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Conserved domains on  [gi|485191044|ref|YP_007905734|]
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polyprotein [Rodent pegivirus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Pegivirus_RdRp cd23203
RNA-dependent RNA polymerase (RdRp) in the genus Pegivirus, within the family Flaviviridae of ...
 2923-3398 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: 877.36  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 2923 WSGRAIAVDEPKRPPISRPLTAQLGAKADKVYITNPQDITKRIAKVTIDQTVAEVDQCFRDAYNCAIAKAKRVTQPGWTY 3002
Cdd:cd23203     1 WSGAPLGVGRPKPPPVTRPVGSHLRADATKVYVTDPDDVGERIEKVTIWRTPRVVDKFLRDAYNLALAKASATPSPGWTY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3003 DEAVAKLRPGSAKGHVAKVTVADMKSGAGRPFVEQVINDLAAGTLEHPFMLRPKAEVFPQTKETHKPPRLIVYPSLEFRV 3082
Cdd:cd23203    81 EEAVAKVRPGAAMGHGSKVTVADLKTPAGKKAVEECLNQIIAGGEEVPFTLTAKQEVFFQDKKTRKPPRLIVYPPLEFRV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3083 AEKMILGDPSLVAKAVMGASYGFQYPPHKRAEVLVNMWNSKRVPTAYTVDGTCFDSTVTPEDIAREGEIFAAASTNPELV 3162
Cdd:cd23203   161 AEKMILGDPGRVAKAVLGKAYGFQYTPNQRVKVLVDMWKSKRHPCAITVDATCFDSSITEEDVARETEIYAAASDDPELV 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3163 RRLHELYAGSPMMDPSGNIVGYRRCRASGTLTTSAGNSITCYLKVSAACRKAGLINPSYLIHGDDVVIVCEKTECDQSQA 3242
Cdd:cd23203   241 RALGKYYAEGPMVNPEGVPVGERRCRASGVLTTSSSNSITCYLKVKAACRKAGLKNPSFLIHGDDCLIICERPEEDPCDA 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3243 LGAALRSYGYECEPTRHADLTTAESCSSSLDTVRTVRGLKHVLRCDMRRGLGRTVAECGDPVGTAWGYTINYPTHPIVMY 3322
Cdd:cd23203   321 LKAALASYGYDCEPQYHASLDTAESCSAYLAECNAGGGRHYFLSTDMRRPLARASSEYGDPVASALGYILLYPWHPITRY 400

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 485191044 3323 VLLPLLLQTALNNGDGIHQPVTIDVRGNSVTLPLDTIGRAVRGLHGRDILAVTGHSATVLQETYDTLQFFGMRGLG 3398
Cdd:cd23203   401 VLLPHLLTLAFRGGGTPDDLVTCQVHGNSYKFPLKLLPRILVGLHGPDCLRVTADSTKTLMEAGKALQAFGMRGLA 476
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 1476-1611 4.93e-24

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: 100.70  E-value: 4.93e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 1476 APTGSGKSTKFPAKLAQDGHN----VLVLNPSVVTTKAMGPYMKklvGKTPNIFAGtgasAMQIKTGSK--ITYCTYGRF 1549
Cdd:cd17931     8 LHPGAGKTTRVLPQIIREAIKkrlrTLVLAPTRVVAAEMYEALR---GLPIRYRTG----AVKEEHGGNeiVDYMCHGTF 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 485191044 1550 LvnpQGFLDQKAV-----VVCDECHATDGTSILGIGVARALAEkAGVRLLVFATATPPGTQFTPHAS 1611
Cdd:cd17931    81 T---CRLLSPKRVpnynlIIMDEAHFTDPASIAARGYIHTRVE-MGEAAVIFMTATPPGTVTPFPQS 143
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 1612-1744 2.22e-20

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: 90.01  E-value: 2.22e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 1612 ITEETLDGDGDIPFYGVSLkaSTYLKGRHVIFCHSKAECVRVAESLAGAGVKAVTYWRG---TRHDVLTDDADLTVVATD 1688
Cdd:cd18806     1 IEDVALEIPGRIWFYGKAW--ITIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKlddTEYPKIKTIDWDFVVTTD 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 485191044 1689 AISTGYTGNFATCTDCCSVVEETVDVDLNptFTINL-ITKAADAALRMQRRGRCGRG 1744
Cdd:cd18806    79 ISEMGANFDADRVIDCRTCVKPTILFSGD--FRVILtGPVPQTAASAAQRRGRTGRN 133
HCV_NS4b super family cl03062
Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. ...
 2052-2203 2.23e-18

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


The actual alignment was detected with superfamily member pfam01001:

Pssm-ID: 110032  Cd Length: 192  Bit Score: 85.89  E-value: 2.23e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044  2052 HITALLAGGMAIASASSSPVFATLAALLSGASVTLPSKVAWALTLAGSAAAGLCGGARAGLA-VGAGFyVGSHLAGLSVV 2130
Cdd:pfam01001   40 NFRSGIQYLAGLYTLPRNPPLAVLASFLAGMTSPLPTHVRLALALLGGWGATQLGTPSGGLAfVGAGF-AGAAVGSSWLG 118

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 485191044  2131 DTAINLAAGYEACVSTCAFVLDLFDGKATMAHFLPCLAGVLA-PGAACAGVAFALILRASATGDSSTWMNRLLS 2203
Cdd:pfam01001  119 RVLVDVLGGYEAAVNAASLTFKIMSGELPTAEDLWNLLPCLLsPGASVVGVALAALLRSHKGEGAVQWMNRLLT 192
GBV-C_env super family cl15089
GB virus C genotype envelope; This the envelope protein from the ssRNA GB virus genotype C.
 443-591 1.88e-08

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


The actual alignment was detected with superfamily member pfam12786:

Pssm-ID: 193262  Cd Length: 413  Bit Score: 59.81  E-value: 1.88e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044   443 NGTT-CDCPFGV----------------IIRHFNNDtdpyldIPAICPESFpYTNFSWLCGWGSWWWVAHGVERPYSHPY 505
Cdd:pfam12786  111 NGTVvCDCPFGPmvwlpalcsglawrdgDREGTVND------LPLVCPREV-LGTVSVMCVWGSAYWFWRTGDWVDLWSE 183

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044   506 MPPSpfsAICYILTNRTvlynatiypntyaGVGRYPNytASVLGP--APVTSCMLDRRPAMCGDCFGGCFYRDGSHSRPF 583
Cdd:pfam12786  184 LPGS---ALCTFAALGT-------------SDRDHPD--VDVLSPsgIPCASCVVDRRPASCGSCVRDCWETTGPKRLPF 245


                   ....*...
gi 485191044   584 GVCGGGVR 591
Cdd:pfam12786  246 EECGLGPR 253
ComEC super family cl33995
DNA uptake channel protein ComEC, N-terminal domain [Intracellular trafficking, secretion, and ...
 891-1210 3.05e-03

DNA uptake channel protein ComEC, N-terminal domain [Intracellular trafficking, secretion, and vesicular transport];


The actual alignment was detected with superfamily member COG0658:

Pssm-ID: 440423 [Multi-domain]  Cd Length: 543  Bit Score: 43.25  E-value: 3.05e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044  891 NWLGFIAAFVVRP-TALALVAIVIAGCAGLPLRTHFPYRAFAVAFHLASVSLIESGVVFGLAWWAADWFARAGADAALSR 969
Cdd:COG0658   182 SLVSLLANLLAVPlVSLIVVPGLLLALLLLPLLPPLALLLLLLALLLLLLLLLLLLALLLLLLLLLLLLLLLLLLLLLLL 261

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044  970 AVLASPVVGWAIRLPSWPEVILGVVCVALYMRVVGQARLAALVAYKLSRGLAGAALVVLLVCRGPERGALGYQLCLPEWD 1049
Cdd:COG0658   262 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLGLLGGVGVGGGDGGLLLGGRGLLGVLGGLLLLLLLLLLL 341

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 1050 ASIDLDDVWWYAAAFFTFCCISISLLTRRGVVFKLRVYARWCRLYCWLQLVVGHTPAGDYFRWRGASSLLWLAAGVLWPA 1129
Cdd:COG0658   342 LLLLLLGLLLVLLLLLLLALLLGLLLLLLAALLGLAAALLLLLALLALLALLALALLLGALVGLLVVLLLALRSLLLGGG 421

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 1130 EVAVVSMIIVCFAAVLDVFDALLERLLTASPSLRPLVNLANTLHSCLSDPELAAFLRARWHRGELLYDHAGQVAASLRER 1209
Cdd:COG0658   422 LLLLLLLLLLLLALALLLLLLALLSLLLLLLLLLALLLLLLGSLLLSLLLLLALASSALASLSSSSSGAAVLAAAGAVAL 501


                  .
gi 485191044 1210 V 1210
Cdd:COG0658   502 L 502
 
Name Accession Description Interval E-value
Pegivirus_RdRp cd23203
RNA-dependent RNA polymerase (RdRp) in the genus Pegivirus, within the family Flaviviridae of ...
 2923-3398 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: 877.36  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 2923 WSGRAIAVDEPKRPPISRPLTAQLGAKADKVYITNPQDITKRIAKVTIDQTVAEVDQCFRDAYNCAIAKAKRVTQPGWTY 3002
Cdd:cd23203     1 WSGAPLGVGRPKPPPVTRPVGSHLRADATKVYVTDPDDVGERIEKVTIWRTPRVVDKFLRDAYNLALAKASATPSPGWTY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3003 DEAVAKLRPGSAKGHVAKVTVADMKSGAGRPFVEQVINDLAAGTLEHPFMLRPKAEVFPQTKETHKPPRLIVYPSLEFRV 3082
Cdd:cd23203    81 EEAVAKVRPGAAMGHGSKVTVADLKTPAGKKAVEECLNQIIAGGEEVPFTLTAKQEVFFQDKKTRKPPRLIVYPPLEFRV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3083 AEKMILGDPSLVAKAVMGASYGFQYPPHKRAEVLVNMWNSKRVPTAYTVDGTCFDSTVTPEDIAREGEIFAAASTNPELV 3162
Cdd:cd23203   161 AEKMILGDPGRVAKAVLGKAYGFQYTPNQRVKVLVDMWKSKRHPCAITVDATCFDSSITEEDVARETEIYAAASDDPELV 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3163 RRLHELYAGSPMMDPSGNIVGYRRCRASGTLTTSAGNSITCYLKVSAACRKAGLINPSYLIHGDDVVIVCEKTECDQSQA 3242
Cdd:cd23203   241 RALGKYYAEGPMVNPEGVPVGERRCRASGVLTTSSSNSITCYLKVKAACRKAGLKNPSFLIHGDDCLIICERPEEDPCDA 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3243 LGAALRSYGYECEPTRHADLTTAESCSSSLDTVRTVRGLKHVLRCDMRRGLGRTVAECGDPVGTAWGYTINYPTHPIVMY 3322
Cdd:cd23203   321 LKAALASYGYDCEPQYHASLDTAESCSAYLAECNAGGGRHYFLSTDMRRPLARASSEYGDPVASALGYILLYPWHPITRY 400

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 485191044 3323 VLLPLLLQTALNNGDGIHQPVTIDVRGNSVTLPLDTIGRAVRGLHGRDILAVTGHSATVLQETYDTLQFFGMRGLG 3398
Cdd:cd23203   401 VLLPHLLTLAFRGGGTPDDLVTCQVHGNSYKFPLKLLPRILVGLHGPDCLRVTADSTKTLMEAGKALQAFGMRGLA 476
RdRP_3 pfam00998
Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase ...
 2920-3413 5.05e-78

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: 268.72  E-value: 5.05e-78
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044  2920 SYVWSGRAIAVDEpKRPPISRPLTAQLGAKADKVYITNPQDITKRIAKVTIDQTVAEVDQCF-RDAYNCAIAKAKRVTQP 2998
Cdd:pfam00998    1 SYVWTGARPAKER-KILPITGPGSGLLFGVHNNSLVNLRRGLVERVFKVTFDRGGQLVPPKPyPGAFKELKYFASALVSK 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044  2999 GWtydEAVAKLRPGSAKGHV---AKVTVADMKSGAGRPfVEQVINDLAAGTLEHPFMLRPKAEVFPQtKETHKPPRLIVY 3075
Cdd:pfam00998   80 LG---EATPLTPEHFAASYTgrkRKIYVKALESLAVKP-VQRRDAILKTFVKAEKINITAKPDPAPR-VIQPRPPRYNVE 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044  3076 PSLEFRVAEKMILGDpslVAKAVMGASYGFQYPPHKRAEVLVNMWNSKRVPTAYTVDGTCFDSTVTPEDIAREGEIFAAA 3155
Cdd:pfam00998  155 PGRYLRPCEKMIYKA---IDKAFGGPTVLKGYTPEQRGEILLKKWDSFKKPVAIGLDASRFDQHVSVEALRFEHSIYLAA 231

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044  3156 STNPELVRRL--HELYAGSPMMDPSGNI-VGYRRCRASGTLTTSAGNSITCYLKVSAACRKAGlINPSYLIHGDDVVIVC 3232
Cdd:pfam00998  232 FLGPEELIRLltWQLYNGGPMYASDGQIkYGVRGCRMSGDMNTSLGNCLLMCLKVHAACKALG-IDARLLNNGDDCVVIC 310

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044  3233 EKTECDQ-SQALGAALRSYGYEC---EPTRHADLTtaESCSSSLDTVRTVRGLKH-VLRCDMRRGLGRTVAECGDPVGTA 3307
Cdd:pfam00998  311 ESADLDEvKEALTEAFARYGFTMkveEPVYELELI--EFCQSNPVFDGGKYGMVRnPLTSDSKDPLSRASWETATPAKSW 388

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044  3308 WGYTINYPTHPIVMYVLLPLLLQtALNNGDGIHQPVTIDVRGNSVtlplDTIGRAvrgLHGRDILAVtgHSATVLQETyd 3387
Cdd:pfam00998  389 LGAIGECGLSLWGGVPVLQHFYS-CLLRNGGLEKAVSFEMYGKVY----SDSGFR---LHGLGAGSR--HSYEPTEEA-- 456

                          490       500
                   ....*....|....*....|....*....
gi 485191044  3388 TLQF---FGMRGLGHWRRSRRKVKLRLLR 3413
Cdd:pfam00998  457 RVSFwlaFGITPDEQWALEAYYDRLKLLR 485
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 1476-1611 4.93e-24

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: 100.70  E-value: 4.93e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 1476 APTGSGKSTKFPAKLAQDGHN----VLVLNPSVVTTKAMGPYMKklvGKTPNIFAGtgasAMQIKTGSK--ITYCTYGRF 1549
Cdd:cd17931     8 LHPGAGKTTRVLPQIIREAIKkrlrTLVLAPTRVVAAEMYEALR---GLPIRYRTG----AVKEEHGGNeiVDYMCHGTF 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 485191044 1550 LvnpQGFLDQKAV-----VVCDECHATDGTSILGIGVARALAEkAGVRLLVFATATPPGTQFTPHAS 1611
Cdd:cd17931    81 T---CRLLSPKRVpnynlIIMDEAHFTDPASIAARGYIHTRVE-MGEAAVIFMTATPPGTVTPFPQS 143
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 1612-1744 2.22e-20

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: 90.01  E-value: 2.22e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 1612 ITEETLDGDGDIPFYGVSLkaSTYLKGRHVIFCHSKAECVRVAESLAGAGVKAVTYWRG---TRHDVLTDDADLTVVATD 1688
Cdd:cd18806     1 IEDVALEIPGRIWFYGKAW--ITIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKlddTEYPKIKTIDWDFVVTTD 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 485191044 1689 AISTGYTGNFATCTDCCSVVEETVDVDLNptFTINL-ITKAADAALRMQRRGRCGRG 1744
Cdd:cd18806    79 ISEMGANFDADRVIDCRTCVKPTILFSGD--FRVILtGPVPQTAASAAQRRGRTGRN 133
HCV_NS4b pfam01001
Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. ...
 2052-2203 2.23e-18

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


Pssm-ID: 110032  Cd Length: 192  Bit Score: 85.89  E-value: 2.23e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044  2052 HITALLAGGMAIASASSSPVFATLAALLSGASVTLPSKVAWALTLAGSAAAGLCGGARAGLA-VGAGFyVGSHLAGLSVV 2130
Cdd:pfam01001   40 NFRSGIQYLAGLYTLPRNPPLAVLASFLAGMTSPLPTHVRLALALLGGWGATQLGTPSGGLAfVGAGF-AGAAVGSSWLG 118

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 485191044  2131 DTAINLAAGYEACVSTCAFVLDLFDGKATMAHFLPCLAGVLA-PGAACAGVAFALILRASATGDSSTWMNRLLS 2203
Cdd:pfam01001  119 RVLVDVLGGYEAAVNAASLTFKIMSGELPTAEDLWNLLPCLLsPGASVVGVALAALLRSHKGEGAVQWMNRLLT 192
DEXDc smart00487
DEAD-like helicases superfamily;
1467-1603 2.73e-12

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 68.67  E-value: 2.73e-12
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044   1467 SGYKEVPYFAPTGSGKSTKFPAKLAQDGHN-----VLVLNPSVVTTKAMGPYMKKLVGKTPNIFAG--TGAS----AMQI 1535
Cdd:smart00487   22 SGLRDVILAAPTGSGKTLAALLPALEALKRgkggrVLVLVPTRELAEQWAEELKKLGPSLGLKVVGlyGGDSkreqLRKL 101

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 485191044   1536 KTG-SKITYCTYGRF---LVNPQGFLDQKAVVVCDECHATDGTSILGIgVARALAEKAGVRLLVFATATPPG 1603
Cdd:smart00487  102 ESGkTDILVTTPGRLldlLENDKLSLSNVDLVILDEAHRLLDGGFGDQ-LEKLLKLLPKNVQLLLLSATPPE 172
GBV-C_env pfam12786
GB virus C genotype envelope; This the envelope protein from the ssRNA GB virus genotype C.
 443-591 1.88e-08

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


Pssm-ID: 193262  Cd Length: 413  Bit Score: 59.81  E-value: 1.88e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044   443 NGTT-CDCPFGV----------------IIRHFNNDtdpyldIPAICPESFpYTNFSWLCGWGSWWWVAHGVERPYSHPY 505
Cdd:pfam12786  111 NGTVvCDCPFGPmvwlpalcsglawrdgDREGTVND------LPLVCPREV-LGTVSVMCVWGSAYWFWRTGDWVDLWSE 183

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044   506 MPPSpfsAICYILTNRTvlynatiypntyaGVGRYPNytASVLGP--APVTSCMLDRRPAMCGDCFGGCFYRDGSHSRPF 583
Cdd:pfam12786  184 LPGS---ALCTFAALGT-------------SDRDHPD--VDVLSPsgIPCASCVVDRRPASCGSCVRDCWETTGPKRLPF 245


                   ....*...
gi 485191044   584 GVCGGGVR 591
Cdd:pfam12786  246 EECGLGPR 253
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
1479-1605 6.08e-05

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 45.79  E-value: 6.08e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044  1479 GSGKSTKFPAKLAQD----GHNVLVLNPSVVTTKAMGPYMKKLvgktpNIFAGTGASAMQIKTGSKIT---YCTYGRFLV 1551
Cdd:pfam07652   12 GAGKTRKVLPELVREcidrRLRTLVLAPTRVVLAEMEEALRGL-----PIRYHTPAVSSEHTGREIVDvmcHATFTQRLL 86

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 485191044  1552 NPQGFLDQkAVVVCDECHATDGTSILGIGVARALAEKaGVRLLVFATATPPGTQ 1605
Cdd:pfam07652   87 SPVRVPNY-EVIIMDEAHFTDPASIAARGYISTLVEL-GEAAAIFMTATPPGTS 138
ComEC COG0658
DNA uptake channel protein ComEC, N-terminal domain [Intracellular trafficking, secretion, and ...
 891-1210 3.05e-03

DNA uptake channel protein ComEC, N-terminal domain [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 440423 [Multi-domain]  Cd Length: 543  Bit Score: 43.25  E-value: 3.05e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044  891 NWLGFIAAFVVRP-TALALVAIVIAGCAGLPLRTHFPYRAFAVAFHLASVSLIESGVVFGLAWWAADWFARAGADAALSR 969
Cdd:COG0658   182 SLVSLLANLLAVPlVSLIVVPGLLLALLLLPLLPPLALLLLLLALLLLLLLLLLLLALLLLLLLLLLLLLLLLLLLLLLL 261

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044  970 AVLASPVVGWAIRLPSWPEVILGVVCVALYMRVVGQARLAALVAYKLSRGLAGAALVVLLVCRGPERGALGYQLCLPEWD 1049
Cdd:COG0658   262 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLGLLGGVGVGGGDGGLLLGGRGLLGVLGGLLLLLLLLLLL 341

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 1050 ASIDLDDVWWYAAAFFTFCCISISLLTRRGVVFKLRVYARWCRLYCWLQLVVGHTPAGDYFRWRGASSLLWLAAGVLWPA 1129
Cdd:COG0658   342 LLLLLLGLLLVLLLLLLLALLLGLLLLLLAALLGLAAALLLLLALLALLALLALALLLGALVGLLVVLLLALRSLLLGGG 421

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 1130 EVAVVSMIIVCFAAVLDVFDALLERLLTASPSLRPLVNLANTLHSCLSDPELAAFLRARWHRGELLYDHAGQVAASLRER 1209
Cdd:COG0658   422 LLLLLLLLLLLLALALLLLLLALLSLLLLLLLLLALLLLLLGSLLLSLLLLLALASSALASLSSSSSGAAVLAAAGAVAL 501


                  .
gi 485191044 1210 V 1210
Cdd:COG0658   502 L 502
 
Name Accession Description Interval E-value
Pegivirus_RdRp cd23203
RNA-dependent RNA polymerase (RdRp) in the genus Pegivirus, within the family Flaviviridae of ...
 2923-3398 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: 877.36  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 2923 WSGRAIAVDEPKRPPISRPLTAQLGAKADKVYITNPQDITKRIAKVTIDQTVAEVDQCFRDAYNCAIAKAKRVTQPGWTY 3002
Cdd:cd23203     1 WSGAPLGVGRPKPPPVTRPVGSHLRADATKVYVTDPDDVGERIEKVTIWRTPRVVDKFLRDAYNLALAKASATPSPGWTY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3003 DEAVAKLRPGSAKGHVAKVTVADMKSGAGRPFVEQVINDLAAGTLEHPFMLRPKAEVFPQTKETHKPPRLIVYPSLEFRV 3082
Cdd:cd23203    81 EEAVAKVRPGAAMGHGSKVTVADLKTPAGKKAVEECLNQIIAGGEEVPFTLTAKQEVFFQDKKTRKPPRLIVYPPLEFRV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3083 AEKMILGDPSLVAKAVMGASYGFQYPPHKRAEVLVNMWNSKRVPTAYTVDGTCFDSTVTPEDIAREGEIFAAASTNPELV 3162
Cdd:cd23203   161 AEKMILGDPGRVAKAVLGKAYGFQYTPNQRVKVLVDMWKSKRHPCAITVDATCFDSSITEEDVARETEIYAAASDDPELV 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3163 RRLHELYAGSPMMDPSGNIVGYRRCRASGTLTTSAGNSITCYLKVSAACRKAGLINPSYLIHGDDVVIVCEKTECDQSQA 3242
Cdd:cd23203   241 RALGKYYAEGPMVNPEGVPVGERRCRASGVLTTSSSNSITCYLKVKAACRKAGLKNPSFLIHGDDCLIICERPEEDPCDA 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3243 LGAALRSYGYECEPTRHADLTTAESCSSSLDTVRTVRGLKHVLRCDMRRGLGRTVAECGDPVGTAWGYTINYPTHPIVMY 3322
Cdd:cd23203   321 LKAALASYGYDCEPQYHASLDTAESCSAYLAECNAGGGRHYFLSTDMRRPLARASSEYGDPVASALGYILLYPWHPITRY 400

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 485191044 3323 VLLPLLLQTALNNGDGIHQPVTIDVRGNSVTLPLDTIGRAVRGLHGRDILAVTGHSATVLQETYDTLQFFGMRGLG 3398
Cdd:cd23203   401 VLLPHLLTLAFRGGGTPDDLVTCQVHGNSYKFPLKLLPRILVGLHGPDCLRVTADSTKTLMEAGKALQAFGMRGLA 476
Hepacivirus_RdRp cd23202
RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ...
 2932-3427 1.91e-117

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: 383.81  E-value: 1.91e-117
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 2932 EPKRPPISrPLTAQLGAKADKVYITNPQDITKRIAKVTIDQtVAEVDQCFRDAYNCAIAKAKRVTQPGWTYDEAVAKLRP 3011
Cdd:cd23202     4 EEEKLPIS-PLSNSLLRHHNLVYSTTSRSASERQKKVTFDR-LQVLDPHYDDVLKEAKARASGVKARLLSVEEACSLTPP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3012 GSAKgHVAKVTVADMKSGAGRPF--VEQVINDLAAGTLEH-PFMLRPKAEVF---PQtKETHKPPRLIVYPSLEFRVAEK 3085
Cdd:cd23202    82 HSAR-SKFGYGAKDVRSLSRKAVnhINSVWEDLLEDSETPiPTTIMAKNEVFcvtPE-KGGRKPARLIVYPDLGVRVCEK 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3086 MILGD--PSLVaKAVMGASYGFQYPPHKRAEVLVNMWNSKRVPTAYTVDGTCFDSTVTPEDIAREGEIFAAASTNPE--- 3160
Cdd:cd23202   160 MALYDvaPKLP-KAVMGEAYGFQYSPAQRVEFLLKMWRSKKTPMGFSYDTRCFDSTVTERDIRTEESIYQCCDLDPEark 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3161 LVRRLHE-LYAGSPMMDPSGNIVGYRRCRASGTLTTSAGNSITCYLKVSAACRKAGLINPSYLIHGDDVVIVCEK--TEC 3237
Cdd:cd23202   239 AIRSLTErLYVGGPMTNSKGQSCGYRRCRASGVFTTSSGNTLTCYLKASAACRAAGLKDPTMLVCGDDLVVIAESagVEE 318

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3238 DQSqALGA---ALRSYGyeC----EPTRHADLTTAESCSSSLDTVRTVRG-LKHVLRCDMRRGLGRTVAECGD--PVGTA 3307
Cdd:cd23202   319 DAA-ALRAfteAMTRYS--AppgdPPQPEYDLELITSCSSNVSVAHDATGkRYYYLTRDPTTPLARAAWETARhtPVNSW 395

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3308 WGYTI-NYPThpivMYVLLPLLLQ--TALNNGDGIHQPVTIDVRGNSVTLPLDTIGRAVRGLHGRDILAVTGHSATVLQE 3384
Cdd:cd23202   396 LGNIImYAPT----LWVRMVLMTHffSILLAQEQLEKALDFEMYGNTYSIPPLDLPAIIQRLHGLSAFSLHGYSPRELNR 471

                         490       500       510       520
                  ....*....|....*....|....*....|....*....|...
gi 485191044 3385 TYDTLQFFGMRGLGHWRRSRRKVKLRLLRAGKAWAKLARELLW 3427
Cdd:cd23202   472 VAAALRKLGVPPLRAWRHRARAVRAKLIAQGGKAAICGKYLFN 514
ps-ssRNAv_Flaviviridae_RdRp cd23178
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of ...
 3050-3317 1.09e-103

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: 334.49  E-value: 1.09e-103
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3050 PFMLRPKAEVFPQTKE--THKPPRLIVYPSLEFRVAEKMILGDPSLVAKAV-MGASYGFQYPPHKRAEVLVNMWNSKRVP 3126
Cdd:cd23178     2 PTTIMPKNEVFCVEPGkgGRKPPRLIVYPDLGVRVAEKMALYDPVEVLPQVvGGSYYGFQYSPNQRVEILRKAWKSKKGP 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3127 TAYTVDGTCFDSTVTPEDIAREGEIFAAAST---NPELVRRLHELYAGSPMMDPSGNIVGYRRCRASGTLTTSAGNSITC 3203
Cdd:cd23178    82 MAYSYDTRCFDSTVTEDDIQVEEEIYQACSLkeaRQAIVSITERLYVEGPMVNSDGQICGRRRCRASGVLTTSAGNT*TC 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3204 YLKVSAACRKAGLINPSYLIHGDDVVIVCEKTECDQSQALGAALRSYGYECEPTRHA------DLTTAESCSSSLDTVRT 3277
Cdd:cd23178   162 YLK*LAACREAGIRLPTMLVCGDDCVVICESDGTQEDAALLAAFTEALTRYGKPPKDppqpeyDLELIESCSHTVSEVRM 241

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 485191044 3278 VRGLKHVLRC-DMRRGLGRTVAECGD--PVGTAWGYTINYPTH 3317
Cdd:cd23178   242 KDGRRLYYLTrDPTTPLARAAWETGRhePINSWLGYIIMYALT 284
RdRP_3 pfam00998
Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase ...
 2920-3413 5.05e-78

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: 268.72  E-value: 5.05e-78
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044  2920 SYVWSGRAIAVDEpKRPPISRPLTAQLGAKADKVYITNPQDITKRIAKVTIDQTVAEVDQCF-RDAYNCAIAKAKRVTQP 2998
Cdd:pfam00998    1 SYVWTGARPAKER-KILPITGPGSGLLFGVHNNSLVNLRRGLVERVFKVTFDRGGQLVPPKPyPGAFKELKYFASALVSK 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044  2999 GWtydEAVAKLRPGSAKGHV---AKVTVADMKSGAGRPfVEQVINDLAAGTLEHPFMLRPKAEVFPQtKETHKPPRLIVY 3075
Cdd:pfam00998   80 LG---EATPLTPEHFAASYTgrkRKIYVKALESLAVKP-VQRRDAILKTFVKAEKINITAKPDPAPR-VIQPRPPRYNVE 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044  3076 PSLEFRVAEKMILGDpslVAKAVMGASYGFQYPPHKRAEVLVNMWNSKRVPTAYTVDGTCFDSTVTPEDIAREGEIFAAA 3155
Cdd:pfam00998  155 PGRYLRPCEKMIYKA---IDKAFGGPTVLKGYTPEQRGEILLKKWDSFKKPVAIGLDASRFDQHVSVEALRFEHSIYLAA 231

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044  3156 STNPELVRRL--HELYAGSPMMDPSGNI-VGYRRCRASGTLTTSAGNSITCYLKVSAACRKAGlINPSYLIHGDDVVIVC 3232
Cdd:pfam00998  232 FLGPEELIRLltWQLYNGGPMYASDGQIkYGVRGCRMSGDMNTSLGNCLLMCLKVHAACKALG-IDARLLNNGDDCVVIC 310

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044  3233 EKTECDQ-SQALGAALRSYGYEC---EPTRHADLTtaESCSSSLDTVRTVRGLKH-VLRCDMRRGLGRTVAECGDPVGTA 3307
Cdd:pfam00998  311 ESADLDEvKEALTEAFARYGFTMkveEPVYELELI--EFCQSNPVFDGGKYGMVRnPLTSDSKDPLSRASWETATPAKSW 388

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044  3308 WGYTINYPTHPIVMYVLLPLLLQtALNNGDGIHQPVTIDVRGNSVtlplDTIGRAvrgLHGRDILAVtgHSATVLQETyd 3387
Cdd:pfam00998  389 LGAIGECGLSLWGGVPVLQHFYS-CLLRNGGLEKAVSFEMYGKVY----SDSGFR---LHGLGAGSR--HSYEPTEEA-- 456

                          490       500
                   ....*....|....*....|....*....
gi 485191044  3388 TLQF---FGMRGLGHWRRSRRKVKLRLLR 3413
Cdd:pfam00998  457 RVSFwlaFGITPDEQWALEAYYDRLKLLR 485
RNA_dep_RNAP cd01699
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
 3035-3261 2.05e-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: 152.44  E-value: 2.05e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3035 VEQVInDLAAGTLEHPFMLRPKAEVFPQTKETHKPPRLIVYPSLEFRVAEKMILGDPSLVAKAVMGAS-YGFQYPPH-KR 3112
Cdd:cd01699     5 VESLE-DLPLIRPDLVFTTFLKDELRPLEKVEAGKTRLIQPRPLDYNIALRMYLGPFEAKLMKNRGGLpIAVGINPYsRD 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3113 AEVLVNMWNSKrVPTAYTVDGTCFDSTVTPEDIAREGEIFAAASTNPELVRR--LHELYAGSPMMDPSGNIVGYRRCRAS 3190
Cdd:cd01699    84 WTILANKLRSF-SPVAIALDYSRFDSSLSPQLLEAEHSIYNALYDDDDELERrnLLRSLTNNSLHIGFNEVYKVRGGRPS 162

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 485191044 3191 GTLTTSAGNSITCYLKVSAACRKAG----LINPSYLIHGDDVVIVCEKTECDQSQ-ALGAALRSYGYECEPTRHAD 3261
Cdd:cd01699   163 GDPLTSIGNSIINCILVRYAFRKLGgksfFKNVRLLNYGDDCLLSVEKADDKFNLeTLAEWLKEYGLTMTDEDKVE 238
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 1476-1611 4.93e-24

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: 100.70  E-value: 4.93e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 1476 APTGSGKSTKFPAKLAQDGHN----VLVLNPSVVTTKAMGPYMKklvGKTPNIFAGtgasAMQIKTGSK--ITYCTYGRF 1549
Cdd:cd17931     8 LHPGAGKTTRVLPQIIREAIKkrlrTLVLAPTRVVAAEMYEALR---GLPIRYRTG----AVKEEHGGNeiVDYMCHGTF 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 485191044 1550 LvnpQGFLDQKAV-----VVCDECHATDGTSILGIGVARALAEkAGVRLLVFATATPPGTQFTPHAS 1611
Cdd:cd17931    81 T---CRLLSPKRVpnynlIIMDEAHFTDPASIAARGYIHTRVE-MGEAAVIFMTATPPGTVTPFPQS 143
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 1612-1744 2.22e-20

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: 90.01  E-value: 2.22e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 1612 ITEETLDGDGDIPFYGVSLkaSTYLKGRHVIFCHSKAECVRVAESLAGAGVKAVTYWRG---TRHDVLTDDADLTVVATD 1688
Cdd:cd18806     1 IEDVALEIPGRIWFYGKAW--ITIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKlddTEYPKIKTIDWDFVVTTD 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 485191044 1689 AISTGYTGNFATCTDCCSVVEETVDVDLNptFTINL-ITKAADAALRMQRRGRCGRG 1744
Cdd:cd18806    79 ISEMGANFDADRVIDCRTCVKPTILFSGD--FRVILtGPVPQTAASAAQRRGRTGRN 133
HCV_NS4b pfam01001
Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. ...
 2052-2203 2.23e-18

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


Pssm-ID: 110032  Cd Length: 192  Bit Score: 85.89  E-value: 2.23e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044  2052 HITALLAGGMAIASASSSPVFATLAALLSGASVTLPSKVAWALTLAGSAAAGLCGGARAGLA-VGAGFyVGSHLAGLSVV 2130
Cdd:pfam01001   40 NFRSGIQYLAGLYTLPRNPPLAVLASFLAGMTSPLPTHVRLALALLGGWGATQLGTPSGGLAfVGAGF-AGAAVGSSWLG 118

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 485191044  2131 DTAINLAAGYEACVSTCAFVLDLFDGKATMAHFLPCLAGVLA-PGAACAGVAFALILRASATGDSSTWMNRLLS 2203
Cdd:pfam01001  119 RVLVDVLGGYEAAVNAASLTFKIMSGELPTAEDLWNLLPCLLsPGASVVGVALAALLRSHKGEGAVQWMNRLLT 192
DEXDc smart00487
DEAD-like helicases superfamily;
1467-1603 2.73e-12

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 68.67  E-value: 2.73e-12
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044   1467 SGYKEVPYFAPTGSGKSTKFPAKLAQDGHN-----VLVLNPSVVTTKAMGPYMKKLVGKTPNIFAG--TGAS----AMQI 1535
Cdd:smart00487   22 SGLRDVILAAPTGSGKTLAALLPALEALKRgkggrVLVLVPTRELAEQWAEELKKLGPSLGLKVVGlyGGDSkreqLRKL 101

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 485191044   1536 KTG-SKITYCTYGRF---LVNPQGFLDQKAVVVCDECHATDGTSILGIgVARALAEKAGVRLLVFATATPPG 1603
Cdd:smart00487  102 ESGkTDILVTTPGRLldlLENDKLSLSNVDLVILDEAHRLLDGGFGDQ-LEKLLKLLPKNVQLLLLSATPPE 172
ps_ssRNAv_Tolivirales_RdRp cd23179
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Toliovirales of ...
 3056-3234 7.41e-12

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: 67.93  E-value: 7.41e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3056 KAEVFPQTKEtHKPPRLIVYPSLEFRVA--------EKMILGDPS-------LVAKAvmgasygfqYPPHKRAEVLVNMW 3120
Cdd:cd23179     8 KAEKYNPLAK-NKKPRMIQPRSPRYNLElarylkpiEHALYGALDagrggtrVVAKG---------LNPRQRANLIRRKW 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3121 NSKRVPTAYTVDGTCFDSTVTPEDIAREGEIFAAA-STNPELVRRLhelyagSPMMDPSG---NIVGYRR--CRASGTLT 3194
Cdd:cd23179    78 DEFDDPVVFSLDASRFDAHVSVELLRLEHSVYLACyPGDPELRKLL------KWQLVNKGrtsNGVKYKTrgGRMSGDMN 151

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 485191044 3195 TSAGNSITCYLKVSAACRKAGlINPSYLIHGDDVVIVCEK 3234
Cdd:cd23179   152 TGLGNCLIMLAMVYAVLRELG-IKYDLLVDGDDALVFVER 190
GBV-C_env pfam12786
GB virus C genotype envelope; This the envelope protein from the ssRNA GB virus genotype C.
 443-591 1.88e-08

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


Pssm-ID: 193262  Cd Length: 413  Bit Score: 59.81  E-value: 1.88e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044   443 NGTT-CDCPFGV----------------IIRHFNNDtdpyldIPAICPESFpYTNFSWLCGWGSWWWVAHGVERPYSHPY 505
Cdd:pfam12786  111 NGTVvCDCPFGPmvwlpalcsglawrdgDREGTVND------LPLVCPREV-LGTVSVMCVWGSAYWFWRTGDWVDLWSE 183

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044   506 MPPSpfsAICYILTNRTvlynatiypntyaGVGRYPNytASVLGP--APVTSCMLDRRPAMCGDCFGGCFYRDGSHSRPF 583
Cdd:pfam12786  184 LPGS---ALCTFAALGT-------------SDRDHPD--VDVLSPsgIPCASCVVDRRPASCGSCVRDCWETTGPKRLPF 245


                   ....*...
gi 485191044   584 GVCGGGVR 591
Cdd:pfam12786  246 EECGLGPR 253
Alphanecrovirus_RdRp cd23237
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Alphanecrovirus of ...
 3043-3262 1.96e-08

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: 59.66  E-value: 1.96e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3043 AAGTLEH-PFMLRP-------KAEVFPQTKETHKPPRLIVYPSLEFRVAEKMILGDPSLVAKAVMGASYG----FQ-YPP 3109
Cdd:cd23237    64 AVDSLSHqPLSLRDaklktfvKAEKLNLSKKPDPAPRVIQPRSPRYNVCLGRYLRHYEHHAFKTIAKCFGeitvFKgFTL 143

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3110 HKRAEVLVNMWNSKRVPTAYTVDGTCFDSTVTPEDIAREGEIFAAASTN-PELVRRLHELYAGSPMMDPSGNIVGYRR-- 3186
Cdd:cd23237   144 EQQGEIMRSKWKKYVNPVAVGLDASRFDQHVSVEALQYEHEFYLRDYPNdKQLKWLLKQQLCNIGTAFASDGIIKYKKeg 223

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 485191044 3187 CRASGTLTTSAGNSITCYLKVSAACRKAGlINPSYLIHGDDVVIVCEKTECDQ-SQALGAALRSYGYECEPTRHADL 3262
Cdd:cd23237   224 CRMSGDMNTSLGNCILMCAMVYGLKEHLG-INLSLANNGDDCVIVCEKADLKKlTSSIEPYFKQFGFKMEVEKPVDI 299
Regressovirinae_RdRp cd23235
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Regressovirinae ...
 3009-3239 1.30e-07

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Regressovirinae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the subfamily Regressovirinae, family Tombusviridae, order Tolivirales. Dianthovirus is a genus of plant viruses within this subfamily. All the genera in the family Tombusviridae have monopartite (+)ssRNA genomes, except the dianthoviruses which have bipartite (+)ssRNA genomes. The dianthoviruses are distributed worldwide. The genus Dianthovirus is composed of three viruses: Carnation ringspot virus, Red clover necrotic mosaic virus, and Sweet clover necrotic mosaic virus. The amino acid (aa) sequence of dianthovirus RdRp has higher homology with that of the luteoviruses, while the amino acid sequence of dianthovirus coat protein (CP) has high homology with those of the tombusviruses and aureusviruses that belong to the subfamily Procedovirinae. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438085 [Multi-domain]  Cd Length: 472  Bit Score: 57.24  E-value: 1.30e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3009 LRPGSAKGHVAKVTVADM---KSGAGRPFVEQvindlAAGTLEH-PFMLR-PKAEVFPQTK----ETHKP-PRLIVYPSL 3078
Cdd:cd23235    41 LKKLYSKGPVLKSSIDDVvacYSSEKRKLYQK-----AAATLSHkPLHWRdSKVRAFIKVEklecDKKDPvPRTIQPRSK 115

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3079 EF--------RVAEKMILGDPSLV--AKAVMGAsygfqYPPHKRAEVLVNMWNSKRVPTAYTVDGTCFDSTVTPEDIARE 3148
Cdd:cd23235   116 RYnlcigqylRLNEKRMLDAIDAVfgEKTVLSG-----LDNKAQGRAIAKKWSKYESPIGIGLDASRFDQHCSKDALKFE 190

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3149 GEIFAAASTNPELVRRL---HELYAGSPMMdPSGNIVGYRR--CRASGTLTTSAGNSITCYLKVSAACRKAGlINPSYLI 3223
Cdd:cd23235   191 HSFYRECFPDDKTLEDLldwQLENEGSALM-PTGELVKYRTkgCRMSGDINTGLGNKILMCSMVHAYLKEVG-VNASLAN 268

                         250
                  ....*....|....*.
gi 485191044 3224 HGDDVVIVCEKTECDQ 3239
Cdd:cd23235   269 NGDDCVLFCEKGDFNR 284
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 1476-1600 5.43e-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: 45.86  E-value: 5.43e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 1476 APTGSGKSTKFPAKLAQD----GHNVLVLNPSVVTTKAMGPYMKKLVGKTPNIFAGTGASAMQIKTG-----SKITYCTY 1546
Cdd:cd00046     8 APTGSGKTLAALLAALLLllkkGKKVLVLVPTKALALQTAERLRELFGPGIRVAVLVGGSSAEEREKnklgdADIIIATP 87

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 485191044 1547 GRF----LVNPQGFLDQKAVVVCDECHATDGTS----ILGIGVARALAEKAGVrllVFATAT 1600
Cdd:cd00046    88 DMLlnllLREDRLFLKDLKLIIVDEAHALLIDSrgalILDLAVRKAGLKNAQV---ILLSAT 146
Tombusvirus-like_RdRp cd23236
RNA-dependent RNA polymerase (RdRp) in the genus Tombusvirus of positive-sense single-stranded ...
 3107-3242 5.83e-05

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


Pssm-ID: 438086 [Multi-domain]  Cd Length: 474  Bit Score: 48.86  E-value: 5.83e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3107 YPPHKRAEVLVNMWNSKRVPTAYTVDGTCFDSTVTPEDIAREGEIFAAASTNPELVRRLHE--LYAGSPMMDPSGNIVgY 3184
Cdd:cd23236   181 YTADEVGAIFRDKWDRFDKPVAIGLDASRFDQHCSVEALQFEHSFYRAMYPGNKLLSKLLEwqLHNKGKGYVPDGTIT-Y 259

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3185 RR--CRASGTLTTSAGNSITCYLKVSAACRKAGLINPSYLIHGDDVVIVCEKTECDQSQA 3242
Cdd:cd23236   260 RKegCRMSGDINTSLGNYLLMCAMVYGYMRHLGINEFSLANCGDDCVLIVERRNLKQVQG 319
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
1479-1605 6.08e-05

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 45.79  E-value: 6.08e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044  1479 GSGKSTKFPAKLAQD----GHNVLVLNPSVVTTKAMGPYMKKLvgktpNIFAGTGASAMQIKTGSKIT---YCTYGRFLV 1551
Cdd:pfam07652   12 GAGKTRKVLPELVREcidrRLRTLVLAPTRVVLAEMEEALRGL-----PIRYHTPAVSSEHTGREIVDvmcHATFTQRLL 86

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 485191044  1552 NPQGFLDQkAVVVCDECHATDGTSILGIGVARALAEKaGVRLLVFATATPPGTQ 1605
Cdd:pfam07652   87 SPVRVPNY-EVIIMDEAHFTDPASIAARGYISTLVEL-GEAAAIFMTATPPGTS 138
Carmotetraviridae_RdRp cd23205
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Carmotetraviridae ...
 3111-3247 8.48e-05

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: 47.32  E-value: 8.48e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3111 KRAEVLVNMWNSKRVPTAYTVDGTCFDSTVTPEDIAREGEIFAAASTNPELVRRLHELyagspMMDPSGNIVGYRRC--- 3187
Cdd:cd23205    67 QRANLLQRMWHLYERPVSISFDLSRWDMHVQVPLLKRVLEIYSQHVTCPLLLDMCQNL-----LKNVCYTNKGIRYHvdg 141

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 485191044 3188 -RASGTLTTSAGNSItcylkvsAACRKAGLINPSYLIHGDDVVIVCEKTECDQSQALGAAL 3247
Cdd:cd23205   142 gIMSGDMTTGLGNCI-------AVLVIVMSFRLSILDDGDDHVIICEKSHTWICERVLPLW 195
Luteovirus_RdRp cd23233
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Luteovirus of ...
 3107-3270 9.42e-05

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: 47.81  E-value: 9.42e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3107 YPPHKRAEVLVNMWNSKRVPTAYTVDGTCFDSTVTPEDIAREGEIFAAASTNPELVRRLHELYAGSPMMDPSGNIVGY-- 3184
Cdd:cd23233    91 YDNFKVGRIIAKKWQKFANPVAIGVDASRFDQHVSEQALKWEHSIYNGIFGDPELAELLEWQLDNKIKLFVEDKMLRFkv 170

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3185 RRCRASGTLTTSAGNS-ITC-----YLKVSAAcrKAGLINpsyliHGDDVVIVCEKTECDQSQALGAALRSYGYE--CEP 3256
Cdd:cd23233   171 KGHRMSGDINTSMGNKlIMCgmmhaYFKELGV--EAELCN-----NGDDCVIICERKDEKKFSGMYDWFLDYGFNmvTEK 243

                         170
                  ....*....|....
gi 485191044 3257 TRHaDLTTAESCSS 3270
Cdd:cd23233   244 PVY-ELEKLEFCQS 256
Betacarmovirus_RdRp cd23240
RNA-dependent RNA polymerase (RdRp) in the genus Betacarmovirus of positive-sense ...
 3115-3271 2.48e-04

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: 46.76  E-value: 2.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3115 VLVNMWNSKRVPTAYTVDGTCFDSTVTPEDIAREGEIFAAASTNPELVRRLHELYAGSPMMDPSGNIVGYR--RCRASGT 3192
Cdd:cd23240   172 IMHNHWSQFQKPCAVGFDMKRFDQHVSVDALRFEHSVYNRSFCSPELARLLEWQLLNSGVGHASDGFIRYKvdGCRMSGD 251

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3193 LTTSAGN-----SITCYLKVSAACRkagLINpsyliHGDDVVIVCEKTECDQSQALGAALRSYGYEC---EPTRhaDLTT 3264
Cdd:cd23240   252 VNTALGNcllacLITKYLLKGIRCR---LIN-----NGDDCVLFFEAPDLAAVTERLAHWLDFGFQCvveEPVY--ELEK 321


                  ....*..
gi 485191044 3265 AESCSSS 3271
Cdd:cd23240   322 VEFCQMK 328
Parechovirus_RdRp cd23217
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Parechovirus of ...
 3025-3253 4.75e-04

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


Pssm-ID: 438067  Cd Length: 371  Bit Score: 45.63  E-value: 4.75e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3025 DMKSGAGRPFVEQVINDLAAGTLEhPFMLRPKAEVFPQTK----ETHKPPRLIVYPSL--EFRVAEKMILG--------- 3089
Cdd:cd23217    12 DLSTSPGYKYVKSGYKKRDLLSLE-PFSVSPQLEKDVKDKlhavYKGNQPTTIFNACLkdELRKLDKIAQGktrcieacs 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3090 -DPSLVAKAVMGASYG--FQYPPHKRA-EVLVNMWN------SKRVPTAYTVDGTCFDSTVTPEDIAREGEIFAAASTNP 3159
Cdd:cd23217    91 iDYVIAYRVVMSSLYEaiYQTPCQELGlAVGMNPWTdwdfmiNALNPYNYGLDYSSYDGSLSEMLMWEAVEVLAYCHESP 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3160 ELVRRLHELYAGSP--MMDPSGNIVGyrrCRASGTLTTSAGNSItCYLKVsaaCR-KAGLINPSY----LIHGDDVVIVC 3232
Cdd:cd23217   171 DLVMQLHKPVINSDhvVMDERWLVHG---GMPSGSPCTTVLNSI-CNLLV---CIyLAYLQSPGIeclpIVYGDDVIFSV 243

                         250       260
                  ....*....|....*....|.
gi 485191044 3233 EKtECDQSQALGAALRSYGYE 3253
Cdd:cd23217   244 SS-EIDPEYLVSSAADSFGME 263
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
 3025-3252 6.22e-04

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


Pssm-ID: 425815  Cd Length: 450  Bit Score: 45.48  E-value: 6.22e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044  3025 DMKSGAGRPFVEQ------VINDLAAGTLEHPFMLRPKAEVFPQTKETHKPPRLIVYPSLEFRVAEK-------MILGDP 3091
Cdd:pfam00680   97 NWDTSAGYPYVGLggkkgdLIEHLKDGTEARELAERLAADWEVLQNGTPLKLVYQTCLKDELRPLEKvekgktrLVWGEP 176

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044  3092 ---SLVAKAVMG-ASYGFQYPPHKR-AEVLVNM----W---------NSKRVptaYTVDGTCFDSTVTPEDIAREGEI-- 3151
Cdd:pfam00680  177 veyLLLERAFFDpFNQAFMLNNGFHpIQVGINPfdrgWprllrrlarFGDYV---YELDYSGFDSSVPPWLIRFAFEIlr 253

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044  3152 -FAAASTNPELVRRLHELYAGSPMMDPSGNIVGYRRCRASGTLTTSAGNSITCYLKVSAACRKAgLINPSY--------- 3221
Cdd:pfam00680  254 eLLGFPSNVKEWRAILELLIYTPIALPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYALLKS-LENDGPrvcnldkyf 332

                          250       260       270
                   ....*....|....*....|....*....|...
gi 485191044  3222 --LIHGDDVVIVCEKTECDQSQALGAALRSYGY 3252
Cdd:pfam00680  333 dfFTYGDDSLVAVSPDFDPVLDRLSPHLKELGL 365
Caliciviridae_RdRp cd23192
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Caliciviridae of ...
 3117-3268 6.36e-04

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Caliciviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Caliciviridae, order Picornavirales. Member viruses have a viral (+)ssRNA genome, which is not segmented. The family Caliciviridae, includes eleven genera: seven genera of which infect mammals (Lagovirus, Norovirus, Nebovirus, Recovirus, Sapovirus, Valovirus, and Vesivirus), two genera of which infect birds (Bavovirus, Nacovirus), and two genera of which infect fish (Minovirus and Salovirus). Each genus includes 1-2 species. Human noroviruses are a leading cause of acute gastroenteritis in humans. Furthermore, unclassified caliciviruses have been detected in geese, yellowfin seabream, greater green snake, arctic lamprey, frogs and various Australian birds, highlighting the wide host range of viruses in the family Caliciviridae. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438042  Cd Length: 310  Bit Score: 44.95  E-value: 6.36e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3117 VNMWNS--KRVPTAYTVDGTCFDSTVTPEDIAREGEIFAAASTNPELVRRLHELYAGSPMMDPSGNIVGYRRCRASGTLT 3194
Cdd:cd23192    67 VEVIFErlSGFRYHYCLDYSKWDSTQSPAVTAAAIDILADLSEETPLRDSVVETLSSPPMGIFDDVIFVTKRGLPSGMPF 146

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3195 TSAGNSITCYLKVSAACRKA--------GLINPSYLIH--GDD-VVIVCEKTECDqSQALGAALRSYGYecEPTRhADLT 3263
Cdd:cd23192   147 TSVINSLNHWLLFSAAVLKAyelvgiytGNVFDEADFFtyGDDgVYAMPPATASV-MDEIIENLKSYGL--KPTA-ADKT 222


                  ....*
gi 485191044 3264 TAESC 3268
Cdd:cd23192   223 ENPDI 227
ps-ssRNAv_Hepelivirales_RdRp cd23209
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Hepelivirales of ...
 3077-3232 9.59e-04

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Hepelivirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the order Hepelivirales, class Alsuviricetes. This Hepelivirales order consists of four families: Alphatetraviridae, Benyviridae, Hepeviridae, and Matonaviridae. 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: 438059 [Multi-domain]  Cd Length: 183  Bit Score: 42.86  E-value: 9.59e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3077 SLEFRVAEKMILgdpslvakavMGASYGFQYPPHKRAEVLVNMWNSKRVPTAYTVDGTCFDSTVTPEDIAREGEIFAAAS 3156
Cdd:cd23209    40 GPWFRALEKILR----------RALKPNVLYANGHEAEPFVDKINQAHSAVFIENDFTEFDSTQNLFSLLVELEILEACG 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3157 TNPELVRRLHELYAGSPMMDPSGNI-VGYRrcRASGTLTTSAGNSI-------TCYlkvSAACRKAGLINpsylihGDDV 3228
Cdd:cd23209   110 MPPALAELYRALRAKWTLQAREGSLeGTCK--KTSGEPGTLLHNTIwnmavmmHMV---RGGVRKAAAFK------GDDS 178


                  ....
gi 485191044 3229 VIVC 3232
Cdd:cd23209   179 VVCC 182
ps-ssRNAv_RdRp-like cd23167
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
 3187-3233 1.01e-03

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


Pssm-ID: 438017 [Multi-domain]  Cd Length: 73  Bit Score: 40.40  E-value: 1.01e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 485191044 3187 CRASGTLTTSAGNSITCYLKVSAACRKAG-----LINPSYLIHGDDVVIVCE 3233
Cdd:cd23167    22 GQPSGSPNTSADNSLINLLLARLALRKACgraefLNSVGILVYGDDSLVSVP 73
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 1476-1602 1.08e-03

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: 42.61  E-value: 1.08e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044  1476 APTGSGKSTKF--PA----KLAQDGHNVLVLNPsvvtTKA--------MGPYMKKLVGKTPNIFAGTGASAMQIK-TGSK 1540
Cdd:pfam00270   21 APTGSGKTLAFllPAlealDKLDNGPQALVLAP----TRElaeqiyeeLKKLGKGLGLKVASLLGGDSRKEQLEKlKGPD 96

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 485191044  1541 ITYCTYGRFL--VNPQGFLDQKAVVVCDECHATDGTSiLGIGVARALAEKAGVRLLVFATATPP 1602
Cdd:pfam00270   97 ILVGTPGRLLdlLQERKLLKNLKLLVLDEAHRLLDMG-FGPDLEEILRRLPKKRQILLLSATLP 159
Aquamavirus_RdRp cd23220
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Aquamavirus of ...
 2998-3230 2.29e-03

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


Pssm-ID: 438070  Cd Length: 338  Bit Score: 43.16  E-value: 2.29e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 2998 PGWTYDEAVAKLRPgSAKGHVAKVTvADMKSGAGRPFVEQVINDlaagtlehpfmlrpkaEVFPQTKETHKPPRLIVYPS 3077
Cdd:cd23220    23 PGMNRRQLLLPLNP-QVRDDVVKLA-GDVGNGTATVVFETFMKD----------------ELRPKEKIESGKTRIVESCP 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3078 LEFRVAEKMIL---------GDPSLVAKAVmGASYGFQYPPhkraevLVNMWNSKRvptaYTVDGTCFDSTVTPEDIARE 3148
Cdd:cd23220    85 LDYLLLYRMVMlksmiwwynSDCIKTGVAP-GMNVYTDFVP------MVKQFKKIK----YCLDFSAYDSTLSDEILAAG 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3149 GEIFAAASTNPELVRRLHelyagSPMMDP---SGNIVGY-RRCRASGTLTTSAGNSITCYLKVSAACRKAGLINPSYLIH 3224
Cdd:cd23220   154 VEVLACTSAVPSYVRKLH-----APIICShhwHNNVVDLvLGGMPSGAPCTSVLNSIVNVLMARYICALMDIDYPVMVAY 228


                  ....*.
gi 485191044 3225 GDDVVI 3230
Cdd:cd23220   229 GDDNVV 234
Alphacarmovirus_RdRp cd23239
RNA-dependent RNA polymerase (RdRp) in the genus Alphacarmovirus of positive-sense ...
 3113-3258 2.34e-03

RNA-dependent RNA polymerase (RdRp) in the genus Alphacarmovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Alphacarmovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. The Alphacarmovirus genus was split in 2015 into three genera, each retaining -carmovirus as part of their name: Alphacarmovirus, Betacarmovirus, and Gammacarmovirus. Different carmoviruses infect a wide range of both monocotyledonous and dicotyledonous plants. Viruses tend to remain localized, forming necrosis in artificially infected hosts. There are 8 species in the genus Alphacarmovirus: Adonis mosaic virus, Angelonia flower break virus, Calibrachoa mottle virus, Carnation mottle virus, Honeysuckle ringspot virus, Nootka lupine vein clearing virus, Pelargonium flower break virus, and Saguaro cactus virus. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438089 [Multi-domain]  Cd Length: 470  Bit Score: 43.58  E-value: 2.34e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3113 AEVLVNMWNSKRVPTAYTVDGTCFDSTVTPEDIAREGEIFAAA-STNPELVRRLHELYAGSPMMDPSGNIVGYRR--CRA 3189
Cdd:cd23239   190 AQHISSAWDQFQIPVAIGFDMSRFDQHVSVPALQFEHSCYLACfPGDRHLAQLLSWQLKNFGVGFASNGMIRYKKegCRM 269

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 485191044 3190 SGTLTTSAGNSITCYLKVSAACR--KAGLINpsyliHGDDVVIVCEKTECDQSQA-LGAALRSYGYEC---EPTR 3258
Cdd:cd23239   270 SGDMNTALGNCLLACLITKHLMKgvNCRLIN-----NGDDCVLICERKDLGFVVSnLTTGWRRFGFTCiaeEPVY 339
ps-ssRNA_Picornaviridae cd23193
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Picornaviridae of ...
 3071-3234 2.41e-03

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: 43.31  E-value: 2.41e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3071 RLIVYPSLEFRVAEKMILGdpSLVAKavMGASYGFQY------PPHKRAEVLVNMWNSKRVptaYTVDGTCFDSTVTPED 3144
Cdd:cd23193    80 RVIEAAPLDYVIAGRMVFG--RLFAQ--FHSNPGILTgsavgcNPDTDWTRLFASLKQDNV---YDLDYSGFDASLSSQL 152

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3145 IAREGEIFAAASTNPELVRRLHElyagsPMMDpSGNIVGYRRCR-----ASGTLTTSAGNSITCYLKVSAACRKAGLINP 3219
Cdd:cd23193   153 FEAAVEVLAECHGDPELVLRYLE-----PIIN-SKHVVGDERYTveggmPSGCPCTSILNSICNNLVVRYALLETGKFDP 226

                         170
                  ....*....|....*...
gi 485191044 3220 SY---LIHGDDVVIVCEK 3234
Cdd:cd23193   227 DEyyiLAYGDDVLVSTDE 244
Pelarspovirus_RdRp cd23241
RNA-dependent RNA polymerase (RdRp) in the genus Pelarspovirus of positive-sense ...
 3114-3254 2.61e-03

RNA-dependent RNA polymerase (RdRp) in the genus Pelarspovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Pelarspovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. The genus name "Pelarspovirus" is derived from the pelargonium ringspot virus, which was the first virus to be named. There are 8 species in the Pelarspovirus genus: Clematis chlorotic mottle virus, Elderberry latent virus, Jasmine mosaic-associated virus, Jasmine virus H, Pelargonium chlorotic ring pattern virus, Pelargonium line pattern virus, Pelargonium ringspot virus, and Rosa rugosa leaf distortion virus. Members of the Pelarspovirus have monopartite genomes encoding five open reading frames (ORFs) that include two 5'-proximal replication proteins, two centrally located movement proteins (MP1 and MP2) and a 3'-proximal coat protein that, at least for pelargonium line pattern virus (PLPV), has been shown to act also as suppressor of RNA silencing. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438091 [Multi-domain]  Cd Length: 497  Bit Score: 43.58  E-value: 2.61e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3114 EVLVNMWNSKRVPTAYTVDGTCFDSTVTPEDIAREGEIFAAASTNPELVRRLHELyagspMMDPSGniVGYRR------- 3186
Cdd:cd23241   189 NIIRDKWNKYQKPAAIGFDMSRFDQHVSVDALKFEHKIYRRCFSNDGNLARLLGH-----QIENRG--VAYAKdgwlkyk 261

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 485191044 3187 ---CRASGTLTTSAGN-----SITCYLKVSAACrKAGLINpsyliHGDDVVIVCEKTECDQSQA-LGAALRSYGYEC 3254
Cdd:cd23241   262 vegKRMSGDVNTALGNcilacCITKELMGGIGI-KCSLIN-----NGDDCVLIGESRDCRAVEDiLTEGWLRFGFTC 332
ComEC COG0658
DNA uptake channel protein ComEC, N-terminal domain [Intracellular trafficking, secretion, and ...
 891-1210 3.05e-03

DNA uptake channel protein ComEC, N-terminal domain [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 440423 [Multi-domain]  Cd Length: 543  Bit Score: 43.25  E-value: 3.05e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044  891 NWLGFIAAFVVRP-TALALVAIVIAGCAGLPLRTHFPYRAFAVAFHLASVSLIESGVVFGLAWWAADWFARAGADAALSR 969
Cdd:COG0658   182 SLVSLLANLLAVPlVSLIVVPGLLLALLLLPLLPPLALLLLLLALLLLLLLLLLLLALLLLLLLLLLLLLLLLLLLLLLL 261

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044  970 AVLASPVVGWAIRLPSWPEVILGVVCVALYMRVVGQARLAALVAYKLSRGLAGAALVVLLVCRGPERGALGYQLCLPEWD 1049
Cdd:COG0658   262 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLGLLGGVGVGGGDGGLLLGGRGLLGVLGGLLLLLLLLLLL 341

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 1050 ASIDLDDVWWYAAAFFTFCCISISLLTRRGVVFKLRVYARWCRLYCWLQLVVGHTPAGDYFRWRGASSLLWLAAGVLWPA 1129
Cdd:COG0658   342 LLLLLLGLLLVLLLLLLLALLLGLLLLLLAALLGLAAALLLLLALLALLALLALALLLGALVGLLVVLLLALRSLLLGGG 421

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 1130 EVAVVSMIIVCFAAVLDVFDALLERLLTASPSLRPLVNLANTLHSCLSDPELAAFLRARWHRGELLYDHAGQVAASLRER 1209
Cdd:COG0658   422 LLLLLLLLLLLLALALLLLLLALLSLLLLLLLLLALLLLLLGSLLLSLLLLLALASSALASLSSSSSGAAVLAAAGAVAL 501


                  .
gi 485191044 1210 V 1210
Cdd:COG0658   502 L 502
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 1476-1601 3.16e-03

DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part 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: 350684 [Multi-domain]  Cd Length: 146  Bit Score: 40.75  E-value: 3.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 1476 APTGSGKST---KFPAKLAQdgHNVLVLNPSVV-TTKAMGPYMKKLVGKTPNIFaGTGASAMqiKTGSKITYCTY---GR 1548
Cdd:cd17926    25 LPTGSGKTLtalALIAYLKE--LRTLIVVPTDAlLDQWKERFEDFLGDSSIGLI-GGGKKKD--FDDANVVVATYqslSN 99

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 485191044 1549 FLVNPQGFLDQKAVVVCDECHATDGTSIlgigvaRALAEKAGVRLLVFATATP 1601
Cdd:cd17926   100 LAEEEKDLFDQFGLLIVDEAHHLPAKTF------SEILKELNAKYRLGLTATP 146
Gammacarmovirus_RdRp cd23242
RNA-dependent RNA polymerase (RdRp) in the genus Gammacarmovirus of positive-sense ...
 3120-3255 5.79e-03

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: 42.42  E-value: 5.79e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485191044 3120 WNSKRVPTAYTVDGTCFDSTVTPEDIAREGEIFAAASTN-PELVRRLHELYAGSPMMDPSGNIVGYRR--CRASGTLTTS 3196
Cdd:cd23242   187 WDSFVSPVAIGFDMKRFDQHVSRDALEWEHSVYLDAFCNdPYLAELLSWQLENKGVGYASDGSIKYKVdgCRMSGDMNTA 266

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 485191044 3197 AGNSITCYLKVSAACR----KAGLINpsyliHGDDVVIVCEKTECDQSQA-LGAALRSYGYECE 3255
Cdd:cd23242   267 MGNCLLACAITWDFFKgrgiKARLLN-----NGDDCVVITEKECAAAVVAgMVRHWRRFGFQCE 325
 
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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