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Conserved domains on  [gi|9628706|ref|NP_043570|]
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polyprotein precursor [GB virus C]

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 ...
 2316-2790 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: 944.00  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2316 WSGVPLTRATPAKPPVVRPVGSLLVADTTKVYVTNPDNVGRRVDKVTFWRAPRVHDKYLVDSIERAKRAAQACLSMGYTY 2395
Cdd:cd23203    1 WSGAPLGVGRPKPPPVTRPVGSHLRADATKVYVTDPDDVGERIEKVTIWRTPRVVDKFLRDAYNLALAKASATPSPGWTY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2396 EEAIRTVRPHAAMGWGSKVSVKDLATPAGKMAVHDRL-QEILEGTPVPFTLTVKKEVFFKDRKEEKAPRLIVFPPLDFRI 2474
Cdd:cd23203   81 EEAVAKVRPGAAMGHGSKVTVADLKTPAGKKAVEECLnQIIAGGEEVPFTLTAKQEVFFQDKKTRKPPRLIVYPPLEFRV 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2475 AEKLILGDPGRVAKAVLGGAYAFQYTPNQRVKEMLKLWESKKTPCAICVDATCFDSSITEEDVALETELYALASDHPEWV 2554
Cdd:cd23203  161 AEKMILGDPGRVAKAVLGKAYGFQYTPNQRVKVLVDMWKSKRHPCAITVDATCFDSSITEEDVARETEIYAAASDDPELV 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2555 RALGKYYASGTMVTPEGVPVGERYCRSSGVLTTSASNCLTCYIKVKAACERVGLKNVSLLIAGDDCLIICERPVCDPSDA 2634
Cdd:cd23203  241 RALGKYYAEGPMVNPEGVPVGERRCRASGVLTTSSSNSITCYLKVKAACRKAGLKNPSFLIHGDDCLIICERPEEDPCDA 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2635 LGRALASYGYACEPSYHASLDTAPFCSTWLAECNADGKRHFFLTTDFRRPLARMSSEYSDPMASAIGYILLYPWHPITRW 2714
Cdd:cd23203  321 LKAALASYGYDCEPQYHASLDTAESCSAYLAECNAGGGRHYFLSTDMRRPLARASSEYGDPVASALGYILLYPWHPITRY 400

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 9628706  2715 VIIPHVLTCAFRGGGTPSDPVWCQVHGNYYKFPLDKLPNIIVALHGPAALRVTADTTKTKMEAGKVLSDLKLPGLA 2790
Cdd:cd23203  401 VLLPHLLTLAFRGGGTPDDLVTCQVHGNSYKFPLKLLPRILVGLHGPDCLRVTADSTKTLMEAGKALQAFGMRGLA 476
GBV-C_env pfam12786
GB virus C genotype envelope; This the envelope protein from the ssRNA GB virus genotype C.
 151-574 0e+00

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


:

Pssm-ID: 193262  Cd Length: 413  Bit Score: 594.85  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706     151 RVYPVPNLTCAVACELKWESEFWRWTEQLASNYWILEYLWKVPFDFWRGVISLTPLLVCVAALLLLEQRIVMVFLLVTMA 230
Cdd:pfam12786    1 RVYPLPNLTCAVECDLAWSYEGWSWTEDMADFDWAFEYLWTLPFDLWRGLMAASVLLVLVAALLLLEQRLVMAFLLLTVA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706     231 GMSQGApasvlgsrpfdyglTWQTCSCRANGSRFSTGEKVWDRGNVTLQCDCPNGPWVWLPAFCQAIGWGDPITywSHGQ 310
Cdd:pfam12786   81 GEAQGG--------------FFDGCHCAYWGSRVPPGAKPWDRGNGTVVCDCPFGPMVWLPALCSGLAWRDGDR--EGTV 144

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706     311 NQWPLSCPQYVYGSATVTCVWGSASWFASTSGRdskIDVWSLVPvGSATCTIAALGSSDRD--TVPGLSEWGIPCVTCVL 388
Cdd:pfam12786  145 NDLPLVCPREVLGTVSVMCVWGSAYWFWRTGDW---VDLWSELP-GSALCTFAALGTSDRDhpDVDVLSPSGIPCASCVV 220

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706     389 DRRPASCGTCVRDCWPETGSVRFPFHRCGVGPRLTKDLEAVPF-----VNRTTPFTIRGPLGNQGRGNPVRSPLGFGSYA 463
Cdd:pfam12786  221 DRRPASCGSCVRDCWETTGPKRLPFEECGLGPRLTEHLEAVLVdggveSKVTTPFGERPKYGGQHGGGTYYGAVRKLSRN 300

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706     464 MTRIRDTLHLVECPTPAIEPPTGTFGFFPGTPPLNNCMLLGTEVSEALGGAGLTGGFYEPLVRRCSKLMGSRNPVCPGFA 543
Cdd:pfam12786  301 MTVIDIGGYWHALPCPCPEFPPGTLPFRIPGPPVNACLLLGGEVSHPFGAWGAPGGFYAPVFTKCNWPTGSGVDVCPGFA 380

                          410       420       430
                   ....*....|....*....|....*....|.
gi 9628706     544 WLSSGRPDGFIHVQGHLQEVDAGNFIPPPRW 574
Cdd:pfam12786  381 FDFPGDHNGFIHVKGGRQQVDSGQRRPSPRW 411
Peptidase_S29 pfam02907
Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a ...
 955-1102 8.17e-73

Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a trypsin-like fold. The non-structural (NS) protein NS3 is one of the NS proteins involved in replication of the HCV genome. NS2-3 proteinase, a zinc-dependent enzyme, performs a single proteolytic cut to release the N-terminus of NS3. The action of NS3 proteinase (NS3P), which resides in the N-terminal one-third of the NS3 protein, then yields all remaining non-structural proteins. The C-terminal two-thirds of the NS3 protein contain a helicase. The functional relationship between the proteinase and helicase domains is unknown. NS3 has a structural zinc-binding site and requires cofactor NS4A.


:

Pssm-ID: 427049  Cd Length: 149  Bit Score: 240.02  E-value: 8.17e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706     955 GNVMVLGTATSRSMGTCLNGLLFTTFHGASSRTIATPVGALNPRWWSASDDVTVYPLPDGATSLTPCTCQAESCWVIRSD 1034
Cdd:pfam02907    2 GEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTRD 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 9628706    1035 GALCHGLSKGD-KVELDVAMEVSDFRGSSGSPVLCDEGHAVGMLVSVLHSGGRVTAARFTrPWTQVPTD 1102
Cdd:pfam02907   82 GDLIPGRRRGDpRVSLLSPRPLSYLKGSSGGPILCPSGHVVGMFRAAVHSGGVVKAVRFV-PWETLPTT 149
HCV_NS4b super family cl03062
Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. ...
 1653-1847 1.42e-58

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: 201.06  E-value: 1.42e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706    1653 QAKTAEAYTATAKWLAGCYTGTRAVptvsiVDKLFAGGWAAVVGHCHSVIAAAVAAYGASRSPPLAAAASYLMGLGVGGN 1732
Cdd:pfam01001    1 FAFKALGLLPPAIDKAESITPAVAS-----LDTKFEQFWAKHMWNFRSGIQYLAGLYTLPRNPPLAVLASFLAGMTSPLP 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706    1733 AQTRLASALLLGAAGTALGTPVVGLTMAGAFMGGASVSPS-LVTILLGAVGGWEGVVNAASLVFDFMAGKL-SSEDLWYA 1810
Cdd:pfam01001   76 THVRLALALLGGWGATQLGTPSGGLAFVGAGFAGAAVGSSwLGRVLVDVLGGYEAAVNAASLTFKIMSGELpTAEDLWNL 155

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 9628706    1811 IPVLTSPGAGLAGIALGLVLYSANNSGTTTWLNRLLT 1847
Cdd:pfam01001  156 LPCLLSPGASVVGVALAALLRSHKGEGAVQWMNRLLT 192
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 1269-1378 3.35e-19

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: 86.55  E-value: 3.35e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  1269 GEIPFYGHGIPLERmrTGRHLVFCHSKAECERLAGQFSARGVNAIAYYRGKDSSIIKD----GDLVVCATDALSTGYTGN 1344
Cdd:cd18806   10 GRIWFYGKAWITIY--GGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEYPKiktiDWDFVVTTDISEMGANFD 87

                         90       100       110
                 ....*....|....*....|....*....|....
gi 9628706  1345 FDSVTDCGLVVEEVVEVTLDPTItISLRTVPASA 1378
Cdd:cd18806   88 ADRVIDCRTCVKPTILFSGDFRV-ILTGPVPQTA 120
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 1123-1260 3.99e-19

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: 86.45  E-value: 3.99e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  1123 LFMPTGAGKSTRVPLEY----DNMGHKVLILNPSVATVRAMGPYMErlaGKHPSIYCGHDTTafTRITDSPLTYSTYGRF 1198
Cdd:cd17931    6 LDLHPGAGKTTRVLPQIireaIKKRLRTLVLAPTRVVAAEMYEALR---GLPIRYRTGAVKE--EHGGNEIVDYMCHGTF 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 9628706  1199 LAnprQMLRGVSV-----VICDECHSHDSTVLLGIGRVRELARgCGVQLVLYATATPPGSPMTQHPS 1260
Cdd:cd17931   81 TC---RLLSPKRVpnynlIIMDEAHFTDPASIAARGYIHTRVE-MGEAAVIFMTATPPGTVTPFPQS 143
 
Name Accession Description Interval E-value
Pegivirus_RdRp cd23203
RNA-dependent RNA polymerase (RdRp) in the genus Pegivirus, within the family Flaviviridae of ...
 2316-2790 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: 944.00  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2316 WSGVPLTRATPAKPPVVRPVGSLLVADTTKVYVTNPDNVGRRVDKVTFWRAPRVHDKYLVDSIERAKRAAQACLSMGYTY 2395
Cdd:cd23203    1 WSGAPLGVGRPKPPPVTRPVGSHLRADATKVYVTDPDDVGERIEKVTIWRTPRVVDKFLRDAYNLALAKASATPSPGWTY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2396 EEAIRTVRPHAAMGWGSKVSVKDLATPAGKMAVHDRL-QEILEGTPVPFTLTVKKEVFFKDRKEEKAPRLIVFPPLDFRI 2474
Cdd:cd23203   81 EEAVAKVRPGAAMGHGSKVTVADLKTPAGKKAVEECLnQIIAGGEEVPFTLTAKQEVFFQDKKTRKPPRLIVYPPLEFRV 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2475 AEKLILGDPGRVAKAVLGGAYAFQYTPNQRVKEMLKLWESKKTPCAICVDATCFDSSITEEDVALETELYALASDHPEWV 2554
Cdd:cd23203  161 AEKMILGDPGRVAKAVLGKAYGFQYTPNQRVKVLVDMWKSKRHPCAITVDATCFDSSITEEDVARETEIYAAASDDPELV 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2555 RALGKYYASGTMVTPEGVPVGERYCRSSGVLTTSASNCLTCYIKVKAACERVGLKNVSLLIAGDDCLIICERPVCDPSDA 2634
Cdd:cd23203  241 RALGKYYAEGPMVNPEGVPVGERRCRASGVLTTSSSNSITCYLKVKAACRKAGLKNPSFLIHGDDCLIICERPEEDPCDA 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2635 LGRALASYGYACEPSYHASLDTAPFCSTWLAECNADGKRHFFLTTDFRRPLARMSSEYSDPMASAIGYILLYPWHPITRW 2714
Cdd:cd23203  321 LKAALASYGYDCEPQYHASLDTAESCSAYLAECNAGGGRHYFLSTDMRRPLARASSEYGDPVASALGYILLYPWHPITRY 400

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 9628706  2715 VIIPHVLTCAFRGGGTPSDPVWCQVHGNYYKFPLDKLPNIIVALHGPAALRVTADTTKTKMEAGKVLSDLKLPGLA 2790
Cdd:cd23203  401 VLLPHLLTLAFRGGGTPDDLVTCQVHGNSYKFPLKLLPRILVGLHGPDCLRVTADSTKTLMEAGKALQAFGMRGLA 476
GBV-C_env pfam12786
GB virus C genotype envelope; This the envelope protein from the ssRNA GB virus genotype C.
 151-574 0e+00

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


Pssm-ID: 193262  Cd Length: 413  Bit Score: 594.85  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706     151 RVYPVPNLTCAVACELKWESEFWRWTEQLASNYWILEYLWKVPFDFWRGVISLTPLLVCVAALLLLEQRIVMVFLLVTMA 230
Cdd:pfam12786    1 RVYPLPNLTCAVECDLAWSYEGWSWTEDMADFDWAFEYLWTLPFDLWRGLMAASVLLVLVAALLLLEQRLVMAFLLLTVA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706     231 GMSQGApasvlgsrpfdyglTWQTCSCRANGSRFSTGEKVWDRGNVTLQCDCPNGPWVWLPAFCQAIGWGDPITywSHGQ 310
Cdd:pfam12786   81 GEAQGG--------------FFDGCHCAYWGSRVPPGAKPWDRGNGTVVCDCPFGPMVWLPALCSGLAWRDGDR--EGTV 144

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706     311 NQWPLSCPQYVYGSATVTCVWGSASWFASTSGRdskIDVWSLVPvGSATCTIAALGSSDRD--TVPGLSEWGIPCVTCVL 388
Cdd:pfam12786  145 NDLPLVCPREVLGTVSVMCVWGSAYWFWRTGDW---VDLWSELP-GSALCTFAALGTSDRDhpDVDVLSPSGIPCASCVV 220

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706     389 DRRPASCGTCVRDCWPETGSVRFPFHRCGVGPRLTKDLEAVPF-----VNRTTPFTIRGPLGNQGRGNPVRSPLGFGSYA 463
Cdd:pfam12786  221 DRRPASCGSCVRDCWETTGPKRLPFEECGLGPRLTEHLEAVLVdggveSKVTTPFGERPKYGGQHGGGTYYGAVRKLSRN 300

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706     464 MTRIRDTLHLVECPTPAIEPPTGTFGFFPGTPPLNNCMLLGTEVSEALGGAGLTGGFYEPLVRRCSKLMGSRNPVCPGFA 543
Cdd:pfam12786  301 MTVIDIGGYWHALPCPCPEFPPGTLPFRIPGPPVNACLLLGGEVSHPFGAWGAPGGFYAPVFTKCNWPTGSGVDVCPGFA 380

                          410       420       430
                   ....*....|....*....|....*....|.
gi 9628706     544 WLSSGRPDGFIHVQGHLQEVDAGNFIPPPRW 574
Cdd:pfam12786  381 FDFPGDHNGFIHVKGGRQQVDSGQRRPSPRW 411
RdRP_3 pfam00998
Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase ...
 2313-2806 2.97e-153

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: 485.20  E-value: 2.97e-153
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706    2313 SYIWSGVPLTrATPAKPPVVRPVGSLLVADTTKVYVTNPDNVGRRVDKVTFWRAPRVHD-KYLVDSIERAKRAAQACLSM 2391
Cdd:pfam00998    1 SYVWTGARPA-KERKILPITGPGSGLLFGVHNNSLVNLRRGLVERVFKVTFDRGGQLVPpKPYPGAFKELKYFASALVSK 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706    2392 GYtyeEAIRTVRPHAA---MGWGSKVSVKDLATpAGKMAVHDRlQEILEG--TPVPFTLTVKKEVFFKdRKEEKAPRLIV 2466
Cdd:pfam00998   80 LG---EATPLTPEHFAasyTGRKRKIYVKALES-LAVKPVQRR-DAILKTfvKAEKINITAKPDPAPR-VIQPRPPRYNV 153

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706    2467 FPPLDFRIAEKLILGDpgrVAKAVLGGAYAFQYTPNQRVKEMLKLWESKKTPCAICVDATCFDSSITEEDVALETELYAL 2546
Cdd:pfam00998  154 EPGRYLRPCEKMIYKA---IDKAFGGPTVLKGYTPEQRGEILLKKWDSFKKPVAIGLDASRFDQHVSVEALRFEHSIYLA 230

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706    2547 ASDHP-EWVRALG-KYYASGTMVTPEG-VPVGERYCRSSGVLTTSASNCLTCYIKVKAACERVGlKNVSLLIAGDDCLII 2623
Cdd:pfam00998  231 AFLGPeELIRLLTwQLYNGGPMYASDGqIKYGVRGCRMSGDMNTSLGNCLLMCLKVHAACKALG-IDARLLNNGDDCVVI 309

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706    2624 CERPVCDP-SDALGRALASYG---YACEPSYHASLDTapFCSTWLAECN-ADGKRHFFLTTDFRRPLARMSSEYSDPMAS 2698
Cdd:pfam00998  310 CESADLDEvKEALTEAFARYGftmKVEEPVYELELIE--FCQSNPVFDGgKYGMVRNPLTSDSKDPLSRASWETATPAKS 387

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706    2699 AIGYILLYPWHPITRWVIIPHVLTCAFRGGGtPSDPVWCQVHGNYYKFpldklpnIIVALHGPAALRVTADTTKTKMEAG 2778
Cdd:pfam00998  388 WLGAIGECGLSLWGGVPVLQHFYSCLLRNGG-LEKAVSFEMYGKVYSD-------SGFRLHGLGAGSRHSYEPTEEARVS 459

                          490       500
                   ....*....|....*....|....*...
gi 9628706    2779 KVLsDLKLPGLAVHRKKAGALRTRMLRS 2806
Cdd:pfam00998  460 FWL-AFGITPDEQWALEAYYDRLKLLRQ 486
Peptidase_S29 pfam02907
Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a ...
 955-1102 8.17e-73

Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a trypsin-like fold. The non-structural (NS) protein NS3 is one of the NS proteins involved in replication of the HCV genome. NS2-3 proteinase, a zinc-dependent enzyme, performs a single proteolytic cut to release the N-terminus of NS3. The action of NS3 proteinase (NS3P), which resides in the N-terminal one-third of the NS3 protein, then yields all remaining non-structural proteins. The C-terminal two-thirds of the NS3 protein contain a helicase. The functional relationship between the proteinase and helicase domains is unknown. NS3 has a structural zinc-binding site and requires cofactor NS4A.


Pssm-ID: 427049  Cd Length: 149  Bit Score: 240.02  E-value: 8.17e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706     955 GNVMVLGTATSRSMGTCLNGLLFTTFHGASSRTIATPVGALNPRWWSASDDVTVYPLPDGATSLTPCTCQAESCWVIRSD 1034
Cdd:pfam02907    2 GEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTRD 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 9628706    1035 GALCHGLSKGD-KVELDVAMEVSDFRGSSGSPVLCDEGHAVGMLVSVLHSGGRVTAARFTrPWTQVPTD 1102
Cdd:pfam02907   82 GDLIPGRRRGDpRVSLLSPRPLSYLKGSSGGPILCPSGHVVGMFRAAVHSGGVVKAVRFV-PWETLPTT 149
HCV_NS4b pfam01001
Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. ...
 1653-1847 1.42e-58

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: 201.06  E-value: 1.42e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706    1653 QAKTAEAYTATAKWLAGCYTGTRAVptvsiVDKLFAGGWAAVVGHCHSVIAAAVAAYGASRSPPLAAAASYLMGLGVGGN 1732
Cdd:pfam01001    1 FAFKALGLLPPAIDKAESITPAVAS-----LDTKFEQFWAKHMWNFRSGIQYLAGLYTLPRNPPLAVLASFLAGMTSPLP 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706    1733 AQTRLASALLLGAAGTALGTPVVGLTMAGAFMGGASVSPS-LVTILLGAVGGWEGVVNAASLVFDFMAGKL-SSEDLWYA 1810
Cdd:pfam01001   76 THVRLALALLGGWGATQLGTPSGGLAFVGAGFAGAAVGSSwLGRVLVDVLGGYEAAVNAASLTFKIMSGELpTAEDLWNL 155

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 9628706    1811 IPVLTSPGAGLAGIALGLVLYSANNSGTTTWLNRLLT 1847
Cdd:pfam01001  156 LPCLLSPGASVVGVALAALLRSHKGEGAVQWMNRLLT 192
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 1269-1378 3.35e-19

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: 86.55  E-value: 3.35e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  1269 GEIPFYGHGIPLERmrTGRHLVFCHSKAECERLAGQFSARGVNAIAYYRGKDSSIIKD----GDLVVCATDALSTGYTGN 1344
Cdd:cd18806   10 GRIWFYGKAWITIY--GGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEYPKiktiDWDFVVTTDISEMGANFD 87

                         90       100       110
                 ....*....|....*....|....*....|....
gi 9628706  1345 FDSVTDCGLVVEEVVEVTLDPTItISLRTVPASA 1378
Cdd:cd18806   88 ADRVIDCRTCVKPTILFSGDFRV-ILTGPVPQTA 120
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 1123-1260 3.99e-19

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: 86.45  E-value: 3.99e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  1123 LFMPTGAGKSTRVPLEY----DNMGHKVLILNPSVATVRAMGPYMErlaGKHPSIYCGHDTTafTRITDSPLTYSTYGRF 1198
Cdd:cd17931    6 LDLHPGAGKTTRVLPQIireaIKKRLRTLVLAPTRVVAAEMYEALR---GLPIRYRTGAVKE--EHGGNEIVDYMCHGTF 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 9628706  1199 LAnprQMLRGVSV-----VICDECHSHDSTVLLGIGRVRELARgCGVQLVLYATATPPGSPMTQHPS 1260
Cdd:cd17931   81 TC---RLLSPKRVpnynlIIMDEAHFTDPASIAARGYIHTRVE-MGEAAVIFMTATPPGTVTPFPQS 143
DEXDc smart00487
DEAD-like helicases superfamily;
1123-1252 1.68e-13

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 71.75  E-value: 1.68e-13
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706     1123 LFMPTGAGKSTRVPL-----EYDNMGHKVLILNPSVATVRAMGPYMERLA----GKHPSIYCGHDTTAFTRIT---DSPL 1190
Cdd:smart00487   29 LAAPTGSGKTLAALLpaleaLKRGKGGRVLVLVPTRELAEQWAEELKKLGpslgLKVVGLYGGDSKREQLRKLesgKTDI 108

                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 9628706     1191 TYSTYGRF---LANPRQMLRGVSVVICDECHSHDS----TVLLGIGRVRELARgcgvqLVLYATATPPG 1252
Cdd:smart00487  109 LVTTPGRLldlLENDKLSLSNVDLVILDEAHRLLDggfgDQLEKLLKLLPKNV-----QLLLLSATPPE 172
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 1125-1251 2.88e-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: 49.93  E-value: 2.88e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706    1125 MPTGAGKST--RVP----LEYDNMGHKVLILNPSVA----TVRAMGPYMERLAGKHPSIYCGHDTTA-FTRITDSPLTYS 1193
Cdd:pfam00270   21 APTGSGKTLafLLPaleaLDKLDNGPQALVLAPTRElaeqIYEELKKLGKGLGLKVASLLGGDSRKEqLEKLKGPDILVG 100

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 9628706    1194 TYGRFLA--NPRQMLRGVSVVICDECHshdstVLLGIGRVRELARGCG-----VQLVLYaTATPP 1251
Cdd:pfam00270  101 TPGRLLDllQERKLLKNLKLLVLDEAH-----RLLDMGFGPDLEEILRrlpkkRQILLL-SATLP 159
 
Name Accession Description Interval E-value
Pegivirus_RdRp cd23203
RNA-dependent RNA polymerase (RdRp) in the genus Pegivirus, within the family Flaviviridae of ...
 2316-2790 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: 944.00  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2316 WSGVPLTRATPAKPPVVRPVGSLLVADTTKVYVTNPDNVGRRVDKVTFWRAPRVHDKYLVDSIERAKRAAQACLSMGYTY 2395
Cdd:cd23203    1 WSGAPLGVGRPKPPPVTRPVGSHLRADATKVYVTDPDDVGERIEKVTIWRTPRVVDKFLRDAYNLALAKASATPSPGWTY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2396 EEAIRTVRPHAAMGWGSKVSVKDLATPAGKMAVHDRL-QEILEGTPVPFTLTVKKEVFFKDRKEEKAPRLIVFPPLDFRI 2474
Cdd:cd23203   81 EEAVAKVRPGAAMGHGSKVTVADLKTPAGKKAVEECLnQIIAGGEEVPFTLTAKQEVFFQDKKTRKPPRLIVYPPLEFRV 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2475 AEKLILGDPGRVAKAVLGGAYAFQYTPNQRVKEMLKLWESKKTPCAICVDATCFDSSITEEDVALETELYALASDHPEWV 2554
Cdd:cd23203  161 AEKMILGDPGRVAKAVLGKAYGFQYTPNQRVKVLVDMWKSKRHPCAITVDATCFDSSITEEDVARETEIYAAASDDPELV 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2555 RALGKYYASGTMVTPEGVPVGERYCRSSGVLTTSASNCLTCYIKVKAACERVGLKNVSLLIAGDDCLIICERPVCDPSDA 2634
Cdd:cd23203  241 RALGKYYAEGPMVNPEGVPVGERRCRASGVLTTSSSNSITCYLKVKAACRKAGLKNPSFLIHGDDCLIICERPEEDPCDA 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2635 LGRALASYGYACEPSYHASLDTAPFCSTWLAECNADGKRHFFLTTDFRRPLARMSSEYSDPMASAIGYILLYPWHPITRW 2714
Cdd:cd23203  321 LKAALASYGYDCEPQYHASLDTAESCSAYLAECNAGGGRHYFLSTDMRRPLARASSEYGDPVASALGYILLYPWHPITRY 400

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 9628706  2715 VIIPHVLTCAFRGGGTPSDPVWCQVHGNYYKFPLDKLPNIIVALHGPAALRVTADTTKTKMEAGKVLSDLKLPGLA 2790
Cdd:cd23203  401 VLLPHLLTLAFRGGGTPDDLVTCQVHGNSYKFPLKLLPRILVGLHGPDCLRVTADSTKTLMEAGKALQAFGMRGLA 476
GBV-C_env pfam12786
GB virus C genotype envelope; This the envelope protein from the ssRNA GB virus genotype C.
 151-574 0e+00

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


Pssm-ID: 193262  Cd Length: 413  Bit Score: 594.85  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706     151 RVYPVPNLTCAVACELKWESEFWRWTEQLASNYWILEYLWKVPFDFWRGVISLTPLLVCVAALLLLEQRIVMVFLLVTMA 230
Cdd:pfam12786    1 RVYPLPNLTCAVECDLAWSYEGWSWTEDMADFDWAFEYLWTLPFDLWRGLMAASVLLVLVAALLLLEQRLVMAFLLLTVA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706     231 GMSQGApasvlgsrpfdyglTWQTCSCRANGSRFSTGEKVWDRGNVTLQCDCPNGPWVWLPAFCQAIGWGDPITywSHGQ 310
Cdd:pfam12786   81 GEAQGG--------------FFDGCHCAYWGSRVPPGAKPWDRGNGTVVCDCPFGPMVWLPALCSGLAWRDGDR--EGTV 144

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706     311 NQWPLSCPQYVYGSATVTCVWGSASWFASTSGRdskIDVWSLVPvGSATCTIAALGSSDRD--TVPGLSEWGIPCVTCVL 388
Cdd:pfam12786  145 NDLPLVCPREVLGTVSVMCVWGSAYWFWRTGDW---VDLWSELP-GSALCTFAALGTSDRDhpDVDVLSPSGIPCASCVV 220

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706     389 DRRPASCGTCVRDCWPETGSVRFPFHRCGVGPRLTKDLEAVPF-----VNRTTPFTIRGPLGNQGRGNPVRSPLGFGSYA 463
Cdd:pfam12786  221 DRRPASCGSCVRDCWETTGPKRLPFEECGLGPRLTEHLEAVLVdggveSKVTTPFGERPKYGGQHGGGTYYGAVRKLSRN 300

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706     464 MTRIRDTLHLVECPTPAIEPPTGTFGFFPGTPPLNNCMLLGTEVSEALGGAGLTGGFYEPLVRRCSKLMGSRNPVCPGFA 543
Cdd:pfam12786  301 MTVIDIGGYWHALPCPCPEFPPGTLPFRIPGPPVNACLLLGGEVSHPFGAWGAPGGFYAPVFTKCNWPTGSGVDVCPGFA 380

                          410       420       430
                   ....*....|....*....|....*....|.
gi 9628706     544 WLSSGRPDGFIHVQGHLQEVDAGNFIPPPRW 574
Cdd:pfam12786  381 FDFPGDHNGFIHVKGGRQQVDSGQRRPSPRW 411
RdRP_3 pfam00998
Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase ...
 2313-2806 2.97e-153

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: 485.20  E-value: 2.97e-153
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706    2313 SYIWSGVPLTrATPAKPPVVRPVGSLLVADTTKVYVTNPDNVGRRVDKVTFWRAPRVHD-KYLVDSIERAKRAAQACLSM 2391
Cdd:pfam00998    1 SYVWTGARPA-KERKILPITGPGSGLLFGVHNNSLVNLRRGLVERVFKVTFDRGGQLVPpKPYPGAFKELKYFASALVSK 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706    2392 GYtyeEAIRTVRPHAA---MGWGSKVSVKDLATpAGKMAVHDRlQEILEG--TPVPFTLTVKKEVFFKdRKEEKAPRLIV 2466
Cdd:pfam00998   80 LG---EATPLTPEHFAasyTGRKRKIYVKALES-LAVKPVQRR-DAILKTfvKAEKINITAKPDPAPR-VIQPRPPRYNV 153

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706    2467 FPPLDFRIAEKLILGDpgrVAKAVLGGAYAFQYTPNQRVKEMLKLWESKKTPCAICVDATCFDSSITEEDVALETELYAL 2546
Cdd:pfam00998  154 EPGRYLRPCEKMIYKA---IDKAFGGPTVLKGYTPEQRGEILLKKWDSFKKPVAIGLDASRFDQHVSVEALRFEHSIYLA 230

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706    2547 ASDHP-EWVRALG-KYYASGTMVTPEG-VPVGERYCRSSGVLTTSASNCLTCYIKVKAACERVGlKNVSLLIAGDDCLII 2623
Cdd:pfam00998  231 AFLGPeELIRLLTwQLYNGGPMYASDGqIKYGVRGCRMSGDMNTSLGNCLLMCLKVHAACKALG-IDARLLNNGDDCVVI 309

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706    2624 CERPVCDP-SDALGRALASYG---YACEPSYHASLDTapFCSTWLAECN-ADGKRHFFLTTDFRRPLARMSSEYSDPMAS 2698
Cdd:pfam00998  310 CESADLDEvKEALTEAFARYGftmKVEEPVYELELIE--FCQSNPVFDGgKYGMVRNPLTSDSKDPLSRASWETATPAKS 387

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706    2699 AIGYILLYPWHPITRWVIIPHVLTCAFRGGGtPSDPVWCQVHGNYYKFpldklpnIIVALHGPAALRVTADTTKTKMEAG 2778
Cdd:pfam00998  388 WLGAIGECGLSLWGGVPVLQHFYSCLLRNGG-LEKAVSFEMYGKVYSD-------SGFRLHGLGAGSRHSYEPTEEARVS 459

                          490       500
                   ....*....|....*....|....*...
gi 9628706    2779 KVLsDLKLPGLAVHRKKAGALRTRMLRS 2806
Cdd:pfam00998  460 FWL-AFGITPDEQWALEAYYDRLKLLRQ 486
Hepacivirus_RdRp cd23202
RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ...
 2322-2818 4.32e-108

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: 356.47  E-value: 4.32e-108
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2322 TRATPAKPPVvRPVGSLLVADTTKVYVTNPDNVGRRVDKVTFWRApRVHDKYLVDSIERAKRAAQACLSMGYTYEEAIRT 2401
Cdd:cd23202    1 CAAEEEKLPI-SPLSNSLLRHHNLVYSTTSRSASERQKKVTFDRL-QVLDPHYDDVLKEAKARASGVKARLLSVEEACSL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2402 VRPHAA---MGWGSKvSVKDLATPAGK--MAVHDRLQEILEgTPVPFTLTVKKEVFFKDRKEE--KAPRLIVFPPLDFRI 2474
Cdd:cd23202   79 TPPHSArskFGYGAK-DVRSLSRKAVNhiNSVWEDLLEDSE-TPIPTTIMAKNEVFCVTPEKGgrKPARLIVYPDLGVRV 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2475 AEKLILGDPGR-VAKAVLGGAYAFQYTPNQRVKEMLKLWESKKTPCAICVDATCFDSSITEEDVALETELYALASDHPE- 2552
Cdd:cd23202  157 CEKMALYDVAPkLPKAVMGEAYGFQYSPAQRVEFLLKMWRSKKTPMGFSYDTRCFDSTVTERDIRTEESIYQCCDLDPEa 236

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2553 --WVRALGK-YYASGTMVTPEGVPVGERYCRSSGVLTTSASNCLTCYIKVKAACERVGLKNVSLLIAGDDCLIICERpvC 2629
Cdd:cd23202  237 rkAIRSLTErLYVGGPMTNSKGQSCGYRRCRASGVFTTSSGNTLTCYLKASAACRAAGLKDPTMLVCGDDLVVIAES--A 314

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2630 DPSD---ALGR---ALASY----GYACEPSYHASLDTApfCSTWLAECN-ADGKRHFFLTTDFRRPLARMSSEYSD--PM 2696
Cdd:cd23202  315 GVEEdaaALRAfteAMTRYsappGDPPQPEYDLELITS--CSSNVSVAHdATGKRYYYLTRDPTTPLARAAWETARhtPV 392

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2697 ASAIGYILLY-P--WhpiTRWVIIPHVLTcAFRGGGTPSDPVWCQVHGNYYKFPLDKLPNIIVALHGPAALRVTADTTKT 2773
Cdd:cd23202  393 NSWLGNIIMYaPtlW---VRMVLMTHFFS-ILLAQEQLEKALDFEMYGNTYSIPPLDLPAIIQRLHGLSAFSLHGYSPRE 468

                        490       500       510       520
                 ....*....|....*....|....*....|....*....|....*.
gi 9628706  2774 KMEAGKVLSDLKLPGLAVHRKKAGALRTRMLRSRG-WAELARGLLW 2818
Cdd:cd23202  469 LNRVAAALRKLGVPPLRAWRHRARAVRAKLIAQGGkAAICGKYLFN 514
ps-ssRNAv_Flaviviridae_RdRp cd23178
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of ...
 2441-2709 9.27e-87

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: 285.95  E-value: 9.27e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2441 VPFTLTVKKEVFF--KDRKEEKAPRLIVFPPLDFRIAEKLILGDPGRVAKAVLGG-AYAFQYTPNQRVKEMLKLWESKKT 2517
Cdd:cd23178    1 IPTTIMPKNEVFCvePGKGGRKPPRLIVYPDLGVRVAEKMALYDPVEVLPQVVGGsYYGFQYSPNQRVEILRKAWKSKKG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2518 PCAICVDATCFDSSITEEDVALETELYALAS---DHPEWVRALGKYYASGTMVTPEGVPVGERYCRSSGVLTTSASNCLT 2594
Cdd:cd23178   81 PMAYSYDTRCFDSTVTEDDIQVEEEIYQACSlkeARQAIVSITERLYVEGPMVNSDGQICGRRRCRASGVLTTSAGNT*T 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2595 CYIKVKAACERVGLKNVSLLIAGDDCLIICERPVCDPSDALGRALASYGYACEPSYHA------SLDTAPFCSTWLAEC- 2667
Cdd:cd23178  161 CYLK*LAACREAGIRLPTMLVCGDDCVVICESDGTQEDAALLAAFTEALTRYGKPPKDppqpeyDLELIESCSHTVSEVr 240

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 9628706  2668 NADGKRHFFLTTDFRRPLARMSSEYSD--PMASAIGYILLYPWH 2709
Cdd:cd23178  241 MKDGRRLYYLTRDPTTPLARAAWETGRhePINSWLGYIIMYALT 284
Peptidase_S29 pfam02907
Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a ...
 955-1102 8.17e-73

Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a trypsin-like fold. The non-structural (NS) protein NS3 is one of the NS proteins involved in replication of the HCV genome. NS2-3 proteinase, a zinc-dependent enzyme, performs a single proteolytic cut to release the N-terminus of NS3. The action of NS3 proteinase (NS3P), which resides in the N-terminal one-third of the NS3 protein, then yields all remaining non-structural proteins. The C-terminal two-thirds of the NS3 protein contain a helicase. The functional relationship between the proteinase and helicase domains is unknown. NS3 has a structural zinc-binding site and requires cofactor NS4A.


Pssm-ID: 427049  Cd Length: 149  Bit Score: 240.02  E-value: 8.17e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706     955 GNVMVLGTATSRSMGTCLNGLLFTTFHGASSRTIATPVGALNPRWWSASDDVTVYPLPDGATSLTPCTCQAESCWVIRSD 1034
Cdd:pfam02907    2 GEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTRD 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 9628706    1035 GALCHGLSKGD-KVELDVAMEVSDFRGSSGSPVLCDEGHAVGMLVSVLHSGGRVTAARFTrPWTQVPTD 1102
Cdd:pfam02907   82 GDLIPGRRRGDpRVSLLSPRPLSYLKGSSGGPILCPSGHVVGMFRAAVHSGGVVKAVRFV-PWETLPTT 149
HCV_NS4b pfam01001
Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. ...
 1653-1847 1.42e-58

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: 201.06  E-value: 1.42e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706    1653 QAKTAEAYTATAKWLAGCYTGTRAVptvsiVDKLFAGGWAAVVGHCHSVIAAAVAAYGASRSPPLAAAASYLMGLGVGGN 1732
Cdd:pfam01001    1 FAFKALGLLPPAIDKAESITPAVAS-----LDTKFEQFWAKHMWNFRSGIQYLAGLYTLPRNPPLAVLASFLAGMTSPLP 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706    1733 AQTRLASALLLGAAGTALGTPVVGLTMAGAFMGGASVSPS-LVTILLGAVGGWEGVVNAASLVFDFMAGKL-SSEDLWYA 1810
Cdd:pfam01001   76 THVRLALALLGGWGATQLGTPSGGLAFVGAGFAGAAVGSSwLGRVLVDVLGGYEAAVNAASLTFKIMSGELpTAEDLWNL 155

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 9628706    1811 IPVLTSPGAGLAGIALGLVLYSANNSGTTTWLNRLLT 1847
Cdd:pfam01001  156 LPCLLSPGASVVGVALAALLRSHKGEGAVQWMNRLLT 192
RNA_dep_RNAP cd01699
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
 2427-2698 1.84e-51

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: 184.02  E-value: 1.84e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2427 AVHDRLQEILEGTPVPFTLTVKKEVFFKDRKEEKAPRLIVFPPLDFRIAEKLILGDPGRVAKAV-LGGAYAFQYTPNQR- 2504
Cdd:cd01699    4 AVESLEDLPLIRPDLVFTTFLKDELRPLEKVEAGKTRLIQPRPLDYNIALRMYLGPFEAKLMKNrGGLPIAVGINPYSRd 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2505 VKEMLKLWESKKtPCAICVDATCFDSSITEEDVALETELYALASDHPEWvRALGKYYASGTM-VTPEG--VPVGERYCRS 2581
Cdd:cd01699   84 WTILANKLRSFS-PVAIALDYSRFDSSLSPQLLEAEHSIYNALYDDDDE-LERRNLLRSLTNnSLHIGfnEVYKVRGGRP 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2582 SGVLTTSASNCLTCYIKVKAACERVG----LKNVSLLIAGDDCLIICERPV-CDPSDALGRALASYGYACEPSYHASLDT 2656
Cdd:cd01699  162 SGDPLTSIGNSIINCILVRYAFRKLGgksfFKNVRLLNYGDDCLLSVEKADdKFNLETLAEWLKEYGLTMTDEDKVESPF 241

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 9628706  2657 APFcstwlaECNADGKRHFFLTTDFR-RPLARMSSEYSDPMAS 2698
Cdd:cd01699  242 RPL------EEVEFLKRRFVLDEGGGwRAPLDPSSILSKLSWS 278
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 1269-1378 3.35e-19

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: 86.55  E-value: 3.35e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  1269 GEIPFYGHGIPLERmrTGRHLVFCHSKAECERLAGQFSARGVNAIAYYRGKDSSIIKD----GDLVVCATDALSTGYTGN 1344
Cdd:cd18806   10 GRIWFYGKAWITIY--GGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEYPKiktiDWDFVVTTDISEMGANFD 87

                         90       100       110
                 ....*....|....*....|....*....|....
gi 9628706  1345 FDSVTDCGLVVEEVVEVTLDPTItISLRTVPASA 1378
Cdd:cd18806   88 ADRVIDCRTCVKPTILFSGDFRV-ILTGPVPQTA 120
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 1123-1260 3.99e-19

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: 86.45  E-value: 3.99e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  1123 LFMPTGAGKSTRVPLEY----DNMGHKVLILNPSVATVRAMGPYMErlaGKHPSIYCGHDTTafTRITDSPLTYSTYGRF 1198
Cdd:cd17931    6 LDLHPGAGKTTRVLPQIireaIKKRLRTLVLAPTRVVAAEMYEALR---GLPIRYRTGAVKE--EHGGNEIVDYMCHGTF 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 9628706  1199 LAnprQMLRGVSV-----VICDECHSHDSTVLLGIGRVRELARgCGVQLVLYATATPPGSPMTQHPS 1260
Cdd:cd17931   81 TC---RLLSPKRVpnynlIIMDEAHFTDPASIAARGYIHTRVE-MGEAAVIFMTATPPGTVTPFPQS 143
Tombusviridae_RdRp cd23206
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tombusviridae of ...
 2447-2650 2.39e-17

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: 83.70  E-value: 2.39e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2447 VKKEVFFKDRKEEKAPRLIvfPPLD----------FRIAEKLILGDPGRV--AKAVLGGayafqYTPNQRVKEMLKLWES 2514
Cdd:cd23206    8 VKAEKINLTKKPDPAPRVI--QPRSprynvelgryLKPLEHRLYKAIDRVfgSPTVMKG-----YNAEERGRILREKWDS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2515 KKTPCAICVDATCFDSSITEEdvALETE--LY-ALASDHPEWVRAL-------GKYYASGTMVtpegvpvgeRY----CR 2580
Cdd:cd23206   81 FRDPVAVGLDASRFDQHVSVD--ALKWEhsVYlRIFPDDKELSRLLrwqlhnkGVARCKDGKV---------KYkvkgGR 149

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 9628706  2581 SSGVLTTSASNCLT-CYIkVKAACERVGLKnVSLLIAGDDCLIICERPVCDP-SDALGRALASYGYAC---EPSY 2650
Cdd:cd23206  150 MSGDMNTSLGNCLImCAM-VYAYLEELGIK-AELANNGDDCVLIMERSDLLRfLDGLEEWFLRFGFTMvveEPVY 222
DEXDc smart00487
DEAD-like helicases superfamily;
1123-1252 1.68e-13

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 71.75  E-value: 1.68e-13
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706     1123 LFMPTGAGKSTRVPL-----EYDNMGHKVLILNPSVATVRAMGPYMERLA----GKHPSIYCGHDTTAFTRIT---DSPL 1190
Cdd:smart00487   29 LAAPTGSGKTLAALLpaleaLKRGKGGRVLVLVPTRELAEQWAEELKKLGpslgLKVVGLYGGDSKREQLRKLesgKTDI 108

                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 9628706     1191 TYSTYGRF---LANPRQMLRGVSVVICDECHSHDS----TVLLGIGRVRELARgcgvqLVLYATATPPG 1252
Cdd:smart00487  109 LVTTPGRLldlLENDKLSLSNVDLVILDEAHRLLDggfgDQLEKLLKLLPKNV-----QLLLLSATPPE 172
Betanecrovirus_RdRp cd23244
RNA-dependent RNA polymerase (RdRp) in the genus Betanecrosvirus of positive-sense ...
 2425-2626 9.17e-13

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: 73.78  E-value: 9.17e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2425 KMAVHDRLQEILEGTPVP-----FTLTVKKEVFFKDRKEEKAPRLIvfPPLD----------FRIAEKLILgdpgRVAKA 2489
Cdd:cd23244   98 KLERYQQAVESLEIRPIGekdawLSTFVKAEKLNITAKPDPAPRVI--QPRDprynvevgrfLRHAEEHLF----DAINR 171

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2490 VLGGAYAFQ-YTPNQRVKEMLKLWESKKTPCAICVDATCFDSSITEEDVALETELYAL---ASDHPEWVRALG-KYYASG 2564
Cdd:cd23244  172 VFGGRTIFKgLNADQAGMEMKAMWDSFDDPVGIGMDASRFDQHISKEALEFEHKMWLSmfpGSDRKELARLLGmQIHNRG 251

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 9628706  2565 TMVTPEGVPvgeRY----CRSSGVLTTSASNCLTCYIKVKAACERVGLKNVSLLIAGDDCLIICER 2626
Cdd:cd23244  252 LARCPDGEI---RYtvegCRMSGDMNTSSGNCYIMCATVHNWCSRLGVKHFRLANNGDDCMLVVER 314
ps_ssRNAv_Tolivirales_RdRp cd23179
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Toliovirales of ...
 2447-2626 3.72e-11

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: 65.62  E-value: 3.72e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2447 VKKEvFFKDRKEEKAPRLIVF--PPLDFRIA------EKLILG--DPGR-----VAKAvlggayafqYTPNQRVKEMLKL 2511
Cdd:cd23179    7 LKAE-KYNPLAKNKKPRMIQPrsPRYNLELArylkpiEHALYGalDAGRggtrvVAKG---------LNPRQRANLIRRK 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2512 WESKKTPCAICVDATCFDSSITEEDVALETELY-ALASDHPEwVRALGKYYASGTMVTPEGVpvgeRY----CRSSGVLT 2586
Cdd:cd23179   77 WDEFDDPVVFSLDASRFDAHVSVELLRLEHSVYlACYPGDPE-LRKLLKWQLVNKGRTSNGV----KYktrgGRMSGDMN 151

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 9628706  2587 TSASNCLTCYIKVKAACERVGLKnVSLLIAGDDCLIICER 2626
Cdd:cd23179  152 TGLGNCLIMLAMVYAVLRELGIK-YDLLVDGDDALVFVER 190
Alphanecrovirus_RdRp cd23237
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Alphanecrovirus of ...
 2499-2626 2.04e-09

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: 62.74  E-value: 2.04e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2499 YTPNQRVKEMLKLWESKKTPCAICVDATCFDSSITEEDVALETELYALASDHPEWVRALGKYYAS--GTMVTPEG-VPVG 2575
Cdd:cd23237  141 FTLEQQGEIMRSKWKKYVNPVAVGLDASRFDQHVSVEALQYEHEFYLRDYPNDKQLKWLLKQQLCniGTAFASDGiIKYK 220

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 9628706  2576 ERYCRSSGVLTTSASNCLTCYIKVKAACERVGLkNVSLLIAGDDCLIICER 2626
Cdd:cd23237  221 KEGCRMSGDMNTSLGNCILMCAMVYGLKEHLGI-NLSLANNGDDCVIVCEK 270
Gammacarmovirus_RdRp cd23242
RNA-dependent RNA polymerase (RdRp) in the genus Gammacarmovirus of positive-sense ...
 2499-2647 3.01e-09

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: 62.45  E-value: 3.01e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2499 YTPNQRVKEMLKLWESKKTPCAICVDATCFDSSITEEDVALETELYALASDHPEWVRAL--------GKYYASGTMVtpe 2570
Cdd:cd23242  174 YTVEQIGNIAEDAWDSFVSPVAIGFDMKRFDQHVSRDALEWEHSVYLDAFCNDPYLAELlswqlenkGVGYASDGSI--- 250

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2571 gvpvgeRY----CRSSGVLTTSASNCL-TCYIkVKAACERVGLKnVSLLIAGDDCLIICERPVCDPSDA-LGRALASYGY 2644
Cdd:cd23242  251 ------KYkvdgCRMSGDMNTAMGNCLlACAI-TWDFFKGRGIK-ARLLNNGDDCVVITEKECAAAVVAgMVRHWRRFGF 322


                 ...
gi 9628706  2645 ACE 2647
Cdd:cd23242  323 QCE 325
Panicovirus_RdRp cd23238
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Panicovirus of ...
 2518-2650 8.73e-08

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Panicovirus 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 Panicovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. Viruses in Panicovirus are non-enveloped, with icosahedral and spherical geometries, and T=3 symmetry. Their host range is restricted to monocotyledonous plants. There are 3 species in this genus: Cocksfoot mild mosaic virus, Panicum mosaic virus, and Thin paspalum asymptomatic virus. The virus typically forms a systemic mosaic. 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: 438088 [Multi-domain]  Cd Length: 692  Bit Score: 57.99  E-value: 8.73e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2518 PCAICVDATCFDSSITEEDVALETELYALASDHPEWVRALGKY--YASGTMVTPEG-VPVGERYCRSSGVLTTSASNCLT 2594
Cdd:cd23238  388 PCAIGFDASRFDQHVSVEALRFEHSIYKSIHGYPELLNLLLKWqiHNQGTAHANDGfFKYSVDGKRMSGDMNTSLGNCIL 467

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 9628706  2595 CYIKVKAACERVGLkNVSLLIAGDDCLIICErpvCDPSDALGRALAS----YGY---ACEPSY 2650
Cdd:cd23238  468 ASLISKDLVDSLGI-DAQLVNNGDDNVLICS---VDDEEVVVKALYDhwmkYGFevvAEQPVY 526
DEXHc_HrpB cd17990
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ...
 1126-1237 7.68e-07

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: 51.56  E-value: 7.68e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  1126 PTGAGKSTRVPL----EYDNMGHKVLILNPSVATVRAMGPYMERLAGKHPSIYCGHDTTAFTRIT-DSPLTYSTYG---- 1196
Cdd:cd17990   25 PPGAGKTTRVPLallaELWIAGGKIIVLEPRRVAARAAARRLATLLGEAPGETVGYRVRGESRVGrRTRVEVVTEGvllr 104

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 9628706  1197 RFLANPRqmLRGVSVVICDECHSHDSTVLLGIGRVRELARG 1237
Cdd:cd17990  105 RLQRDPE--LSGVGAVILDEFHERSLDADLALALLLEVQQL 143
ps-ssRNAv_RdRp-like cd23167
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
 2521-2625 1.90e-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: 47.72  E-value: 1.90e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2521 ICVDATCFDSSIteedvaletelyalasdHPEWVRAlgkyyasgtmvtpegvpvgeryCRSSGVLTTSASNCLTCYIKVK 2600
Cdd:cd23167    3 VESDYSGFDSSI-----------------SPDLLKA----------------------GQPSGSPNTSADNSLINLLLAR 43

                         90       100       110
                 ....*....|....*....|....*....|
gi 9628706  2601 AACERVG-----LKNVSLLIAGDDCLIICE 2625
Cdd:cd23167   44 LALRKACgraefLNSVGILVYGDDSLVSVP 73
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 1125-1251 2.88e-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: 49.93  E-value: 2.88e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706    1125 MPTGAGKST--RVP----LEYDNMGHKVLILNPSVA----TVRAMGPYMERLAGKHPSIYCGHDTTA-FTRITDSPLTYS 1193
Cdd:pfam00270   21 APTGSGKTLafLLPaleaLDKLDNGPQALVLAPTRElaeqIYEELKKLGKGLGLKVASLLGGDSRKEqLEKLKGPDILVG 100

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 9628706    1194 TYGRFLA--NPRQMLRGVSVVICDECHshdstVLLGIGRVRELARGCG-----VQLVLYaTATPP 1251
Cdd:pfam00270  101 TPGRLLDllQERKLLKNLKLLVLDEAH-----RLLDMGFGPDLEEILRrlpkkRQILLL-SATLP 159
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 1125-1249 6.69e-06

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: 48.17  E-value: 6.69e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  1125 MPTGAGKSTRVPL----EYDNMGHKVLILNPSVATVRAMGPYMERLAGKHPSI-YCGHDTTAFTR----ITDSPLTYSTY 1195
Cdd:cd00046    8 APTGSGKTLAALLaallLLLKKGKKVLVLVPTKALALQTAERLRELFGPGIRVaVLVGGSSAEEReknkLGDADIIIATP 87

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 9628706  1196 GRF----LANPRQMLRGVSVVICDECH----SHDSTVLLGIgRVRELARGcGVQLVLyATAT 1249
Cdd:cd00046   88 DMLlnllLREDRLFLKDLKLIIVDEAHalliDSRGALILDL-AVRKAGLK-NAQVIL-LSAT 146
Pelarspovirus_RdRp cd23241
RNA-dependent RNA polymerase (RdRp) in the genus Pelarspovirus of positive-sense ...
 2447-2646 1.02e-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: 50.89  E-value: 1.02e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2447 VKKEVFFKDRKEEKAPRLIvfPPLDFRIAEKLilgdpGRVAKAVLGGAY-AFQ-----------YTpnqrVKEMLKL--- 2511
Cdd:cd23241  125 VKCEKLNFSKKPDPAPRVI--QPRDPRYNVEL-----GRYLKPFEHHCYrALDklwggptvmkgYT----VQEMGNIird 193

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2512 -WESKKTPCAICVDATCFDSSITEEDVALETELY-ALASDHPEWVRALG-KYYASGTMVTPEGVPvgeRY----CRSSGV 2584
Cdd:cd23241  194 kWNKYQKPAAIGFDMSRFDQHVSVDALKFEHKIYrRCFSNDGNLARLLGhQIENRGVAYAKDGWL---KYkvegKRMSGD 270

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 9628706  2585 LTTSASNC-LTCYIkVKAACERVGLKnVSLLIAGDDCLIICERPVCDP-SDALGRALASYGYAC 2646
Cdd:cd23241  271 VNTALGNCiLACCI-TKELMGGIGIK-CSLINNGDDCVLIGESRDCRAvEDILTEGWLRFGFTC 332
Tombusvirus-like_RdRp cd23236
RNA-dependent RNA polymerase (RdRp) in the genus Tombusvirus of positive-sense single-stranded ...
 2512-2626 1.79e-05

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: 50.01  E-value: 1.79e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2512 WESKKTPCAICVDATCFDSSITEEDVALETELY-------ALASDHPEWvralgKYYASGTMVTPEG-VPVGERYCRSSG 2583
Cdd:cd23236  194 WDRFDKPVAIGLDASRFDQHCSVEALQFEHSFYramypgnKLLSKLLEW-----QLHNKGKGYVPDGtITYRKEGCRMSG 268

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 9628706  2584 VLTTSASNCLTCYIKVKAACERVGLKNVSLLIAGDDCLIICER 2626
Cdd:cd23236  269 DINTSLGNYLLMCAMVYGYMRHLGINEFSLANCGDDCVLIVER 311
Betacarmovirus_RdRp cd23240
RNA-dependent RNA polymerase (RdRp) in the genus Betacarmovirus of positive-sense ...
 2499-2660 4.19e-05

RNA-dependent RNA polymerase (RdRp) in the genus Betacarmovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Betacarmovirus 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. 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 Betacarmovirus: Cardamine chlorotic fleck virus, Hibiscus chlorotic ringspot virus, Japanese iris necrotic ring virus, and Turnip crinkle 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: 438090  Cd Length: 451  Bit Score: 48.69  E-value: 4.19e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2499 YTPNQRVKEMLKLWESKKTPCAICVDATCFDSSITEEDVALETELYALASDHPEWVRALG-KYYASGTMVTPEGVPvgeR 2577
Cdd:cd23240  164 YTVEELGNIMHNHWSQFQKPCAVGFDMKRFDQHVSVDALRFEHSVYNRSFCSPELARLLEwQLLNSGVGHASDGFI---R 240

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2578 Y----CRSSGVLTTSASNC-LTCYIkVKAACErvGLKnVSLLIAGDDCLIICERP-VCDPSDALGRALaSYGYAC---EP 2648
Cdd:cd23240  241 YkvdgCRMSGDVNTALGNClLACLI-TKYLLK--GIR-CRLINNGDDCVLFFEAPdLAAVTERLAHWL-DFGFQCvveEP 315

                        170
                 ....*....|..
gi 9628706  2649 SYhaSLDTAPFC 2660
Cdd:cd23240  316 VY--ELEKVEFC 325
Alphacarmovirus_RdRp cd23239
RNA-dependent RNA polymerase (RdRp) in the genus Alphacarmovirus of positive-sense ...
 2447-2650 6.93e-05

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: 48.21  E-value: 6.93e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2447 VKKEVFFKDRKEEKAPRLIvfPPLDFRIAEKLilgdpGRVAKAVLGGAY-AFQ-----------YTPNQRVKEMLKLWES 2514
Cdd:cd23239  127 IKAEKFCVSLKPDPAPRVI--QPRSPRYNVEL-----GRYLKKFEHHAYrALDkiwggptvmkgYTVEEVAQHISSAWDQ 199

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2515 KKTPCAICVDATCFDSSITEEDVALETELY-ALASDHPE------W-VRALGKYYASGTMVtpegvpvgeRY----CRSS 2582
Cdd:cd23239  200 FQIPVAIGFDMSRFDQHVSVPALQFEHSCYlACFPGDRHlaqllsWqLKNFGVGFASNGMI---------RYkkegCRMS 270

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 9628706  2583 GVLTTSASNC-LTCYIkVKAACERVglkNVSLLIAGDDCLIICERPVCDP-SDALGRALASYGYAC---EPSY 2650
Cdd:cd23239  271 GDMNTALGNClLACLI-TKHLMKGV---NCRLINNGDDCVLICERKDLGFvVSNLTTGWRRFGFTCiaeEPVY 339
Regressovirinae_RdRp cd23235
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Regressovirinae ...
 2512-2626 3.19e-04

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: 46.07  E-value: 3.19e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2512 WESKKTPCAICVDATCFDSSITEEDVALETELYALASDHPEWVRALGKYYAS--GTMVTPEGVPVGERY--CRSSGVLTT 2587
Cdd:cd23235  162 WSKYESPIGIGLDASRFDQHCSKDALKFEHSFYRECFPDDKTLEDLLDWQLEneGSALMPTGELVKYRTkgCRMSGDINT 241

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 9628706  2588 SASNCLTCYIKVKAACERVGLkNVSLLIAGDDCLIICER 2626
Cdd:cd23235  242 GLGNKILMCSMVHAYLKEVGV-NASLANNGDDCVLFCEK 279
Aureusvirus_RdRp cd23243
RNA-dependent RNA polymerase (RdRp) in the genus Aureusvirus of positive-sense single-stranded ...
 2516-2660 7.86e-04

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: 44.83  E-value: 7.86e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2516 KTPCAICVDATCFDSSITEEDVALETELY-ALASDhpEWVRALGKYYAS--GTMVTPEGVPvgeRY----CRSSGVLTTS 2588
Cdd:cd23243  202 REPVFVGLDASRFDQHCSRQALEWEHSVYnAIFRD--PYLAELLTWQIDnvGTAYLKDGFV---RYrvdgCRMSGDMNTS 276

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 9628706  2589 ASNCLTCYIKVKAACERVGLKnVSLLIAGDDCLIICERPVCDPSDALGRALASYGYAC---EPSYHasLDTAPFC 2660
Cdd:cd23243  277 MGNYLIMSCLVYQFCKEVGLD-ASLANCGDDCVLFLEKKDLGKLKHLPQWFVKMGYTMkveKPVYE--VEEIEFC 348
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 1289-1336 1.87e-03

C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an evolutionarily conserved class of enzymes, dedicated to preserving genomic integrity by operating in telomere maintenance, DNA repair, and replication. They 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: 350181 [Multi-domain]  Cd Length: 134  Bit Score: 41.04  E-value: 1.87e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 9628706  1289 LVFCHSKAECERLAGQFSARGVNAIAYYRGKDSSI--------IKDGDLVVCATDA 1336
Cdd:cd18794   34 IIYCLSRKECEQVAARLQSKGISAAAYHAGLEPSDrrdvqrkwLRDKIQVIVATVA 89
Calvusvirinae_RdRp cd23234
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Calvusvirinae of ...
 2510-2626 8.45e-03

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: 41.65  E-value: 8.45e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9628706  2510 KLWESKKTPCAICVDATCFDSSITEEDVALETELYALASDHPEWVRALGKYYAS-GTMVTPEG-VPVGERYCRSSGVLTT 2587
Cdd:cd23234  189 KKWKMFRDPVCVGLDASRFDQHVSVEALRFTHSVYKRFIKSREFNKLLQWMYTNrGLGTAKDGfVKYKVKGCRMSGDMDT 268

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 9628706  2588 SASNCLTCYIKVKAACERVGLKNvSLLIAGDDCLIICER 2626
Cdd:cd23234  269 ALGNCVLMVLMTRHLCKSLSIPH-ELMDNGDDCIVIFDK 306
 
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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