGMPF 1553
Cdd:cd23172     78 KGNYFVEFDWTRFDGTIPAELFRHIRKLRWSFldPEKTEENRKV---YDWYVHNLLNrYVLLPTgevtrvTKGNPSGQIS 154
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 1934859774 1554 TSVINSICHWLLW---SAAVYKACDEIglfCSNLYEDAPFFVYGDD 1596
Cdd:cd23172    155 TTMDNCMVNTFLTafeFAYVYGPKTGT---LKELWDNYDTIVYGDD 197
ps-ssRNAv_RdRp-like cd23167
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
1486-1602 4.28e-04

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


Pssm-ID: 438017 [Multi-domain]  Cd Length: 73  Bit Score: 40.78  E-value: 4.28e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1486 DFLCLDYSKWDSTMSPcvvrlaidiladcceqteltksvvltlkslpmtvlDAMIVptkrGLPSGMPFTSVINSICHWLL 1565
Cdd:cd23167      1 HVVESDYSGFDSSISP-----------------------------------DLLKA----GQPSGSPNTSADNSLINLLL 41
                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1934859774 1566 WSAAVYKACDEIGLFcSNLYedapFFVYGDDGVYAMT 1602
Cdd:cd23167     42 ARLALRKACGRAEFL-NSVG----ILVYGDDSLVSVP 73
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
504-630 9.28e-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: 9.28e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774   504 RPQPVAIIfkGAPGIGKTYLVHRLAKDLGCPHPSNINFGLDHFDSYTGED---VAIADEFNTSGDERWVELFIQMVNTNP 580
Cdd:smart00382    1 PGEVILIV--GPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQlllIIVGGKKASGSGELRLRLALALARKLK 78
                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1934859774   581 CPL---------------------NCDKVENKNKVFNSKYLLCTTNSSMVLNATHPRAtAFYRRVIIVDVR 630
Cdd:smart00382   79 PDVlildeitslldaeqealllllEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLIL 148
Zeta_toxin pfam06414
Zeta toxin; This family consists of several bacterial zeta toxin proteins. Zeta toxin is ...
501-572 3.70e-03

Zeta toxin; This family consists of several bacterial zeta toxin proteins. Zeta toxin is thought to be part of a postregulational killing system in bacteria. It relies on antitoxin/toxin systems that secure stable inheritance of low and medium copy number plasmids during cell division and kill cells that have lost the plasmid.


Pssm-ID: 428926  Cd Length: 192  Bit Score: 40.81  E-value: 3.70e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1934859774  501 TKQRPQPVAIIFKGAPGIGKTYLVHRLAKDLGcPHPSNINFGLDHFDSYTGEDVAIADEfntsGDERWVELF 572
Cdd:pfam06414    5 TTSQERPKAILLGGQPGAGKTELARALLDELG-RQGNVVRIDPDDFRELHPHYRELQAA----DPKTASEYT 71
FN3 COG3401
Fibronectin type 3 domain [General function prediction only];
1929-2146 7.85e-03

Fibronectin type 3 domain [General function prediction only];


Pssm-ID: 442628 [Multi-domain]  Cd Length: 603  Bit Score: 41.53  E-value: 7.85e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 1929 YHPTGNPGLVPTLVVSVYNNLINPFGGTTSAIQVTVETRPS-EDFEFVLIRAPSSKTVESVNPSWLLTTPVLTGAGSDNR 2007
Cdd:COG3401      5 YLTSLDAGIAASAAANTAVNALSKAGGSGKTILVYLAVVLSvTTKESPGTLLVAAGLSSGGGLGTGGRAGTTSGVAAVAV 84
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1934859774 2008 WGAPIVGLQPVPG-GFSTCNRHWNMNGETYGWSSPRFDDIDHPSGNVSYPTGSATNT---------IETWYANAGTATTN 2077
Cdd:COG3401     85 AAAPPTATGLTTLtGSGSVGGATNTGLTSSDEVPSPAVGTATTATAVAGGAATAGTYalgaglygvDGANASGTTASSVA 164
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1934859774 2078 PISNVAPDGFPDMGAIPFSGTTIPTGAWVGFGQVWNasNGTPYVGTVQAYELGfANGAPSNIRPVTTTT 2146
Cdd:COG3401    165 GAGVVVSPDTSATAAVATTSLTVTSTTLVDGGGDIE--PGTTYYYRVAATDTG-GESAPSNEVSVTTPT 230
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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