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Conserved domains on  [gi|2828598|gb|AAC40501|]
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polyprotein [Pegivirus platyrrhini]

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 ...
 2415-2886 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: 934.37  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2415 WSGAPLGCGRVVPPPITRPIGTHLTHDTTKVYVTDPDRAAERAEKVTIWRGQRVYDEHYASVVGEALKKAAATTSPGWTY 2494
Cdd:cd23203    1 WSGAPLGVGRPKPPPVTRPVGSHLRADATKVYVTDPDDVGERIEKVTIWRTPRVVDKFLRDAYNLALAKASATPSPGWTY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2495 AMAISKVRKRAAAGYGSKVTVATLETGWPHV---RTMIDKIRCHEEVPFTFVTKREVFFS-KTTRKPPRFIVYPPLDFRI 2570
Cdd:cd23203   81 EEAVAKVRPGAAMGHGSKVTVADLKTPAGKKaveECLNQIIAGGEEVPFTLTAKQEVFFQdKKTRKPPRLIVYPPLEFRV 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2571 AEKMILGDPGIVAKAILGPAYLFQYTPNQRVKLLVSTWESKTHPAAITVDATCFDSSIDERDMEVEAEIFAAASDQPELV 2650
Cdd:cd23203  161 AEKMILGDPGRVAKAVLGKAYGFQYTPNQRVKVLVDMWKSKRHPCAITVDATCFDSSITEEDVARETEIYAAASDDPELV 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2651 KALCRYYAEGPMVTPDGVPIGFRKCRSSGVLTTSSANSITCYIKVKAACAKVGLKDPSFFIAGDDCLIIYEDDGADPCER 2730
Cdd:cd23203  241 RALGKYYAEGPMVNPEGVPVGERRCRASGVLTTSSSNSITCYLKVKAACRKAGLKNPSFLIHGDDCLIICERPEEDPCDA 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2731 LRLALGNYGYRCEPSKHASLDTAECCSAYLAECTAGGSRRWWLSTDMRKPLARAAAEYSDPVGSALGTILMYPWHPIVRY 2810
Cdd:cd23203  321 LKAALASYGYDCEPQYHASLDTAESCSAYLAECNAGGGRHYFLSTDMRRPLARASSEYGDPVASALGYILLYPWHPITRY 400

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2828598  2811 VLIPHVLIMAFRGGGTPDELVMCQVQGNTYSFPLKILPRVLVSLHGPWCLQVTTDSTKTRMEAGNALRDLGMKSLS 2886
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.
 121-523 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: 669.97  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598     121 RLGRLPNLTCHLKCDFAFSYPGISV-----DFDWAFKKILELPSRLWCGLSRAGVLALLVVMMLGLEQRLVLALLLLIVV 195
Cdd:pfam12786    1 RVYPLPNLTCAVECDLAWSYEGWSWtedmaDFDWAFEYLWTLPFDLWRGLMAASVLLVLVAALLLLEQRLVMAFLLLTVA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598     196 GEAYCDVFEACHCAHWGGRPPPRITPWVRGNGSVECTCPFGRMVWNPVLCSGLIWKDGSREGNVYDLPPVCPSEVLGTVA 275
Cdd:pfam12786   81 GEAQGGFFDGCHCAYWGSRVPPGAKPWDRGNGTVVCDCPFGPMVWLPALCSGLAWRDGDREGTVNDLPLVCPREVLGTVS 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598     276 VMCRWGSAYWAWRLGDWVELHRELPRSALCVFHSFTQRMNMWPkDVDFLTPEGTPCASCVVDQRPAWCGSCVRDCWETGG 355
Cdd:pfam12786  161 VMCVWGSAYWFWRTGDWVDLWSELPGSALCTFAALGTSDRDHP-DVDVLSPSGIPCASCVVDRRPASCGSCVRDCWETTG 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598     356 P---DFASCGIGTQVTEHLEAVLVHGGVESVVTTPRGERPKYLGHHGQGAYYGAVSKLSTNYTVTQIGGYWHALKCPCVE 432
Cdd:pfam12786  240 PkrlPFEECGLGPRLTEHLEAVLVDGGVESKVTTPFGERPKYGGQHGGGTYYGAVRKLSRNMTVIDIGGYWHALPCPCPE 319

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598     433 FPSGDLPRRIPGIPVNACLS--GAGPHPFTAW-APGGWYAPVFTKCNWPTTPGVDVCRGFAYDFPGDHNGFIHVVGARQQ 509
Cdd:pfam12786  320 FPPGTLPFRIPGPPVNACLLlgGEVSHPFGAWgAPGGFYAPVFTKCNWPTGSGVDVCPGFAFDFPGDHNGFIHVKGGRQQ 399

                          410
                   ....*....|....
gi 2828598     510 *YSGVMRSSPAWLL 523
Cdd:pfam12786  400 VDSGQRRPSPRWLL 413
HCV_NS4b pfam01001
Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. ...
 1710-1899 5.15e-85

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: 276.95  E-value: 5.15e-85
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598    1710 QAWSSGMFVPPPAASAEHMPSIIQSLDTAFTRAWDTVFTHGRSLLVGFTAAYGAKRNPPLGVGASFLLGMSAGHSVHVRL 1789
Cdd:pfam01001    1 FAFKALGLLPPAIDKAESITPAVASLDTKFEQFWAKHMWNFRSGIQYLAGLYTLPRNPPLAVLASFLAGMTSPLPTHVRL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598    1790 AAALLLGVGGTMLGQASTGLAMAGAYFAGGSITSSWLS-VIVALLGGWEGAVNAASLTFDLLSGRAE-AKDAWCIISCLA 1867
Cdd:pfam01001   81 ALALLGGWGATQLGTPSGGLAFVGAGFAGAAVGSSWLGrVLVDVLGGYEAAVNAASLTFKIMSGELPtAEDLWNLLPCLL 160

                          170       180       190
                   ....*....|....*....|....*....|..
gi 2828598    1868 SPGASVAGAALGVLLWSMKKGVGQDWVNRLLT 1899
Cdd:pfam01001  161 SPGASVVGVALAALLRSHKGEGAVQWMNRLLT 192
HCV_NS2 pfam01538
Hepatitis C virus non-structural protein NS2; The viral genome is translated into a single ...
 749-946 2.50e-76

Hepatitis C virus non-structural protein NS2; The viral genome is translated into a single polyprotein of about 3000 amino acids. Generation of the mature non-structural proteins relies on the activity of viral proteases. Cleavage at the NS2/NS3 junction is accomplished by a metal-dependent autoprotease encoded within NS2 and the N-terminus of NS3.


:

Pssm-ID: 366698  Cd Length: 195  Bit Score: 252.21  E-value: 2.50e-76
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598     749 DWADHLWFASWVLSWGLLMLGLLSQRGKDEKLRAYGRWCILYQRLRKLVAWSPVGRYGRWPWLPKLWLVAAwfwPREIAA 828
Cdd:pfam01538    1 DTEDAGWLGAAVLSWITLFTLTPTYKGLLAKLLWWLQYCIARQEARLHVWVPPLGVRGGRDAVILLWCLAH---PDLVFD 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598     829 VCVAFILGFGFFdvvdYILEVVLVSSPNLVRLARVLDSLVA----AGDKLATTWLVEKLRKRNCFLYAHAGQVTRRTAEQ 904
Cdd:pfam01538   78 VTKILLAILGPL----YLLQASLLRVPYFVRAARLLRSCVLvrhlAGGKYVQMALLKLGRWTGTYLYDHLGPLSDWAAEG 153

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 2828598     905 LRQWGFALEPVAVHPEDCAMVRDAARTLSCGQSVHGKPVVAR 946
Cdd:pfam01538  154 LRDLAVALEPVVFSPMECKIITWGADTAACGDIVHGLPVSAR 195
Peptidase_S29 super family cl03772
Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a ...
 999-1145 3.31e-69

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.


The actual alignment was detected with superfamily member pfam02907:

Pssm-ID: 427049  Cd Length: 149  Bit Score: 229.62  E-value: 3.31e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598     999 GNVVVLGTSTTRSMGTCVNGVMYTTYHGSNARTLAAQMGPVNSRWWSASDDVAVYPLPVGAKCLEPCKCQPQGVWVIRND 1078
Cdd:pfam02907    2 GEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTRD 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2828598    1079 GALCHGTL--GRTVELDLPAELCDFRGSSGSPILCDEGHAVGMLISVLHRGSRVTGIRYTkPWETLPRE 1145
Cdd:pfam02907   82 GDLIPGRRrgDPRVSLLSPRPLSYLKGSSGGPILCPSGHVVGMFRAAVHSGGVVKAVRFV-PWETLPTT 149
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 1304-1435 2.30e-23

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: 98.49  E-value: 2.30e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  1304 IREEMLGVEGEVVFYGHKLPAARymTGRHLLFCHSKVECNRLASALTSCGISAITYYRGGEQAIPE-----GDVCVCATD 1378
Cdd:cd18806    1 IEDVALEIPGRIWFYGKAWITIY--GGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEYPkiktiDWDFVVTTD 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 2828598  1379 ALSTGFTGNFDTVTDCGLMVEEVVEVTLDPTITVSlRTVPAPAELRSQRRGRCGRGK 1435
Cdd:cd18806   79 ISEMGANFDADRVIDCRTCVKPTILFSGDFRVILT-GPVPQTAASAAQRRGRTGRNP 134
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 1166-1307 8.15e-23

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: 97.23  E-value: 8.15e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  1166 LYLPTGSGKSTRIPWEYVKSGH----RVLVLNPSIATVRAMGPYMEQLtgqhPSIYcghDTTAYSRTTQ--SGLTYCTYG 1239
Cdd:cd17931    6 LDLHPGAGKTTRVLPQIIREAIkkrlRTLVLAPTRVVAAEMYEALRGL----PIRY---RTGAVKEEHGgnEIVDYMCHG 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  1240 RFManprkyMRGC--------DVVICDECHSTDPVSILGMG----RARLLAkdckvRLLLFATATPPGAPIAPHE---NI 1304
Cdd:cd17931   79 TFT------CRLLspkrvpnyNLIIMDEAHFTDPASIAARGyihtRVEMGE-----AAVIFMTATPPGTVTPFPQsnhPI 147


                 ...
gi 2828598  1305 REE 1307
Cdd:cd17931  148 EDF 150
 
Name Accession Description Interval E-value
Pegivirus_RdRp cd23203
RNA-dependent RNA polymerase (RdRp) in the genus Pegivirus, within the family Flaviviridae of ...
 2415-2886 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: 934.37  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2415 WSGAPLGCGRVVPPPITRPIGTHLTHDTTKVYVTDPDRAAERAEKVTIWRGQRVYDEHYASVVGEALKKAAATTSPGWTY 2494
Cdd:cd23203    1 WSGAPLGVGRPKPPPVTRPVGSHLRADATKVYVTDPDDVGERIEKVTIWRTPRVVDKFLRDAYNLALAKASATPSPGWTY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2495 AMAISKVRKRAAAGYGSKVTVATLETGWPHV---RTMIDKIRCHEEVPFTFVTKREVFFS-KTTRKPPRFIVYPPLDFRI 2570
Cdd:cd23203   81 EEAVAKVRPGAAMGHGSKVTVADLKTPAGKKaveECLNQIIAGGEEVPFTLTAKQEVFFQdKKTRKPPRLIVYPPLEFRV 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2571 AEKMILGDPGIVAKAILGPAYLFQYTPNQRVKLLVSTWESKTHPAAITVDATCFDSSIDERDMEVEAEIFAAASDQPELV 2650
Cdd:cd23203  161 AEKMILGDPGRVAKAVLGKAYGFQYTPNQRVKVLVDMWKSKRHPCAITVDATCFDSSITEEDVARETEIYAAASDDPELV 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2651 KALCRYYAEGPMVTPDGVPIGFRKCRSSGVLTTSSANSITCYIKVKAACAKVGLKDPSFFIAGDDCLIIYEDDGADPCER 2730
Cdd:cd23203  241 RALGKYYAEGPMVNPEGVPVGERRCRASGVLTTSSSNSITCYLKVKAACRKAGLKNPSFLIHGDDCLIICERPEEDPCDA 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2731 LRLALGNYGYRCEPSKHASLDTAECCSAYLAECTAGGSRRWWLSTDMRKPLARAAAEYSDPVGSALGTILMYPWHPIVRY 2810
Cdd:cd23203  321 LKAALASYGYDCEPQYHASLDTAESCSAYLAECNAGGGRHYFLSTDMRRPLARASSEYGDPVASALGYILLYPWHPITRY 400

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2828598  2811 VLIPHVLIMAFRGGGTPDELVMCQVQGNTYSFPLKILPRVLVSLHGPWCLQVTTDSTKTRMEAGNALRDLGMKSLS 2886
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.
 121-523 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: 669.97  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598     121 RLGRLPNLTCHLKCDFAFSYPGISV-----DFDWAFKKILELPSRLWCGLSRAGVLALLVVMMLGLEQRLVLALLLLIVV 195
Cdd:pfam12786    1 RVYPLPNLTCAVECDLAWSYEGWSWtedmaDFDWAFEYLWTLPFDLWRGLMAASVLLVLVAALLLLEQRLVMAFLLLTVA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598     196 GEAYCDVFEACHCAHWGGRPPPRITPWVRGNGSVECTCPFGRMVWNPVLCSGLIWKDGSREGNVYDLPPVCPSEVLGTVA 275
Cdd:pfam12786   81 GEAQGGFFDGCHCAYWGSRVPPGAKPWDRGNGTVVCDCPFGPMVWLPALCSGLAWRDGDREGTVNDLPLVCPREVLGTVS 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598     276 VMCRWGSAYWAWRLGDWVELHRELPRSALCVFHSFTQRMNMWPkDVDFLTPEGTPCASCVVDQRPAWCGSCVRDCWETGG 355
Cdd:pfam12786  161 VMCVWGSAYWFWRTGDWVDLWSELPGSALCTFAALGTSDRDHP-DVDVLSPSGIPCASCVVDRRPASCGSCVRDCWETTG 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598     356 P---DFASCGIGTQVTEHLEAVLVHGGVESVVTTPRGERPKYLGHHGQGAYYGAVSKLSTNYTVTQIGGYWHALKCPCVE 432
Cdd:pfam12786  240 PkrlPFEECGLGPRLTEHLEAVLVDGGVESKVTTPFGERPKYGGQHGGGTYYGAVRKLSRNMTVIDIGGYWHALPCPCPE 319

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598     433 FPSGDLPRRIPGIPVNACLS--GAGPHPFTAW-APGGWYAPVFTKCNWPTTPGVDVCRGFAYDFPGDHNGFIHVVGARQQ 509
Cdd:pfam12786  320 FPPGTLPFRIPGPPVNACLLlgGEVSHPFGAWgAPGGFYAPVFTKCNWPTGSGVDVCPGFAFDFPGDHNGFIHVKGGRQQ 399

                          410
                   ....*....|....
gi 2828598     510 *YSGVMRSSPAWLL 523
Cdd:pfam12786  400 VDSGQRRPSPRWLL 413
RdRP_3 pfam00998
Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase ...
 2412-2902 1.75e-151

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: 480.19  E-value: 1.75e-151
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598    2412 SYIWSGAPLgCGRVVPPPITRPIGTHLTHDTTKVYVTDPDRAAERAEKVTIWRGQRVYD-EHYASVVGEALKKAAATTSP 2490
Cdd:pfam00998    1 SYVWTGARP-AKERKILPITGPGSGLLFGVHNNSLVNLRRGLVERVFKVTFDRGGQLVPpKPYPGAFKELKYFASALVSK 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598    2491 GWTyamAISKVRKRAAA---GYGSKVTVATLET-GWPHVRTMIDKIRCHE-EVPFTFVTKREVFFSKTTRKPPRFIVYPP 2565
Cdd:pfam00998   80 LGE---ATPLTPEHFAAsytGRKRKIYVKALESlAVKPVQRRDAILKTFVkAEKINITAKPDPAPRVIQPRPPRYNVEPG 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598    2566 LDFRIAEKMILGDpgiVAKAILGPAYLFQYTPNQRVKLLVSTWESKTHPAAITVDATCFDSSIDERDMEVEAEIFAAASD 2645
Cdd:pfam00998  157 RYLRPCEKMIYKA---IDKAFGGPTVLKGYTPEQRGEILLKKWDSFKKPVAIGLDASRFDQHVSVEALRFEHSIYLAAFL 233

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598    2646 QP-ELVKALC-RYYAEGPMVTPDG-VPIGFRKCRSSGVLTTSSANSITCYIKVKAACAKVGlKDPSFFIAGDDCLIIYED 2722
Cdd:pfam00998  234 GPeELIRLLTwQLYNGGPMYASDGqIKYGVRGCRMSGDMNTSLGNCLLMCLKVHAACKALG-IDARLLNNGDDCVVICES 312

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598    2723 DGADPC-ERLRLALGNYG---YRCEPSKHASLDTAecCSAYLAEC-TAGGSRRWWLSTDMRKPLARAAAEYSDPVGSALG 2797
Cdd:pfam00998  313 ADLDEVkEALTEAFARYGftmKVEEPVYELELIEF--CQSNPVFDgGKYGMVRNPLTSDSKDPLSRASWETATPAKSWLG 390

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598    2798 TILMYPWHPIVRYVLIPHVLIMAFRGGGtPDELVMCQVQGNTYSFplkilprVLVSLHGPWCLQVTTDSTKTRMEAGNAL 2877
Cdd:pfam00998  391 AIGECGLSLWGGVPVLQHFYSCLLRNGG-LEKAVSFEMYGKVYSD-------SGFRLHGLGAGSRHSYEPTEEARVSFWL 462

                          490       500
                   ....*....|....*....|....*
gi 2828598    2878 rDLGMKSLSWHRRRAGNVRTRLLRG 2902
Cdd:pfam00998  463 -AFGITPDEQWALEAYYDRLKLLRQ 486
HCV_NS4b pfam01001
Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. ...
 1710-1899 5.15e-85

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: 276.95  E-value: 5.15e-85
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598    1710 QAWSSGMFVPPPAASAEHMPSIIQSLDTAFTRAWDTVFTHGRSLLVGFTAAYGAKRNPPLGVGASFLLGMSAGHSVHVRL 1789
Cdd:pfam01001    1 FAFKALGLLPPAIDKAESITPAVASLDTKFEQFWAKHMWNFRSGIQYLAGLYTLPRNPPLAVLASFLAGMTSPLPTHVRL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598    1790 AAALLLGVGGTMLGQASTGLAMAGAYFAGGSITSSWLS-VIVALLGGWEGAVNAASLTFDLLSGRAE-AKDAWCIISCLA 1867
Cdd:pfam01001   81 ALALLGGWGATQLGTPSGGLAFVGAGFAGAAVGSSWLGrVLVDVLGGYEAAVNAASLTFKIMSGELPtAEDLWNLLPCLL 160

                          170       180       190
                   ....*....|....*....|....*....|..
gi 2828598    1868 SPGASVAGAALGVLLWSMKKGVGQDWVNRLLT 1899
Cdd:pfam01001  161 SPGASVVGVALAALLRSHKGEGAVQWMNRLLT 192
HCV_NS2 pfam01538
Hepatitis C virus non-structural protein NS2; The viral genome is translated into a single ...
 749-946 2.50e-76

Hepatitis C virus non-structural protein NS2; The viral genome is translated into a single polyprotein of about 3000 amino acids. Generation of the mature non-structural proteins relies on the activity of viral proteases. Cleavage at the NS2/NS3 junction is accomplished by a metal-dependent autoprotease encoded within NS2 and the N-terminus of NS3.


Pssm-ID: 366698  Cd Length: 195  Bit Score: 252.21  E-value: 2.50e-76
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598     749 DWADHLWFASWVLSWGLLMLGLLSQRGKDEKLRAYGRWCILYQRLRKLVAWSPVGRYGRWPWLPKLWLVAAwfwPREIAA 828
Cdd:pfam01538    1 DTEDAGWLGAAVLSWITLFTLTPTYKGLLAKLLWWLQYCIARQEARLHVWVPPLGVRGGRDAVILLWCLAH---PDLVFD 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598     829 VCVAFILGFGFFdvvdYILEVVLVSSPNLVRLARVLDSLVA----AGDKLATTWLVEKLRKRNCFLYAHAGQVTRRTAEQ 904
Cdd:pfam01538   78 VTKILLAILGPL----YLLQASLLRVPYFVRAARLLRSCVLvrhlAGGKYVQMALLKLGRWTGTYLYDHLGPLSDWAAEG 153

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 2828598     905 LRQWGFALEPVAVHPEDCAMVRDAARTLSCGQSVHGKPVVAR 946
Cdd:pfam01538  154 LRDLAVALEPVVFSPMECKIITWGADTAACGDIVHGLPVSAR 195
Peptidase_S29 pfam02907
Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a ...
 999-1145 3.31e-69

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: 229.62  E-value: 3.31e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598     999 GNVVVLGTSTTRSMGTCVNGVMYTTYHGSNARTLAAQMGPVNSRWWSASDDVAVYPLPVGAKCLEPCKCQPQGVWVIRND 1078
Cdd:pfam02907    2 GEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTRD 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2828598    1079 GALCHGTL--GRTVELDLPAELCDFRGSSGSPILCDEGHAVGMLISVLHRGSRVTGIRYTkPWETLPRE 1145
Cdd:pfam02907   82 GDLIPGRRrgDPRVSLLSPRPLSYLKGSSGGPILCPSGHVVGMFRAAVHSGGVVKAVRFV-PWETLPTT 149
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 1304-1435 2.30e-23

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: 98.49  E-value: 2.30e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  1304 IREEMLGVEGEVVFYGHKLPAARymTGRHLLFCHSKVECNRLASALTSCGISAITYYRGGEQAIPE-----GDVCVCATD 1378
Cdd:cd18806    1 IEDVALEIPGRIWFYGKAWITIY--GGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEYPkiktiDWDFVVTTD 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 2828598  1379 ALSTGFTGNFDTVTDCGLMVEEVVEVTLDPTITVSlRTVPAPAELRSQRRGRCGRGK 1435
Cdd:cd18806   79 ISEMGANFDADRVIDCRTCVKPTILFSGDFRVILT-GPVPQTAASAAQRRGRTGRNP 134
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 1166-1307 8.15e-23

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: 97.23  E-value: 8.15e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  1166 LYLPTGSGKSTRIPWEYVKSGH----RVLVLNPSIATVRAMGPYMEQLtgqhPSIYcghDTTAYSRTTQ--SGLTYCTYG 1239
Cdd:cd17931    6 LDLHPGAGKTTRVLPQIIREAIkkrlRTLVLAPTRVVAAEMYEALRGL----PIRY---RTGAVKEEHGgnEIVDYMCHG 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  1240 RFManprkyMRGC--------DVVICDECHSTDPVSILGMG----RARLLAkdckvRLLLFATATPPGAPIAPHE---NI 1304
Cdd:cd17931   79 TFT------CRLLspkrvpnyNLIIMDEAHFTDPASIAARGyihtRVEMGE-----AAVIFMTATPPGTVTPFPQsnhPI 147


                 ...
gi 2828598  1305 REE 1307
Cdd:cd17931  148 EDF 150
DEXDc smart00487
DEAD-like helicases superfamily;
1158-1296 1.01e-14

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 75.22  E-value: 1.01e-14
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598     1158 RSGYREAPLYLPTGSGKSTRIP---WEYVKSGH--RVLVLNPSIATVRAMGPYMEQLT----GQHPSIYCGHDTTAYSRT 1228
Cdd:smart00487   21 LSGLRDVILAAPTGSGKTLAALlpaLEALKRGKggRVLVLVPTRELAEQWAEELKKLGpslgLKVVGLYGGDSKREQLRK 100

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2828598     1229 TQSG---LTYCTYGRF---MANPRKYMRGCDVVICDECHstdpvSILGMGR----ARLLAKDCKVRLLLFATATPPGA 1296
Cdd:smart00487  101 LESGktdILVTTPGRLldlLENDKLSLSNVDLVILDEAH-----RLLDGGFgdqlEKLLKLLPKNVQLLLLSATPPEE 173
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
1171-1295 1.88e-06

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 50.03  E-value: 1.88e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598    1171 GSGKSTRIPWEYVK----SGHRVLVLNPSIATVRAMGpymEQLTGQhPSIYcghDTTAYSRTTQSG-----LTYCTYGRF 1241
Cdd:pfam07652   12 GAGKTRKVLPELVRecidRRLRTLVLAPTRVVLAEME---EALRGL-PIRY---HTPAVSSEHTGReivdvMCHATFTQR 84

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2828598    1242 MANPRKYMRgCDVVICDECHSTDPVSILGMGRARLLAK--DCKvrlLLFATATPPG 1295
Cdd:pfam07652   85 LLSPVRVPN-YEVIIMDEAHFTDPASIAARGYISTLVElgEAA---AIFMTATPPG 136
 
Name Accession Description Interval E-value
Pegivirus_RdRp cd23203
RNA-dependent RNA polymerase (RdRp) in the genus Pegivirus, within the family Flaviviridae of ...
 2415-2886 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: 934.37  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2415 WSGAPLGCGRVVPPPITRPIGTHLTHDTTKVYVTDPDRAAERAEKVTIWRGQRVYDEHYASVVGEALKKAAATTSPGWTY 2494
Cdd:cd23203    1 WSGAPLGVGRPKPPPVTRPVGSHLRADATKVYVTDPDDVGERIEKVTIWRTPRVVDKFLRDAYNLALAKASATPSPGWTY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2495 AMAISKVRKRAAAGYGSKVTVATLETGWPHV---RTMIDKIRCHEEVPFTFVTKREVFFS-KTTRKPPRFIVYPPLDFRI 2570
Cdd:cd23203   81 EEAVAKVRPGAAMGHGSKVTVADLKTPAGKKaveECLNQIIAGGEEVPFTLTAKQEVFFQdKKTRKPPRLIVYPPLEFRV 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2571 AEKMILGDPGIVAKAILGPAYLFQYTPNQRVKLLVSTWESKTHPAAITVDATCFDSSIDERDMEVEAEIFAAASDQPELV 2650
Cdd:cd23203  161 AEKMILGDPGRVAKAVLGKAYGFQYTPNQRVKVLVDMWKSKRHPCAITVDATCFDSSITEEDVARETEIYAAASDDPELV 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2651 KALCRYYAEGPMVTPDGVPIGFRKCRSSGVLTTSSANSITCYIKVKAACAKVGLKDPSFFIAGDDCLIIYEDDGADPCER 2730
Cdd:cd23203  241 RALGKYYAEGPMVNPEGVPVGERRCRASGVLTTSSSNSITCYLKVKAACRKAGLKNPSFLIHGDDCLIICERPEEDPCDA 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2731 LRLALGNYGYRCEPSKHASLDTAECCSAYLAECTAGGSRRWWLSTDMRKPLARAAAEYSDPVGSALGTILMYPWHPIVRY 2810
Cdd:cd23203  321 LKAALASYGYDCEPQYHASLDTAESCSAYLAECNAGGGRHYFLSTDMRRPLARASSEYGDPVASALGYILLYPWHPITRY 400

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2828598  2811 VLIPHVLIMAFRGGGTPDELVMCQVQGNTYSFPLKILPRVLVSLHGPWCLQVTTDSTKTRMEAGNALRDLGMKSLS 2886
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.
 121-523 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: 669.97  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598     121 RLGRLPNLTCHLKCDFAFSYPGISV-----DFDWAFKKILELPSRLWCGLSRAGVLALLVVMMLGLEQRLVLALLLLIVV 195
Cdd:pfam12786    1 RVYPLPNLTCAVECDLAWSYEGWSWtedmaDFDWAFEYLWTLPFDLWRGLMAASVLLVLVAALLLLEQRLVMAFLLLTVA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598     196 GEAYCDVFEACHCAHWGGRPPPRITPWVRGNGSVECTCPFGRMVWNPVLCSGLIWKDGSREGNVYDLPPVCPSEVLGTVA 275
Cdd:pfam12786   81 GEAQGGFFDGCHCAYWGSRVPPGAKPWDRGNGTVVCDCPFGPMVWLPALCSGLAWRDGDREGTVNDLPLVCPREVLGTVS 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598     276 VMCRWGSAYWAWRLGDWVELHRELPRSALCVFHSFTQRMNMWPkDVDFLTPEGTPCASCVVDQRPAWCGSCVRDCWETGG 355
Cdd:pfam12786  161 VMCVWGSAYWFWRTGDWVDLWSELPGSALCTFAALGTSDRDHP-DVDVLSPSGIPCASCVVDRRPASCGSCVRDCWETTG 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598     356 P---DFASCGIGTQVTEHLEAVLVHGGVESVVTTPRGERPKYLGHHGQGAYYGAVSKLSTNYTVTQIGGYWHALKCPCVE 432
Cdd:pfam12786  240 PkrlPFEECGLGPRLTEHLEAVLVDGGVESKVTTPFGERPKYGGQHGGGTYYGAVRKLSRNMTVIDIGGYWHALPCPCPE 319

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598     433 FPSGDLPRRIPGIPVNACLS--GAGPHPFTAW-APGGWYAPVFTKCNWPTTPGVDVCRGFAYDFPGDHNGFIHVVGARQQ 509
Cdd:pfam12786  320 FPPGTLPFRIPGPPVNACLLlgGEVSHPFGAWgAPGGFYAPVFTKCNWPTGSGVDVCPGFAFDFPGDHNGFIHVKGGRQQ 399

                          410
                   ....*....|....
gi 2828598     510 *YSGVMRSSPAWLL 523
Cdd:pfam12786  400 VDSGQRRPSPRWLL 413
RdRP_3 pfam00998
Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase ...
 2412-2902 1.75e-151

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: 480.19  E-value: 1.75e-151
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598    2412 SYIWSGAPLgCGRVVPPPITRPIGTHLTHDTTKVYVTDPDRAAERAEKVTIWRGQRVYD-EHYASVVGEALKKAAATTSP 2490
Cdd:pfam00998    1 SYVWTGARP-AKERKILPITGPGSGLLFGVHNNSLVNLRRGLVERVFKVTFDRGGQLVPpKPYPGAFKELKYFASALVSK 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598    2491 GWTyamAISKVRKRAAA---GYGSKVTVATLET-GWPHVRTMIDKIRCHE-EVPFTFVTKREVFFSKTTRKPPRFIVYPP 2565
Cdd:pfam00998   80 LGE---ATPLTPEHFAAsytGRKRKIYVKALESlAVKPVQRRDAILKTFVkAEKINITAKPDPAPRVIQPRPPRYNVEPG 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598    2566 LDFRIAEKMILGDpgiVAKAILGPAYLFQYTPNQRVKLLVSTWESKTHPAAITVDATCFDSSIDERDMEVEAEIFAAASD 2645
Cdd:pfam00998  157 RYLRPCEKMIYKA---IDKAFGGPTVLKGYTPEQRGEILLKKWDSFKKPVAIGLDASRFDQHVSVEALRFEHSIYLAAFL 233

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598    2646 QP-ELVKALC-RYYAEGPMVTPDG-VPIGFRKCRSSGVLTTSSANSITCYIKVKAACAKVGlKDPSFFIAGDDCLIIYED 2722
Cdd:pfam00998  234 GPeELIRLLTwQLYNGGPMYASDGqIKYGVRGCRMSGDMNTSLGNCLLMCLKVHAACKALG-IDARLLNNGDDCVVICES 312

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598    2723 DGADPC-ERLRLALGNYG---YRCEPSKHASLDTAecCSAYLAEC-TAGGSRRWWLSTDMRKPLARAAAEYSDPVGSALG 2797
Cdd:pfam00998  313 ADLDEVkEALTEAFARYGftmKVEEPVYELELIEF--CQSNPVFDgGKYGMVRNPLTSDSKDPLSRASWETATPAKSWLG 390

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598    2798 TILMYPWHPIVRYVLIPHVLIMAFRGGGtPDELVMCQVQGNTYSFplkilprVLVSLHGPWCLQVTTDSTKTRMEAGNAL 2877
Cdd:pfam00998  391 AIGECGLSLWGGVPVLQHFYSCLLRNGG-LEKAVSFEMYGKVYSD-------SGFRLHGLGAGSRHSYEPTEEARVSFWL 462

                          490       500
                   ....*....|....*....|....*
gi 2828598    2878 rDLGMKSLSWHRRRAGNVRTRLLRG 2902
Cdd:pfam00998  463 -AFGITPDEQWALEAYYDRLKLLRQ 486
Hepacivirus_RdRp cd23202
RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ...
 2444-2915 6.88e-119

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: 387.67  E-value: 6.88e-119
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2444 KVYVTDPDRAAERAEKVTIWRgQRVYDEHYASVVGEALKKAAATTSPGWTYAMAISKVR---KRAAAGYGSKVTVATLET 2520
Cdd:cd23202   23 LVYSTTSRSASERQKKVTFDR-LQVLDPHYDDVLKEAKARASGVKARLLSVEEACSLTPphsARSKFGYGAKDVRSLSRK 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2521 GWPHVRTMIDKIR--CHEEVPFTFVTKREVFF---SKTTRKPPRFIVYPPLDFRIAEKMILGDPG-IVAKAILGPAYLFQ 2594
Cdd:cd23202  102 AVNHINSVWEDLLedSETPIPTTIMAKNEVFCvtpEKGGRKPARLIVYPDLGVRVCEKMALYDVApKLPKAVMGEAYGFQ 181

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2595 YTPNQRVKLLVSTWESKTHPAAITVDATCFDSSIDERDMEVEAEIFAAASDQPE---LVKALC-RYYAEGPMVTPDGVPI 2670
Cdd:cd23202  182 YSPAQRVEFLLKMWRSKKTPMGFSYDTRCFDSTVTERDIRTEESIYQCCDLDPEarkAIRSLTeRLYVGGPMTNSKGQSC 261

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2671 GFRKCRSSGVLTTSSANSITCYIKVKAACAKVGLKDPSFFIAGDDCLIIYEDDG-ADPCERLRL---ALGNYGyrC---- 2742
Cdd:cd23202  262 GYRRCRASGVFTTSSGNTLTCYLKASAACRAAGLKDPTMLVCGDDLVVIAESAGvEEDAAALRAfteAMTRYS--Appgd 339

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2743 EPSKHASLDTAECCSAYLAEC-TAGGSRRWWLSTDMRKPLARAAAEYSD--PVGSALGTILMY-P--WhpiVRYVLIPHV 2816
Cdd:cd23202  340 PPQPEYDLELITSCSSNVSVAhDATGKRYYYLTRDPTTPLARAAWETARhtPVNSWLGNIIMYaPtlW---VRMVLMTHF 416

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2817 LIMaFRGGGTPDELVMCQVQGNTYSFPLKILPRVLVSLHGPWCLQVTTDSTKTRMEAGNALRDLGMKSLSWHRRRAGNVR 2896
Cdd:cd23202  417 FSI-LLAQEQLEKALDFEMYGNTYSIPPLDLPAIIQRLHGLSAFSLHGYSPRELNRVAAALRKLGVPPLRAWRHRARAVR 495

                        490       500
                 ....*....|....*....|
gi 2828598  2897 TRLL-RGGKAwGHLARCLLW 2915
Cdd:cd23202  496 AKLIaQGGKA-AICGKYLFN 514
ps-ssRNAv_Flaviviridae_RdRp cd23178
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of ...
 2538-2805 1.02e-111

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: 357.60  E-value: 1.02e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2538 VPFTFVTKREVFFSKT---TRKPPRFIVYPPLDFRIAEKMILGDPGIVAKAILGP-AYLFQYTPNQRVKLLVSTWESKTH 2613
Cdd:cd23178    1 IPTTIMPKNEVFCVEPgkgGRKPPRLIVYPDLGVRVAEKMALYDPVEVLPQVVGGsYYGFQYSPNQRVEILRKAWKSKKG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2614 PAAITVDATCFDSSIDERDMEVEAEIFAAAS---DQPELVKALCRYYAEGPMVTPDGVPIGFRKCRSSGVLTTSSANSIT 2690
Cdd:cd23178   81 PMAYSYDTRCFDSTVTEDDIQVEEEIYQACSlkeARQAIVSITERLYVEGPMVNSDGQICGRRRCRASGVLTTSAGNT*T 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2691 CYIKVKAACAKVGLKDPSFFIAGDDCLIIYEDDGADPCERLRLALGNYGYRCEPSKHA------SLDTAECCSAYLAECT 2764
Cdd:cd23178  161 CYLK*LAACREAGIRLPTMLVCGDDCVVICESDGTQEDAALLAAFTEALTRYGKPPKDppqpeyDLELIESCSHTVSEVR 240

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 2828598  2765 AGGSRRWWLS-TDMRKPLARAAAEYSD--PVGSALGTILMYPWH 2805
Cdd:cd23178  241 MKDGRRLYYLtRDPTTPLARAAWETGRhePINSWLGYIIMYALT 284
HCV_NS4b pfam01001
Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. ...
 1710-1899 5.15e-85

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: 276.95  E-value: 5.15e-85
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598    1710 QAWSSGMFVPPPAASAEHMPSIIQSLDTAFTRAWDTVFTHGRSLLVGFTAAYGAKRNPPLGVGASFLLGMSAGHSVHVRL 1789
Cdd:pfam01001    1 FAFKALGLLPPAIDKAESITPAVASLDTKFEQFWAKHMWNFRSGIQYLAGLYTLPRNPPLAVLASFLAGMTSPLPTHVRL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598    1790 AAALLLGVGGTMLGQASTGLAMAGAYFAGGSITSSWLS-VIVALLGGWEGAVNAASLTFDLLSGRAE-AKDAWCIISCLA 1867
Cdd:pfam01001   81 ALALLGGWGATQLGTPSGGLAFVGAGFAGAAVGSSWLGrVLVDVLGGYEAAVNAASLTFKIMSGELPtAEDLWNLLPCLL 160

                          170       180       190
                   ....*....|....*....|....*....|..
gi 2828598    1868 SPGASVAGAALGVLLWSMKKGVGQDWVNRLLT 1899
Cdd:pfam01001  161 SPGASVVGVALAALLRSHKGEGAVQWMNRLLT 192
HCV_NS2 pfam01538
Hepatitis C virus non-structural protein NS2; The viral genome is translated into a single ...
 749-946 2.50e-76

Hepatitis C virus non-structural protein NS2; The viral genome is translated into a single polyprotein of about 3000 amino acids. Generation of the mature non-structural proteins relies on the activity of viral proteases. Cleavage at the NS2/NS3 junction is accomplished by a metal-dependent autoprotease encoded within NS2 and the N-terminus of NS3.


Pssm-ID: 366698  Cd Length: 195  Bit Score: 252.21  E-value: 2.50e-76
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598     749 DWADHLWFASWVLSWGLLMLGLLSQRGKDEKLRAYGRWCILYQRLRKLVAWSPVGRYGRWPWLPKLWLVAAwfwPREIAA 828
Cdd:pfam01538    1 DTEDAGWLGAAVLSWITLFTLTPTYKGLLAKLLWWLQYCIARQEARLHVWVPPLGVRGGRDAVILLWCLAH---PDLVFD 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598     829 VCVAFILGFGFFdvvdYILEVVLVSSPNLVRLARVLDSLVA----AGDKLATTWLVEKLRKRNCFLYAHAGQVTRRTAEQ 904
Cdd:pfam01538   78 VTKILLAILGPL----YLLQASLLRVPYFVRAARLLRSCVLvrhlAGGKYVQMALLKLGRWTGTYLYDHLGPLSDWAAEG 153

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 2828598     905 LRQWGFALEPVAVHPEDCAMVRDAARTLSCGQSVHGKPVVAR 946
Cdd:pfam01538  154 LRDLAVALEPVVFSPMECKIITWGADTAACGDIVHGLPVSAR 195
Peptidase_S29 pfam02907
Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a ...
 999-1145 3.31e-69

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: 229.62  E-value: 3.31e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598     999 GNVVVLGTSTTRSMGTCVNGVMYTTYHGSNARTLAAQMGPVNSRWWSASDDVAVYPLPVGAKCLEPCKCQPQGVWVIRND 1078
Cdd:pfam02907    2 GEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTRD 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2828598    1079 GALCHGTL--GRTVELDLPAELCDFRGSSGSPILCDEGHAVGMLISVLHRGSRVTGIRYTkPWETLPRE 1145
Cdd:pfam02907   82 GDLIPGRRrgDPRVSLLSPRPLSYLKGSSGGPILCPSGHVVGMFRAAVHSGGVVKAVRFV-PWETLPTT 149
RNA_dep_RNAP cd01699
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
 2522-2787 2.42e-40

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: 152.05  E-value: 2.42e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2522 WPHVRTMIDKIRCHEEVPFTFVTKREVFF-SKTTRKPPRFIVYPPLDFRIAEKMILGDPGIVAKAI-LGPAYLFQYTPNQ 2599
Cdd:cd01699    2 EKAVESLEDLPLIRPDLVFTTFLKDELRPlEKVEAGKTRLIQPRPLDYNIALRMYLGPFEAKLMKNrGGLPIAVGINPYS 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2600 R-VKLLVSTWESKThPAAITVDATCFDSSIDERDMEVEAEIFAAASDQP------ELVKALCRYYaegpmvTPDGVPIGF 2672
Cdd:cd01699   82 RdWTILANKLRSFS-PVAIALDYSRFDSSLSPQLLEAEHSIYNALYDDDdelerrNLLRSLTNNS------LHIGFNEVY 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2673 RK--CRSSGVLTTSSANSITCYIKVKAACAKVG----LKDPSFFIAGDDCLIIYE-DDGADPCERLRLALGNYGYRCEPS 2745
Cdd:cd01699  155 KVrgGRPSGDPLTSIGNSIINCILVRYAFRKLGgksfFKNVRLLNYGDDCLLSVEkADDKFNLETLAEWLKEYGLTMTDE 234

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 2828598  2746 KHasldtAECCSAYLAECT-------AGGSRRWWLSTDMRKPLARAAAE 2787
Cdd:cd01699  235 DK-----VESPFRPLEEVEflkrrfvLDEGGGWRAPLDPSSILSKLSWS 278
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 1304-1435 2.30e-23

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: 98.49  E-value: 2.30e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  1304 IREEMLGVEGEVVFYGHKLPAARymTGRHLLFCHSKVECNRLASALTSCGISAITYYRGGEQAIPE-----GDVCVCATD 1378
Cdd:cd18806    1 IEDVALEIPGRIWFYGKAWITIY--GGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEYPkiktiDWDFVVTTD 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 2828598  1379 ALSTGFTGNFDTVTDCGLMVEEVVEVTLDPTITVSlRTVPAPAELRSQRRGRCGRGK 1435
Cdd:cd18806   79 ISEMGANFDADRVIDCRTCVKPTILFSGDFRVILT-GPVPQTAASAAQRRGRTGRNP 134
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 1166-1307 8.15e-23

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: 97.23  E-value: 8.15e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  1166 LYLPTGSGKSTRIPWEYVKSGH----RVLVLNPSIATVRAMGPYMEQLtgqhPSIYcghDTTAYSRTTQ--SGLTYCTYG 1239
Cdd:cd17931    6 LDLHPGAGKTTRVLPQIIREAIkkrlRTLVLAPTRVVAAEMYEALRGL----PIRY---RTGAVKEEHGgnEIVDYMCHG 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  1240 RFManprkyMRGC--------DVVICDECHSTDPVSILGMG----RARLLAkdckvRLLLFATATPPGAPIAPHE---NI 1304
Cdd:cd17931   79 TFT------CRLLspkrvpnyNLIIMDEAHFTDPASIAARGyihtRVEMGE-----AAVIFMTATPPGTVTPFPQsnhPI 147


                 ...
gi 2828598  1305 REE 1307
Cdd:cd17931  148 EDF 150
DEXDc smart00487
DEAD-like helicases superfamily;
1158-1296 1.01e-14

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 75.22  E-value: 1.01e-14
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598     1158 RSGYREAPLYLPTGSGKSTRIP---WEYVKSGH--RVLVLNPSIATVRAMGPYMEQLT----GQHPSIYCGHDTTAYSRT 1228
Cdd:smart00487   21 LSGLRDVILAAPTGSGKTLAALlpaLEALKRGKggRVLVLVPTRELAEQWAEELKKLGpslgLKVVGLYGGDSKREQLRK 100

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2828598     1229 TQSG---LTYCTYGRF---MANPRKYMRGCDVVICDECHstdpvSILGMGR----ARLLAKDCKVRLLLFATATPPGA 1296
Cdd:smart00487  101 LESGktdILVTTPGRLldlLENDKLSLSNVDLVILDEAH-----RLLDGGFgdqlEKLLKLLPKNVQLLLLSATPPEE 173
ps_ssRNAv_Tolivirales_RdRp cd23179
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Toliovirales of ...
 2542-2721 1.83e-09

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: 60.61  E-value: 1.83e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2542 FVtKREVFFSKTTRKPPRFIVY--PPLDFRIA------EKMI---LGDPG----IVAKAilgpaylfqYTPNQRVKLLVS 2606
Cdd:cd23179    6 FL-KAEKYNPLAKNKKPRMIQPrsPRYNLELArylkpiEHALygaLDAGRggtrVVAKG---------LNPRQRANLIRR 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2607 TWESKTHPAAITVDATCFDSSIDERDMEVEAEIFAAA-SDQPELVKaLCRYYAEGPMVTPDGVPIGFRKCRSSGVLTTSS 2685
Cdd:cd23179   76 KWDEFDDPVVFSLDASRFDAHVSVELLRLEHSVYLACyPGDPELRK-LLKWQLVNKGRTSNGVKYKTRGGRMSGDMNTGL 154

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 2828598  2686 ANSITCYIKVKAACaKVGLKDPSFFIAGDDCLIIYE 2721
Cdd:cd23179  155 GNCLIMLAMVYAVL-RELGIKYDLLVDGDDALVFVE 189
Tombusviridae_RdRp cd23206
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tombusviridae of ...
 2595-2743 1.94e-08

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: 57.51  E-value: 1.94e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2595 YTPNQRVKLLVSTWESKTHPAAITVDATCFDSSIDERDMEVEAEIF-AAASDQPELVKAL-CRYYAEGPMVTPDGVpIGF 2672
Cdd:cd23206   65 YNAEERGRILREKWDSFRDPVAVGLDASRFDQHVSVDALKWEHSVYlRIFPDDKELSRLLrWQLHNKGVARCKDGK-VKY 143

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2673 RK--CRSSGVLTTSSAN-SITCYIkVKAACAKVGLKdPSFFIAGDDCLIIyeddgadpCERLRLAL---------GNYGY 2740
Cdd:cd23206  144 KVkgGRMSGDMNTSLGNcLIMCAM-VYAYLEELGIK-AELANNGDDCVLI--------MERSDLLRfldgleewfLRFGF 213


                 ...
gi 2828598  2741 RCE 2743
Cdd:cd23206  214 TMV 216
Betanecrovirus_RdRp cd23244
RNA-dependent RNA polymerase (RdRp) in the genus Betanecrosvirus of positive-sense ...
 2608-2721 8.31e-07

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: 54.52  E-value: 8.31e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2608 WESKTHPAAITVDATCFDSSIDERDMEVEAEIFAA---ASDQPELVKAL-CRYYAEGPMVTPDGvPIGFR--KCRSSGVL 2681
Cdd:cd23244  195 WDSFDDPVGIGMDASRFDQHISKEALEFEHKMWLSmfpGSDRKELARLLgMQIHNRGLARCPDG-EIRYTveGCRMSGDM 273

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 2828598  2682 TTSSANsitCYI---KVKAACAKVGLKDPSFFIAGDDCLIIYE 2721
Cdd:cd23244  274 NTSSGN---CYImcaTVHNWCSRLGVKHFRLANNGDDCMLVVE 313
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
1171-1295 1.88e-06

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 50.03  E-value: 1.88e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598    1171 GSGKSTRIPWEYVK----SGHRVLVLNPSIATVRAMGpymEQLTGQhPSIYcghDTTAYSRTTQSG-----LTYCTYGRF 1241
Cdd:pfam07652   12 GAGKTRKVLPELVRecidRRLRTLVLAPTRVVLAEME---EALRGL-PIRY---HTPAVSSEHTGReivdvMCHATFTQR 84

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2828598    1242 MANPRKYMRgCDVVICDECHSTDPVSILGMGRARLLAK--DCKvrlLLFATATPPG 1295
Cdd:pfam07652   85 LLSPVRVPN-YEVIIMDEAHFTDPASIAARGYISTLVElgEAA---AIFMTATPPG 136
Alphanecrovirus_RdRp cd23237
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Alphanecrovirus of ...
 2595-2721 2.04e-06

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Alphanecrovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the Alphanecrovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. Alphanecroviruses are non-enveloped, with icosahedral and spherical geometries, and T=3 symmetry, and a diameter of around 28 nm. Their genomes are linear, around 4 kb in length. In the Alphanecrovirus genus plants serve as natural hosts. There are 4 species in this genus: Olive latent virus 1, Olive mild mosaic virus, Potato necrosis virus, and Tobacco necrosis virus A. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438087  Cd Length: 439  Bit Score: 53.11  E-value: 2.04e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2595 YTPNQRVKLLVSTWESKTHPAAITVDATCFDSSIDERDMEVEAEIFaaASDQPE-------LVKALCRYyaeGPMVTPDG 2667
Cdd:cd23237  141 FTLEQQGEIMRSKWKKYVNPVAVGLDASRFDQHVSVEALQYEHEFY--LRDYPNdkqlkwlLKQQLCNI---GTAFASDG 215

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2828598  2668 VpIGFRK--CRSSGVLTTSSANSITcyikvkaACAKV-GLKDP-----SFFIAGDDCLIIYE 2721
Cdd:cd23237  216 I-IKYKKegCRMSGDMNTSLGNCIL-------MCAMVyGLKEHlginlSLANNGDDCVIVCE 269
Tombusvirus-like_RdRp cd23236
RNA-dependent RNA polymerase (RdRp) in the genus Tombusvirus of positive-sense single-stranded ...
 2595-2783 2.93e-06

RNA-dependent RNA polymerase (RdRp) in the genus Tombusvirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within Procedovirinae subfamily; and related RdRps; This group contains the RdRp of RNA viruses belonging to the Tombusvirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. Tombusvirus is a genus of plant viruses. There are 17 species in the Tombusvirus genus: Artichoke mottled crinkle virus, Carnation Italian ringspot virus, Cucumber Bulgarian virus, Cucumber necrosis virus, Cymbidium ringspot virus, Eggplant mottled crinkle virus, Grapevine Algerian latent virus, Havel River virus, Lato River virus, Limonium flower distortion virus, Moroccan pepper virus, Neckar River virus, Pelargonium leaf curl virus, Pelargonium necrotic spot virus, Petunia asteroid mosaic virus, Sikte waterborne virus, and Tomato bushy stunt virus. Symptoms associated with this genus include mosaic. The name of the genus comes from Tomato bushy stunt virus. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438086 [Multi-domain]  Cd Length: 474  Bit Score: 52.71  E-value: 2.93e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2595 YTPNQRVKLLVSTWESKTHPAAITVDATCFDSSIDERDMEVEAEIFAAASDQPELVKALCRY--YAEGPMVTPDGVpIGF 2672
Cdd:cd23236  181 YTADEVGAIFRDKWDRFDKPVAIGLDASRFDQHCSVEALQFEHSFYRAMYPGNKLLSKLLEWqlHNKGKGYVPDGT-ITY 259

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2673 RK--CRSSGVLTTSSANSITCYIKVKAACAKVGLKDPSFFIAGDDCLIIYEDDGADPCER-LRLALGNYGY--RCEPSKH 2747
Cdd:cd23236  260 RKegCRMSGDINTSLGNYLLMCAMVYGYMRHLGINEFSLANCGDDCVLIVERRNLKQVQGtLPEYFLNLGYtmKVEPPVF 339

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 2828598  2748 aSLDTAECCSAYLAECTAGgsrrWWLSTDMRKPLAR 2783
Cdd:cd23236  340 -QLEEVEFCQAHPVQFQGG----WKMVRNVRTAMSK 370
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 1169-1294 2.28e-05

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: 47.24  E-value: 2.28e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598    1169 PTGSGKST--RIP----WEYVKSGHRVLVLNPSIA----TVRAMGPYMEQLTGQHPSIYCGHDTTA-YSRTTQSGLTYCT 1237
Cdd:pfam00270   22 PTGSGKTLafLLPaleaLDKLDNGPQALVLAPTRElaeqIYEELKKLGKGLGLKVASLLGGDSRKEqLEKLKGPDILVGT 101

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2828598    1238 YGRF--MANPRKYMRGCDVVICDECHstdpvSILGMGR----ARLLAKDCKVRLLLFATATPP 1294
Cdd:pfam00270  102 PGRLldLLQERKLLKNLKLLVLDEAH-----RLLDMGFgpdlEEILRRLPKKRQILLLSATLP 159
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 1169-1292 3.92e-05

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: 46.24  E-value: 3.92e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  1169 PTGSGKSTRIP----WEYVKSGHRVLVLNPSIATVRAMGPYMEQLTGQHPSI-YCGHDTTAYSRTTQSG----LTYCTYG 1239
Cdd:cd00046    9 PTGSGKTLAALlaalLLLLKKGKKVLVLVPTKALALQTAERLRELFGPGIRVaVLVGGSSAEEREKNKLgdadIIIATPD 88

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2828598  1240 RF----MANPRKYMRGCDVVICDECHSTDP--VSILGMGRA--RLLAKDCKVrllLFATAT 1292
Cdd:cd00046   89 MLlnllLREDRLFLKDLKLIIVDEAHALLIdsRGALILDLAvrKAGLKNAQV---ILLSAT 146
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
 2619-2746 7.62e-05

Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase found in many positive strand RNA eukaryotic viruses. Structural studies indicate that these proteins form the "right hand" structure found in all oligonucleotide polymerases, containing thumb, finger and palm domains, and also the additional bridging finger and thumb domains unique to RNA-directed RNA polymerases.


Pssm-ID: 425815  Cd Length: 450  Bit Score: 48.18  E-value: 7.62e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598    2619 VDATCFDSSIDERDMEVEAEIFAAASDQPELVKALCRYYAE---GPMVTPDGVPigFRKCR--SSGVLTTSSANSITCYI 2693
Cdd:pfam00680  231 LDYSGFDSSVPPWLIRFAFEILRELLGFPSNVKEWRAILELliyTPIALPNGTV--FKKTGglPSGSPFTSIINSIVNYL 308

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2828598    2694 KVKAA----CAKVGL------KDPSFFIAGDDCLIIYEDDGADPCERLRLALGNYGYRCEPSK 2746
Cdd:pfam00680  309 LILYAllksLENDGPrvcnldKYFDFFTYGDDSLVAVSPDFDPVLDRLSPHLKELGLTITPAK 371
ps-ssRNA_Picornaviridae cd23193
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Picornaviridae of ...
 2487-2723 9.72e-05

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Picornaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Picornaviridae, order Picornavirales. The Picornaviridae family consists of small, icosahedral viruses with (+)ssRNA genomes. Characteristic features of all members of the family Picornaviridae are three capsid proteins with beta-barrel folding, polyprotein processing by virus-encoded cysteine proteinase(s), and replication by an RdRp with a YGDD sequence motif. The family Picornaviridae comprises 68 genera containing 158 species, but many viruses are presently awaiting classification. The established genera of the family include: Aphthovirus, Avisivirus, Crohivirus, Enterovirus, Teschovirus, Cardiovirus, Erbovirus, Kobuvirus, Hepatovirus, Parechovirus, Aquamavirus, Avihepatovirus, Avisivirus, Cosavirus, Dicipivirus, Fipivirus, Gallivirus, Hunnivirus, Kunsagivirus, Limnipivirus, Megrivirus, Mischivirus, Mosavirus, Oscivirus, Pasivirus, Passerivirus, Rabovirus, Rosavirus, Sakobuvirus, Salivirus, Sapelovirus, Senecavirus, Sicinivirus, and Tremovirus. The Picornaviridae contains many important human and animal pathogens including enteroviruses (such as poliovirus, enterovirus, coxsackievirus, and rhinovirus), cardioviruses (such as encephalomyocarditis virus and Theiler's virus), hepatitis A virus and foot-and-mouth disease virus. Infection with various picornaviruses may cause encephalitis, febrile rash illnesses (hand-foot-and-mouth disease), aseptic meningitis, hepatitis, conjunctivitis, herpangina, myositis and myocarditis, and the common cold. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438043  Cd Length: 345  Bit Score: 47.54  E-value: 9.72e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2487 TTSPGWTYAmaISKVRKRaaagygSKVTVATLETGWPHVRtMIDKIRCHEEVPFTFVT--KRE------VFFSKTtrkpp 2558
Cdd:cd23193   14 NTSPGYPYT--TQGLRRR------DLIDNDKGGVSPLLEE-EEQVLLDLDGPDVVFTTflKDElrpkekVKAGKT----- 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2559 RFIVYPPLDFRIAEKMILGdpGIVAKAILGPAYLF----------QYTPnqrvklLVSTWESKThpaAITVDATCFDSSI 2628
Cdd:cd23193   80 RVIEAAPLDYVIAGRMVFG--RLFAQFHSNPGILTgsavgcnpdtDWTR------LFASLKQDN---VYDLDYSGFDASL 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2629 DERDMEVEAEIFAAASDQPELVKAL-------------CRYYAEGPMvtPDGvpigfrkcrSSGvltTSSANSITCYIKV 2695
Cdd:cd23193  149 SSQLFEAAVEVLAECHGDPELVLRYlepiinskhvvgdERYTVEGGM--PSG---------CPC---TSILNSICNNLVV 214

                        250       260       270
                 ....*....|....*....|....*....|.
gi 2828598  2696 KAACAKVGLKDPSFF--IA-GDDCLIIYEDD 2723
Cdd:cd23193  215 RYALLETGKFDPDEYyiLAyGDDVLVSTDEP 245
Gammacarmovirus_RdRp cd23242
RNA-dependent RNA polymerase (RdRp) in the genus Gammacarmovirus of positive-sense ...
 2588-2743 1.10e-04

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: 47.82  E-value: 1.10e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2588 GPAYLFQYTPNQRVKLLVSTWESKTHPAAITVDATCFDSSIDERDMEVEAEIFAAASDQPELVKALCRYYAE--GPMVTP 2665
Cdd:cd23242  167 GPTVIKGYTVEQIGNIAEDAWDSFVSPVAIGFDMKRFDQHVSRDALEWEHSVYLDAFCNDPYLAELLSWQLEnkGVGYAS 246

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2666 DG-VPIGFRKCRSSGVLTTSSANS-ITCYIkVKAACAKVGLKdPSFFIAGDDCLIIYEDDGADP--CERLRLALgNYGYR 2741
Cdd:cd23242  247 DGsIKYKVDGCRMSGDMNTAMGNClLACAI-TWDFFKGRGIK-ARLLNNGDDCVVITEKECAAAvvAGMVRHWR-RFGFQ 323


                 ..
gi 2828598  2742 CE 2743
Cdd:cd23242  324 CE 325
ps-ssRNAv_RdRp-like cd23167
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
 2675-2721 3.25e-04

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


Pssm-ID: 438017 [Multi-domain]  Cd Length: 73  Bit Score: 41.56  E-value: 3.25e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 2828598  2675 CRSSGVLTTSSANSITCYIKVKAACAKVG-----LKDPSFFIAGDDCLIIYE 2721
Cdd:cd23167   22 GQPSGSPNTSADNSLINLLLARLALRKACgraefLNSVGILVYGDDSLVSVP 73
DEXHc_HrpB cd17990
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ...
 1169-1299 8.98e-04

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: 42.70  E-value: 8.98e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  1169 PTGSGKSTRIP-----WEYVKSGhRVLVLNPSIATVRAMGPYMEQLTGQHPSIYCGHDTTAYSRTTQSG-LTYCTYG--- 1239
Cdd:cd17990   25 PPGAGKTTRVPlallaELWIAGG-KIIVLEPRRVAARAAARRLATLLGEAPGETVGYRVRGESRVGRRTrVEVVTEGvll 103

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2828598  1240 -RFMANPRkyMRGCDVVICDECH--STDPVSILGMGR--ARLLAKDCKvrlLLFATATPPGAPIA 1299
Cdd:cd17990  104 rRLQRDPE--LSGVGAVILDEFHerSLDADLALALLLevQQLLRDDLR---LLAMSATLDGDGLA 163
Luteovirus_RdRp cd23233
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Luteovirus of ...
 2589-2730 1.30e-03

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Luteovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Luteovirus genus within the family Tombusviridae, order Tolivirales. There are 13 species in the Luteovirus genus: Apple associated luteovirus, Apple luteovirus 1, Barley yellow dwarf virus kerII, Barley yellow dwarf virus kerIII, Barley yellow dwarf virus MAV, Barley yellow dwarf virus PAS, Barley yellow dwarf virus PAV, Bean leafroll virus, Cherry associated luteovirus, Nectarine stem pitting associated virus, Red clover associated luteovirus, Rose spring dwarf-associated virus, and Soybean dwarf virus. Plants serve as natural hosts. The geographical distribution of Luteoviruses is widespread, with the virus primarily infecting plants via transmission by aphid vectors. The virus only replicates within the host cell and not within the vector. The name 'luteovirus' is derived from the Latin luteus (yellow) due to the symptomatic yellowing of the plant that occurs as a result of infection. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438083  Cd Length: 407  Bit Score: 43.96  E-value: 1.30e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2589 PAYLFQYTPNQRVKLLVSTWESKTHPAAITVDATCFDSSIDERDMEVEAEIFAAASDQPELVKAL-------CRYYAEGP 2661
Cdd:cd23233   85 PTVLSGYDNFKVGRIIAKKWQKFANPVAIGVDASRFDQHVSEQALKWEHSIYNGIFGDPELAELLewqldnkIKLFVEDK 164

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2828598  2662 MVTpdgvpIGFRKCRSSGVLTTSSANS-ITC-----YIK---VKAA-CAKvglkdpsffiaGDDCLIIyeddgadpCER 2730
Cdd:cd23233  165 MLR-----FKVKGHRMSGDINTSMGNKlIMCgmmhaYFKelgVEAElCNN-----------GDDCVII--------CER 219
Panicovirus_RdRp cd23238
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Panicovirus of ...
 2612-2740 1.32e-03

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: 44.51  E-value: 1.32e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2612 THPAAITVDATCFDSSIDERDMEVEAEIFAAASDQPELVKALCRY--YAEGPMVTPDGVpigFRK----CRSSGVLTTSS 2685
Cdd:cd23238  386 SRPCAIGFDASRFDQHVSVEALRFEHSIYKSIHGYPELLNLLLKWqiHNQGTAHANDGF---FKYsvdgKRMSGDMNTSL 462

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 2828598  2686 ANSITCYIKVKAACAKVGLkDPSFFIAGDD-CLIIYEDDGADPCERLRLALGNYGY 2740
Cdd:cd23238  463 GNCILASLISKDLVDSLGI-DAQLVNNGDDnVLICSVDDEEVVVKALYDHWMKYGF 517
Betacarmovirus_RdRp cd23240
RNA-dependent RNA polymerase (RdRp) in the genus Betacarmovirus of positive-sense ...
 2588-2744 1.88e-03

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: 43.68  E-value: 1.88e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2588 GPAYLFQYTPNQRVKLLVSTWESKTHPAAITVDATCFDSSIDERDMEVEAEIFAAASDQPELVKALC-RYYAEGPMVTPD 2666
Cdd:cd23240  157 GPTVLKGYTVEELGNIMHNHWSQFQKPCAVGFDMKRFDQHVSVDALRFEHSVYNRSFCSPELARLLEwQLLNSGVGHASD 236

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2667 G-VPIGFRKCRSSGVLTTSSAN-----SITCYIKVKAACAKVGlkdpsffiAGDDCLIIYE-DDGADPCERLRLALgNYG 2739
Cdd:cd23240  237 GfIRYKVDGCRMSGDVNTALGNcllacLITKYLLKGIRCRLIN--------NGDDCVLFFEaPDLAAVTERLAHWL-DFG 307


                 ....*...
gi 2828598  2740 YRC---EP 2744
Cdd:cd23240  308 FQCvveEP 315
Carmotetraviridae_RdRp cd23205
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Carmotetraviridae ...
 2598-2730 7.60e-03

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Carmotetraviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, and related Erinaceus virus H14; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Carmotetraviridae, and related Erinaceus virus H14, order Tolivirales. Carmotetraviridae includes only one genus, Alphacarmotetravirus, which has one species: Providence virus. Lepidopteran insects serve as the natural host. Recent studies indicated that Providence virus, a non-enveloped insect RNA virus, isolated from a lepidopteran midgut cell line can establish a productive infection in plants as well as in animal cells. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438055  Cd Length: 268  Bit Score: 41.15  E-value: 7.60e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2828598  2598 NQRVKLLVSTWESKTHPAAITVDATCFDSSIDERDMEVEAEIFAAASDQPELVKaLCRYYAEGPMVTPDGVPIGFRKCRS 2677
Cdd:cd23205   66 DQRANLLQRMWHLYERPVSISFDLSRWDMHVQVPLLKRVLEIYSQHVTCPLLLD-MCQNLLKNVCYTNKGIRYHVDGGIM 144

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 2828598  2678 SGVLTTSSANSITCYIKVKAACAKVgLKDpsffiaGDDCLIIYEDDGADPCER 2730
Cdd:cd23205  145 SGDMTTGLGNCIAVLVIVMSFRLSI-LDD------GDDHVIICEKSHTWICER 190
 
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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