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Conserved domains on  [gi|482876020|gb|AGK41017|]
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polyprotein [Bat pegivirus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Pegivirus_RdRp cd23203
RNA-dependent RNA polymerase (RdRp) in the genus Pegivirus, within the family Flaviviridae of ...
 2757-3232 0e+00

RNA-dependent RNA polymerase (RdRp) in the genus Pegivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the RdRp of RNA viruses belonging to the Pegivirus genus within the family Flaviviridae, order Amarillovirales. Members of the Pegivirus genus are widely distributed in a range of mammalian species, in which they cause persistent infections. To date, they have not been clearly associated with disease. Virions of Pegivirus have a single, small, basic capsid (C) protein and two envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. 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: 438053  Cd Length: 476  Bit Score: 892.77  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2757 WSGAPITVQEPKQPPVTRAVTGALRASADRVYVTNPEDIHKRIAKVTIEQKVAEKDRYFLDAYNLALANASRILSPGFSY 2836
Cdd:cd23203     1 WSGAPLGVGRPKPPPVTRPVGSHLRADATKVYVTDPDDVGERIEKVTIWRTPRVVDKFLRDAYNLALAKASATPSPGWTY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2837 EEAIAKVKPNTAKGHVARITAADLKTEVGRKAVEKCLDDIRGGVAYAPFMLRPKSEVFPQTRETFKPPRLITYPSLEFRV 2916
Cdd:cd23203    81 EEAVAKVRPGAAMGHGSKVTVADLKTPAGKKAVEECLNQIIAGGEEVPFTLTAKQEVFFQDKKTRKPPRLIVYPPLEFRV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2917 AEKMILGDPSLVAKAVMGPAYGFQYPPHERAEVLTKMWTSKKSPVAYTVDGVCFDSTITPEDIDREANIFAAASDDPMAV 2996
Cdd:cd23203   161 AEKMILGDPGRVAKAVLGKAYGFQYTPNQRVKVLVDMWKSKRHPCAITVDATCFDSSITEEDVARETEIYAAASDDPELV 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2997 RRLHDHYASGPLMDPSGKIVGVRNCRASGTLTTSAGNSITCYLKVTAACRKAGIKNPSFLIHGDDCVIICEKEEVDKSDA 3076
Cdd:cd23203   241 RALGKYYAEGPMVNPEGVPVGERRCRASGVLTTSSSNSITCYLKVKAACRKAGLKNPSFLIHGDDCLIICERPEEDPCDA 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 3077 LGEALRSYGYECEPTIHADLSTAESCSASLDRVRTVRGLRPTLKPDMRRAIGRVIAEHGDSVGCAWGYIIQYPTHPISMY 3156
Cdd:cd23203   321 LKAALASYGYDCEPQYHASLDTAESCSAYLAECNAGGGRHYFLSTDMRRPLARASSEYGDPVASALGYILLYPWHPITRY 400

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 482876020 3157 VLLPILLTIALNNGDSARQPVTIDVRGNQITLPLNRLGSAIRGLHGPDVLAITGHSAAVIEESHQTLQFFRMRGLN 3232
Cdd:cd23203   401 VLLPHLLTLAFRGGGTPDDLVTCQVHGNSYKFPLKLLPRILVGLHGPDCLRVTADSTKTLMEAGKALQAFGMRGLA 476
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 1406-1540 2.60e-25

N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase superfamily is a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. The N-terminal domain contains the ATP-binding region.


The actual alignment was detected with superfamily member cd17931:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 151  Bit Score: 104.55  E-value: 2.60e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 1406 APTGSGKSTKFPSKLVQEGH----RVLVLNPSVVTTRAMFKYMKdstGDAPNVYAGtgkgAISRETGSK--LTYCTYGRF 1479
Cdd:cd17931     8 LHPGAGKTTRVLPQIIREAIkkrlRTLVLAPTRVVAAEMYEALR---GLPIRYRTG----AVKEEHGGNeiVDYMCHGTF 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 482876020 1480 ---LVSPGRfLQRVNVVICDECHAVDGTTILGIGAVRALAQdAGVRLVVFATATPPGTQLQPHP 1540
Cdd:cd17931    81 tcrLLSPKR-VPNYNLIIMDEAHFTDPASIAARGYIHTRVE-MGEAAVIFMTATPPGTVTPFPQ 142
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 1542-1674 4.20e-21

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


The actual alignment was detected with superfamily member cd18806:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 145  Bit Score: 92.32  E-value: 4.20e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 1542 ITETPLDSDGDVPFYGLTLKSAnyKAGRHVIFCHSKVECQRVAKELTSRGVNTVTYWRG-----KPADTLTDdpDLTVVA 1616
Cdd:cd18806     1 IEDVALEIPGRIWFYGKAWITI--YGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKlddteYPKIKTID--WDFVVT 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 482876020 1617 TDAISTGYTGNFASVTDCCSAVAEEVEVDLNptFTISL-FTGPADAALRMQRRGRTGRG 1674
Cdd:cd18806    77 TDISEMGANFDADRVIDCRTCVKPTILFSGD--FRVILtGPVPQTAASAAQRRGRTGRN 133
HCV_NS4b super family cl03062
Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. ...
 1956-2113 6.79e-18

Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. However, it is known that NS4b interacts with NS4a and NS3 to form a large replicase complex to direct the viral RNA replication.


The actual alignment was detected with superfamily member pfam01001:

Pssm-ID: 110032  Cd Length: 192  Bit Score: 84.35  E-value: 6.79e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020  1956 LDLIAANLSAMVAGGVAICGARASPAFASLAALVAGAQVCTSSNIIWGLTLAGGLAATLLGGAGAGFGVATSFFIGSKLA 2035
Cdd:pfam01001   34 WAKHMWNFRSGIQYLAGLYTLPRNPPLAVLASFLAGMTSPLPTHVRLALALLGGWGATQLGTPSGGLAFVGAGFAGAAVG 113

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 482876020  2036 GLSWVETIVGCFAGYEACVNFCALTLDLLDGKLALETAAPCLV-GLLAPGAAVAGIVMAMLLRSTQGGDVTPWMNRLLS 2113
Cdd:pfam01001  114 SSWLGRVLVDVLGGYEAAVNAASLTFKIMSGELPTAEDLWNLLpCLLSPGASVVGVALAALLRSHKGEGAVQWMNRLLT 192
GBV-C_env super family cl15089
GB virus C genotype envelope; This the envelope protein from the ssRNA GB virus genotype C.
 271-513 1.43e-07

GB virus C genotype envelope; This the envelope protein from the ssRNA GB virus genotype C.


The actual alignment was detected with superfamily member pfam12786:

Pssm-ID: 193262  Cd Length: 413  Bit Score: 56.73  E-value: 1.43e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020   271 PDLVCNRTCSV-FALDWWSDNAPTLAALWSVVTL--LPEAVWGVLTAMPPLFGGLLLFYLCRGWWVQAVLLFLAV----P 343
Cdd:pfam12786    6 PNLTCAVECDLaWSYEGWSWTEDMADFDWAFEYLwtLPFDLWRGLMAASVLLVLVAALLLLEQRLVMAFLLLTVAgeaqG 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020   344 GVLADCYDAEYDEIASLSCNMTHFRKANITCPCPYG--VWMREFNAS----DPAQAHL--NLTIRCPeRYNHSQDYWTCG 415
Cdd:pfam12786   86 GFFDGCHCAYWGSRVPPGAKPWDRGNGTVVCDCPFGpmVWLPALCSGlawrDGDREGTvnDLPLVCP-REVLGTVSVMCV 164

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020   416 WGS--WWWQ-HDNVEVpYSHPymppePLTAICYITNNFTGLFNRSFHLELGVSGrlfagsAYITTCILDRRPSFCGDCFG 492
Cdd:pfam12786  165 WGSayWFWRtGDWVDL-WSEL-----PGSALCTFAALGTSDRDHPDVDVLSPSG------IPCASCVVDRRPASCGSCVR 232

                          250       260
                   ....*....|....*....|.
gi 482876020   493 GCFHSTGRHDMGFGVCGGGYR 513
Cdd:pfam12786  233 DCWETTGPKRLPFEECGLGPR 253
HCV_NS5a_1a super family cl07056
Hepatitis C virus non-structural 5a zinc finger domain; The molecular function of the ...
 2196-2257 6.41e-06

Hepatitis C virus non-structural 5a zinc finger domain; The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR. This domain corresponds to the N-terminal zinc binding domain.


The actual alignment was detected with superfamily member pfam08300:

Pssm-ID: 369801  Cd Length: 62  Bit Score: 46.20  E-value: 6.41e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 482876020  2196 MPLVSCDKGWSGPWLGTGTGITTCACGHRVTVTVTSPKKPVIrASRACRHAWQHTFPVNVTT 2257
Cdd:pfam08300    1 IPFMGCQKGWAGPWEGDGHMEARCHCGAEITGEIKDGELHIV-GPRTCKDMVSGTFFCNAYS 61
 
Name Accession Description Interval E-value
Pegivirus_RdRp cd23203
RNA-dependent RNA polymerase (RdRp) in the genus Pegivirus, within the family Flaviviridae of ...
 2757-3232 0e+00

RNA-dependent RNA polymerase (RdRp) in the genus Pegivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the RdRp of RNA viruses belonging to the Pegivirus genus within the family Flaviviridae, order Amarillovirales. Members of the Pegivirus genus are widely distributed in a range of mammalian species, in which they cause persistent infections. To date, they have not been clearly associated with disease. Virions of Pegivirus have a single, small, basic capsid (C) protein and two envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. 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: 438053  Cd Length: 476  Bit Score: 892.77  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2757 WSGAPITVQEPKQPPVTRAVTGALRASADRVYVTNPEDIHKRIAKVTIEQKVAEKDRYFLDAYNLALANASRILSPGFSY 2836
Cdd:cd23203     1 WSGAPLGVGRPKPPPVTRPVGSHLRADATKVYVTDPDDVGERIEKVTIWRTPRVVDKFLRDAYNLALAKASATPSPGWTY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2837 EEAIAKVKPNTAKGHVARITAADLKTEVGRKAVEKCLDDIRGGVAYAPFMLRPKSEVFPQTRETFKPPRLITYPSLEFRV 2916
Cdd:cd23203    81 EEAVAKVRPGAAMGHGSKVTVADLKTPAGKKAVEECLNQIIAGGEEVPFTLTAKQEVFFQDKKTRKPPRLIVYPPLEFRV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2917 AEKMILGDPSLVAKAVMGPAYGFQYPPHERAEVLTKMWTSKKSPVAYTVDGVCFDSTITPEDIDREANIFAAASDDPMAV 2996
Cdd:cd23203   161 AEKMILGDPGRVAKAVLGKAYGFQYTPNQRVKVLVDMWKSKRHPCAITVDATCFDSSITEEDVARETEIYAAASDDPELV 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2997 RRLHDHYASGPLMDPSGKIVGVRNCRASGTLTTSAGNSITCYLKVTAACRKAGIKNPSFLIHGDDCVIICEKEEVDKSDA 3076
Cdd:cd23203   241 RALGKYYAEGPMVNPEGVPVGERRCRASGVLTTSSSNSITCYLKVKAACRKAGLKNPSFLIHGDDCLIICERPEEDPCDA 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 3077 LGEALRSYGYECEPTIHADLSTAESCSASLDRVRTVRGLRPTLKPDMRRAIGRVIAEHGDSVGCAWGYIIQYPTHPISMY 3156
Cdd:cd23203   321 LKAALASYGYDCEPQYHASLDTAESCSAYLAECNAGGGRHYFLSTDMRRPLARASSEYGDPVASALGYILLYPWHPITRY 400

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 482876020 3157 VLLPILLTIALNNGDSARQPVTIDVRGNQITLPLNRLGSAIRGLHGPDVLAITGHSAAVIEESHQTLQFFRMRGLN 3232
Cdd:cd23203   401 VLLPHLLTLAFRGGGTPDDLVTCQVHGNSYKFPLKLLPRILVGLHGPDCLRVTADSTKTLMEAGKALQAFGMRGLA 476
RdRP_3 pfam00998
Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase ...
 2754-3245 4.23e-80

Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase enzymes from hepatitis C virus and various plant viruses.


Pssm-ID: 395794 [Multi-domain]  Cd Length: 486  Bit Score: 274.50  E-value: 4.23e-80
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020  2754 SYVWSGAPITVQEpKQPPVTRAVTGALRASADRVYVTNPEDIHKRIAKVTI-EQKVAEKDRYFLDAYNLALANASRILSP 2832
Cdd:pfam00998    1 SYVWTGARPAKER-KILPITGPGSGLLFGVHNNSLVNLRRGLVERVFKVTFdRGGQLVPPKPYPGAFKELKYFASALVSK 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020  2833 GFsyeEAIAKVKPNTAKGHVAR---ITAADLKTeVGRKAVEKCLDDIRGGVAYAPFMLRPKSEVFPQTRETfKPPRLITY 2909
Cdd:pfam00998   80 LG---EATPLTPEHFAASYTGRkrkIYVKALES-LAVKPVQRRDAILKTFVKAEKINITAKPDPAPRVIQP-RPPRYNVE 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020  2910 PSLEFRVAEKMILGDpslVAKAVMGPAYGFQYPPHERAEVLTKMWTSKKSPVAYTVDGVCFDSTITPEDIDREANIFAAA 2989
Cdd:pfam00998  155 PGRYLRPCEKMIYKA---IDKAFGGPTVLKGYTPEQRGEILLKKWDSFKKPVAIGLDASRFDQHVSVEALRFEHSIYLAA 231

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020  2990 SDDPMAVRRL--HDHYASGPLMDPSGKI-VGVRNCRASGTLTTSAGNSITCYLKVTAACRKAGIkNPSFLIHGDDCVIIC 3066
Cdd:pfam00998  232 FLGPEELIRLltWQLYNGGPMYASDGQIkYGVRGCRMSGDMNTSLGNCLLMCLKVHAACKALGI-DARLLNNGDDCVVIC 310

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020  3067 EKEEVDK-SDALGEALRSYGYEC---EPTIHadLSTAESCSASL----DRVRTVRGLRPTlkpDMRRAIGRVIAEHGDSV 3138
Cdd:pfam00998  311 ESADLDEvKEALTEAFARYGFTMkveEPVYE--LELIEFCQSNPvfdgGKYGMVRNPLTS---DSKDPLSRASWETATPA 385

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020  3139 GCAWGYIIQYPTHPISMYVLLPILLTIALNNGDSARqPVTIDVRGNQITLplnrlgsAIRGLHGPDVLAITGHSAAVIEE 3218
Cdd:pfam00998  386 KSWLGAIGECGLSLWGGVPVLQHFYSCLLRNGGLEK-AVSFEMYGKVYSD-------SGFRLHGLGAGSRHSYEPTEEAR 457

                          490       500
                   ....*....|....*....|....*..
gi 482876020  3219 SHQTLQfFRMRGLNHWRRQRRKVQLRM 3245
Cdd:pfam00998  458 VSFWLA-FGITPDEQWALEAYYDRLKL 483
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 1406-1540 2.60e-25

DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional protein found in pestiviruses that contains an N-terminal protease and a C-terminal helicase. The N-terminal domain is a chymotrypsin-like serine protease, which is responsible for most of the maturation cleavages of the polyprotein precursor in the cytosolic side of the endoplasmic reticulum membrane. The C-terminal domain, about two-thirds of NS3, is a helicase belonging to superfamily 2 (SF2) thought to be important for unwinding highly structured regions of the RNA genome during replication. NS3 plays an essential role in viral polyprotein processing and genome replication. NS3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350689 [Multi-domain]  Cd Length: 151  Bit Score: 104.55  E-value: 2.60e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 1406 APTGSGKSTKFPSKLVQEGH----RVLVLNPSVVTTRAMFKYMKdstGDAPNVYAGtgkgAISRETGSK--LTYCTYGRF 1479
Cdd:cd17931     8 LHPGAGKTTRVLPQIIREAIkkrlRTLVLAPTRVVAAEMYEALR---GLPIRYRTG----AVKEEHGGNeiVDYMCHGTF 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 482876020 1480 ---LVSPGRfLQRVNVVICDECHAVDGTTILGIGAVRALAQdAGVRLVVFATATPPGTQLQPHP 1540
Cdd:cd17931    81 tcrLLSPKR-VPNYNLIIMDEAHFTDPASIAARGYIHTRVE-MGEAAVIFMTATPPGTVTPFPQ 142
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 1542-1674 4.20e-21

C-terminal helicase domain of viral helicase; Viral helicases in this family here are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350193 [Multi-domain]  Cd Length: 145  Bit Score: 92.32  E-value: 4.20e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 1542 ITETPLDSDGDVPFYGLTLKSAnyKAGRHVIFCHSKVECQRVAKELTSRGVNTVTYWRG-----KPADTLTDdpDLTVVA 1616
Cdd:cd18806     1 IEDVALEIPGRIWFYGKAWITI--YGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKlddteYPKIKTID--WDFVVT 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 482876020 1617 TDAISTGYTGNFASVTDCCSAVAEEVEVDLNptFTISL-FTGPADAALRMQRRGRTGRG 1674
Cdd:cd18806    77 TDISEMGANFDADRVIDCRTCVKPTILFSGD--FRVILtGPVPQTAASAAQRRGRTGRN 133
HCV_NS4b pfam01001
Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. ...
 1956-2113 6.79e-18

Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. However, it is known that NS4b interacts with NS4a and NS3 to form a large replicase complex to direct the viral RNA replication.


Pssm-ID: 110032  Cd Length: 192  Bit Score: 84.35  E-value: 6.79e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020  1956 LDLIAANLSAMVAGGVAICGARASPAFASLAALVAGAQVCTSSNIIWGLTLAGGLAATLLGGAGAGFGVATSFFIGSKLA 2035
Cdd:pfam01001   34 WAKHMWNFRSGIQYLAGLYTLPRNPPLAVLASFLAGMTSPLPTHVRLALALLGGWGATQLGTPSGGLAFVGAGFAGAAVG 113

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 482876020  2036 GLSWVETIVGCFAGYEACVNFCALTLDLLDGKLALETAAPCLV-GLLAPGAAVAGIVMAMLLRSTQGGDVTPWMNRLLS 2113
Cdd:pfam01001  114 SSWLGRVLVDVLGGYEAAVNAASLTFKIMSGELPTAEDLWNLLpCLLSPGASVVGVALAALLRSHKGEGAVQWMNRLLT 192
DEXDc smart00487
DEAD-like helicases superfamily;
1397-1533 4.15e-13

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 70.98  E-value: 4.15e-13
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020   1397 NGYKEVPYIAPTGSGKSTKFP-----SKLVQEGHRVLVLNPSVVTTRAMFKYMKDSTGDAPNVYAGTGKGAISRETGSKL 1471
Cdd:smart00487   22 SGLRDVILAAPTGSGKTLAALlpaleALKRGKGGRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKL 101

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 482876020   1472 -------TYCTYGRF---LVSPGRFLQRVNVVICDECHAVD----GTTILGIGAVRalaqdAGVRLVVFATATPPG 1533
Cdd:smart00487  102 esgktdiLVTTPGRLldlLENDKLSLSNVDLVILDEAHRLLdggfGDQLEKLLKLL-----PKNVQLLLLSATPPE 172
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
1409-1541 4.59e-09

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 57.73  E-value: 4.59e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020  1409 GSGKSTKFPSKLVQE----GHRVLVLNPsvvtTRAMFKYMKDSTGDAPNVYAgtgKGAISRE-TGSKLT----YCTYGRF 1479
Cdd:pfam07652   12 GAGKTRKVLPELVREcidrRLRTLVLAP----TRVVLAEMEEALRGLPIRYH---TPAVSSEhTGREIVdvmcHATFTQR 84

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 482876020  1480 LVSPGRfLQRVNVVICDECHAVDGTTILGIGAVRALAqDAGVRLVVFATATPPGTQlQPHPD 1541
Cdd:pfam07652   85 LLSPVR-VPNYEVIIMDEAHFTDPASIAARGYISTLV-ELGEAAAIFMTATPPGTS-DPFPE 143
GBV-C_env pfam12786
GB virus C genotype envelope; This the envelope protein from the ssRNA GB virus genotype C.
 271-513 1.43e-07

GB virus C genotype envelope; This the envelope protein from the ssRNA GB virus genotype C.


Pssm-ID: 193262  Cd Length: 413  Bit Score: 56.73  E-value: 1.43e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020   271 PDLVCNRTCSV-FALDWWSDNAPTLAALWSVVTL--LPEAVWGVLTAMPPLFGGLLLFYLCRGWWVQAVLLFLAV----P 343
Cdd:pfam12786    6 PNLTCAVECDLaWSYEGWSWTEDMADFDWAFEYLwtLPFDLWRGLMAASVLLVLVAALLLLEQRLVMAFLLLTVAgeaqG 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020   344 GVLADCYDAEYDEIASLSCNMTHFRKANITCPCPYG--VWMREFNAS----DPAQAHL--NLTIRCPeRYNHSQDYWTCG 415
Cdd:pfam12786   86 GFFDGCHCAYWGSRVPPGAKPWDRGNGTVVCDCPFGpmVWLPALCSGlawrDGDREGTvnDLPLVCP-REVLGTVSVMCV 164

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020   416 WGS--WWWQ-HDNVEVpYSHPymppePLTAICYITNNFTGLFNRSFHLELGVSGrlfagsAYITTCILDRRPSFCGDCFG 492
Cdd:pfam12786  165 WGSayWFWRtGDWVDL-WSEL-----PGSALCTFAALGTSDRDHPDVDVLSPSG------IPCASCVVDRRPASCGSCVR 232

                          250       260
                   ....*....|....*....|.
gi 482876020   493 GCFHSTGRHDMGFGVCGGGYR 513
Cdd:pfam12786  233 DCWETTGPKRLPFEECGLGPR 253
HCV_NS5a_1a pfam08300
Hepatitis C virus non-structural 5a zinc finger domain; The molecular function of the ...
 2196-2257 6.41e-06

Hepatitis C virus non-structural 5a zinc finger domain; The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR. This domain corresponds to the N-terminal zinc binding domain.


Pssm-ID: 369801  Cd Length: 62  Bit Score: 46.20  E-value: 6.41e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 482876020  2196 MPLVSCDKGWSGPWLGTGTGITTCACGHRVTVTVTSPKKPVIrASRACRHAWQHTFPVNVTT 2257
Cdd:pfam08300    1 IPFMGCQKGWAGPWEGDGHMEARCHCGAEITGEIKDGELHIV-GPRTCKDMVSGTFFCNAYS 61
 
Name Accession Description Interval E-value
Pegivirus_RdRp cd23203
RNA-dependent RNA polymerase (RdRp) in the genus Pegivirus, within the family Flaviviridae of ...
 2757-3232 0e+00

RNA-dependent RNA polymerase (RdRp) in the genus Pegivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the RdRp of RNA viruses belonging to the Pegivirus genus within the family Flaviviridae, order Amarillovirales. Members of the Pegivirus genus are widely distributed in a range of mammalian species, in which they cause persistent infections. To date, they have not been clearly associated with disease. Virions of Pegivirus have a single, small, basic capsid (C) protein and two envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. 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: 438053  Cd Length: 476  Bit Score: 892.77  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2757 WSGAPITVQEPKQPPVTRAVTGALRASADRVYVTNPEDIHKRIAKVTIEQKVAEKDRYFLDAYNLALANASRILSPGFSY 2836
Cdd:cd23203     1 WSGAPLGVGRPKPPPVTRPVGSHLRADATKVYVTDPDDVGERIEKVTIWRTPRVVDKFLRDAYNLALAKASATPSPGWTY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2837 EEAIAKVKPNTAKGHVARITAADLKTEVGRKAVEKCLDDIRGGVAYAPFMLRPKSEVFPQTRETFKPPRLITYPSLEFRV 2916
Cdd:cd23203    81 EEAVAKVRPGAAMGHGSKVTVADLKTPAGKKAVEECLNQIIAGGEEVPFTLTAKQEVFFQDKKTRKPPRLIVYPPLEFRV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2917 AEKMILGDPSLVAKAVMGPAYGFQYPPHERAEVLTKMWTSKKSPVAYTVDGVCFDSTITPEDIDREANIFAAASDDPMAV 2996
Cdd:cd23203   161 AEKMILGDPGRVAKAVLGKAYGFQYTPNQRVKVLVDMWKSKRHPCAITVDATCFDSSITEEDVARETEIYAAASDDPELV 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2997 RRLHDHYASGPLMDPSGKIVGVRNCRASGTLTTSAGNSITCYLKVTAACRKAGIKNPSFLIHGDDCVIICEKEEVDKSDA 3076
Cdd:cd23203   241 RALGKYYAEGPMVNPEGVPVGERRCRASGVLTTSSSNSITCYLKVKAACRKAGLKNPSFLIHGDDCLIICERPEEDPCDA 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 3077 LGEALRSYGYECEPTIHADLSTAESCSASLDRVRTVRGLRPTLKPDMRRAIGRVIAEHGDSVGCAWGYIIQYPTHPISMY 3156
Cdd:cd23203   321 LKAALASYGYDCEPQYHASLDTAESCSAYLAECNAGGGRHYFLSTDMRRPLARASSEYGDPVASALGYILLYPWHPITRY 400

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 482876020 3157 VLLPILLTIALNNGDSARQPVTIDVRGNQITLPLNRLGSAIRGLHGPDVLAITGHSAAVIEESHQTLQFFRMRGLN 3232
Cdd:cd23203   401 VLLPHLLTLAFRGGGTPDDLVTCQVHGNSYKFPLKLLPRILVGLHGPDCLRVTADSTKTLMEAGKALQAFGMRGLA 476
Hepacivirus_RdRp cd23202
RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ...
 2787-3261 3.75e-114

RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the RdRp of RNA viruses belonging to the Hepacivirus genus within the family Flaviviridae, order Amarillovirales. The genus Hepacivirus includes hepatitis C virus, a major human pathogen causing progressive liver disease, and several other viruses of unknown pathogenicity that infect horses, rodents, bats, cows and primates. Infections are typically persistent and target the liver. Virions of Hepacivirus have a single, small, basic capsid (C) protein and two envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. 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: 438052  Cd Length: 518  Bit Score: 374.18  E-value: 3.75e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2787 VYVTNPEDIHKRIAKVTIEqKVAEKDRYFLDAYNLALANASRILSPGFSYEEAIAKVKPNTAKgHVARITAADLKtEVGR 2866
Cdd:cd23202    24 VYSTTSRSASERQKKVTFD-RLQVLDPHYDDVLKEAKARASGVKARLLSVEEACSLTPPHSAR-SKFGYGAKDVR-SLSR 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2867 KAV-------EKCLDDIrggVAYAPFMLRPKSEVFPQTRE--TFKPPRLITYPSLEFRVAEKMILGD--PSLVaKAVMGP 2935
Cdd:cd23202   101 KAVnhinsvwEDLLEDS---ETPIPTTIMAKNEVFCVTPEkgGRKPARLIVYPDLGVRVCEKMALYDvaPKLP-KAVMGE 176

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2936 AYGFQYPPHERAEVLTKMWTSKKSPVAYTVDGVCFDSTITPEDIDREANIFAAASDDPMA---VRRLHDH-YASGPLMDP 3011
Cdd:cd23202   177 AYGFQYSPAQRVEFLLKMWRSKKTPMGFSYDTRCFDSTVTERDIRTEESIYQCCDLDPEArkaIRSLTERlYVGGPMTNS 256

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 3012 SGKIVGVRNCRASGTLTTSAGNSITCYLKVTAACRKAGIKNPSFLIHGDDCVIICEKE--EVDKS--DALGEALRSYGye 3087
Cdd:cd23202   257 KGQSCGYRRCRASGVFTTSSGNTLTCYLKASAACRAAGLKDPTMLVCGDDLVVIAESAgvEEDAAalRAFTEAMTRYS-- 334

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 3088 C----EPTIHADLSTAESCSASLDRVRTVRGLR-PTLKPDMRRAIGRVIAE---HgDSVGcAW-GYIIQY-PTHPISMyV 3157
Cdd:cd23202   335 AppgdPPQPEYDLELITSCSSNVSVAHDATGKRyYYLTRDPTTPLARAAWEtarH-TPVN-SWlGNIIMYaPTLWVRM-V 411

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 3158 LLPILLTIaLNNGDSARQPVTIDVRGNQITLPLNRLGSAIRGLHGPDVLAITGHSAAVIEESHQTLQFFRMRGLNHWRRQ 3237
Cdd:cd23202   412 LMTHFFSI-LLAQEQLEKALDFEMYGNTYSIPPLDLPAIIQRLHGLSAFSLHGYSPRELNRVAAALRKLGVPPLRAWRHR 490

                         490       500
                  ....*....|....*....|....
gi 482876020 3238 RRKVQLRMRRAGKEWADLARELLW 3261
Cdd:cd23202   491 ARAVRAKLIAQGGKAAICGKYLFN 514
ps-ssRNAv_Flaviviridae_RdRp cd23178
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of ...
 2884-3151 4.35e-102

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Flaviviridae, order Amarillovirales. Flaviviridae, is a family of small, enveloped viruses with RNA genomes of 9-13 kb. Most infect mammals and birds. Many flaviviruses are host-specific and pathogenic, such as hepatitis C virus in the genus Hepacivirus. The majority of known members in the genus Flavivirus are arthropod borne, and many are important human and veterinary pathogens (e.g., yellow fever virus, dengue virus). Virions are typically spherical in shape with a lipid envelope. Virions have a single, small, basic capsid (C) protein and two (genera Flavivirus, Hepacivirus and Pegivirus) or three (genus Pestivirus) envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. Translational initiation of genomic RNA is cap dependent in the case of members of the genus Flavivirus. 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: 438028  Cd Length: 284  Bit Score: 329.86  E-value: 4.35e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2884 PFMLRPKSEVFPQTRE--TFKPPRLITYPSLEFRVAEKMILGDPSLVAKAVMGP-AYGFQYPPHERAEVLTKMWTSKKSP 2960
Cdd:cd23178     2 PTTIMPKNEVFCVEPGkgGRKPPRLIVYPDLGVRVAEKMALYDPVEVLPQVVGGsYYGFQYSPNQRVEILRKAWKSKKGP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2961 VAYTVDGVCFDSTITPEDIDREANIFAAAS---DDPMAVRRLHDHYASGPLMDPSGKIVGVRNCRASGTLTTSAGNSITC 3037
Cdd:cd23178    82 MAYSYDTRCFDSTVTEDDIQVEEEIYQACSlkeARQAIVSITERLYVEGPMVNSDGQICGRRRCRASGVLTTSAGNT*TC 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 3038 YLKVTAACRKAGIKNPSFLIHGDDCVIICEKEEVDKSDALGEALRSYGYECEPTIHA------DLSTAESCSASLDRVRT 3111
Cdd:cd23178   162 YLK*LAACREAGIRLPTMLVCGDDCVVICESDGTQEDAALLAAFTEALTRYGKPPKDppqpeyDLELIESCSHTVSEVRM 241

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 482876020 3112 VRGLRPTLKP-DMRRAIGRVIAEHGDS--VGCAWGYIIQYPTH 3151
Cdd:cd23178   242 KDGRRLYYLTrDPTTPLARAAWETGRHepINSWLGYIIMYALT 284
RdRP_3 pfam00998
Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase ...
 2754-3245 4.23e-80

Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase enzymes from hepatitis C virus and various plant viruses.


Pssm-ID: 395794 [Multi-domain]  Cd Length: 486  Bit Score: 274.50  E-value: 4.23e-80
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020  2754 SYVWSGAPITVQEpKQPPVTRAVTGALRASADRVYVTNPEDIHKRIAKVTI-EQKVAEKDRYFLDAYNLALANASRILSP 2832
Cdd:pfam00998    1 SYVWTGARPAKER-KILPITGPGSGLLFGVHNNSLVNLRRGLVERVFKVTFdRGGQLVPPKPYPGAFKELKYFASALVSK 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020  2833 GFsyeEAIAKVKPNTAKGHVAR---ITAADLKTeVGRKAVEKCLDDIRGGVAYAPFMLRPKSEVFPQTRETfKPPRLITY 2909
Cdd:pfam00998   80 LG---EATPLTPEHFAASYTGRkrkIYVKALES-LAVKPVQRRDAILKTFVKAEKINITAKPDPAPRVIQP-RPPRYNVE 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020  2910 PSLEFRVAEKMILGDpslVAKAVMGPAYGFQYPPHERAEVLTKMWTSKKSPVAYTVDGVCFDSTITPEDIDREANIFAAA 2989
Cdd:pfam00998  155 PGRYLRPCEKMIYKA---IDKAFGGPTVLKGYTPEQRGEILLKKWDSFKKPVAIGLDASRFDQHVSVEALRFEHSIYLAA 231

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020  2990 SDDPMAVRRL--HDHYASGPLMDPSGKI-VGVRNCRASGTLTTSAGNSITCYLKVTAACRKAGIkNPSFLIHGDDCVIIC 3066
Cdd:pfam00998  232 FLGPEELIRLltWQLYNGGPMYASDGQIkYGVRGCRMSGDMNTSLGNCLLMCLKVHAACKALGI-DARLLNNGDDCVVIC 310

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020  3067 EKEEVDK-SDALGEALRSYGYEC---EPTIHadLSTAESCSASL----DRVRTVRGLRPTlkpDMRRAIGRVIAEHGDSV 3138
Cdd:pfam00998  311 ESADLDEvKEALTEAFARYGFTMkveEPVYE--LELIEFCQSNPvfdgGKYGMVRNPLTS---DSKDPLSRASWETATPA 385

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020  3139 GCAWGYIIQYPTHPISMYVLLPILLTIALNNGDSARqPVTIDVRGNQITLplnrlgsAIRGLHGPDVLAITGHSAAVIEE 3218
Cdd:pfam00998  386 KSWLGAIGECGLSLWGGVPVLQHFYSCLLRNGGLEK-AVSFEMYGKVYSD-------SGFRLHGLGAGSRHSYEPTEEAR 457

                          490       500
                   ....*....|....*....|....*..
gi 482876020  3219 SHQTLQfFRMRGLNHWRRQRRKVQLRM 3245
Cdd:pfam00998  458 VSFWLA-FGITPDEQWALEAYYDRLKL 483
RNA_dep_RNAP cd01699
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
 2866-3122 1.55e-41

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: 155.52  E-value: 1.55e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2866 RKAVEKCLDDIrGGVAYAPFMLRPKSEVFPQTRETFKPPRLITYPSLEFRVAEKMILGDPSLVAKAVM-GPAYGFQYPPH 2944
Cdd:cd01699     2 EKAVESLEDLP-LIRPDLVFTTFLKDELRPLEKVEAGKTRLIQPRPLDYNIALRMYLGPFEAKLMKNRgGLPIAVGINPY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2945 ER-AEVLTKMWTSKKsPVAYTVDGVCFDSTITPEDIDREANIFAAASDDPMAVRR--LHDHYASGPLMDPSGKIVGVRNC 3021
Cdd:cd01699    81 SRdWTILANKLRSFS-PVAIALDYSRFDSSLSPQLLEAEHSIYNALYDDDDELERrnLLRSLTNNSLHIGFNEVYKVRGG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 3022 RASGTLTTSAGNSITCYLKVTAACRKAG----IKNPSFLIHGDDCVIICEKEEVDK-SDALGEALRSYGYECEP-----T 3091
Cdd:cd01699   160 RPSGDPLTSIGNSIINCILVRYAFRKLGgksfFKNVRLLNYGDDCLLSVEKADDKFnLETLAEWLKEYGLTMTDedkveS 239

                         250       260       270
                  ....*....|....*....|....*....|.
gi 482876020 3092 IHADLSTAESCSASLdRVRTVRGLRPTLKPD 3122
Cdd:cd01699   240 PFRPLEEVEFLKRRF-VLDEGGGWRAPLDPS 269
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 1406-1540 2.60e-25

DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional protein found in pestiviruses that contains an N-terminal protease and a C-terminal helicase. The N-terminal domain is a chymotrypsin-like serine protease, which is responsible for most of the maturation cleavages of the polyprotein precursor in the cytosolic side of the endoplasmic reticulum membrane. The C-terminal domain, about two-thirds of NS3, is a helicase belonging to superfamily 2 (SF2) thought to be important for unwinding highly structured regions of the RNA genome during replication. NS3 plays an essential role in viral polyprotein processing and genome replication. NS3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350689 [Multi-domain]  Cd Length: 151  Bit Score: 104.55  E-value: 2.60e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 1406 APTGSGKSTKFPSKLVQEGH----RVLVLNPSVVTTRAMFKYMKdstGDAPNVYAGtgkgAISRETGSK--LTYCTYGRF 1479
Cdd:cd17931     8 LHPGAGKTTRVLPQIIREAIkkrlRTLVLAPTRVVAAEMYEALR---GLPIRYRTG----AVKEEHGGNeiVDYMCHGTF 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 482876020 1480 ---LVSPGRfLQRVNVVICDECHAVDGTTILGIGAVRALAQdAGVRLVVFATATPPGTQLQPHP 1540
Cdd:cd17931    81 tcrLLSPKR-VPNYNLIIMDEAHFTDPASIAARGYIHTRVE-MGEAAVIFMTATPPGTVTPFPQ 142
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 1542-1674 4.20e-21

C-terminal helicase domain of viral helicase; Viral helicases in this family here are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350193 [Multi-domain]  Cd Length: 145  Bit Score: 92.32  E-value: 4.20e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 1542 ITETPLDSDGDVPFYGLTLKSAnyKAGRHVIFCHSKVECQRVAKELTSRGVNTVTYWRG-----KPADTLTDdpDLTVVA 1616
Cdd:cd18806     1 IEDVALEIPGRIWFYGKAWITI--YGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKlddteYPKIKTID--WDFVVT 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 482876020 1617 TDAISTGYTGNFASVTDCCSAVAEEVEVDLNptFTISL-FTGPADAALRMQRRGRTGRG 1674
Cdd:cd18806    77 TDISEMGANFDADRVIDCRTCVKPTILFSGD--FRVILtGPVPQTAASAAQRRGRTGRN 133
HCV_NS4b pfam01001
Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. ...
 1956-2113 6.79e-18

Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. However, it is known that NS4b interacts with NS4a and NS3 to form a large replicase complex to direct the viral RNA replication.


Pssm-ID: 110032  Cd Length: 192  Bit Score: 84.35  E-value: 6.79e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020  1956 LDLIAANLSAMVAGGVAICGARASPAFASLAALVAGAQVCTSSNIIWGLTLAGGLAATLLGGAGAGFGVATSFFIGSKLA 2035
Cdd:pfam01001   34 WAKHMWNFRSGIQYLAGLYTLPRNPPLAVLASFLAGMTSPLPTHVRLALALLGGWGATQLGTPSGGLAFVGAGFAGAAVG 113

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 482876020  2036 GLSWVETIVGCFAGYEACVNFCALTLDLLDGKLALETAAPCLV-GLLAPGAAVAGIVMAMLLRSTQGGDVTPWMNRLLS 2113
Cdd:pfam01001  114 SSWLGRVLVDVLGGYEAAVNAASLTFKIMSGELPTAEDLWNLLpCLLSPGASVVGVALAALLRSHKGEGAVQWMNRLLT 192
ps_ssRNAv_Tolivirales_RdRp cd23179
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Toliovirales of ...
 2902-3073 1.05e-14

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Toliovirales of positive-sense single-stranded RNA (+ssRNA) viruses; This family contains the catalytic core domain of RdRp of Tolivirales, an order of (+)ssRNA viruses which infect insects and plants. The virions are non-enveloped, spherical, and have an icosahedral capsid. The name Tolivirales, is derived from "tombusvirus-like" with the suffix -virales indicating a virus order. This order includes two families: Carmotetraviridae and Tombusviridae. 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: 438029  Cd Length: 227  Bit Score: 76.02  E-value: 1.05e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2902 KPPRLITYPSLEFRVA--------EKMILGDPS-------LVAKAvmgpaygfqYPPHERAEVLTKMWTSKKSPVAYTVD 2966
Cdd:cd23179    19 KKPRMIQPRSPRYNLElarylkpiEHALYGALDagrggtrVVAKG---------LNPRQRANLIRRKWDEFDDPVVFSLD 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2967 GVCFDSTITPEDIDREANIFAAA-SDDPMaVRRLHDH--YASGPLMDpsGKIVGVRNCRASGTLTTSAGNSITCYLKVTA 3043
Cdd:cd23179    90 ASRFDAHVSVELLRLEHSVYLACyPGDPE-LRKLLKWqlVNKGRTSN--GVKYKTRGGRMSGDMNTGLGNCLIMLAMVYA 166

                         170       180       190
                  ....*....|....*....|....*....|
gi 482876020 3044 ACRKAGIKNpSFLIHGDDCVIICEKEEVDK 3073
Cdd:cd23179   167 VLRELGIKY-DLLVDGDDALVFVEREDLER 195
DEXDc smart00487
DEAD-like helicases superfamily;
1397-1533 4.15e-13

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 70.98  E-value: 4.15e-13
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020   1397 NGYKEVPYIAPTGSGKSTKFP-----SKLVQEGHRVLVLNPSVVTTRAMFKYMKDSTGDAPNVYAGTGKGAISRETGSKL 1471
Cdd:smart00487   22 SGLRDVILAAPTGSGKTLAALlpaleALKRGKGGRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKL 101

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 482876020   1472 -------TYCTYGRF---LVSPGRFLQRVNVVICDECHAVD----GTTILGIGAVRalaqdAGVRLVVFATATPPG 1533
Cdd:smart00487  102 esgktdiLVTTPGRLldlLENDKLSLSNVDLVILDEAHRLLdggfGDQLEKLLKLL-----PKNVQLLLLSATPPE 172
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
1409-1541 4.59e-09

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 57.73  E-value: 4.59e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020  1409 GSGKSTKFPSKLVQE----GHRVLVLNPsvvtTRAMFKYMKDSTGDAPNVYAgtgKGAISRE-TGSKLT----YCTYGRF 1479
Cdd:pfam07652   12 GAGKTRKVLPELVREcidrRLRTLVLAP----TRVVLAEMEEALRGLPIRYH---TPAVSSEhTGREIVdvmcHATFTQR 84

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 482876020  1480 LVSPGRfLQRVNVVICDECHAVDGTTILGIGAVRALAqDAGVRLVVFATATPPGTQlQPHPD 1541
Cdd:pfam07652   85 LLSPVR-VPNYEVIIMDEAHFTDPASIAARGYISTLV-ELGEAAAIFMTATPPGTS-DPFPE 143
Regressovirinae_RdRp cd23235
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Regressovirinae ...
 2946-3089 7.01e-09

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Regressovirinae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the subfamily Regressovirinae, family Tombusviridae, order Tolivirales. Dianthovirus is a genus of plant viruses within this subfamily. All the genera in the family Tombusviridae have monopartite (+)ssRNA genomes, except the dianthoviruses which have bipartite (+)ssRNA genomes. The dianthoviruses are distributed worldwide. The genus Dianthovirus is composed of three viruses: Carnation ringspot virus, Red clover necrotic mosaic virus, and Sweet clover necrotic mosaic virus. The amino acid (aa) sequence of dianthovirus RdRp has higher homology with that of the luteoviruses, while the amino acid sequence of dianthovirus coat protein (CP) has high homology with those of the tombusviruses and aureusviruses that belong to the subfamily Procedovirinae. 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: 438085 [Multi-domain]  Cd Length: 472  Bit Score: 61.48  E-value: 7.01e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2946 RAEVLTKMWTSKKSPVAYTVDGVCFDSTITPEDIDREANIFAAASDDPMAVRRLHDHYAS--GPLMDPSGKIVGVRN--C 3021
Cdd:cd23235   154 QGRAIAKKWSKYESPIGIGLDASRFDQHCSKDALKFEHSFYRECFPDDKTLEDLLDWQLEneGSALMPTGELVKYRTkgC 233

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 482876020 3022 RASGTLTTSAGNSITCYLKVTAACRKAGIkNPSFLIHGDDCVIICEKEEVDK-SDALGEALRSYGYECE 3089
Cdd:cd23235   234 RMSGDINTGLGNKILMCSMVHAYLKEVGV-NASLANNGDDCVLFCEKGDFNRiNDSLREWFLCRGFNMV 301
Tombusviridae_RdRp cd23206
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tombusviridae of ...
 2945-3089 9.56e-09

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tombusviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Tombusviridae, order Tolivirales. The family Tombusviridae comprises plant viruses, and is classified into 3 subfamilies (Calvusvirinae, Procedovirinae, and Regressovirinae), 17 genera, and 95 species. One genus is unassigned to a subfamily: Luteovirus. The name of the family is derived from Tomato bushy stunt virus (TBSV). Members of Tombusviridae replicate in the cytoplasm, by use of negative strand templates. The replication process leaves a surplus of positive- sense (+)RNA strands, and it is thought that not only does the viral RNA act as a template for replication, but is also able to manipulate and regulate RNA synthesis. 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: 438056  Cd Length: 231  Bit Score: 58.66  E-value: 9.56e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2945 ERAEVLTKMWTSKKSPVAYTVDGVCFDSTITPEDIDREANIFAAASDDPMAVRRLHDH------YASGPlmdpSGKIV-G 3017
Cdd:cd23206    69 ERGRILREKWDSFRDPVAVGLDASRFDQHVSVDALKWEHSVYLRIFPDDKELSRLLRWqlhnkgVARCK----DGKVKyK 144

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 482876020 3018 VRNCRASGTLTTSAGN-SITCYLkVTAACRKAGIKNpSFLIHGDDCVIICEKEEVDK-SDALGEALRSYGYECE 3089
Cdd:cd23206   145 VKGGRMSGDMNTSLGNcLIMCAM-VYAYLEELGIKA-ELANNGDDCVLIMERSDLLRfLDGLEEWFLRFGFTMV 216
Luteovirus_RdRp cd23233
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Luteovirus of ...
 2948-3102 4.10e-08

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Luteovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Luteovirus genus within the family Tombusviridae, order Tolivirales. There are 13 species in the Luteovirus genus: Apple associated luteovirus, Apple luteovirus 1, Barley yellow dwarf virus kerII, Barley yellow dwarf virus kerIII, Barley yellow dwarf virus MAV, Barley yellow dwarf virus PAS, Barley yellow dwarf virus PAV, Bean leafroll virus, Cherry associated luteovirus, Nectarine stem pitting associated virus, Red clover associated luteovirus, Rose spring dwarf-associated virus, and Soybean dwarf virus. Plants serve as natural hosts. The geographical distribution of Luteoviruses is widespread, with the virus primarily infecting plants via transmission by aphid vectors. The virus only replicates within the host cell and not within the vector. The name 'luteovirus' is derived from the Latin luteus (yellow) due to the symptomatic yellowing of the plant that occurs as a result of infection. 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: 438083  Cd Length: 407  Bit Score: 58.59  E-value: 4.10e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2948 EVLTKMWTSKKSPVAYTVDGVCFDSTITPEDIDREANIFAAASDDPMAVRRLHDHYASGPLMDPSGKIV--GVRNCRASG 3025
Cdd:cd23233    98 RIIAKKWQKFANPVAIGVDASRFDQHVSEQALKWEHSIYNGIFGDPELAELLEWQLDNKIKLFVEDKMLrfKVKGHRMSG 177

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 3026 TLTTSAGNS-ITCYLkVTAACRKAGIKnPSFLIHGDDCVIICEKEEVDKSDALGEALRSYGYE--CEPTIHaDLSTAESC 3102
Cdd:cd23233   178 DINTSMGNKlIMCGM-MHAYFKELGVE-AELCNNGDDCVIICERKDEKKFSGMYDWFLDYGFNmvTEKPVY-ELEKLEFC 254
Gammacarmovirus_RdRp cd23242
RNA-dependent RNA polymerase (RdRp) in the genus Gammacarmovirus of positive-sense ...
 2948-3089 8.94e-08

RNA-dependent RNA polymerase (RdRp) in the genus Gammacarmovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Gammacarmovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. The single genus Carmovirus was split in 2015 into three genera, each retaining -carmovirus as part of their name: Alphacarmovirus, Betacarmovirus, and Gammacarmovirus. Most species have a narrow natural host range. However, different carmoviruses infect a wide range of both monocotyledonous and dicotyledonous plants. Viruses tend to remain localized, forming necrosis in artificially infected hosts. There are 4 species in the genus Gammacarmovirus: Cowpea mottle virus, Melon necrotic spot virus, Pea stem necrosis virus, and Soybean yellow mottle mosaic virus. 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: 438092  Cd Length: 476  Bit Score: 57.83  E-value: 8.94e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2948 EVLTKMWTSKKSPVAYTVDGVCFDSTITPEDIDREANIFAAA-SDDPMAVRRLH---DHYASGPLMDpsGKI-VGVRNCR 3022
Cdd:cd23242   181 NIAEDAWDSFVSPVAIGFDMKRFDQHVSRDALEWEHSVYLDAfCNDPYLAELLSwqlENKGVGYASD--GSIkYKVDGCR 258

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 482876020 3023 ASGTLTTSAGNSITCYLKVTAACRKAGIKnPSFLIHGDDCVIICEKE--EVDKSDALgEALRSYGYECE 3089
Cdd:cd23242   259 MSGDMNTAMGNCLLACAITWDFFKGRGIK-ARLLNNGDDCVVITEKEcaAAVVAGMV-RHWRRFGFQCE 325
GBV-C_env pfam12786
GB virus C genotype envelope; This the envelope protein from the ssRNA GB virus genotype C.
 271-513 1.43e-07

GB virus C genotype envelope; This the envelope protein from the ssRNA GB virus genotype C.


Pssm-ID: 193262  Cd Length: 413  Bit Score: 56.73  E-value: 1.43e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020   271 PDLVCNRTCSV-FALDWWSDNAPTLAALWSVVTL--LPEAVWGVLTAMPPLFGGLLLFYLCRGWWVQAVLLFLAV----P 343
Cdd:pfam12786    6 PNLTCAVECDLaWSYEGWSWTEDMADFDWAFEYLwtLPFDLWRGLMAASVLLVLVAALLLLEQRLVMAFLLLTVAgeaqG 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020   344 GVLADCYDAEYDEIASLSCNMTHFRKANITCPCPYG--VWMREFNAS----DPAQAHL--NLTIRCPeRYNHSQDYWTCG 415
Cdd:pfam12786   86 GFFDGCHCAYWGSRVPPGAKPWDRGNGTVVCDCPFGpmVWLPALCSGlawrDGDREGTvnDLPLVCP-REVLGTVSVMCV 164

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020   416 WGS--WWWQ-HDNVEVpYSHPymppePLTAICYITNNFTGLFNRSFHLELGVSGrlfagsAYITTCILDRRPSFCGDCFG 492
Cdd:pfam12786  165 WGSayWFWRtGDWVDL-WSEL-----PGSALCTFAALGTSDRDHPDVDVLSPSG------IPCASCVVDRRPASCGSCVR 232

                          250       260
                   ....*....|....*....|.
gi 482876020   493 GCFHSTGRHDMGFGVCGGGYR 513
Cdd:pfam12786  233 DCWETTGPKRLPFEECGLGPR 253
Betanecrovirus_RdRp cd23244
RNA-dependent RNA polymerase (RdRp) in the genus Betanecrosvirus of positive-sense ...
 2945-3123 2.69e-06

RNA-dependent RNA polymerase (RdRp) in the genus Betanecrosvirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Betanecrosvirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. In the Betanecrosvirus genus plants serve as natural hosts, and transmission routes are mechanical, seed borne, and by contact. There are three species in this genus: Beet black scorch virus, Leek white stripe virus, and Tobacco necrosis virus D. Viral replication is cytoplasmic. Entry into the host cell is achieved by penetration into the host cell. Replication follows the positive stranded RNA virus replication model. Positive stranded RNA virus transcription, using the premature termination model of subgenomic RNA transcription is the method of transcription. The virus exits the host cell by tubule-guided viral movement. 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: 438094  Cd Length: 500  Bit Score: 52.98  E-value: 2.69e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2945 ERAEVLTKMWTSKKSPVAYTVDGVCFDSTITPEDIDREANIFAaaSDDPMAVRRLHDHYASGPLMD------PSGKI-VG 3017
Cdd:cd23244   186 QAGMEMKAMWDSFDDPVGIGMDASRFDQHISKEALEFEHKMWL--SMFPGSDRKELARLLGMQIHNrglarcPDGEIrYT 263

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 3018 VRNCRASGTLTTSAGNsitCYL---KVTAACRKAGIKNPSFLIHGDDCVIICE-KEEVDKSDALGEALRSYGY--ECEPT 3091
Cdd:cd23244   264 VEGCRMSGDMNTSSGN---CYImcaTVHNWCSRLGVKHFRLANNGDDCMLVVErKDEARVRQGLIEYYRELGFtmKVEPT 340

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 482876020 3092 IHAdLSTAESCSASLDRV----RTVRGLRPTLKPDM 3123
Cdd:cd23244   341 VDV-LERLEFCQTRPVLVdgayRMVRNLHQGMSKDL 375
Alphanecrovirus_RdRp cd23237
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Alphanecrovirus of ...
 2945-3089 3.67e-06

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Alphanecrovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the Alphanecrovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. Alphanecroviruses are non-enveloped, with icosahedral and spherical geometries, and T=3 symmetry, and a diameter of around 28 nm. Their genomes are linear, around 4 kb in length. In the Alphanecrovirus genus plants serve as natural hosts. There are 4 species in this genus: Olive latent virus 1, Olive mild mosaic virus, Potato necrosis virus, and Tobacco necrosis virus A. 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: 438087  Cd Length: 439  Bit Score: 52.34  E-value: 3.67e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2945 ERAEVLTKMWTSKKSPVAYTVDGVCFDSTITPEDIDREANIFAAASDDPMAVRRLHDHYAS--GPLMDPSGKI-VGVRNC 3021
Cdd:cd23237   145 QQGEIMRSKWKKYVNPVAVGLDASRFDQHVSVEALQYEHEFYLRDYPNDKQLKWLLKQQLCniGTAFASDGIIkYKKEGC 224

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 482876020 3022 RASGTLTTSAGNSITCYLKVTAACRKAGIkNPSFLIHGDDCVIICEKEEVDK-SDALGEALRSYGYECE 3089
Cdd:cd23237   225 RMSGDMNTSLGNCILMCAMVYGLKEHLGI-NLSLANNGDDCVIVCEKADLKKlTSSIEPYFKQFGFKME 292
DEXHc_HrpB cd17990
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ...
 1405-1517 3.92e-06

DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA two-partner secretion (TPS) system, a secretion pathway important to the secretion of large virulence-associated proteins. HrpB belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438711 [Multi-domain]  Cd Length: 174  Bit Score: 49.64  E-value: 3.92e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 1405 IAPTGSGKSTKFPSKLVQE----GHRVLVLNPSVVTTRAMFKYMKDSTGDAPNVYAG---TGKGAISRETgsKLTYCTYG 1477
Cdd:cd17990    23 EAPPGAGKTTRVPLALLAElwiaGGKIIVLEPRRVAARAAARRLATLLGEAPGETVGyrvRGESRVGRRT--RVEVVTEG 100

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 482876020 1478 RFLvspgRFLQR------VNVVICDECHAVDGTTILGIGAVRALAQ 1517
Cdd:cd17990   101 VLL----RRLQRdpelsgVGAVILDEFHERSLDADLALALLLEVQQ 142
ps-ssRNAv_RdRp-like cd23167
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
 3019-3067 5.81e-06

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


Pssm-ID: 438017 [Multi-domain]  Cd Length: 73  Bit Score: 46.56  E-value: 5.81e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 482876020 3019 RNCRASGTLTTSAGNSITCYLKVTAACRKAGI-----KNPSFLIHGDDCVIICE 3067
Cdd:cd23167    20 KAGQPSGSPNTSADNSLINLLLARLALRKACGraeflNSVGILVYGDDSLVSVP 73
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 1405-1532 5.82e-06

DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 49.16  E-value: 5.82e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020  1405 IAPTGSGKSTKF--P----SKLVQEGHRVLVLNPsvvtTRA--------MFKYMKDSTGDAPNVYAGTGKGAISRE-TGS 1469
Cdd:pfam00270   20 QAPTGSGKTLAFllPaleaLDKLDNGPQALVLAP----TRElaeqiyeeLKKLGKGLGLKVASLLGGDSRKEQLEKlKGP 95

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 482876020  1470 KLTYCTYGRFL--VSPGRFLQRVNVVICDECHAVDGttiLGIGAV--RALAQDAGVRLVVFATATPP 1532
Cdd:pfam00270   96 DILVGTPGRLLdlLQERKLLKNLKLLVLDEAHRLLD---MGFGPDleEILRRLPKKRQILLLSATLP 159
HCV_NS5a_1a pfam08300
Hepatitis C virus non-structural 5a zinc finger domain; The molecular function of the ...
 2196-2257 6.41e-06

Hepatitis C virus non-structural 5a zinc finger domain; The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR. This domain corresponds to the N-terminal zinc binding domain.


Pssm-ID: 369801  Cd Length: 62  Bit Score: 46.20  E-value: 6.41e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 482876020  2196 MPLVSCDKGWSGPWLGTGTGITTCACGHRVTVTVTSPKKPVIrASRACRHAWQHTFPVNVTT 2257
Cdd:pfam08300    1 IPFMGCQKGWAGPWEGDGHMEARCHCGAEITGEIKDGELHIV-GPRTCKDMVSGTFFCNAYS 61
Tombusvirus-like_RdRp cd23236
RNA-dependent RNA polymerase (RdRp) in the genus Tombusvirus of positive-sense single-stranded ...
 2941-3123 8.71e-06

RNA-dependent RNA polymerase (RdRp) in the genus Tombusvirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within Procedovirinae subfamily; and related RdRps; This group contains the RdRp of RNA viruses belonging to the Tombusvirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. Tombusvirus is a genus of plant viruses. There are 17 species in the Tombusvirus genus: Artichoke mottled crinkle virus, Carnation Italian ringspot virus, Cucumber Bulgarian virus, Cucumber necrosis virus, Cymbidium ringspot virus, Eggplant mottled crinkle virus, Grapevine Algerian latent virus, Havel River virus, Lato River virus, Limonium flower distortion virus, Moroccan pepper virus, Neckar River virus, Pelargonium leaf curl virus, Pelargonium necrotic spot virus, Petunia asteroid mosaic virus, Sikte waterborne virus, and Tomato bushy stunt virus. Symptoms associated with this genus include mosaic. The name of the genus comes from Tomato bushy stunt virus. 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: 438086 [Multi-domain]  Cd Length: 474  Bit Score: 51.17  E-value: 8.71e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2941 YPPHERAEVLTKMWTSKKSPVAYTVDGVCFDSTITPEDIDREANIFAAASDDPMAVRRLHDH--YASGPLMDPSGKIVGV 3018
Cdd:cd23236   181 YTADEVGAIFRDKWDRFDKPVAIGLDASRFDQHCSVEALQFEHSFYRAMYPGNKLLSKLLEWqlHNKGKGYVPDGTITYR 260

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 3019 RN-CRASGTLTTSAGNSITCYLKVTAACRKAGIKNPSFLIHGDDCVIICEKEEVDKSDA-LGEALRSYGY--ECEPTIHa 3094
Cdd:cd23236   261 KEgCRMSGDINTSLGNYLLMCAMVYGYMRHLGINEFSLANCGDDCVLIVERRNLKQVQGtLPEYFLNLGYtmKVEPPVF- 339

                         170       180       190
                  ....*....|....*....|....*....|...
gi 482876020 3095 DLSTAESCSASLDRV----RTVRGLRPTLKPDM 3123
Cdd:cd23236   340 QLEEVEFCQAHPVQFqggwKMVRNVRTAMSKDV 372
Aureusvirus_RdRp cd23243
RNA-dependent RNA polymerase (RdRp) in the genus Aureusvirus of positive-sense single-stranded ...
 2958-3122 3.97e-05

RNA-dependent RNA polymerase (RdRp) in the genus Aureusvirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Aureusvirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. In the Aureusvirus genus plants serve as natural hosts. There are six species in this genus: Cucumber leaf spot virus (CLSV), Elderberry aureusvirus 1, Johnsongrass chlorotic stripe mosaic virus (JCSMV), Maize white line mosaic virus (MWLMV), Pothos latent virus (PoLV), and Yam spherical virus (YSV). Aureusviruses infect various natural host plants but their individual range is generally restricted to a few species, pothos and pigeon pea or lisianthus for PoLV, yam for YSV, sesame for SNMV, cucumber, melon or squash for CLSV and various Poaceae species, mainly maize (MWLMV) or johnsongrass (JCSMV). Aureusviruses are transmitted mechanically and by seeds. Transmission through the soil or by the water circulating in hydroponic systems for PoLV, CLSV and MWLMV, or by the fungus Olpidium bornovanus (for CLSV) have also been reported. 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: 438093  Cd Length: 488  Bit Score: 49.06  E-value: 3.97e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2958 KSPVAYTVDGVCFDSTITPEDIDREANIFAAASDDPMAVRRLH---DHYASGPLMDpsGKI-VGVRNCRASGTLTTSAGN 3033
Cdd:cd23243   202 REPVFVGLDASRFDQHCSRQALEWEHSVYNAIFRDPYLAELLTwqiDNVGTAYLKD--GFVrYRVDGCRMSGDMNTSMGN 279

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 3034 SITCYLKVTAACRKAGIKnPSFLIHGDDCVIICEKEEVDKSDALGEALRSYGY--ECEPTIHaDLSTAESCsaSLDRVRT 3111
Cdd:cd23243   280 YLIMSCLVYQFCKEVGLD-ASLANCGDDCVLFLEKKDLGKLKHLPQWFVKMGYtmKVEKPVY-EVEEIEFC--QQHPVQL 355

                         170
                  ....*....|.
gi 482876020 3112 VRGLRPTLKPD 3122
Cdd:cd23243   356 SRGWVMVRRPD 366
ps-ssRNA_Picornaviridae cd23193
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Picornaviridae of ...
 2905-3075 8.35e-05

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: 47.93  E-value: 8.35e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2905 RLITYPSLEFRVAEKMILGdpSLVAK-----------AV-MGPAYGFqyppheraevlTKMWTSKKSPVAYTVDGVCFDS 2972
Cdd:cd23193    80 RVIEAAPLDYVIAGRMVFG--RLFAQfhsnpgiltgsAVgCNPDTDW-----------TRLFASLKQDNVYDLDYSGFDA 146

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2973 TITPEDIDREANIFAAASDDPMAVRRLHD------HYasgplmdpsgkivgVRNCR-------ASGTLTTSAGNSITCYL 3039
Cdd:cd23193   147 SLSSQLFEAAVEVLAECHGDPELVLRYLEpiinskHV--------------VGDERytveggmPSGCPCTSILNSICNNL 212

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 482876020 3040 KVTAACRKAGIKNPS---FLIHGDDcVIICEKEEVDKSD 3075
Cdd:cd23193   213 VVRYALLETGKFDPDeyyILAYGDD-VLVSTDEPIDPSD 250
Pelarspovirus_RdRp cd23241
RNA-dependent RNA polymerase (RdRp) in the genus Pelarspovirus of positive-sense ...
 2934-3088 8.43e-05

RNA-dependent RNA polymerase (RdRp) in the genus Pelarspovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Pelarspovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. The genus name "Pelarspovirus" is derived from the pelargonium ringspot virus, which was the first virus to be named. There are 8 species in the Pelarspovirus genus: Clematis chlorotic mottle virus, Elderberry latent virus, Jasmine mosaic-associated virus, Jasmine virus H, Pelargonium chlorotic ring pattern virus, Pelargonium line pattern virus, Pelargonium ringspot virus, and Rosa rugosa leaf distortion virus. Members of the Pelarspovirus have monopartite genomes encoding five open reading frames (ORFs) that include two 5'-proximal replication proteins, two centrally located movement proteins (MP1 and MP2) and a 3'-proximal coat protein that, at least for pelargonium line pattern virus (PLPV), has been shown to act also as suppressor of RNA silencing. 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: 438091 [Multi-domain]  Cd Length: 497  Bit Score: 48.20  E-value: 8.43e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2934 GPAYGFQYPPHERAEVLTKMWTSKKSPVAYTVDGVCFDSTITPEDIDREANIFAAASDDPMAVRRLHDH--------YAS 3005
Cdd:cd23241   175 GPTVMKGYTVQEMGNIIRDKWNKYQKPAAIGFDMSRFDQHVSVDALKFEHKIYRRCFSNDGNLARLLGHqienrgvaYAK 254

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 3006 -GPLmdpSGKIVGVRncrASGTLTTSAGN-----SITCYLkvtaaCRKAGIKNpSFLIHGDDCVIICEKEEVDK-SDALG 3078
Cdd:cd23241   255 dGWL---KYKVEGKR---MSGDVNTALGNcilacCITKEL-----MGGIGIKC-SLINNGDDCVLIGESRDCRAvEDILT 322

                         170
                  ....*....|
gi 482876020 3079 EALRSYGYEC 3088
Cdd:cd23241   323 EGWLRFGFTC 332
Calvusvirinae_RdRp cd23234
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Calvusvirinae of ...
 2945-3084 9.77e-05

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Calvusvirinae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the subfamily Calvusvirinae, family Tombusviridae, order Tolivirales. Umbravirus is a genus of plant viruses assigned to this subfamily. The genus includes nine distinct virus species: Carrot mottle mimic virus (CMoMV), Groundnut rosette virus (GRV), Ethiopian tobacco bushy top virus (ETBTV), Lettuce speckles mottle virus (LSMV), Opium poppy mosaic virus (OPMV), Pea enation mosaic virus-2 (PEMV-2), Tobacco mottle virus (TMoV), and Tobacco bushy top virus (TBTV). Umbraviruses differ from other plant viruses in that they do not encode a coat protein (CP), and thus no conventional virus particles are formed in the infected plants. However, they encode RdRp domain typical to that of other members of the family Tombusviridae, allowing to classify the genus Umbravirus within this family. 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: 438084  Cd Length: 471  Bit Score: 47.81  E-value: 9.77e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2945 ERAEVLTKMWTSKKSPVAYTVDGVCFDSTITPEDIDREANIFAAASDDPMAVRRLHDHYASGPLMDPSGKIV--GVRNCR 3022
Cdd:cd23234   182 ETGEIIAKKWKMFRDPVCVGLDASRFDQHVSVEALRFTHSVYKRFIKSREFNKLLQWMYTNRGLGTAKDGFVkyKVKGCR 261

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 482876020 3023 ASGTLTTSAGNSITCYLKVTAACRKAGIKNpSFLIHGDDCVIICEKEEVDKsdaLGEALRSY 3084
Cdd:cd23234   262 MSGDMDTALGNCVLMVLMTRHLCKSLSIPH-ELMDNGDDCIVIFDKEHLSK---FNAAVKPY 319
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
 2831-3086 4.50e-04

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: 45.86  E-value: 4.50e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020  2831 SPGFSYE-------EAIAKVKPNTAKGHVARITAADlktevgRKAVEKCLDDIrggVAYAPFM---LRPKSEVfpQTRET 2900
Cdd:pfam00680  101 SAGYPYVglggkkgDLIEHLKDGTEARELAERLAAD------WEVLQNGTPLK---LVYQTCLkdeLRPLEKV--EKGKT 169

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020  2901 fkppRLITYPSLEFRVAEKMILGD---------PSLVAKAVMGPAYGfqypphERAEVLTKMwtSKKSPVAYTVDGVCFD 2971
Cdd:pfam00680  170 ----RLVWGEPVEYLLLERAFFDPfnqafmlnnGFHPIQVGINPFDR------GWPRLLRRL--ARFGDYVYELDYSGFD 237

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020  2972 STITPEDIdREA----NIFAAASDDPMAVRRLHDHYASGPLMDPSGKIVGVRNCRASGTLTTSAGNSITCYLKVTAA--- 3044
Cdd:pfam00680  238 SSVPPWLI-RFAfeilRELLGFPSNVKEWRAILELLIYTPIALPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYAllk 316

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*....
gi 482876020  3045 -CRKAGIKNPS------FLIHGDDCVIICEKEEVDKSDALGEALRSYGY 3086
Cdd:pfam00680  317 sLENDGPRVCNldkyfdFFTYGDDSLVAVSPDFDPVLDRLSPHLKELGL 365
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 1406-1530 9.69e-04

N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region.


Pssm-ID: 350668 [Multi-domain]  Cd Length: 146  Bit Score: 42.39  E-value: 9.69e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 1406 APTGSGKSTKFPSKLVQE----GHRVLVLNPSVVTTRAMFKYMKD-STGDAP------NVYAGTGKGAISREtgSKLTYC 1474
Cdd:cd00046     8 APTGSGKTLAALLAALLLllkkGKKVLVLVPTKALALQTAERLRElFGPGIRvavlvgGSSAEEREKNKLGD--ADIIIA 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 482876020 1475 TYGRFLVS----PGRFLQRVNVVICDECHAVD----GTTILGIGAVRALAQDAGvrlVVFATAT 1530
Cdd:cd00046    86 TPDMLLNLllreDRLFLKDLKLIIVDEAHALLidsrGALILDLAVRKAGLKNAQ---VILLSAT 146
Aquamavirus_RdRp cd23220
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Aquamavirus of ...
 2832-3069 2.20e-03

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: 43.16  E-value: 2.20e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2832 PGFSYEEAIAKVKPnTAKGHVARitaadLKTEVGRKAvekclddirGGVAYAPFMlrpKSEVFPQTRETFKPPRLITYPS 2911
Cdd:cd23220    23 PGMNRRQLLLPLNP-QVRDDVVK-----LAGDVGNGT---------ATVVFETFM---KDELRPKEKIESGKTRIVESCP 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2912 LEFRVAEKMILgdpslvAKAVMgpaYGFQYPPHERAEVLTKMWTSKKSPVA-------YTVDGVCFDSTITPEDIDREAN 2984
Cdd:cd23220    85 LDYLLLYRMVM------LKSMI---WWYNSDCIKTGVAPGMNVYTDFVPMVkqfkkikYCLDFSAYDSTLSDEILAAGVE 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2985 IFAAASDDPMAVRRLH-----DHYASGPLMDPsgkivgVRNCRASGTLTTSAGNSITCYLKVTAACRKAGIKNPSFLIHG 3059
Cdd:cd23220   156 VLACTSAVPSYVRKLHapiicSHHWHNNVVDL------VLGGMPSGAPCTSVLNSIVNVLMARYICALMDIDYPVMVAYG 229

                         250
                  ....*....|
gi 482876020 3060 DDCVIICEKE 3069
Cdd:cd23220   230 DDNVVSFDEE 239
Alphacarmovirus_RdRp cd23239
RNA-dependent RNA polymerase (RdRp) in the genus Alphacarmovirus of positive-sense ...
 3018-3088 2.43e-03

RNA-dependent RNA polymerase (RdRp) in the genus Alphacarmovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Alphacarmovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. The Alphacarmovirus genus was split in 2015 into three genera, each retaining -carmovirus as part of their name: Alphacarmovirus, Betacarmovirus, and Gammacarmovirus. Different carmoviruses infect a wide range of both monocotyledonous and dicotyledonous plants. Viruses tend to remain localized, forming necrosis in artificially infected hosts. There are 8 species in the genus Alphacarmovirus: Adonis mosaic virus, Angelonia flower break virus, Calibrachoa mottle virus, Carnation mottle virus, Honeysuckle ringspot virus, Nootka lupine vein clearing virus, Pelargonium flower break virus, and Saguaro cactus virus. 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: 438089 [Multi-domain]  Cd Length: 470  Bit Score: 43.58  E-value: 2.43e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 482876020 3018 VRNCRASGTLTTSAGNS-----ITCYLKVTAACRkagiknpsfLIH-GDDCVIICEKEEVDK-SDALGEALRSYGYEC 3088
Cdd:cd23239   264 KEGCRMSGDMNTALGNCllaclITKHLMKGVNCR---------LINnGDDCVLICERKDLGFvVSNLTTGWRRFGFTC 332
Carmotetraviridae_RdRp cd23205
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Carmotetraviridae ...
 2945-3085 8.47e-03

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Carmotetraviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, and related Erinaceus virus H14; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Carmotetraviridae, and related Erinaceus virus H14, order Tolivirales. Carmotetraviridae includes only one genus, Alphacarmotetravirus, which has one species: Providence virus. Lepidopteran insects serve as the natural host. Recent studies indicated that Providence virus, a non-enveloped insect RNA virus, isolated from a lepidopteran midgut cell line can establish a productive infection in plants as well as in animal cells. 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: 438055  Cd Length: 268  Bit Score: 41.15  E-value: 8.47e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 482876020 2945 ERAEVLTKMWTSKKSPVAYTVDGVCFDSTITPEDIDREANIFAAASDDPMAVRRLHDHyasgpLMDPSGKIVGVR----N 3020
Cdd:cd23205    67 QRANLLQRMWHLYERPVSISFDLSRWDMHVQVPLLKRVLEIYSQHVTCPLLLDMCQNL-----LKNVCYTNKGIRyhvdG 141

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 482876020 3021 CRASGTLTTSAGNSItcylkvtAACRKAGIKNPSFLIHGDDCVIICEKEEVDKS--------DALGEALRSYG 3085
Cdd:cd23205   142 GIMSGDMTTGLGNCI-------AVLVIVMSFRLSILDDGDDHVIICEKSHTWICervlplwwTAMGHSLRVDG 207
 
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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