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Conserved domains on  [gi|113720390|gb|ABI36965|]
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polyprotein [Hepatitis C virus subtype 6i]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Hepacivirus_RdRp cd23202
RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ...
 2439-2956 0e+00

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: 1159.99  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2439 CAAEEEKLPINPLSNSLIRHHNLVYSTSSKSAGLRQKKVTFDRVQLVDQHYYDTLKEIKLQASQVQARLLTTEEACDLTP 2518
Cdd:cd23202     1 CAAEEEKLPISPLSNSLLRHHNLVYSTTSRSASERQKKVTFDRLQVLDPHYDDVLKEAKARASGVKARLLSVEEACSLTP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2519 SHSARSKFGYGAKDVRSHTRKAINHINSVWEDLLEDTQTPIPTTIMAKNEVFCVDTSKGGRKPARLIVYPDLGVRVCEKK 2598
Cdd:cd23202    81 PHSARSKFGYGAKDVRSLSRKAVNHINSVWEDLLEDSETPIPTTIMAKNEVFCVTPEKGGRKPARLIVYPDLGVRVCEKM 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2599 ALFDITRKLPVAVMGDAYGFQYSPKQRVERLLRMWRSKKTPMGFSYDTRCFDSTVTERDIRTEQDIYLCCQLDPEAQQAI 2678
Cdd:cd23202   161 ALYDVAPKLPKAVMGEAYGFQYSPAQRVEFLLKMWRSKKTPMGFSYDTRCFDSTVTERDIRTEESIYQCCDLDPEARKAI 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2679 KSLTERLYVGGPMYNSKGQLCGQRRCRASGVLPTSMGNTITCFLKAKAACRAAGFTNFDMLVCGDDLVVISESAGVNEDI 2758
Cdd:cd23202   241 RSLTERLYVGGPMTNSKGQSCGYRRCRASGVFTTSSGNTLTCYLKASAACRAAGLKDPTMLVCGDDLVVIAESAGVEEDA 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2759 ANLRAFTEAMTRYSATPGDLPSPSYDLELITSCSSNVSVAHDGDGRKYYYLTRDPVTPLARAAWETARHTPVNSWLGNII 2838
Cdd:cd23202   321 AALRAFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDATGKRYYYLTRDPTTPLARAAWETARHTPVNSWLGNII 400

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2839 MYAPAIWVRMVLMTHFFQTLQAQETLDKVLDFDIYGVTYSITPLDLPVIIQRLHGMAAFSLHGYSPGELNRVAACLRKLG 2918
Cdd:cd23202   401 MYAPTLWVRMVLMTHFFSILLAQEQLEKALDFEMYGNTYSIPPLDLPAIIQRLHGLSAFSLHGYSPRELNRVAAALRKLG 480

                         490       500       510
                  ....*....|....*....|....*....|....*...
gi 113720390 2919 APPLRAWRHRARAVRAQLITRGGKAAICGRYLFNWAVK 2956
Cdd:cd23202   481 VPPLRAWRHRARAVRAKLIAQGGKAAICGKYLFNWAVK 518
HCV_NS1 super family cl03263
Hepatitis C virus non-structural protein E2/NS1; The hypervariable region of the E2/NS1 region ...
 386-731 0e+00

Hepatitis C virus non-structural protein E2/NS1; The hypervariable region of the E2/NS1 region of hepatitis C virus varies greatly between viral isolates. E2 is thought to encode a structurally unconstrained envelope protein.


The actual alignment was detected with superfamily member pfam01560:

Pssm-ID: 110557  Cd Length: 344  Bit Score: 643.06  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390   386 YISGSSAGSTVNGLTGLFTRGPQQNLQLINSNGSWHVNRTALNCNDSLQTGFFVPLFYKQNINTSGCVERMSSCKPLDQF 465
Cdd:pfam01560    1 HVTGGSAARTTRGLVSLFSPGAKQNIQLINTNGSWHINRTALNCNDSLQTGFLASLFYTHRFNSSGCPERLASCRSIDDF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390   466 DQGWGPLSYFNVSgPSEERPYCWHYPPRPCEVVPAESVCGPVYCFTPSPVVIGTTDKRGLPTFTWGENETDVFLLGSARP 545
Cdd:pfam01560   81 RQGWGPITYEETN-PEDQRPYCWHYPPRPCGIVPASSVCGPVYCFTPSPVVVGTTDRSGAPTYSWGENETDVFLLNNTRP 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390   546 PQGSWFGCTWMNGTGYVKTCGAPPCLTQPTkGNNTLVCPTDCFRKHPDTTFGKCGSGPWLTPRCLVDYPYRLWHYPCTVN 625
Cdd:pfam01560  160 PQGNWFGCTWMNSTGFTKTCGAPPCRIGGD-GNNTLLCPTDCFRKHPDATYTKCGSGPWLTPRCMVDYPYRLWHYPCTVN 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390   626 FTIHKVRMFVGGIEHRFGAACNWTRGDRCELDDRDRVEMSPLLFSTTQMAILPCTFTTMPALSTGLIHLHQNIVDVQYLY 705
Cdd:pfam01560  239 FTIFKVRMYVGGVEHRLNAACNWTRGERCDLEDRDRSELSPLLLSTTEWQVLPCSFTTLPALSTGLIHLHQNIVDVQYLY 318

                          330       340
                   ....*....|....*....|....*.
gi 113720390   706 GISTAIVSWALKWEYVVLAFLVLADS 731
Cdd:pfam01560  319 GLGSAVTSFAIKWEYVVLLFLLLADA 344
HCV_NS2 pfam01538
Hepatitis C virus non-structural protein NS2; The viral genome is translated into a single ...
 813-1007 9.95e-110

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


:

Pssm-ID: 366698  Cd Length: 195  Bit Score: 347.74  E-value: 9.95e-110
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390   813 DTDQAASVGLLALGIITIFTLTPAYKQLLVGVLWWTQYFIARAEAMLHVWIPPLQVRGGRDAVILLSCLFHPQLGFEVTK 892
Cdd:pfam01538    1 DTEDAGWLGAAVLSWITLFTLTPTYKGLLAKLLWWLQYCIARQEARLHVWVPPLGVRGGRDAVILLWCLAHPDLVFDVTK 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390   893 ILMALLGSMYLLQYSFLKTPYFVRAHILLRACMLFRGLASGKY*QALLLRLGAWTGTYVYDHLTPLTDWACDGLRDLAVA 972
Cdd:pfam01538   81 ILLAILGPLYLLQASLLRVPYFVRAARLLRSCVLVRHLAGGKYVQMALLKLGRWTGTYLYDHLGPLSDWAAEGLRDLAVA 160

                          170       180       190
                   ....*....|....*....|....*....|....*
gi 113720390   973 VEPVVFSPMEKKVITWGADTAACGDIIEGLPVSAR 1007
Cdd:pfam01538  161 LEPVVFSPMECKIITWGADTAACGDIVHGLPVSAR 195
HCV_env super family cl03255
Hepatitis C virus envelope glycoprotein E1;
195-382 2.27e-91

Hepatitis C virus envelope glycoprotein E1;


The actual alignment was detected with superfamily member pfam01539:

Pssm-ID: 110536  Cd Length: 190  Bit Score: 294.86  E-value: 2.27e-91
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390   195 KNASGVYHLTNDCPNSSIVYEAESIILHLPGCVPCVRSKNVSRCWYSVSPTLAVFDASTPVHGFRRHVDLIVGAAAFCSA 274
Cdd:pfam01539    3 RNISGSYHVTNDCSNSSITWQLADAVLHTPGCVPCEREGNTSRCWIAVTPNVAVRHRGALTTSLRTHVDMLVMAATLCSA 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390   275 MYIGDLCGGVFLVGQVFTLRPKIHTTVQDCNCSIYTGHITGHRMAWDMMMNWSPTVTYVVSSALRTPQLLLEIFLGAHWG 354
Cdd:pfam01539   83 LYVGDLCGSVMLVSQLFTVSPQRHWFTQDCNCSIYPGHITGHRMAWDMMMNWSPTATMILAYALRVPEAVLDIIAGAHWG 162

                          170       180
                   ....*....|....*....|....*...
gi 113720390   355 VLGAVVYYCMVANWAKVLVVLLMFAGVD 382
Cdd:pfam01539  163 VLFGLAYFSMQGAWAKVLVILLLFAGVD 190
HCV_NS4b pfam01001
Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. ...
 1730-1923 1.54e-90

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: 292.74  E-value: 1.54e-90
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  1730 FKQKVLGLIQTSAKQAEELKPVVTSAWPKLEQFWTKHLWNFVSGIQYLAGLSTLPGNPAIASLMSFSASLTSPLSTSTTL 1809
Cdd:pfam01001    1 FAFKALGLLPPAIDKAESITPAVASLDTKFEQFWAKHMWNFRSGIQYLAGLYTLPRNPPLAVLASFLAGMTSPLPTHVRL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  1810 LLNILGGWVASQLATPTASTSFVVSGLAGAAVGSIGLGKVIVDVLAGYGAGISGALVGFKIMCGETPSAEDMVNLLPALL 1889
Cdd:pfam01001   81 ALALLGGWGATQLGTPSGGLAFVGAGFAGAAVGSSWLGRVLVDVLGGYEAAVNAASLTFKIMSGELPTAEDLWNLLPCLL 160

                          170       180       190
                   ....*....|....*....|....*....|....
gi 113720390  1890 SPGALVVGVVCAAILRRHTGpsEGATQWMNRLIA 1923
Cdd:pfam01001  161 SPGASVVGVALAALLRSHKG--EGAVQWMNRLLT 192
Peptidase_S29 pfam02907
Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a ...
 1058-1205 2.31e-81

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


:

Pssm-ID: 427049  Cd Length: 149  Bit Score: 264.67  E-value: 2.31e-81
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  1058 EGEVQVVSTATQSFLATTLNGVLWTVYHGAGSKTLAGPKGPICQMYTNVEQDLVGWPAPSGARSLTPCSCGSSDLYLVTR 1137
Cdd:pfam02907    1 EGEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTR 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 113720390  1138 NADVIPARRRGDSRAALLSPRPISTLKGSSGGPMLCPSGHVAGIFRAAVCTRGVAKSLDFVPVENMQT 1205
Cdd:pfam02907   81 DGDLIPGRRRGDPRVSLLSPRPLSYLKGSSGGPILCPSGHVVGMFRAAVHSGGVVKAVRFVPWETLPT 148
HCV_NS5a_C super family cl15181
HCV NS5a protein C-terminal region; This is a family of proteins found in the hepatitis C ...
 2181-2425 2.40e-73

HCV NS5a protein C-terminal region; This is a family of proteins found in the hepatitis C virus. This family contains the C-terminal region of the NS5A protein. CC The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR.


The actual alignment was detected with superfamily member pfam12941:

Pssm-ID: 289693  Cd Length: 242  Bit Score: 245.62  E-value: 2.40e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  2181 SHVTAEAAARRLARGSPPSLASSSASQLSALSLKGTCTTHGPHPDAELIEANLLWRQEMGNNITRVESESKVIILDSFDP 2260
Cdd:pfam12941    1 SHITAEAAGRRLARGSPPSMASSSASQLSAPSLKATCTANHDSPDAELIEANLLWRQEMGGNITRVESENKVVILDSFDP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  2261 LVPEYDDREPSLSAECHRPNRpKFPPALPIWARPDYNPPLLEPWKSPDYNPPMVHGCALPPPDKPPVPPPRRRKVVQLDA 2340
Cdd:pfam12941   81 LVAEEDEREVSVPAEILRKSR-RFAPALPVWARPDYNPLLVETWKKPDYEPPVVHGCPLPPPRSPPVPPPRKKRTVVLTE 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  2341 SNVSTVLAQLAEKTFPQPASlttgcgSGQAAHSTGSGEQSEEDGAASEAD--SYSSMPPLEGEPGDPDLSSGSWSTISEE 2418
Cdd:pfam12941  160 STLPTALAELATKSFGSSST------SGITGDNTTTSSEPAPSGCPPDSDveSYSSMPPLEGEPGDPDLSDGSWSTVSSG 233


                   ....*....
gi 113720390  2419 GD--GVVCC 2425
Cdd:pfam12941  234 ADteDVVCC 242
HCV_capsid pfam01543
Hepatitis C virus capsid protein;
2-115 4.05e-70

Hepatitis C virus capsid protein;


:

Pssm-ID: 144947  Cd Length: 121  Bit Score: 231.12  E-value: 4.05e-70
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390     2 STLPKPQRKTKRNTYRRPMDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARPPTGRSWGQPGY 81
Cdd:pfam01543    1 STNPKPQRKTKRNTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARPPEGRSWLSPGT 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 113720390    82 PWP------LYGNEG-CGWAGWLLSPRGSRPNWGPNDPRRR 115
Cdd:pfam01543   81 LGPstamraLYGNDGsCGWAGWLLPPRGSRPSWGQNDPRRR 121
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 1226-1368 1.43e-51

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: 179.28  E-value: 1.43e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 1226 QVGYLHAPTGSGKSTKVPAAYAAQGY----KVLVLNPSVAATLGFGAYMSKAhgiDPNIRTGVRTITTGG--PITYSTYG 1299
Cdd:cd17931     2 QLTVLDLHPGAGKTTRVLPQIIREAIkkrlRTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGGneIVDYMCHG 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 113720390 1300 KFLaDGGCSGGA---YDIIICDECHSTDPTTILGIGTVLDQAETsGARLTVLATATPPGSVTVPH---PNITEEA 1368
Cdd:cd17931    79 TFT-CRLLSPKRvpnYNLIIMDEAHFTDPASIAARGYIHTRVEM-GEAAVIFMTATPPGTVTPFPqsnHPIEDFE 151
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 1364-1505 3.53e-49

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: 172.45  E-value: 3.53e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 1364 ITEEALPTTGEIPFYGKGIPLDFikGGRHLIFCHSKKKCDELAKQLTTLGINAVAFYRGVDVSV---IPTDGDVVVCATD 1440
Cdd:cd18806     1 IEDVALEIPGRIWFYGKAWITIY--GGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 113720390 1441 ALMTGYTGNFDTVIDCNVAVTQVVDFSLDptFTIETT-TLPQDAVSRSQRRGRTGRGKH---GVYRYVS 1505
Cdd:cd18806    79 ISEMGANFDADRVIDCRTCVKPTILFSGD--FRVILTgPVPQTAASAAQRRGRTGRNPAqerDIYRFVG 145
HCV_NS5a_1b pfam08301
Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a ...
 2070-2170 7.50e-48

Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR. This region corresponds to the 1b domain.


:

Pssm-ID: 149382  Cd Length: 102  Bit Score: 166.77  E-value: 7.50e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  2070 GPSVPIPEPNYTRALWRVSAEDYVEVKRVGDSHFVVGATEDNLkCPCQVPAPEFF--TEVDGVRIHRYAPKCKPLLRDEI 2147
Cdd:pfam08301    1 GPAVPLPPPNYGPALWRVGAEDYVEVVRVGDTHYVTATSCYNL-CPCQVPRPEFFapTEVDGVRVSWYAPPCKPLLVYEV 79

                           90       100
                   ....*....|....*....|...
gi 113720390  2148 TFSVGMSSYAMGSQLPCEPEPDV 2170
Cdd:pfam08301   80 GQSVGLDGYGVRSQLPCELEPDV 102
HCV_core super family cl46603
Hepatitis C virus core protein; The viral core protein forms the internal viral coat that ...
 116-190 2.91e-26

Hepatitis C virus core protein; The viral core protein forms the internal viral coat that encapsidates the genomic RNA and is enveloped in a host cell-derived lipid membrane. The core protein has been shown, by yeast two-hybrid assay to interact with cellular DEAD box helicases. The N terminus of the core protein is involved in transcriptional repression.


The actual alignment was detected with superfamily member pfam01542:

Pssm-ID: 480943  Cd Length: 75  Bit Score: 104.38  E-value: 2.91e-26
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 113720390   116 SRNLGKVIDTLTCGLADLMGYIPVLGGPLGGVAAALAHGVRAIEDGVNYATGNLPGCSFSIFILALLSCLTTPVS 190
Cdd:pfam01542    1 MRNLGKPIDKLKCGFADLMGDIKFPGAGLGGAARALAHGRGPLEDGRATAKGNEPGCPFGIFLLALKACLPEGAS 75
HCV_NS4a pfam01006
Hepatitis C virus non-structural protein NS4a; NS4a forms an integral part of the NS3 serine ...
 1660-1713 2.12e-21

Hepatitis C virus non-structural protein NS4a; NS4a forms an integral part of the NS3 serine protease, as it is required in a number of cases as a cofactor of cleavage. It has also been reported that NS4a interacts with NS4b and NS3 to form a multi-subunit replicase complex.


:

Pssm-ID: 366414  Cd Length: 55  Bit Score: 89.44  E-value: 2.12e-21
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 113720390  1660 STWVLVGGVLAALAAYCLSVGCVVICGRVSTSGQP-ALIPDREVLYRQFDEMEEC 1713
Cdd:pfam01006    1 STWVLVGGALAAGAAYCLTTGSVVVVGRWSVNGKPpAVVPDREVLYQQGEEMEEC 55
HCV_p7 cd20903
Hepatitis C virus p7 protein; Hepatitis C virus (HCV) p7 protein is a viroporin essential for ...
 749-806 1.39e-17

Hepatitis C virus p7 protein; Hepatitis C virus (HCV) p7 protein is a viroporin essential for virus production. The p7 monomer is comprised of 2 trans-membrane helices connected by a cytosolic loop, and oligomerizes to form cation-specific ion channels. These ion channels dissipate pH gradients in secretory vesicles potentially protecting acid-labile intracellular virions during egress (the rupturing of the infected cell and release of viral contents). p7 protein has at least two different functions in culture, one via the formation of these ion channels, the other through its specific interaction with the non-structural viral protein NS2. Several compounds targeting p7 have been investigated as anti-HCV drugs.


:

Pssm-ID: 411017  Cd Length: 58  Bit Score: 78.81  E-value: 1.39e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 113720390  749 ALENLIVLNAASAAGNHGLVWGLIFICCVWHVRGRLVPLSTYAFLQLWPLLLLVLALP 806
Cdd:cd20903     1 ALENLVVLNAASAAGTHGLLWFLLFFCAAWYIKGRLVPAATYALLGLWPLLLLLLALP 58
 
Name Accession Description Interval E-value
Hepacivirus_RdRp cd23202
RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ...
 2439-2956 0e+00

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: 1159.99  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2439 CAAEEEKLPINPLSNSLIRHHNLVYSTSSKSAGLRQKKVTFDRVQLVDQHYYDTLKEIKLQASQVQARLLTTEEACDLTP 2518
Cdd:cd23202     1 CAAEEEKLPISPLSNSLLRHHNLVYSTTSRSASERQKKVTFDRLQVLDPHYDDVLKEAKARASGVKARLLSVEEACSLTP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2519 SHSARSKFGYGAKDVRSHTRKAINHINSVWEDLLEDTQTPIPTTIMAKNEVFCVDTSKGGRKPARLIVYPDLGVRVCEKK 2598
Cdd:cd23202    81 PHSARSKFGYGAKDVRSLSRKAVNHINSVWEDLLEDSETPIPTTIMAKNEVFCVTPEKGGRKPARLIVYPDLGVRVCEKM 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2599 ALFDITRKLPVAVMGDAYGFQYSPKQRVERLLRMWRSKKTPMGFSYDTRCFDSTVTERDIRTEQDIYLCCQLDPEAQQAI 2678
Cdd:cd23202   161 ALYDVAPKLPKAVMGEAYGFQYSPAQRVEFLLKMWRSKKTPMGFSYDTRCFDSTVTERDIRTEESIYQCCDLDPEARKAI 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2679 KSLTERLYVGGPMYNSKGQLCGQRRCRASGVLPTSMGNTITCFLKAKAACRAAGFTNFDMLVCGDDLVVISESAGVNEDI 2758
Cdd:cd23202   241 RSLTERLYVGGPMTNSKGQSCGYRRCRASGVFTTSSGNTLTCYLKASAACRAAGLKDPTMLVCGDDLVVIAESAGVEEDA 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2759 ANLRAFTEAMTRYSATPGDLPSPSYDLELITSCSSNVSVAHDGDGRKYYYLTRDPVTPLARAAWETARHTPVNSWLGNII 2838
Cdd:cd23202   321 AALRAFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDATGKRYYYLTRDPTTPLARAAWETARHTPVNSWLGNII 400

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2839 MYAPAIWVRMVLMTHFFQTLQAQETLDKVLDFDIYGVTYSITPLDLPVIIQRLHGMAAFSLHGYSPGELNRVAACLRKLG 2918
Cdd:cd23202   401 MYAPTLWVRMVLMTHFFSILLAQEQLEKALDFEMYGNTYSIPPLDLPAIIQRLHGLSAFSLHGYSPRELNRVAAALRKLG 480

                         490       500       510
                  ....*....|....*....|....*....|....*...
gi 113720390 2919 APPLRAWRHRARAVRAQLITRGGKAAICGRYLFNWAVK 2956
Cdd:cd23202   481 VPPLRAWRHRARAVRAKLIAQGGKAAICGKYLFNWAVK 518
HCV_NS1 pfam01560
Hepatitis C virus non-structural protein E2/NS1; The hypervariable region of the E2/NS1 region ...
 386-731 0e+00

Hepatitis C virus non-structural protein E2/NS1; The hypervariable region of the E2/NS1 region of hepatitis C virus varies greatly between viral isolates. E2 is thought to encode a structurally unconstrained envelope protein.


Pssm-ID: 110557  Cd Length: 344  Bit Score: 643.06  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390   386 YISGSSAGSTVNGLTGLFTRGPQQNLQLINSNGSWHVNRTALNCNDSLQTGFFVPLFYKQNINTSGCVERMSSCKPLDQF 465
Cdd:pfam01560    1 HVTGGSAARTTRGLVSLFSPGAKQNIQLINTNGSWHINRTALNCNDSLQTGFLASLFYTHRFNSSGCPERLASCRSIDDF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390   466 DQGWGPLSYFNVSgPSEERPYCWHYPPRPCEVVPAESVCGPVYCFTPSPVVIGTTDKRGLPTFTWGENETDVFLLGSARP 545
Cdd:pfam01560   81 RQGWGPITYEETN-PEDQRPYCWHYPPRPCGIVPASSVCGPVYCFTPSPVVVGTTDRSGAPTYSWGENETDVFLLNNTRP 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390   546 PQGSWFGCTWMNGTGYVKTCGAPPCLTQPTkGNNTLVCPTDCFRKHPDTTFGKCGSGPWLTPRCLVDYPYRLWHYPCTVN 625
Cdd:pfam01560  160 PQGNWFGCTWMNSTGFTKTCGAPPCRIGGD-GNNTLLCPTDCFRKHPDATYTKCGSGPWLTPRCMVDYPYRLWHYPCTVN 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390   626 FTIHKVRMFVGGIEHRFGAACNWTRGDRCELDDRDRVEMSPLLFSTTQMAILPCTFTTMPALSTGLIHLHQNIVDVQYLY 705
Cdd:pfam01560  239 FTIFKVRMYVGGVEHRLNAACNWTRGERCDLEDRDRSELSPLLLSTTEWQVLPCSFTTLPALSTGLIHLHQNIVDVQYLY 318

                          330       340
                   ....*....|....*....|....*.
gi 113720390   706 GISTAIVSWALKWEYVVLAFLVLADS 731
Cdd:pfam01560  319 GLGSAVTSFAIKWEYVVLLFLLLADA 344
RdRP_3 pfam00998
Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase ...
 2428-2939 0e+00

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: 585.35  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  2428 SYSWTGALItpcAAEEEKLPIN-PLSNSLIRHHNLVYSTSSKSAGLRQKKVTFDRVQLV--DQHYYDTLKEIKLQASQVQ 2504
Cdd:pfam00998    1 SYVWTGARP---AKERKILPITgPGSGLLFGVHNNSLVNLRRGLVERVFKVTFDRGGQLvpPKPYPGAFKELKYFASALV 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  2505 ARLLtteEACDLTPSHSARSKFGYGAK-DVRSHTRKAINHINSVwEDLLEDTQTPIPTTIMAKNEVFCVdtsKGGRKPAR 2583
Cdd:pfam00998   78 SKLG---EATPLTPEHFAASYTGRKRKiYVKALESLAVKPVQRR-DAILKTFVKAEKINITAKPDPAPR---VIQPRPPR 150

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  2584 LIVYPDLGVRVCEKKALFDItrklPVAVMGDAYGFQYSPKQRVERLLRMWRSKKTPMGFSYDTRCFDSTVTERDIRTEQD 2663
Cdd:pfam00998  151 YNVEPGRYLRPCEKMIYKAI----DKAFGGPTVLKGYTPEQRGEILLKKWDSFKKPVAIGLDASRFDQHVSVEALRFEHS 226

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  2664 IYLCCQLDPEaqQAIKSLTERLYVGGPMYNSKGQL-CGQRRCRASGVLPTSMGNTITCFLKAKAACRAAGfTNFDMLVCG 2742
Cdd:pfam00998  227 IYLAAFLGPE--ELIRLLTWQLYNGGPMYASDGQIkYGVRGCRMSGDMNTSLGNCLLMCLKVHAACKALG-IDARLLNNG 303

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  2743 DDLVVISESAGVNEDIanlRAFTEAMTRYSaTPGDLPSPSYDLELITSCSSNVSVAHDGDGRKYYYLTRDPVTPLARAAW 2822
Cdd:pfam00998  304 DDCVVICESADLDEVK---EALTEAFARYG-FTMKVEEPVYELELIEFCQSNPVFDGGKYGMVRNPLTSDSKDPLSRASW 379

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  2823 ETArhTPVNSWLGNIIMYAPAIWVRMVLMTHFFQTLQAQETLDKVLDFDIYGVTYSitpldlpVIIQRLHGMAAFSLHGY 2902
Cdd:pfam00998  380 ETA--TPAKSWLGAIGECGLSLWGGVPVLQHFYSCLLRNGGLEKAVSFEMYGKVYS-------DSGFRLHGLGAGSRHSY 450

                          490       500       510
                   ....*....|....*....|....*....|....*..
gi 113720390  2903 SPGELNRVAACLrKLGAPPLRAWRHRARAVRAQLITR 2939
Cdd:pfam00998  451 EPTEEARVSFWL-AFGITPDEQWALEAYYDRLKLLRQ 486
HCV_NS2 pfam01538
Hepatitis C virus non-structural protein NS2; The viral genome is translated into a single ...
 813-1007 9.95e-110

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


Pssm-ID: 366698  Cd Length: 195  Bit Score: 347.74  E-value: 9.95e-110
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390   813 DTDQAASVGLLALGIITIFTLTPAYKQLLVGVLWWTQYFIARAEAMLHVWIPPLQVRGGRDAVILLSCLFHPQLGFEVTK 892
Cdd:pfam01538    1 DTEDAGWLGAAVLSWITLFTLTPTYKGLLAKLLWWLQYCIARQEARLHVWVPPLGVRGGRDAVILLWCLAHPDLVFDVTK 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390   893 ILMALLGSMYLLQYSFLKTPYFVRAHILLRACMLFRGLASGKY*QALLLRLGAWTGTYVYDHLTPLTDWACDGLRDLAVA 972
Cdd:pfam01538   81 ILLAILGPLYLLQASLLRVPYFVRAARLLRSCVLVRHLAGGKYVQMALLKLGRWTGTYLYDHLGPLSDWAAEGLRDLAVA 160

                          170       180       190
                   ....*....|....*....|....*....|....*
gi 113720390   973 VEPVVFSPMEKKVITWGADTAACGDIIEGLPVSAR 1007
Cdd:pfam01538  161 LEPVVFSPMECKIITWGADTAACGDIVHGLPVSAR 195
HCV_env pfam01539
Hepatitis C virus envelope glycoprotein E1;
195-382 2.27e-91

Hepatitis C virus envelope glycoprotein E1;


Pssm-ID: 110536  Cd Length: 190  Bit Score: 294.86  E-value: 2.27e-91
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390   195 KNASGVYHLTNDCPNSSIVYEAESIILHLPGCVPCVRSKNVSRCWYSVSPTLAVFDASTPVHGFRRHVDLIVGAAAFCSA 274
Cdd:pfam01539    3 RNISGSYHVTNDCSNSSITWQLADAVLHTPGCVPCEREGNTSRCWIAVTPNVAVRHRGALTTSLRTHVDMLVMAATLCSA 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390   275 MYIGDLCGGVFLVGQVFTLRPKIHTTVQDCNCSIYTGHITGHRMAWDMMMNWSPTVTYVVSSALRTPQLLLEIFLGAHWG 354
Cdd:pfam01539   83 LYVGDLCGSVMLVSQLFTVSPQRHWFTQDCNCSIYPGHITGHRMAWDMMMNWSPTATMILAYALRVPEAVLDIIAGAHWG 162

                          170       180
                   ....*....|....*....|....*...
gi 113720390   355 VLGAVVYYCMVANWAKVLVVLLMFAGVD 382
Cdd:pfam01539  163 VLFGLAYFSMQGAWAKVLVILLLFAGVD 190
HCV_NS4b pfam01001
Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. ...
 1730-1923 1.54e-90

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: 292.74  E-value: 1.54e-90
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  1730 FKQKVLGLIQTSAKQAEELKPVVTSAWPKLEQFWTKHLWNFVSGIQYLAGLSTLPGNPAIASLMSFSASLTSPLSTSTTL 1809
Cdd:pfam01001    1 FAFKALGLLPPAIDKAESITPAVASLDTKFEQFWAKHMWNFRSGIQYLAGLYTLPRNPPLAVLASFLAGMTSPLPTHVRL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  1810 LLNILGGWVASQLATPTASTSFVVSGLAGAAVGSIGLGKVIVDVLAGYGAGISGALVGFKIMCGETPSAEDMVNLLPALL 1889
Cdd:pfam01001   81 ALALLGGWGATQLGTPSGGLAFVGAGFAGAAVGSSWLGRVLVDVLGGYEAAVNAASLTFKIMSGELPTAEDLWNLLPCLL 160

                          170       180       190
                   ....*....|....*....|....*....|....
gi 113720390  1890 SPGALVVGVVCAAILRRHTGpsEGATQWMNRLIA 1923
Cdd:pfam01001  161 SPGASVVGVALAALLRSHKG--EGAVQWMNRLLT 192
Peptidase_S29 pfam02907
Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a ...
 1058-1205 2.31e-81

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


Pssm-ID: 427049  Cd Length: 149  Bit Score: 264.67  E-value: 2.31e-81
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  1058 EGEVQVVSTATQSFLATTLNGVLWTVYHGAGSKTLAGPKGPICQMYTNVEQDLVGWPAPSGARSLTPCSCGSSDLYLVTR 1137
Cdd:pfam02907    1 EGEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTR 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 113720390  1138 NADVIPARRRGDSRAALLSPRPISTLKGSSGGPMLCPSGHVAGIFRAAVCTRGVAKSLDFVPVENMQT 1205
Cdd:pfam02907   81 DGDLIPGRRRGDPRVSLLSPRPLSYLKGSSGGPILCPSGHVVGMFRAAVHSGGVVKAVRFVPWETLPT 148
HCV_NS5a_C pfam12941
HCV NS5a protein C-terminal region; This is a family of proteins found in the hepatitis C ...
 2181-2425 2.40e-73

HCV NS5a protein C-terminal region; This is a family of proteins found in the hepatitis C virus. This family contains the C-terminal region of the NS5A protein. CC The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR.


Pssm-ID: 289693  Cd Length: 242  Bit Score: 245.62  E-value: 2.40e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  2181 SHVTAEAAARRLARGSPPSLASSSASQLSALSLKGTCTTHGPHPDAELIEANLLWRQEMGNNITRVESESKVIILDSFDP 2260
Cdd:pfam12941    1 SHITAEAAGRRLARGSPPSMASSSASQLSAPSLKATCTANHDSPDAELIEANLLWRQEMGGNITRVESENKVVILDSFDP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  2261 LVPEYDDREPSLSAECHRPNRpKFPPALPIWARPDYNPPLLEPWKSPDYNPPMVHGCALPPPDKPPVPPPRRRKVVQLDA 2340
Cdd:pfam12941   81 LVAEEDEREVSVPAEILRKSR-RFAPALPVWARPDYNPLLVETWKKPDYEPPVVHGCPLPPPRSPPVPPPRKKRTVVLTE 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  2341 SNVSTVLAQLAEKTFPQPASlttgcgSGQAAHSTGSGEQSEEDGAASEAD--SYSSMPPLEGEPGDPDLSSGSWSTISEE 2418
Cdd:pfam12941  160 STLPTALAELATKSFGSSST------SGITGDNTTTSSEPAPSGCPPDSDveSYSSMPPLEGEPGDPDLSDGSWSTVSSG 233


                   ....*....
gi 113720390  2419 GD--GVVCC 2425
Cdd:pfam12941  234 ADteDVVCC 242
HCV_capsid pfam01543
Hepatitis C virus capsid protein;
2-115 4.05e-70

Hepatitis C virus capsid protein;


Pssm-ID: 144947  Cd Length: 121  Bit Score: 231.12  E-value: 4.05e-70
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390     2 STLPKPQRKTKRNTYRRPMDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARPPTGRSWGQPGY 81
Cdd:pfam01543    1 STNPKPQRKTKRNTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARPPEGRSWLSPGT 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 113720390    82 PWP------LYGNEG-CGWAGWLLSPRGSRPNWGPNDPRRR 115
Cdd:pfam01543   81 LGPstamraLYGNDGsCGWAGWLLPPRGSRPSWGQNDPRRR 121
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 1226-1368 1.43e-51

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: 179.28  E-value: 1.43e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 1226 QVGYLHAPTGSGKSTKVPAAYAAQGY----KVLVLNPSVAATLGFGAYMSKAhgiDPNIRTGVRTITTGG--PITYSTYG 1299
Cdd:cd17931     2 QLTVLDLHPGAGKTTRVLPQIIREAIkkrlRTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGGneIVDYMCHG 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 113720390 1300 KFLaDGGCSGGA---YDIIICDECHSTDPTTILGIGTVLDQAETsGARLTVLATATPPGSVTVPH---PNITEEA 1368
Cdd:cd17931    79 TFT-CRLLSPKRvpnYNLIIMDEAHFTDPASIAARGYIHTRVEM-GEAAVIFMTATPPGTVTPFPqsnHPIEDFE 151
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 1364-1505 3.53e-49

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: 172.45  E-value: 3.53e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 1364 ITEEALPTTGEIPFYGKGIPLDFikGGRHLIFCHSKKKCDELAKQLTTLGINAVAFYRGVDVSV---IPTDGDVVVCATD 1440
Cdd:cd18806     1 IEDVALEIPGRIWFYGKAWITIY--GGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 113720390 1441 ALMTGYTGNFDTVIDCNVAVTQVVDFSLDptFTIETT-TLPQDAVSRSQRRGRTGRGKH---GVYRYVS 1505
Cdd:cd18806    79 ISEMGANFDADRVIDCRTCVKPTILFSGD--FRVILTgPVPQTAASAAQRRGRTGRNPAqerDIYRFVG 145
HCV_NS5a_1b pfam08301
Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a ...
 2070-2170 7.50e-48

Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR. This region corresponds to the 1b domain.


Pssm-ID: 149382  Cd Length: 102  Bit Score: 166.77  E-value: 7.50e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  2070 GPSVPIPEPNYTRALWRVSAEDYVEVKRVGDSHFVVGATEDNLkCPCQVPAPEFF--TEVDGVRIHRYAPKCKPLLRDEI 2147
Cdd:pfam08301    1 GPAVPLPPPNYGPALWRVGAEDYVEVVRVGDTHYVTATSCYNL-CPCQVPRPEFFapTEVDGVRVSWYAPPCKPLLVYEV 79

                           90       100
                   ....*....|....*....|...
gi 113720390  2148 TFSVGMSSYAMGSQLPCEPEPDV 2170
Cdd:pfam08301   80 GQSVGLDGYGVRSQLPCELEPDV 102
HCV_core pfam01542
Hepatitis C virus core protein; The viral core protein forms the internal viral coat that ...
 116-190 2.91e-26

Hepatitis C virus core protein; The viral core protein forms the internal viral coat that encapsidates the genomic RNA and is enveloped in a host cell-derived lipid membrane. The core protein has been shown, by yeast two-hybrid assay to interact with cellular DEAD box helicases. The N terminus of the core protein is involved in transcriptional repression.


Pssm-ID: 460245  Cd Length: 75  Bit Score: 104.38  E-value: 2.91e-26
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 113720390   116 SRNLGKVIDTLTCGLADLMGYIPVLGGPLGGVAAALAHGVRAIEDGVNYATGNLPGCSFSIFILALLSCLTTPVS 190
Cdd:pfam01542    1 MRNLGKPIDKLKCGFADLMGDIKFPGAGLGGAARALAHGRGPLEDGRATAKGNEPGCPFGIFLLALKACLPEGAS 75
HCV_NS4a pfam01006
Hepatitis C virus non-structural protein NS4a; NS4a forms an integral part of the NS3 serine ...
 1660-1713 2.12e-21

Hepatitis C virus non-structural protein NS4a; NS4a forms an integral part of the NS3 serine protease, as it is required in a number of cases as a cofactor of cleavage. It has also been reported that NS4a interacts with NS4b and NS3 to form a multi-subunit replicase complex.


Pssm-ID: 366414  Cd Length: 55  Bit Score: 89.44  E-value: 2.12e-21
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 113720390  1660 STWVLVGGVLAALAAYCLSVGCVVICGRVSTSGQP-ALIPDREVLYRQFDEMEEC 1713
Cdd:pfam01006    1 STWVLVGGALAAGAAYCLTTGSVVVVGRWSVNGKPpAVVPDREVLYQQGEEMEEC 55
HCV_p7 cd20903
Hepatitis C virus p7 protein; Hepatitis C virus (HCV) p7 protein is a viroporin essential for ...
 749-806 1.39e-17

Hepatitis C virus p7 protein; Hepatitis C virus (HCV) p7 protein is a viroporin essential for virus production. The p7 monomer is comprised of 2 trans-membrane helices connected by a cytosolic loop, and oligomerizes to form cation-specific ion channels. These ion channels dissipate pH gradients in secretory vesicles potentially protecting acid-labile intracellular virions during egress (the rupturing of the infected cell and release of viral contents). p7 protein has at least two different functions in culture, one via the formation of these ion channels, the other through its specific interaction with the non-structural viral protein NS2. Several compounds targeting p7 have been investigated as anti-HCV drugs.


Pssm-ID: 411017  Cd Length: 58  Bit Score: 78.81  E-value: 1.39e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 113720390  749 ALENLIVLNAASAAGNHGLVWGLIFICCVWHVRGRLVPLSTYAFLQLWPLLLLVLALP 806
Cdd:cd20903     1 ALENLVVLNAASAAGTHGLLWFLLFFCAAWYIKGRLVPAATYALLGLWPLLLLLLALP 58
DEXDc smart00487
DEAD-like helicases superfamily;
1219-1388 1.02e-15

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 78.30  E-value: 1.02e-15
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390   1219 PAVPQTYQVGYLHAPTGSGKSTKVPAAYAAQGY-----KVLVLNPSVAATLGFGAYMSKAHGIDPNIRTGVRT------- 1286
Cdd:smart00487   18 EALLSGLRDVILAAPTGSGKTLAALLPALEALKrgkggRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGgdskreq 97

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390   1287 ---ITTGGP-ITYSTYGKF---LADGGCSGGAYDIIICDECHSTDP----TTILGIGTVLdqaetSGARLTVLATATPPG 1355
Cdd:smart00487   98 lrkLESGKTdILVTTPGRLldlLENDKLSLSNVDLVILDEAHRLLDggfgDQLEKLLKLL-----PKNVQLLLLSATPPE 172

                           170       180       190
                    ....*....|....*....|....*....|...
gi 113720390   1356 SVtvphPNITEEALptTGEIPFYGKGIPLDFIK 1388
Cdd:smart00487  173 EI----ENLLELFL--NDPVFIDVGFTPLEPIE 199
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
1235-1363 5.48e-06

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 48.49  E-value: 5.48e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  1235 GSGKSTKVPAAYAAQGY----KVLVLNPS--VAATlgfgayMSKA-HGIDPNIRT-GVRTITTGGPIT----YSTYGKFL 1302
Cdd:pfam07652   12 GAGKTRKVLPELVRECIdrrlRTLVLAPTrvVLAE------MEEAlRGLPIRYHTpAVSSEHTGREIVdvmcHATFTQRL 85

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 113720390  1303 ADGGCSGGaYDIIICDECHSTDPTTILGIGTVLDQAETSGARLtVLATATPPGSvTVPHPN 1363
Cdd:pfam07652   86 LSPVRVPN-YEVIIMDEAHFTDPASIAARGYISTLVELGEAAA-IFMTATPPGT-SDPFPE 143
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
1228-1321 1.85e-03

Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 43.86  E-value: 1.85e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 1228 GYLHAPTGSGKST---KVpAAYAAQGYKVLVLNPSVAatLGFGAYmSKAHGIDPNIRTGVRTITTGGPITYSTYGKFLAD 1304
Cdd:COG1061   103 GLVVAPTGTGKTVlalAL-AAELLRGKRVLVLVPRRE--LLEQWA-EELRRFLGDPLAGGGKKDSDAPITVATYQSLARR 178

                          90
                  ....*....|....*....
gi 113720390 1305 GGCS--GGAYDIIICDECH 1321
Cdd:COG1061   179 AHLDelGDRFGLVIIDEAH 197
 
Name Accession Description Interval E-value
Hepacivirus_RdRp cd23202
RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ...
 2439-2956 0e+00

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: 1159.99  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2439 CAAEEEKLPINPLSNSLIRHHNLVYSTSSKSAGLRQKKVTFDRVQLVDQHYYDTLKEIKLQASQVQARLLTTEEACDLTP 2518
Cdd:cd23202     1 CAAEEEKLPISPLSNSLLRHHNLVYSTTSRSASERQKKVTFDRLQVLDPHYDDVLKEAKARASGVKARLLSVEEACSLTP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2519 SHSARSKFGYGAKDVRSHTRKAINHINSVWEDLLEDTQTPIPTTIMAKNEVFCVDTSKGGRKPARLIVYPDLGVRVCEKK 2598
Cdd:cd23202    81 PHSARSKFGYGAKDVRSLSRKAVNHINSVWEDLLEDSETPIPTTIMAKNEVFCVTPEKGGRKPARLIVYPDLGVRVCEKM 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2599 ALFDITRKLPVAVMGDAYGFQYSPKQRVERLLRMWRSKKTPMGFSYDTRCFDSTVTERDIRTEQDIYLCCQLDPEAQQAI 2678
Cdd:cd23202   161 ALYDVAPKLPKAVMGEAYGFQYSPAQRVEFLLKMWRSKKTPMGFSYDTRCFDSTVTERDIRTEESIYQCCDLDPEARKAI 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2679 KSLTERLYVGGPMYNSKGQLCGQRRCRASGVLPTSMGNTITCFLKAKAACRAAGFTNFDMLVCGDDLVVISESAGVNEDI 2758
Cdd:cd23202   241 RSLTERLYVGGPMTNSKGQSCGYRRCRASGVFTTSSGNTLTCYLKASAACRAAGLKDPTMLVCGDDLVVIAESAGVEEDA 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2759 ANLRAFTEAMTRYSATPGDLPSPSYDLELITSCSSNVSVAHDGDGRKYYYLTRDPVTPLARAAWETARHTPVNSWLGNII 2838
Cdd:cd23202   321 AALRAFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDATGKRYYYLTRDPTTPLARAAWETARHTPVNSWLGNII 400

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2839 MYAPAIWVRMVLMTHFFQTLQAQETLDKVLDFDIYGVTYSITPLDLPVIIQRLHGMAAFSLHGYSPGELNRVAACLRKLG 2918
Cdd:cd23202   401 MYAPTLWVRMVLMTHFFSILLAQEQLEKALDFEMYGNTYSIPPLDLPAIIQRLHGLSAFSLHGYSPRELNRVAAALRKLG 480

                         490       500       510
                  ....*....|....*....|....*....|....*...
gi 113720390 2919 APPLRAWRHRARAVRAQLITRGGKAAICGRYLFNWAVK 2956
Cdd:cd23202   481 VPPLRAWRHRARAVRAKLIAQGGKAAICGKYLFNWAVK 518
HCV_NS1 pfam01560
Hepatitis C virus non-structural protein E2/NS1; The hypervariable region of the E2/NS1 region ...
 386-731 0e+00

Hepatitis C virus non-structural protein E2/NS1; The hypervariable region of the E2/NS1 region of hepatitis C virus varies greatly between viral isolates. E2 is thought to encode a structurally unconstrained envelope protein.


Pssm-ID: 110557  Cd Length: 344  Bit Score: 643.06  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390   386 YISGSSAGSTVNGLTGLFTRGPQQNLQLINSNGSWHVNRTALNCNDSLQTGFFVPLFYKQNINTSGCVERMSSCKPLDQF 465
Cdd:pfam01560    1 HVTGGSAARTTRGLVSLFSPGAKQNIQLINTNGSWHINRTALNCNDSLQTGFLASLFYTHRFNSSGCPERLASCRSIDDF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390   466 DQGWGPLSYFNVSgPSEERPYCWHYPPRPCEVVPAESVCGPVYCFTPSPVVIGTTDKRGLPTFTWGENETDVFLLGSARP 545
Cdd:pfam01560   81 RQGWGPITYEETN-PEDQRPYCWHYPPRPCGIVPASSVCGPVYCFTPSPVVVGTTDRSGAPTYSWGENETDVFLLNNTRP 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390   546 PQGSWFGCTWMNGTGYVKTCGAPPCLTQPTkGNNTLVCPTDCFRKHPDTTFGKCGSGPWLTPRCLVDYPYRLWHYPCTVN 625
Cdd:pfam01560  160 PQGNWFGCTWMNSTGFTKTCGAPPCRIGGD-GNNTLLCPTDCFRKHPDATYTKCGSGPWLTPRCMVDYPYRLWHYPCTVN 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390   626 FTIHKVRMFVGGIEHRFGAACNWTRGDRCELDDRDRVEMSPLLFSTTQMAILPCTFTTMPALSTGLIHLHQNIVDVQYLY 705
Cdd:pfam01560  239 FTIFKVRMYVGGVEHRLNAACNWTRGERCDLEDRDRSELSPLLLSTTEWQVLPCSFTTLPALSTGLIHLHQNIVDVQYLY 318

                          330       340
                   ....*....|....*....|....*.
gi 113720390   706 GISTAIVSWALKWEYVVLAFLVLADS 731
Cdd:pfam01560  319 GLGSAVTSFAIKWEYVVLLFLLLADA 344
RdRP_3 pfam00998
Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase ...
 2428-2939 0e+00

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: 585.35  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  2428 SYSWTGALItpcAAEEEKLPIN-PLSNSLIRHHNLVYSTSSKSAGLRQKKVTFDRVQLV--DQHYYDTLKEIKLQASQVQ 2504
Cdd:pfam00998    1 SYVWTGARP---AKERKILPITgPGSGLLFGVHNNSLVNLRRGLVERVFKVTFDRGGQLvpPKPYPGAFKELKYFASALV 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  2505 ARLLtteEACDLTPSHSARSKFGYGAK-DVRSHTRKAINHINSVwEDLLEDTQTPIPTTIMAKNEVFCVdtsKGGRKPAR 2583
Cdd:pfam00998   78 SKLG---EATPLTPEHFAASYTGRKRKiYVKALESLAVKPVQRR-DAILKTFVKAEKINITAKPDPAPR---VIQPRPPR 150

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  2584 LIVYPDLGVRVCEKKALFDItrklPVAVMGDAYGFQYSPKQRVERLLRMWRSKKTPMGFSYDTRCFDSTVTERDIRTEQD 2663
Cdd:pfam00998  151 YNVEPGRYLRPCEKMIYKAI----DKAFGGPTVLKGYTPEQRGEILLKKWDSFKKPVAIGLDASRFDQHVSVEALRFEHS 226

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  2664 IYLCCQLDPEaqQAIKSLTERLYVGGPMYNSKGQL-CGQRRCRASGVLPTSMGNTITCFLKAKAACRAAGfTNFDMLVCG 2742
Cdd:pfam00998  227 IYLAAFLGPE--ELIRLLTWQLYNGGPMYASDGQIkYGVRGCRMSGDMNTSLGNCLLMCLKVHAACKALG-IDARLLNNG 303

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  2743 DDLVVISESAGVNEDIanlRAFTEAMTRYSaTPGDLPSPSYDLELITSCSSNVSVAHDGDGRKYYYLTRDPVTPLARAAW 2822
Cdd:pfam00998  304 DDCVVICESADLDEVK---EALTEAFARYG-FTMKVEEPVYELELIEFCQSNPVFDGGKYGMVRNPLTSDSKDPLSRASW 379

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  2823 ETArhTPVNSWLGNIIMYAPAIWVRMVLMTHFFQTLQAQETLDKVLDFDIYGVTYSitpldlpVIIQRLHGMAAFSLHGY 2902
Cdd:pfam00998  380 ETA--TPAKSWLGAIGECGLSLWGGVPVLQHFYSCLLRNGGLEKAVSFEMYGKVYS-------DSGFRLHGLGAGSRHSY 450

                          490       500       510
                   ....*....|....*....|....*....|....*..
gi 113720390  2903 SPGELNRVAACLrKLGAPPLRAWRHRARAVRAQLITR 2939
Cdd:pfam00998  451 EPTEEARVSFWL-AFGITPDEQWALEAYYDRLKLLRQ 486
ps-ssRNAv_Flaviviridae_RdRp cd23178
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of ...
 2559-2842 6.87e-134

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: 421.16  E-value: 6.87e-134
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2559 IPTTIMAKNEVFCVDTSKGGRKPARLIVYPDLGVRVCEKKALFDITRKLPVAVMGDAYGFQYSPKQRVERLLRMWRSKKT 2638
Cdd:cd23178     1 IPTTIMPKNEVFCVEPGKGGRKPPRLIVYPDLGVRVAEKMALYDPVEVLPQVVGGSYYGFQYSPNQRVEILRKAWKSKKG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2639 PMGFSYDTRCFDSTVTERDIRTEQDIYLCCQLdPEAQQAIKSLTERLYVGGPMYNSKGQLCGQRRCRASGVLPTSMGNTI 2718
Cdd:cd23178    81 PMAYSYDTRCFDSTVTEDDIQVEEEIYQACSL-KEARQAIVSITERLYVEGPMVNSDGQICGRRRCRASGVLTTSAGNT* 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2719 TCFLKAKAACRAAGFTNFDMLVCGDDLVVISESAGVNEDIANLRAFTEAMTRYSATPGDLPSPSYDLELITSCSSNVSVA 2798
Cdd:cd23178   160 TCYLK*LAACREAGIRLPTMLVCGDDCVVICESDGTQEDAALLAAFTEALTRYGKPPKDPPQPEYDLELIESCSHTVSEV 239

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 113720390 2799 HDGDGRKYYYLTRDPVTPLARAAWETARHTPVNSWLGNIIMYAP 2842
Cdd:cd23178   240 RMKDGRRLYYLTRDPTTPLARAAWETGRHEPINSWLGYIIMYAL 283
HCV_NS2 pfam01538
Hepatitis C virus non-structural protein NS2; The viral genome is translated into a single ...
 813-1007 9.95e-110

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


Pssm-ID: 366698  Cd Length: 195  Bit Score: 347.74  E-value: 9.95e-110
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390   813 DTDQAASVGLLALGIITIFTLTPAYKQLLVGVLWWTQYFIARAEAMLHVWIPPLQVRGGRDAVILLSCLFHPQLGFEVTK 892
Cdd:pfam01538    1 DTEDAGWLGAAVLSWITLFTLTPTYKGLLAKLLWWLQYCIARQEARLHVWVPPLGVRGGRDAVILLWCLAHPDLVFDVTK 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390   893 ILMALLGSMYLLQYSFLKTPYFVRAHILLRACMLFRGLASGKY*QALLLRLGAWTGTYVYDHLTPLTDWACDGLRDLAVA 972
Cdd:pfam01538   81 ILLAILGPLYLLQASLLRVPYFVRAARLLRSCVLVRHLAGGKYVQMALLKLGRWTGTYLYDHLGPLSDWAAEGLRDLAVA 160

                          170       180       190
                   ....*....|....*....|....*....|....*
gi 113720390   973 VEPVVFSPMEKKVITWGADTAACGDIIEGLPVSAR 1007
Cdd:pfam01538  161 LEPVVFSPMECKIITWGADTAACGDIVHGLPVSAR 195
Pegivirus_RdRp cd23203
RNA-dependent RNA polymerase (RdRp) in the genus Pegivirus, within the family Flaviviridae of ...
 2431-2922 1.15e-93

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: 313.43  E-value: 1.15e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2431 WTGALITpcAAEEEKLPIN-PLSNSLIRHHNLVYSTSSKSAGLRQKKVTFDRVQLV-DQHYYDTLKEIKLQASQVQARLL 2508
Cdd:cd23203     1 WSGAPLG--VGRPKPPPVTrPVGSHLRADATKVYVTDPDDVGERIEKVTIWRTPRVvDKFLRDAYNLALAKASATPSPGW 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2509 TTEEACDLTPSHSARskfGYGAK----DVRshTRKAINHINSVWEDLLEdTQTPIPTTIMAKNEVFCVDTSKggRKPARL 2584
Cdd:cd23203    79 TYEEAVAKVRPGAAM---GHGSKvtvaDLK--TPAGKKAVEECLNQIIA-GGEEVPFTLTAKQEVFFQDKKT--RKPPRL 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2585 IVYPDLGVRVCEKKALFDITRkLPVAVMGDAYGFQYSPKQRVERLLRMWRSKKTPMGFSYDTRCFDSTVTERDIRTEQDI 2664
Cdd:cd23203   151 IVYPPLEFRVAEKMILGDPGR-VAKAVLGKAYGFQYTPNQRVKVLVDMWKSKRHPCAITVDATCFDSSITEEDVARETEI 229

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2665 YLCCQLDPEAQQAIksltERLYVGGPMYNSKGQLCGQRRCRASGVLPTSMGNTITCFLKAKAACRAAGFTNFDMLVCGDD 2744
Cdd:cd23203   230 YAAASDDPELVRAL----GKYYAEGPMVNPEGVPVGERRCRASGVLTTSSSNSITCYLKVKAACRKAGLKNPSFLIHGDD 305

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2745 LVVISESAGvnEDIAnlRAFTEAMTRYsatpGDLPSPSY--DLELITSCSSNVSVAHDGdGRKYYYLTRDPVTPLARAAW 2822
Cdd:cd23203   306 CLIICERPE--EDPC--DALKAALASY----GYDCEPQYhaSLDTAESCSAYLAECNAG-GGRHYFLSTDMRRPLARASS 376

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2823 ETArhTPVNSWLGNIIMYAPAIWVRMVLMTHFFQT-LQAQETLDKVLDFDIYGVTYSItPLD-LPVIIQRLHGMAAFSLH 2900
Cdd:cd23203   377 EYG--DPVASALGYILLYPWHPITRYVLLPHLLTLaFRGGGTPDDLVTCQVHGNSYKF-PLKlLPRILVGLHGPDCLRVT 453

                         490       500
                  ....*....|....*....|..
gi 113720390 2901 GYSPGELNRVAACLRKLGAPPL 2922
Cdd:cd23203   454 ADSTKTLMEAGKALQAFGMRGL 475
HCV_env pfam01539
Hepatitis C virus envelope glycoprotein E1;
195-382 2.27e-91

Hepatitis C virus envelope glycoprotein E1;


Pssm-ID: 110536  Cd Length: 190  Bit Score: 294.86  E-value: 2.27e-91
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390   195 KNASGVYHLTNDCPNSSIVYEAESIILHLPGCVPCVRSKNVSRCWYSVSPTLAVFDASTPVHGFRRHVDLIVGAAAFCSA 274
Cdd:pfam01539    3 RNISGSYHVTNDCSNSSITWQLADAVLHTPGCVPCEREGNTSRCWIAVTPNVAVRHRGALTTSLRTHVDMLVMAATLCSA 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390   275 MYIGDLCGGVFLVGQVFTLRPKIHTTVQDCNCSIYTGHITGHRMAWDMMMNWSPTVTYVVSSALRTPQLLLEIFLGAHWG 354
Cdd:pfam01539   83 LYVGDLCGSVMLVSQLFTVSPQRHWFTQDCNCSIYPGHITGHRMAWDMMMNWSPTATMILAYALRVPEAVLDIIAGAHWG 162

                          170       180
                   ....*....|....*....|....*...
gi 113720390   355 VLGAVVYYCMVANWAKVLVVLLMFAGVD 382
Cdd:pfam01539  163 VLFGLAYFSMQGAWAKVLVILLLFAGVD 190
HCV_NS4b pfam01001
Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. ...
 1730-1923 1.54e-90

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: 292.74  E-value: 1.54e-90
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  1730 FKQKVLGLIQTSAKQAEELKPVVTSAWPKLEQFWTKHLWNFVSGIQYLAGLSTLPGNPAIASLMSFSASLTSPLSTSTTL 1809
Cdd:pfam01001    1 FAFKALGLLPPAIDKAESITPAVASLDTKFEQFWAKHMWNFRSGIQYLAGLYTLPRNPPLAVLASFLAGMTSPLPTHVRL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  1810 LLNILGGWVASQLATPTASTSFVVSGLAGAAVGSIGLGKVIVDVLAGYGAGISGALVGFKIMCGETPSAEDMVNLLPALL 1889
Cdd:pfam01001   81 ALALLGGWGATQLGTPSGGLAFVGAGFAGAAVGSSWLGRVLVDVLGGYEAAVNAASLTFKIMSGELPTAEDLWNLLPCLL 160

                          170       180       190
                   ....*....|....*....|....*....|....
gi 113720390  1890 SPGALVVGVVCAAILRRHTGpsEGATQWMNRLIA 1923
Cdd:pfam01001  161 SPGASVVGVALAALLRSHKG--EGAVQWMNRLLT 192
Peptidase_S29 pfam02907
Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a ...
 1058-1205 2.31e-81

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


Pssm-ID: 427049  Cd Length: 149  Bit Score: 264.67  E-value: 2.31e-81
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  1058 EGEVQVVSTATQSFLATTLNGVLWTVYHGAGSKTLAGPKGPICQMYTNVEQDLVGWPAPSGARSLTPCSCGSSDLYLVTR 1137
Cdd:pfam02907    1 EGEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTR 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 113720390  1138 NADVIPARRRGDSRAALLSPRPISTLKGSSGGPMLCPSGHVAGIFRAAVCTRGVAKSLDFVPVENMQT 1205
Cdd:pfam02907   81 DGDLIPGRRRGDPRVSLLSPRPLSYLKGSSGGPILCPSGHVVGMFRAAVHSGGVVKAVRFVPWETLPT 148
HCV_NS5a_C pfam12941
HCV NS5a protein C-terminal region; This is a family of proteins found in the hepatitis C ...
 2181-2425 2.40e-73

HCV NS5a protein C-terminal region; This is a family of proteins found in the hepatitis C virus. This family contains the C-terminal region of the NS5A protein. CC The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR.


Pssm-ID: 289693  Cd Length: 242  Bit Score: 245.62  E-value: 2.40e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  2181 SHVTAEAAARRLARGSPPSLASSSASQLSALSLKGTCTTHGPHPDAELIEANLLWRQEMGNNITRVESESKVIILDSFDP 2260
Cdd:pfam12941    1 SHITAEAAGRRLARGSPPSMASSSASQLSAPSLKATCTANHDSPDAELIEANLLWRQEMGGNITRVESENKVVILDSFDP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  2261 LVPEYDDREPSLSAECHRPNRpKFPPALPIWARPDYNPPLLEPWKSPDYNPPMVHGCALPPPDKPPVPPPRRRKVVQLDA 2340
Cdd:pfam12941   81 LVAEEDEREVSVPAEILRKSR-RFAPALPVWARPDYNPLLVETWKKPDYEPPVVHGCPLPPPRSPPVPPPRKKRTVVLTE 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  2341 SNVSTVLAQLAEKTFPQPASlttgcgSGQAAHSTGSGEQSEEDGAASEAD--SYSSMPPLEGEPGDPDLSSGSWSTISEE 2418
Cdd:pfam12941  160 STLPTALAELATKSFGSSST------SGITGDNTTTSSEPAPSGCPPDSDveSYSSMPPLEGEPGDPDLSDGSWSTVSSG 233


                   ....*....
gi 113720390  2419 GD--GVVCC 2425
Cdd:pfam12941  234 ADteDVVCC 242
HCV_capsid pfam01543
Hepatitis C virus capsid protein;
2-115 4.05e-70

Hepatitis C virus capsid protein;


Pssm-ID: 144947  Cd Length: 121  Bit Score: 231.12  E-value: 4.05e-70
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390     2 STLPKPQRKTKRNTYRRPMDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARPPTGRSWGQPGY 81
Cdd:pfam01543    1 STNPKPQRKTKRNTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARPPEGRSWLSPGT 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 113720390    82 PWP------LYGNEG-CGWAGWLLSPRGSRPNWGPNDPRRR 115
Cdd:pfam01543   81 LGPstamraLYGNDGsCGWAGWLLPPRGSRPSWGQNDPRRR 121
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 1226-1368 1.43e-51

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: 179.28  E-value: 1.43e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 1226 QVGYLHAPTGSGKSTKVPAAYAAQGY----KVLVLNPSVAATLGFGAYMSKAhgiDPNIRTGVRTITTGG--PITYSTYG 1299
Cdd:cd17931     2 QLTVLDLHPGAGKTTRVLPQIIREAIkkrlRTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGGneIVDYMCHG 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 113720390 1300 KFLaDGGCSGGA---YDIIICDECHSTDPTTILGIGTVLDQAETsGARLTVLATATPPGSVTVPH---PNITEEA 1368
Cdd:cd17931    79 TFT-CRLLSPKRvpnYNLIIMDEAHFTDPASIAARGYIHTRVEM-GEAAVIFMTATPPGTVTPFPqsnHPIEDFE 151
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 1364-1505 3.53e-49

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: 172.45  E-value: 3.53e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 1364 ITEEALPTTGEIPFYGKGIPLDFikGGRHLIFCHSKKKCDELAKQLTTLGINAVAFYRGVDVSV---IPTDGDVVVCATD 1440
Cdd:cd18806     1 IEDVALEIPGRIWFYGKAWITIY--GGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 113720390 1441 ALMTGYTGNFDTVIDCNVAVTQVVDFSLDptFTIETT-TLPQDAVSRSQRRGRTGRGKH---GVYRYVS 1505
Cdd:cd18806    79 ISEMGANFDADRVIDCRTCVKPTILFSGD--FRVILTgPVPQTAASAAQRRGRTGRNPAqerDIYRFVG 145
HCV_NS5a_1b pfam08301
Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a ...
 2070-2170 7.50e-48

Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR. This region corresponds to the 1b domain.


Pssm-ID: 149382  Cd Length: 102  Bit Score: 166.77  E-value: 7.50e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  2070 GPSVPIPEPNYTRALWRVSAEDYVEVKRVGDSHFVVGATEDNLkCPCQVPAPEFF--TEVDGVRIHRYAPKCKPLLRDEI 2147
Cdd:pfam08301    1 GPAVPLPPPNYGPALWRVGAEDYVEVVRVGDTHYVTATSCYNL-CPCQVPRPEFFapTEVDGVRVSWYAPPCKPLLVYEV 79

                           90       100
                   ....*....|....*....|...
gi 113720390  2148 TFSVGMSSYAMGSQLPCEPEPDV 2170
Cdd:pfam08301   80 GQSVGLDGYGVRSQLPCELEPDV 102
RNA_dep_RNAP cd01699
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
 2542-2823 1.52e-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: 1.52e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2542 NHINSVWEDLLedTQTPIPTTIMAKNEVFCVDtsKGGRKPARLIVYPDLGVRVCEKKALFDITRKLPVAVMGDAYGFQYS 2621
Cdd:cd01699     3 KAVESLEDLPL--IRPDLVFTTFLKDELRPLE--KVEAGKTRLIQPRPLDYNIALRMYLGPFEAKLMKNRGGLPIAVGIN 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2622 PKQR-VERLLRMWRSKKtPMGFSYDTRCFDSTVTERDIRTEQDIYLCCQLDP---EAQQAIKSLTERLYvggPMYNskGQ 2697
Cdd:cd01699    79 PYSRdWTILANKLRSFS-PVAIALDYSRFDSSLSPQLLEAEHSIYNALYDDDdelERRNLLRSLTNNSL---HIGF--NE 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2698 LCGQRRCRASGVLPTSMGNTITCFLKAKAACRAAG----FTNFDMLVCGDDLVVISESAgvnEDIANLRAFTEAMTRYSA 2773
Cdd:cd01699   153 VYKVRGGRPSGDPLTSIGNSIINCILVRYAFRKLGgksfFKNVRLLNYGDDCLLSVEKA---DDKFNLETLAEWLKEYGL 229

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 113720390 2774 TPGDLP---SPSYDLELITSCSSNVSVahdgDGRKYYYLTRDPVTPLARAAWE 2823
Cdd:cd01699   230 TMTDEDkveSPFRPLEEVEFLKRRFVL----DEGGGWRAPLDPSSILSKLSWS 278
HCV_core pfam01542
Hepatitis C virus core protein; The viral core protein forms the internal viral coat that ...
 1-75 9.84e-31

Hepatitis C virus core protein; The viral core protein forms the internal viral coat that encapsidates the genomic RNA and is enveloped in a host cell-derived lipid membrane. The core protein has been shown, by yeast two-hybrid assay to interact with cellular DEAD box helicases. The N terminus of the core protein is involved in transcriptional repression.


Pssm-ID: 460245  Cd Length: 75  Bit Score: 117.09  E-value: 9.84e-31
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 113720390     1 MSTLPKPQRKTKRNTYRRPMDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARPPTGRS 75
Cdd:pfam01542    1 MRNLGKPIDKLKCGFADLMGDIKFPGAGLGGAARALAHGRGPLEDGRATAKGNEPGCPFGIFLLALKACLPEGAS 75
HCV_core pfam01542
Hepatitis C virus core protein; The viral core protein forms the internal viral coat that ...
 116-190 2.91e-26

Hepatitis C virus core protein; The viral core protein forms the internal viral coat that encapsidates the genomic RNA and is enveloped in a host cell-derived lipid membrane. The core protein has been shown, by yeast two-hybrid assay to interact with cellular DEAD box helicases. The N terminus of the core protein is involved in transcriptional repression.


Pssm-ID: 460245  Cd Length: 75  Bit Score: 104.38  E-value: 2.91e-26
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 113720390   116 SRNLGKVIDTLTCGLADLMGYIPVLGGPLGGVAAALAHGVRAIEDGVNYATGNLPGCSFSIFILALLSCLTTPVS 190
Cdd:pfam01542    1 MRNLGKPIDKLKCGFADLMGDIKFPGAGLGGAARALAHGRGPLEDGRATAKGNEPGCPFGIFLLALKACLPEGAS 75
HCV_NS4a pfam01006
Hepatitis C virus non-structural protein NS4a; NS4a forms an integral part of the NS3 serine ...
 1660-1713 2.12e-21

Hepatitis C virus non-structural protein NS4a; NS4a forms an integral part of the NS3 serine protease, as it is required in a number of cases as a cofactor of cleavage. It has also been reported that NS4a interacts with NS4b and NS3 to form a multi-subunit replicase complex.


Pssm-ID: 366414  Cd Length: 55  Bit Score: 89.44  E-value: 2.12e-21
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 113720390  1660 STWVLVGGVLAALAAYCLSVGCVVICGRVSTSGQP-ALIPDREVLYRQFDEMEEC 1713
Cdd:pfam01006    1 STWVLVGGALAAGAAYCLTTGSVVVVGRWSVNGKPpAVVPDREVLYQQGEEMEEC 55
HCV_p7 cd20903
Hepatitis C virus p7 protein; Hepatitis C virus (HCV) p7 protein is a viroporin essential for ...
 749-806 1.39e-17

Hepatitis C virus p7 protein; Hepatitis C virus (HCV) p7 protein is a viroporin essential for virus production. The p7 monomer is comprised of 2 trans-membrane helices connected by a cytosolic loop, and oligomerizes to form cation-specific ion channels. These ion channels dissipate pH gradients in secretory vesicles potentially protecting acid-labile intracellular virions during egress (the rupturing of the infected cell and release of viral contents). p7 protein has at least two different functions in culture, one via the formation of these ion channels, the other through its specific interaction with the non-structural viral protein NS2. Several compounds targeting p7 have been investigated as anti-HCV drugs.


Pssm-ID: 411017  Cd Length: 58  Bit Score: 78.81  E-value: 1.39e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 113720390  749 ALENLIVLNAASAAGNHGLVWGLIFICCVWHVRGRLVPLSTYAFLQLWPLLLLVLALP 806
Cdd:cd20903     1 ALENLVVLNAASAAGTHGLLWFLLFFCAAWYIKGRLVPAATYALLGLWPLLLLLLALP 58
DEXDc smart00487
DEAD-like helicases superfamily;
1219-1388 1.02e-15

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 78.30  E-value: 1.02e-15
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390   1219 PAVPQTYQVGYLHAPTGSGKSTKVPAAYAAQGY-----KVLVLNPSVAATLGFGAYMSKAHGIDPNIRTGVRT------- 1286
Cdd:smart00487   18 EALLSGLRDVILAAPTGSGKTLAALLPALEALKrgkggRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGgdskreq 97

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390   1287 ---ITTGGP-ITYSTYGKF---LADGGCSGGAYDIIICDECHSTDP----TTILGIGTVLdqaetSGARLTVLATATPPG 1355
Cdd:smart00487   98 lrkLESGKTdILVTTPGRLldlLENDKLSLSNVDLVILDEAHRLLDggfgDQLEKLLKLL-----PKNVQLLLLSATPPE 172

                           170       180       190
                    ....*....|....*....|....*....|...
gi 113720390   1356 SVtvphPNITEEALptTGEIPFYGKGIPLDFIK 1388
Cdd:smart00487  173 EI----ENLLELFL--NDPVFIDVGFTPLEPIE 199
ps_ssRNAv_Tolivirales_RdRp cd23179
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Toliovirales of ...
 2620-2792 8.08e-13

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: 70.63  E-value: 8.08e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2620 YSPKQRVERLLRMWRSKKTPMGFSYDTRCFDSTVTERDIRTEQDIYL-CCQLDPEAQqaiKSLTERLYVGGpmYNSKGQL 2698
Cdd:cd23179    64 LNPRQRANLIRRKWDEFDDPVVFSLDASRFDAHVSVELLRLEHSVYLaCYPGDPELR---KLLKWQLVNKG--RTSNGVK 138

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2699 CGQRRCRASGVLPTSMGNTITCFLKAKAACRAAGFTnFDMLVCGDDLVVISESagvnEDIANLRAFTEAMTRYSATPGDL 2778
Cdd:cd23179   139 YKTRGGRMSGDMNTGLGNCLIMLAMVYAVLRELGIK-YDLLVDGDDALVFVER----EDLERLLEEFAEFFLEGGGEETV 213

                         170
                  ....*....|....
gi 113720390 2779 PSPSYDLELITSCS 2792
Cdd:cd23179   214 EKPATVLEEVEFCQ 227
Pestivirus_RdRp cd23201
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Pestivirus, within ...
 2579-2821 3.73e-08

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Pestivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Pestivirus genus within the family Flaviviridae, order Amarillovirales. Members of the genus Pestivirus infect pigs and ruminants, including cattle, sheep, goats and wild ruminants, and are transmitted through contact with infected secretions (respiratory droplets, urine or feces). Infections may be subclinical or cause enteric, hemorrhagic or wasting diseases, including those by the economically important bovine viral diarrhea virus and classical swine fever virus. Virions of Pestivirus have a single, small, basic capsid (C) protein and three 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: 438051  Cd Length: 579  Bit Score: 59.27  E-value: 3.73e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2579 RKPaRLIVYPDLGVRVCEKKALFDITRKLPVAVMGdaYG-----FQYSPKQRVErllrmWRSKKTPMGFSYDTRCFDSTV 2653
Cdd:cd23201   186 KKP-RVIQYPEAKTRLAITKVMYNWVKQKPVVIPG--YEgktplFNIFNKVRKE-----WDQFQEPVAVSFDTKAWDTQV 257

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2654 TERDIRTEQDI--YLccqLDPEAQQAIKSLTERLY------VGGPMYNSKGQlcgqrrcRASGVLPTSMGNTITCFLK-A 2724
Cdd:cd23201   258 TSKDLRLIGEIqkYY---YKKKWHKFIDTLTEHMVevpvitADGEVYIRKGQ-------RGSGQPDTSAGNSMLNVLTmI 327

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2725 KAACRAAG--FTNFDML----VCGDDLVVISESaGVNEDIAN--LRAFTEAMTRYSATPGDLPSPSYDLELITSCSSNVS 2796
Cdd:cd23201   328 YAFCEATGvpYKSFNRVakihVCGDDGFLITEK-GLGEKFASkgVQILHEAGKPQKITEGDKMKVAYRFEDIEFCSHTPI 406

                         250       260
                  ....*....|....*....|....*
gi 113720390 2797 VAHDGDGRKYYYLTRDPVTPLARAA 2821
Cdd:cd23201   407 PVRWSDNTSSYMPGRDTATILSKMA 431
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 1362-1441 3.95e-06

C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an evolutionarily conserved class of enzymes, dedicated to preserving genomic integrity by operating in telomere maintenance, DNA repair, and replication. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350181 [Multi-domain]  Cd Length: 134  Bit Score: 48.74  E-value: 3.95e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 1362 PNITEEALPTTGEIPFYG-KGIPLDFIKGGRHLIFCHSKKKCDELAKQLTTLGINAVAFYRG----VDVSVIP---TDGD 1433
Cdd:cd18794     2 PNLFYSVRPKDKKDEKLDlLKRIKVEHLGGSGIIYCLSRKECEQVAARLQSKGISAAAYHAGlepsDRRDVQRkwlRDKI 81


                  ....*...
gi 113720390 1434 VVVCATDA 1441
Cdd:cd18794    82 QVIVATVA 89
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
1235-1363 5.48e-06

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 48.49  E-value: 5.48e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  1235 GSGKSTKVPAAYAAQGY----KVLVLNPS--VAATlgfgayMSKA-HGIDPNIRT-GVRTITTGGPIT----YSTYGKFL 1302
Cdd:pfam07652   12 GAGKTRKVLPELVRECIdrrlRTLVLAPTrvVLAE------MEEAlRGLPIRYHTpAVSSEHTGREIVdvmcHATFTQRL 85

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 113720390  1303 ADGGCSGGaYDIIICDECHSTDPTTILGIGTVLDQAETSGARLtVLATATPPGSvTVPHPN 1363
Cdd:pfam07652   86 LSPVRVPN-YEVIIMDEAHFTDPASIAARGYISTLVELGEAAA-IFMTATPPGT-SDPFPE 143
ps-ssRNAv_RdRp-like cd23167
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
 2704-2750 1.05e-05

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: 45.79  E-value: 1.05e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 113720390 2704 CRASGVLPTSMGNTITCFLKAKAACRAAGFT-----NFDMLVCGDDLVVISE 2750
Cdd:cd23167    22 GQPSGSPNTSADNSLINLLLARLALRKACGRaeflnSVGILVYGDDSLVSVP 73
Tombusvirus-like_RdRp cd23236
RNA-dependent RNA polymerase (RdRp) in the genus Tombusvirus of positive-sense single-stranded ...
 2525-2827 3.18e-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: 49.24  E-value: 3.18e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2525 KFGY--------GAKdVRSHTRKAIN-HINSVWEdllEDTQTpiptTIMAKNEVfcVDTSKGgrKPARLIVYP------- 2588
Cdd:cd23236    84 RLGYdgflsyysGAK-LRTYTRAVESlHITPVSE---RDSHL----TTFVKAEK--ISTSKG--DPAPRVIQPrnprynv 151

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2589 DLG--VRVCEKKALfditrKLPVAVMGDAYGFQYSPKQRVERLLR-MWRSKKTPMGFSYDTRCFDSTVTERDIRTEQDIY 2665
Cdd:cd23236   152 ELGryLRHMESKLM-----KAVDGVFGETTCIKGYTADEVGAIFRdKWDRFDKPVAIGLDASRFDQHCSVEALQFEHSFY 226

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2666 LCcqLDPEAQQAIKSLTERLYVGGPMYNSKGQLCGQRR-CRASGVLPTSMGNTITCFLKAKAACRAAGFTNFDMLVCGDD 2744
Cdd:cd23236   227 RA--MYPGNKLLSKLLEWQLHNKGKGYVPDGTITYRKEgCRMSGDINTSLGNYLLMCAMVYGYMRHLGINEFSLANCGDD 304

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2745 LVVISESagvnediANLRAFTEAMTRYSATPG---DLPSPSYDLELITSCSS-------------NVSVAHDGDGRKYYY 2808
Cdd:cd23236   305 CVLIVER-------RNLKQVQGTLPEYFLNLGytmKVEPPVFQLEEVEFCQAhpvqfqggwkmvrNVRTAMSKDVHCVNN 377

                         330
                  ....*....|....*....
gi 113720390 2809 LtRDPVTplaRAAWETARH 2827
Cdd:cd23236   378 I-RDLAT---RRAWSNAQH 392
Gammacarmovirus_RdRp cd23242
RNA-dependent RNA polymerase (RdRp) in the genus Gammacarmovirus of positive-sense ...
 2633-2837 3.27e-05

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: 49.36  E-value: 3.27e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2633 WRSKKTPMGFSYDTRCFDSTVTERDIRTEQDIYL--CCQlDPEAQqaiKSLTERLYVGGPMYNSKGQLCGQRR-CRASGV 2709
Cdd:cd23242   187 WDSFVSPVAIGFDMKRFDQHVSRDALEWEHSVYLdaFCN-DPYLA---ELLSWQLENKGVGYASDGSIKYKVDgCRMSGD 262

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2710 LPTSMGNtitCFLKAK---AACRAAGFtNFDMLVCGDDLVVISES---AGVNEDIanLRAFteamTRYSATpGDLPSPSY 2783
Cdd:cd23242   263 MNTAMGN---CLLACAitwDFFKGRGI-KARLLNNGDDCVVITEKecaAAVVAGM--VRHW----RRFGFQ-CELECDVY 331

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 113720390 2784 DLELITSCssNVSVAHDGDgrkYYYLTRDPVTPLAR-----AAWETARHTpvNSWLGNI 2837
Cdd:cd23242   332 ILEHIEFC--QMRPVYDGS---KYTMVRNPLVSLSKdsysvGPWNNIKHA--AKWVNAV 383
Tombusviridae_RdRp cd23206
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tombusviridae of ...
 2620-2751 2.81e-04

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tombusviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Tombusviridae, order Tolivirales. The family Tombusviridae comprises plant viruses, and is classified into 3 subfamilies (Calvusvirinae, Procedovirinae, and Regressovirinae), 17 genera, and 95 species. One genus is unassigned to a subfamily: Luteovirus. The name of the family is derived from Tomato bushy stunt virus (TBSV). Members of Tombusviridae replicate in the cytoplasm, by use of negative strand templates. The replication process leaves a surplus of positive- sense (+)RNA strands, and it is thought that not only does the viral RNA act as a template for replication, but is also able to manipulate and regulate RNA synthesis. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438056  Cd Length: 231  Bit Score: 45.18  E-value: 2.81e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2620 YSPKQRVERLLRMWRSKKTPMGFSYDTRCFDSTVTERDIRTEQDIYL-CCQLDPEAQQAiksLTERLYVGGPMYNSKGQL 2698
Cdd:cd23206    65 YNAEERGRILREKWDSFRDPVAVGLDASRFDQHVSVDALKWEHSVYLrIFPDDKELSRL---LRWQLHNKGVARCKDGKV 141

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 113720390 2699 CGQRR-CRASGVLPTSMGNTIT-CFLkAKAACRAAGFtNFDMLVCGDDLVVISES 2751
Cdd:cd23206   142 KYKVKgGRMSGDMNTSLGNCLImCAM-VYAYLEELGI-KAELANNGDDCVLIMER 194
Alphanecrovirus_RdRp cd23237
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Alphanecrovirus of ...
 2620-2877 3.11e-04

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: 46.18  E-value: 3.11e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2620 YSPKQRVERLLRMWRSKKTPMGFSYDTRCFDSTVTERDIRTEQDIYLccQLDPEAQQAIKSLTERLYVGGPMYNSKGQLC 2699
Cdd:cd23237   141 FTLEQQGEIMRSKWKKYVNPVAVGLDASRFDQHVSVEALQYEHEFYL--RDYPNDKQLKWLLKQQLCNIGTAFASDGIIK 218

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2700 GQRR-CRASGVLPTSMGNtitCFLKAKAACRAAGFTNFDMLVC--GDDLVVISESAgvneDIANLRAFTEAMTRYSATPG 2776
Cdd:cd23237   219 YKKEgCRMSGDMNTSLGN---CILMCAMVYGLKEHLGINLSLAnnGDDCVIVCEKA----DLKKLTSSIEPYFKQFGFKM 291

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2777 DLPSPSYDLELITSCSSNvsVAHDGDG----RKYYYLTRDPVTPLARAAWEtARHTpvnSWLGNIIMYAPAIWVRMVLMT 2852
Cdd:cd23237   292 EVEKPVDIFERIEFCQTQ--PVFDGSQyimvRKPSVVTSKDVTSLIPCQNQ-AQYA---EWLQAVGECGMSINGGIPVMQ 365

                         250       260
                  ....*....|....*....|....*...
gi 113720390 2853 HFFQTLQA---QETLDKVLDFDIYGVTY 2877
Cdd:cd23237   366 NFYQMLQTgvkRTKFTKTGEFQTNGLGY 393
ResIII pfam04851
Type III restriction enzyme, res subunit;
1228-1321 5.05e-04

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 43.43  E-value: 5.05e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390  1228 GYLHAPTGSGK---STKVPAAYAAQGY--KVLVLNPSVA----ATLGFGAYMSKAHGIdPNIRTG--VRTITTGGPITYS 1296
Cdd:pfam04851   26 GLIVMATGSGKtltAAKLIARLFKKGPikKVLFLVPRKDlleqALEEFKKFLPNYVEI-GEIISGdkKDESVDDNKIVVT 104

                           90       100       110
                   ....*....|....*....|....*....|
gi 113720390  1297 TYGKF-----LADGGCSGGAYDIIICDECH 1321
Cdd:pfam04851  105 TIQSLykaleLASLELLPDFFDVIIIDEAH 134
Regressovirinae_RdRp cd23235
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Regressovirinae ...
 2549-2762 7.58e-04

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


Pssm-ID: 438085 [Multi-domain]  Cd Length: 472  Bit Score: 44.91  E-value: 7.58e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2549 EDLLEDTQTPIPTTIMAKNEVF--CVdtskgGRKparlivypdlgVRVCEKKALFDITrklpvAVMGDAYGFQ-YSPKQR 2625
Cdd:cd23235    96 EKLECDKKDPVPRTIQPRSKRYnlCI-----GQY-----------LRLNEKRMLDAID-----AVFGEKTVLSgLDNKAQ 154

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2626 VERLLRMWRSKKTPMGFSYDTRCFDSTVTERDIRTEQDIYLCCQldPEAQQAIKSLTERLYVGGPMYNSKGQLCGQRR-- 2703
Cdd:cd23235   155 GRAIAKKWSKYESPIGIGLDASRFDQHCSKDALKFEHSFYRECF--PDDKTLEDLLDWQLENEGSALMPTGELVKYRTkg 232

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 113720390 2704 CRASGVLPTSMGNTI-TC-----FLKAkAACRAAGFTNfdmlvcGDDLVVISESAGVNEDIANLR 2762
Cdd:cd23235   233 CRMSGDINTGLGNKIlMCsmvhaYLKE-VGVNASLANN------GDDCVLFCEKGDFNRINDSLR 290
Alphacarmovirus_RdRp cd23239
RNA-dependent RNA polymerase (RdRp) in the genus Alphacarmovirus of positive-sense ...
 2620-2856 8.99e-04

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: 44.74  E-value: 8.99e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2620 YSPKQRVERLLRMWRSKKTPMGFSYDTRCFDSTVTERDIRTEQDIYLCC-QLDPEAQQAiksLTERLYVGGPMYNSKGQL 2698
Cdd:cd23239   184 YTVEEVAQHISSAWDQFQIPVAIGFDMSRFDQHVSVPALQFEHSCYLACfPGDRHLAQL---LSWQLKNFGVGFASNGMI 260

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2699 CGQRR-CRASGVLPTSMGNTITCFLKAKAACRAagfTNFDMLVCGDDLVVISESAGVNEDIANLrafTEAMTRYSATpGD 2777
Cdd:cd23239   261 RYKKEgCRMSGDMNTALGNCLLACLITKHLMKG---VNCRLINNGDDCVLICERKDLGFVVSNL---TTGWRRFGFT-CI 333

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2778 LPSPSYDLELITSCssnvSVAHDGDGRKyYYLTRDPVTPLARAA-----WETARHTpvNSWLGNIIMYAPAIWVRMVLMT 2852
Cdd:cd23239   334 AEEPVYELEKIRFC----QMAPVYDGET-WVMVRDPKVSMSKDAfslvhWNNEKNA--KQWMKAVGMCGERITGGVPVVQ 406


                  ....
gi 113720390 2853 HFFQ 2856
Cdd:cd23239   407 EFYQ 410
DEXHc_HrpB cd17990
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ...
 1230-1352 9.83e-04

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


Pssm-ID: 438711 [Multi-domain]  Cd Length: 174  Bit Score: 42.70  E-value: 9.83e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 1230 LHAPTGSGKSTKVPAAYAA----QGYKVLVLNPSVAATLGFGAYMSKAHGIDPNIRTG--VRTITTGGPIT---YSTYGK 1300
Cdd:cd17990    22 LEAPPGAGKTTRVPLALLAelwiAGGKIIVLEPRRVAARAAARRLATLLGEAPGETVGyrVRGESRVGRRTrveVVTEGV 101

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 113720390 1301 FL----ADGGCSGgaYDIIICDECHSTDPTTILGIGTVLDQAETSGARLTVLA-TAT 1352
Cdd:cd17990   102 LLrrlqRDPELSG--VGAVILDEFHERSLDADLALALLLEVQQLLRDDLRLLAmSAT 156
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
1228-1321 1.85e-03

Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 43.86  E-value: 1.85e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 1228 GYLHAPTGSGKST---KVpAAYAAQGYKVLVLNPSVAatLGFGAYmSKAHGIDPNIRTGVRTITTGGPITYSTYGKFLAD 1304
Cdd:COG1061   103 GLVVAPTGTGKTVlalAL-AAELLRGKRVLVLVPRRE--LLEQWA-EELRRFLGDPLAGGGKKDSDAPITVATYQSLARR 178

                          90
                  ....*....|....*....
gi 113720390 1305 GGCS--GGAYDIIICDECH 1321
Cdd:COG1061   179 AHLDelGDRFGLVIIDEAH 197
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 1384-1500 2.78e-03

C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, 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: 350174 [Multi-domain]  Cd Length: 131  Bit Score: 40.57  E-value: 2.78e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 1384 LDFIKGGRHLIFCHSKKKCDELAKQLTTLGINAVAFY------------------------------RGVDVSVIptdgD 1433
Cdd:cd18787    22 LEKLKPGKAIIFVNTKKRVDRLAELLEELGIKVAALHgdlsqeereralkkfrsgkvrvlvatdvaaRGLDIPGV----D 97

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 113720390 1434 VVVcatdalmtgytgNFDtvidcnvavtqvvdfsldptftietttLPQDAVSRSQRRGRTGR-GKHGV 1500
Cdd:cd18787    98 HVI------------NYD---------------------------LPRDAEDYVHRIGRTGRaGRKGT 126
Betacarmovirus_RdRp cd23240
RNA-dependent RNA polymerase (RdRp) in the genus Betacarmovirus of positive-sense ...
 2633-2837 3.09e-03

RNA-dependent RNA polymerase (RdRp) in the genus Betacarmovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Betacarmovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. The single genus Carmovirus was split in 2015 into three genera, each retaining -carmovirus as part of their name: Alphacarmovirus, Betacarmovirus, and Gammacarmovirus. Different carmoviruses infect a wide range of both monocotyledonous and dicotyledonous plants. Viruses tend to remain localized, forming necrosis in artificially infected hosts. There are 4 species in the genus Betacarmovirus: Cardamine chlorotic fleck virus, Hibiscus chlorotic ringspot virus, Japanese iris necrotic ring virus, and Turnip crinkle virus. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438090  Cd Length: 451  Bit Score: 42.91  E-value: 3.09e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2633 WRSKKTPMGFSYDTRCFDSTVTERDIRTEQDIY---LCCqldPEAQQAiksLTERLYVGGPMYNSKG----QLCGqrrCR 2705
Cdd:cd23240   177 WSQFQKPCAVGFDMKRFDQHVSVDALRFEHSVYnrsFCS---PELARL---LEWQLLNSGVGHASDGfiryKVDG---CR 247

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2706 ASGVLPTSMGN-----TITCFLKAKAACRaagftnfdMLVCGDDLVVISESagvnediANLRAFTEAMTRYSatpgDL-- 2778
Cdd:cd23240   248 MSGDVNTALGNcllacLITKYLLKGIRCR--------LINNGDDCVLFFEA-------PDLAAVTERLAHWL----DFgf 308

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 113720390 2779 ----PSPSYDLELITSCssNVSVAHDGDGrkyYYLTRDPVTPLARAAWETARHTPVNS---WLGNI 2837
Cdd:cd23240   309 qcvvEEPVYELEKVEFC--QMKPIFDGEG---WVMVRNPHVSVSKDTYSITPWNNEKDagrWIAAI 369
Carmotetraviridae_RdRp cd23205
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Carmotetraviridae ...
 2624-2793 3.63e-03

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


Pssm-ID: 438055  Cd Length: 268  Bit Score: 41.92  E-value: 3.63e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2624 QRVERLLRMWRSKKTPMGFSYDTRCFDSTVTERDIRTEQDIYLCCQLDPE----AQQAIKSL--TERlyvgGPMYNSKGQ 2697
Cdd:cd23205    67 QRANLLQRMWHLYERPVSISFDLSRWDMHVQVPLLKRVLEIYSQHVTCPLlldmCQNLLKNVcyTNK----GIRYHVDGG 142

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 2698 lcgqrrcRASGVLPTSMGNtitCFLKAKAAcraagFTNFDMLVC-GDDLVVISESAGVNEDIANLRAFTEAMTRYSATPG 2776
Cdd:cd23205   143 -------IMSGDMTTGLGN---CIAVLVIV-----MSFRLSILDdGDDHVIICEKSHTWICERVLPLWWTAMGHSLRVDG 207

                         170
                  ....*....|....*..
gi 113720390 2777 dlpsPSYDLELITSCSS 2793
Cdd:cd23205   208 ----TAEDFEQIEFCQH 220
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 1228-1352 5.15e-03

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: 40.08  E-value: 5.15e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113720390 1228 GYLHAPTGSGKSTKV--PAAYAA--QGYKVLVLNPSVAATL-------GFGAYMSKAHGIDPNIRTGVRTITTGG--PIT 1294
Cdd:cd00046     4 VLITAPTGSGKTLAAllAALLLLlkKGKKVLVLVPTKALALqtaerlrELFGPGIRVAVLVGGSSAEEREKNKLGdaDII 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 113720390 1295 YSTYGKF----LADGGCSGGAYDIIICDECHSTDPTT--ILGIGTVLDQAETSGARLtVLATAT 1352
Cdd:cd00046    84 IATPDMLlnllLREDRLFLKDLKLIIVDEAHALLIDSrgALILDLAVRKAGLKNAQV-ILLSAT 146
 
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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