|
Name |
Accession |
Description |
Interval |
E-value |
| HCV_NS1 |
pfam01560 |
Hepatitis C virus non-structural protein E2/NS1; The hypervariable region of the E2/NS1 region ... |
369-712 |
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: 730.88 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 369 HVTGGSAARGASGLVNLFNPGAQQNIQLINTNGSWHINRTALNCNDSLQTGWLAGLLYTHRFNSSGCSERLASCRPLTDF 448
Cdd:pfam01560 1 HVTGGSAARTTRGLVSLFSPGAKQNIQLINTNGSWHINRTALNCNDSLQTGFLASLFYTHRFNSSGCPERLASCRSIDDF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 449 DQGWGPISYANGSGPDQRPYCWHYPPKPCGIVPAKSVCGPVYCFTPSPVVVGTTDRSGAPTYNWGENETDVFVLNNTRPP 528
Cdd:pfam01560 81 RQGWGPITYEETNPEDQRPYCWHYPPRPCGIVPASSVCGPVYCFTPSPVVVGTTDRSGAPTYSWGENETDVFLLNNTRPP 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 529 LGNWFGCTWMNSTGFTKVCGAPPCVIGGVGNNTLHCPTDCFRKHPEATYSRCGSGPWITPRCLVHYPYRLWHYPCTINYT 608
Cdd:pfam01560 161 QGNWFGCTWMNSTGFTKTCGAPPCRIGGDGNNTLLCPTDCFRKHPDATYTKCGSGPWLTPRCMVDYPYRLWHYPCTVNFT 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 609 IFKVRMYVGGVEHRLEAACNWTRGERCDLEDRDRSELSPLLLSTTQWQVLPCSFTTLPALSTGLIHLHQNIVDVQYLYGV 688
Cdd:pfam01560 241 IFKVRMYVGGVEHRLNAACNWTRGERCDLEDRDRSELSPLLLSTTEWQVLPCSFTTLPALSTGLIHLHQNIVDVQYLYGL 320
|
330 340
....*....|....*....|....
gi 1839358633 689 GSSIASWAIKWEYVVLLFLLLADA 712
Cdd:pfam01560 321 GSAVTSFAIKWEYVVLLFLLLADA 344
|
|
| HCV_env super family |
cl03255 |
Hepatitis C virus envelope glycoprotein E1; |
176-365 |
3.65e-111 |
|
Hepatitis C virus envelope glycoprotein E1;
The actual alignment was detected with superfamily member pfam01539:
Pssm-ID: 110536 Cd Length: 190 Bit Score: 349.95 E-value: 3.65e-111
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 176 QVRNSTGLYHVTNDCPNSSIVYESEGAILHTPGCVPCVREGNISRCWVPMTPTVATRDGKLPATQLRRHIDLLVGSATLC 255
Cdd:pfam01539 1 EVRNISGSYHVTNDCSNSSITWQLADAVLHTPGCVPCEREGNTSRCWIAVTPNVAVRHRGALTTSLRTHVDMLVMAATLC 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 256 SALYVGDLCGSVFLVGQLFTFSPRLYWTTQGCNCSIYPGHITGHRMAWDMMMNWSPTSALVVAQVLRIPQAIVDMIAGAH 335
Cdd:pfam01539 81 SALYVGDLCGSVMLVSQLFTVSPQRHWFTQDCNCSIYPGHITGHRMAWDMMMNWSPTATMILAYALRVPEAVLDIIAGAH 160
|
170 180 190
....*....|....*....|....*....|
gi 1839358633 336 WGVLAGIAYFSMVGNWAKVLVVLLLFAGVD 365
Cdd:pfam01539 161 WGVLFGLAYFSMQGAWAKVLVILLLFAGVD 190
|
|
| HCV_NS2 |
pfam01538 |
Hepatitis C virus non-structural protein NS2; The viral genome is translated into a single ... |
794-988 |
1.37e-104 |
|
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: 331.56 E-value: 1.37e-104
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 794 DTEVAASCGGVVLVGLMALTLSPYYKRYISWCLWWLQYLLTRAEAQLHVWVPPLNVRGGRDAVILLTCVVHPTLVFDITK 873
Cdd:pfam01538 1 DTEDAGWLGAAVLSWITLFTLTPTYKGLLAKLLWWLQYCIARQEARLHVWVPPLGVRGGRDAVILLWCLAHPDLVFDVTK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 874 LLLAVLGPLWILQASLLKVPYFVRVQGLLRLCALARKVVGGHYVQMVIIKLGALTGTYIYNHLTPLRDWAHNGLQDLAVA 953
Cdd:pfam01538 81 ILLAILGPLYLLQASLLRVPYFVRAARLLRSCVLVRHLAGGKYVQMALLKLGRWTGTYLYDHLGPLSDWAAEGLRDLAVA 160
|
170 180 190
....*....|....*....|....*....|....*
gi 1839358633 954 VEPVVFSRMETKLITWGADTAACGDIINGLPVSAR 988
Cdd:pfam01538 161 LEPVVFSPMECKIITWGADTAACGDIVHGLPVSAR 195
|
|
| Peptidase_S29 |
pfam02907 |
Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a ... |
1039-1186 |
1.83e-80 |
|
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: 261.21 E-value: 1.83e-80
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 1039 EGEVQIVSTAAQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDKDLVGWPAPQGARSLTPCTCGSSDLYLVTR 1118
Cdd:pfam02907 1 EGEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTR 80
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1839358633 1119 HADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGIFRAAVCTRGVAKAVDFIPVENLET 1186
Cdd:pfam02907 81 DGDLIPGRRRGDPRVSLLSPRPLSYLKGSSGGPILCPSGHVVGMFRAAVHSGGVVKAVRFVPWETLPT 148
|
|
| HCV_capsid |
pfam01543 |
Hepatitis C virus capsid protein; |
1-98 |
3.18e-60 |
|
Hepatitis C virus capsid protein;
:
Pssm-ID: 144947 Cd Length: 121 Bit Score: 202.23 E-value: 3.18e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 1 RPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARRPEGRTWAQPGYPWP------LYGNEG- 73
Cdd:pfam01543 17 RPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARPPEGRSWLSPGTLGPstamraLYGNDGs 96
|
90 100
....*....|....*....|....*
gi 1839358633 74 CGWAGWLLSPRGPRPSWGPTDPRRR 98
Cdd:pfam01543 97 CGWAGWLLPPRGSRPSWGQNDPRRR 121
|
|
| DEXHc_viral_Ns3 |
cd17931 |
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ... |
1206-1349 |
1.27e-52 |
|
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: 181.59 E-value: 1.27e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 1206 FQVAHLHAPTGSGKSTKVPAAYAAQGY----KVLVLNPSVAATLGFGAYMSKAhgiDPNIRTGVRTITTS--SPITYSTY 1279
Cdd:cd17931 1 GQLTVLDLHPGAGKTTRVLPQIIREAIkkrlRTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGgnEIVDYMCH 77
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1839358633 1280 GKFLaDGGCSGGA---YDIIICDECHSTDATSILGIGTVLDQAETaGARLVVLATATPPGSITVPH---SNIEEVA 1349
Cdd:cd17931 78 GTFT-CRLLSPKRvpnYNLIIMDEAHFTDPASIAARGYIHTRVEM-GEAAVIFMTATPPGTVTPFPqsnHPIEDFE 151
|
|
| P-loop_NTPase super family |
cl38936 |
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ... |
1345-1466 |
8.18e-48 |
|
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: 167.82 E-value: 8.18e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 1345 IEEVALSTTGEIPFYGKAIPLeaIRGGRHLIFCHSRKKCDELAAKLVALGVNAVAYYRGLDVSV---IPTSGDVVVVATD 1421
Cdd:cd18806 1 IEDVALEIPGRIWFYGKAWIT--IYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 1839358633 1422 ALMTGFTGDFDSVIDCNTCVTQTVDFSLDptFTIETT-TLPQDAVS 1466
Cdd:cd18806 79 ISEMGANFDADRVIDCRTCVKPTILFSGD--FRVILTgPVPQTAAS 122
|
|
| HCV_core super family |
cl46603 |
Hepatitis C virus core protein; The viral core protein forms the internal viral coat that ... |
99-173 |
1.68e-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.
The actual alignment was detected with superfamily member pfam01542:
Pssm-ID: 480943 Cd Length: 75 Bit Score: 118.24 E-value: 1.68e-31
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1839358633 99 SRNLGKVIDTLTCGFADLMGYIPLVGAPLGGAARALAHGVRVLEDGVNYATGNLPGCSFSIFLLALLSCLTVPAS 173
Cdd:pfam01542 1 MRNLGKPIDKLKCGFADLMGDIKFPGAGLGGAARALAHGRGPLEDGRATAKGNEPGCPFGIFLLALKACLPEGAS 75
|
|
| HCV_p7 |
cd20903 |
Hepatitis C virus p7 protein; Hepatitis C virus (HCV) p7 protein is a viroporin essential for ... |
730-787 |
7.77e-22 |
|
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: 89.98 E-value: 7.77e-22
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 1839358633 730 ALENLVILNAASLAGTHGLASFLVFFCFAWYLKGKWVPGAVYALYGMWPLLLLLLALP 787
Cdd:cd20903 1 ALENLVVLNAASAAGTHGLLWFLLFFCAAWYIKGRLVPAATYALLGLWPLLLLLLALP 58
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| HCV_NS1 |
pfam01560 |
Hepatitis C virus non-structural protein E2/NS1; The hypervariable region of the E2/NS1 region ... |
369-712 |
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: 730.88 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 369 HVTGGSAARGASGLVNLFNPGAQQNIQLINTNGSWHINRTALNCNDSLQTGWLAGLLYTHRFNSSGCSERLASCRPLTDF 448
Cdd:pfam01560 1 HVTGGSAARTTRGLVSLFSPGAKQNIQLINTNGSWHINRTALNCNDSLQTGFLASLFYTHRFNSSGCPERLASCRSIDDF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 449 DQGWGPISYANGSGPDQRPYCWHYPPKPCGIVPAKSVCGPVYCFTPSPVVVGTTDRSGAPTYNWGENETDVFVLNNTRPP 528
Cdd:pfam01560 81 RQGWGPITYEETNPEDQRPYCWHYPPRPCGIVPASSVCGPVYCFTPSPVVVGTTDRSGAPTYSWGENETDVFLLNNTRPP 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 529 LGNWFGCTWMNSTGFTKVCGAPPCVIGGVGNNTLHCPTDCFRKHPEATYSRCGSGPWITPRCLVHYPYRLWHYPCTINYT 608
Cdd:pfam01560 161 QGNWFGCTWMNSTGFTKTCGAPPCRIGGDGNNTLLCPTDCFRKHPDATYTKCGSGPWLTPRCMVDYPYRLWHYPCTVNFT 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 609 IFKVRMYVGGVEHRLEAACNWTRGERCDLEDRDRSELSPLLLSTTQWQVLPCSFTTLPALSTGLIHLHQNIVDVQYLYGV 688
Cdd:pfam01560 241 IFKVRMYVGGVEHRLNAACNWTRGERCDLEDRDRSELSPLLLSTTEWQVLPCSFTTLPALSTGLIHLHQNIVDVQYLYGL 320
|
330 340
....*....|....*....|....
gi 1839358633 689 GSSIASWAIKWEYVVLLFLLLADA 712
Cdd:pfam01560 321 GSAVTSFAIKWEYVVLLFLLLADA 344
|
|
| HCV_env |
pfam01539 |
Hepatitis C virus envelope glycoprotein E1; |
176-365 |
3.65e-111 |
|
Hepatitis C virus envelope glycoprotein E1;
Pssm-ID: 110536 Cd Length: 190 Bit Score: 349.95 E-value: 3.65e-111
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 176 QVRNSTGLYHVTNDCPNSSIVYESEGAILHTPGCVPCVREGNISRCWVPMTPTVATRDGKLPATQLRRHIDLLVGSATLC 255
Cdd:pfam01539 1 EVRNISGSYHVTNDCSNSSITWQLADAVLHTPGCVPCEREGNTSRCWIAVTPNVAVRHRGALTTSLRTHVDMLVMAATLC 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 256 SALYVGDLCGSVFLVGQLFTFSPRLYWTTQGCNCSIYPGHITGHRMAWDMMMNWSPTSALVVAQVLRIPQAIVDMIAGAH 335
Cdd:pfam01539 81 SALYVGDLCGSVMLVSQLFTVSPQRHWFTQDCNCSIYPGHITGHRMAWDMMMNWSPTATMILAYALRVPEAVLDIIAGAH 160
|
170 180 190
....*....|....*....|....*....|
gi 1839358633 336 WGVLAGIAYFSMVGNWAKVLVVLLLFAGVD 365
Cdd:pfam01539 161 WGVLFGLAYFSMQGAWAKVLVILLLFAGVD 190
|
|
| HCV_NS2 |
pfam01538 |
Hepatitis C virus non-structural protein NS2; The viral genome is translated into a single ... |
794-988 |
1.37e-104 |
|
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: 331.56 E-value: 1.37e-104
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 794 DTEVAASCGGVVLVGLMALTLSPYYKRYISWCLWWLQYLLTRAEAQLHVWVPPLNVRGGRDAVILLTCVVHPTLVFDITK 873
Cdd:pfam01538 1 DTEDAGWLGAAVLSWITLFTLTPTYKGLLAKLLWWLQYCIARQEARLHVWVPPLGVRGGRDAVILLWCLAHPDLVFDVTK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 874 LLLAVLGPLWILQASLLKVPYFVRVQGLLRLCALARKVVGGHYVQMVIIKLGALTGTYIYNHLTPLRDWAHNGLQDLAVA 953
Cdd:pfam01538 81 ILLAILGPLYLLQASLLRVPYFVRAARLLRSCVLVRHLAGGKYVQMALLKLGRWTGTYLYDHLGPLSDWAAEGLRDLAVA 160
|
170 180 190
....*....|....*....|....*....|....*
gi 1839358633 954 VEPVVFSRMETKLITWGADTAACGDIINGLPVSAR 988
Cdd:pfam01538 161 LEPVVFSPMECKIITWGADTAACGDIVHGLPVSAR 195
|
|
| Peptidase_S29 |
pfam02907 |
Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a ... |
1039-1186 |
1.83e-80 |
|
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: 261.21 E-value: 1.83e-80
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 1039 EGEVQIVSTAAQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDKDLVGWPAPQGARSLTPCTCGSSDLYLVTR 1118
Cdd:pfam02907 1 EGEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTR 80
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1839358633 1119 HADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGIFRAAVCTRGVAKAVDFIPVENLET 1186
Cdd:pfam02907 81 DGDLIPGRRRGDPRVSLLSPRPLSYLKGSSGGPILCPSGHVVGMFRAAVHSGGVVKAVRFVPWETLPT 148
|
|
| HCV_capsid |
pfam01543 |
Hepatitis C virus capsid protein; |
1-98 |
3.18e-60 |
|
Hepatitis C virus capsid protein;
Pssm-ID: 144947 Cd Length: 121 Bit Score: 202.23 E-value: 3.18e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 1 RPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARRPEGRTWAQPGYPWP------LYGNEG- 73
Cdd:pfam01543 17 RPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARPPEGRSWLSPGTLGPstamraLYGNDGs 96
|
90 100
....*....|....*....|....*
gi 1839358633 74 CGWAGWLLSPRGPRPSWGPTDPRRR 98
Cdd:pfam01543 97 CGWAGWLLPPRGSRPSWGQNDPRRR 121
|
|
| DEXHc_viral_Ns3 |
cd17931 |
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ... |
1206-1349 |
1.27e-52 |
|
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: 181.59 E-value: 1.27e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 1206 FQVAHLHAPTGSGKSTKVPAAYAAQGY----KVLVLNPSVAATLGFGAYMSKAhgiDPNIRTGVRTITTS--SPITYSTY 1279
Cdd:cd17931 1 GQLTVLDLHPGAGKTTRVLPQIIREAIkkrlRTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGgnEIVDYMCH 77
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1839358633 1280 GKFLaDGGCSGGA---YDIIICDECHSTDATSILGIGTVLDQAETaGARLVVLATATPPGSITVPH---SNIEEVA 1349
Cdd:cd17931 78 GTFT-CRLLSPKRvpnYNLIIMDEAHFTDPASIAARGYIHTRVEM-GEAAVIFMTATPPGTVTPFPqsnHPIEDFE 151
|
|
| SF2_C_viral |
cd18806 |
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ... |
1345-1466 |
8.18e-48 |
|
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: 167.82 E-value: 8.18e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 1345 IEEVALSTTGEIPFYGKAIPLeaIRGGRHLIFCHSRKKCDELAAKLVALGVNAVAYYRGLDVSV---IPTSGDVVVVATD 1421
Cdd:cd18806 1 IEDVALEIPGRIWFYGKAWIT--IYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 1839358633 1422 ALMTGFTGDFDSVIDCNTCVTQTVDFSLDptFTIETT-TLPQDAVS 1466
Cdd:cd18806 79 ISEMGANFDADRVIDCRTCVKPTILFSGD--FRVILTgPVPQTAAS 122
|
|
| HCV_core |
pfam01542 |
Hepatitis C virus core protein; The viral core protein forms the internal viral coat that ... |
99-173 |
1.68e-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: 118.24 E-value: 1.68e-31
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1839358633 99 SRNLGKVIDTLTCGFADLMGYIPLVGAPLGGAARALAHGVRVLEDGVNYATGNLPGCSFSIFLLALLSCLTVPAS 173
Cdd:pfam01542 1 MRNLGKPIDKLKCGFADLMGDIKFPGAGLGGAARALAHGRGPLEDGRATAKGNEPGCPFGIFLLALKACLPEGAS 75
|
|
| HCV_p7 |
cd20903 |
Hepatitis C virus p7 protein; Hepatitis C virus (HCV) p7 protein is a viroporin essential for ... |
730-787 |
7.77e-22 |
|
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: 89.98 E-value: 7.77e-22
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 1839358633 730 ALENLVILNAASLAGTHGLASFLVFFCFAWYLKGKWVPGAVYALYGMWPLLLLLLALP 787
Cdd:cd20903 1 ALENLVVLNAASAAGTHGLLWFLLFFCAAWYIKGRLVPAATYALLGLWPLLLLLLALP 58
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
1211-1338 |
2.85e-14 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 73.30 E-value: 2.85e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 1211 LHAPTGSGKSTKVPAAYAAQGY-----KVLVLNPSVAATLGFGAYMSKAHGIDPNIRTGVRTITTS-----------SPI 1274
Cdd:smart00487 29 LAAPTGSGKTLAALLPALEALKrgkggRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKreqlrklesgkTDI 108
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1839358633 1275 TYSTYGKF---LADGGCSGGAYDIIICDECHSTD----ATSILGIGTVLdqaetAGARLVVLATATPPGSI 1338
Cdd:smart00487 109 LVTTPGRLldlLENDKLSLSNVDLVILDEAHRLLdggfGDQLEKLLKLL-----PKNVQLLLLSATPPEEI 174
|
|
| Flavi_DEAD |
pfam07652 |
Flavivirus DEAD domain; |
1216-1344 |
2.16e-05 |
|
Flavivirus DEAD domain;
Pssm-ID: 400138 [Multi-domain] Cd Length: 146 Bit Score: 46.17 E-value: 2.16e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 1216 GSGKSTKVPAAYAAQGY----KVLVLNPS--VAATlgfgayMSKA-HGIdpnirtGVRTITTSSPITYS----------- 1277
Cdd:pfam07652 12 GAGKTRKVLPELVRECIdrrlRTLVLAPTrvVLAE------MEEAlRGL------PIRYHTPAVSSEHTgreivdvmcha 79
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1839358633 1278 TYGKFLADGGCSGGaYDIIICDECHSTDATSILGIGTVLDQAETAGARLVVLaTATPPGSIT-VPHSN 1344
Cdd:pfam07652 80 TFTQRLLSPVRVPN-YEVIIMDEAHFTDPASIAARGYISTLVELGEAAAIFM-TATPPGTSDpFPESN 145
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
1211-1334 |
4.41e-05 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 48.10 E-value: 4.41e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 1211 LHAPTGSGKST---KVpAAYAAQGYKVLVLNPSVAatLGFGAYmSKAHGIDPNIRTGVRTITTSSPITYSTYGKFLADGG 1287
Cdd:COG1061 105 VVAPTGTGKTVlalAL-AAELLRGKRVLVLVPRRE--LLEQWA-EELRRFLGDPLAGGGKKDSDAPITVATYQSLARRAH 180
|
90 100 110 120
....*....|....*....|....*....|....*....|....*....
gi 1839358633 1288 CS--GGAYDIIICDECHSTDATSILGIgtvldqAETAGARLVVLATATP 1334
Cdd:COG1061 181 LDelGDRFGLVIIDEAHHAGAPSYRRI------LEAFPAAYRLGLTATP 223
|
|
| RecQ |
COG0514 |
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
1365-1423 |
1.58e-04 |
|
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 46.29 E-value: 1.58e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1839358633 1365 LEAIRGGRHLIFCHSRKKCDELAAKLVALGVNAVAYYRGLDVSV--------IptSGDV-VVVATDAL 1423
Cdd:COG0514 225 LKEHPGGSGIVYCLSRKKVEELAEWLREAGIRAAAYHAGLDAEEreanqdrfL--RDEVdVIVATIAF 290
|
|
| PRK11057 |
PRK11057 |
ATP-dependent DNA helicase RecQ; Provisional |
1365-1405 |
1.83e-03 |
|
ATP-dependent DNA helicase RecQ; Provisional
Pssm-ID: 182933 [Multi-domain] Cd Length: 607 Bit Score: 42.78 E-value: 1.83e-03
10 20 30 40
....*....|....*....|....*....|....*....|.
gi 1839358633 1365 LEAIRGGRHLIFCHSRKKCDELAAKLVALGVNAVAYYRGLD 1405
Cdd:PRK11057 231 VQEQRGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLD 271
|
|
| uvsW |
PHA02558 |
UvsW helicase; Provisional |
1211-1320 |
5.69e-03 |
|
UvsW helicase; Provisional
Pssm-ID: 222875 [Multi-domain] Cd Length: 501 Bit Score: 41.15 E-value: 5.69e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 1211 LHAPTGSGKS--TKVPAAYAAQGY--KVLVLNPSVAATL----GFGAYMSKAHGIDPNIRTGvRTITTSSPITYSTY--- 1279
Cdd:PHA02558 134 LNLPTSAGKSliQYLLSRYYLENYegKVLIIVPTTSLVTqmidDFVDYRLFPREAMHKIYSG-TAKDTDAPIVVSTWqsa 212
|
90 100 110 120
....*....|....*....|....*....|....*....|....*
gi 1839358633 1280 ----GKFLADGGCsggaydiIICDECHSTDATSILGIGTVLDQAE 1320
Cdd:PHA02558 213 vkqpKEWFDQFGM-------VIVDECHLFTGKSLTSIITKLDNCK 250
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| HCV_NS1 |
pfam01560 |
Hepatitis C virus non-structural protein E2/NS1; The hypervariable region of the E2/NS1 region ... |
369-712 |
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: 730.88 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 369 HVTGGSAARGASGLVNLFNPGAQQNIQLINTNGSWHINRTALNCNDSLQTGWLAGLLYTHRFNSSGCSERLASCRPLTDF 448
Cdd:pfam01560 1 HVTGGSAARTTRGLVSLFSPGAKQNIQLINTNGSWHINRTALNCNDSLQTGFLASLFYTHRFNSSGCPERLASCRSIDDF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 449 DQGWGPISYANGSGPDQRPYCWHYPPKPCGIVPAKSVCGPVYCFTPSPVVVGTTDRSGAPTYNWGENETDVFVLNNTRPP 528
Cdd:pfam01560 81 RQGWGPITYEETNPEDQRPYCWHYPPRPCGIVPASSVCGPVYCFTPSPVVVGTTDRSGAPTYSWGENETDVFLLNNTRPP 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 529 LGNWFGCTWMNSTGFTKVCGAPPCVIGGVGNNTLHCPTDCFRKHPEATYSRCGSGPWITPRCLVHYPYRLWHYPCTINYT 608
Cdd:pfam01560 161 QGNWFGCTWMNSTGFTKTCGAPPCRIGGDGNNTLLCPTDCFRKHPDATYTKCGSGPWLTPRCMVDYPYRLWHYPCTVNFT 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 609 IFKVRMYVGGVEHRLEAACNWTRGERCDLEDRDRSELSPLLLSTTQWQVLPCSFTTLPALSTGLIHLHQNIVDVQYLYGV 688
Cdd:pfam01560 241 IFKVRMYVGGVEHRLNAACNWTRGERCDLEDRDRSELSPLLLSTTEWQVLPCSFTTLPALSTGLIHLHQNIVDVQYLYGL 320
|
330 340
....*....|....*....|....
gi 1839358633 689 GSSIASWAIKWEYVVLLFLLLADA 712
Cdd:pfam01560 321 GSAVTSFAIKWEYVVLLFLLLADA 344
|
|
| HCV_env |
pfam01539 |
Hepatitis C virus envelope glycoprotein E1; |
176-365 |
3.65e-111 |
|
Hepatitis C virus envelope glycoprotein E1;
Pssm-ID: 110536 Cd Length: 190 Bit Score: 349.95 E-value: 3.65e-111
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 176 QVRNSTGLYHVTNDCPNSSIVYESEGAILHTPGCVPCVREGNISRCWVPMTPTVATRDGKLPATQLRRHIDLLVGSATLC 255
Cdd:pfam01539 1 EVRNISGSYHVTNDCSNSSITWQLADAVLHTPGCVPCEREGNTSRCWIAVTPNVAVRHRGALTTSLRTHVDMLVMAATLC 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 256 SALYVGDLCGSVFLVGQLFTFSPRLYWTTQGCNCSIYPGHITGHRMAWDMMMNWSPTSALVVAQVLRIPQAIVDMIAGAH 335
Cdd:pfam01539 81 SALYVGDLCGSVMLVSQLFTVSPQRHWFTQDCNCSIYPGHITGHRMAWDMMMNWSPTATMILAYALRVPEAVLDIIAGAH 160
|
170 180 190
....*....|....*....|....*....|
gi 1839358633 336 WGVLAGIAYFSMVGNWAKVLVVLLLFAGVD 365
Cdd:pfam01539 161 WGVLFGLAYFSMQGAWAKVLVILLLFAGVD 190
|
|
| HCV_NS2 |
pfam01538 |
Hepatitis C virus non-structural protein NS2; The viral genome is translated into a single ... |
794-988 |
1.37e-104 |
|
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: 331.56 E-value: 1.37e-104
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 794 DTEVAASCGGVVLVGLMALTLSPYYKRYISWCLWWLQYLLTRAEAQLHVWVPPLNVRGGRDAVILLTCVVHPTLVFDITK 873
Cdd:pfam01538 1 DTEDAGWLGAAVLSWITLFTLTPTYKGLLAKLLWWLQYCIARQEARLHVWVPPLGVRGGRDAVILLWCLAHPDLVFDVTK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 874 LLLAVLGPLWILQASLLKVPYFVRVQGLLRLCALARKVVGGHYVQMVIIKLGALTGTYIYNHLTPLRDWAHNGLQDLAVA 953
Cdd:pfam01538 81 ILLAILGPLYLLQASLLRVPYFVRAARLLRSCVLVRHLAGGKYVQMALLKLGRWTGTYLYDHLGPLSDWAAEGLRDLAVA 160
|
170 180 190
....*....|....*....|....*....|....*
gi 1839358633 954 VEPVVFSRMETKLITWGADTAACGDIINGLPVSAR 988
Cdd:pfam01538 161 LEPVVFSPMECKIITWGADTAACGDIVHGLPVSAR 195
|
|
| Peptidase_S29 |
pfam02907 |
Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a ... |
1039-1186 |
1.83e-80 |
|
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: 261.21 E-value: 1.83e-80
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 1039 EGEVQIVSTAAQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDKDLVGWPAPQGARSLTPCTCGSSDLYLVTR 1118
Cdd:pfam02907 1 EGEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTR 80
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1839358633 1119 HADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGIFRAAVCTRGVAKAVDFIPVENLET 1186
Cdd:pfam02907 81 DGDLIPGRRRGDPRVSLLSPRPLSYLKGSSGGPILCPSGHVVGMFRAAVHSGGVVKAVRFVPWETLPT 148
|
|
| HCV_capsid |
pfam01543 |
Hepatitis C virus capsid protein; |
1-98 |
3.18e-60 |
|
Hepatitis C virus capsid protein;
Pssm-ID: 144947 Cd Length: 121 Bit Score: 202.23 E-value: 3.18e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 1 RPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARRPEGRTWAQPGYPWP------LYGNEG- 73
Cdd:pfam01543 17 RPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARPPEGRSWLSPGTLGPstamraLYGNDGs 96
|
90 100
....*....|....*....|....*
gi 1839358633 74 CGWAGWLLSPRGPRPSWGPTDPRRR 98
Cdd:pfam01543 97 CGWAGWLLPPRGSRPSWGQNDPRRR 121
|
|
| DEXHc_viral_Ns3 |
cd17931 |
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ... |
1206-1349 |
1.27e-52 |
|
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: 181.59 E-value: 1.27e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 1206 FQVAHLHAPTGSGKSTKVPAAYAAQGY----KVLVLNPSVAATLGFGAYMSKAhgiDPNIRTGVRTITTS--SPITYSTY 1279
Cdd:cd17931 1 GQLTVLDLHPGAGKTTRVLPQIIREAIkkrlRTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGgnEIVDYMCH 77
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1839358633 1280 GKFLaDGGCSGGA---YDIIICDECHSTDATSILGIGTVLDQAETaGARLVVLATATPPGSITVPH---SNIEEVA 1349
Cdd:cd17931 78 GTFT-CRLLSPKRvpnYNLIIMDEAHFTDPASIAARGYIHTRVEM-GEAAVIFMTATPPGTVTPFPqsnHPIEDFE 151
|
|
| SF2_C_viral |
cd18806 |
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ... |
1345-1466 |
8.18e-48 |
|
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: 167.82 E-value: 8.18e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 1345 IEEVALSTTGEIPFYGKAIPLeaIRGGRHLIFCHSRKKCDELAAKLVALGVNAVAYYRGLDVSV---IPTSGDVVVVATD 1421
Cdd:cd18806 1 IEDVALEIPGRIWFYGKAWIT--IYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 1839358633 1422 ALMTGFTGDFDSVIDCNTCVTQTVDFSLDptFTIETT-TLPQDAVS 1466
Cdd:cd18806 79 ISEMGANFDADRVIDCRTCVKPTILFSGD--FRVILTgPVPQTAAS 122
|
|
| HCV_core |
pfam01542 |
Hepatitis C virus core protein; The viral core protein forms the internal viral coat that ... |
99-173 |
1.68e-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: 118.24 E-value: 1.68e-31
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1839358633 99 SRNLGKVIDTLTCGFADLMGYIPLVGAPLGGAARALAHGVRVLEDGVNYATGNLPGCSFSIFLLALLSCLTVPAS 173
Cdd:pfam01542 1 MRNLGKPIDKLKCGFADLMGDIKFPGAGLGGAARALAHGRGPLEDGRATAKGNEPGCPFGIFLLALKACLPEGAS 75
|
|
| HCV_core |
pfam01542 |
Hepatitis C virus core protein; The viral core protein forms the internal viral coat that ... |
1-58 |
2.03e-24 |
|
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: 98.21 E-value: 2.03e-24
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 1839358633 1 RPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARRPEGRT 58
Cdd:pfam01542 18 LMGDIKFPGAGLGGAARALAHGRGPLEDGRATAKGNEPGCPFGIFLLALKACLPEGAS 75
|
|
| HCV_p7 |
cd20903 |
Hepatitis C virus p7 protein; Hepatitis C virus (HCV) p7 protein is a viroporin essential for ... |
730-787 |
7.77e-22 |
|
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: 89.98 E-value: 7.77e-22
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 1839358633 730 ALENLVILNAASLAGTHGLASFLVFFCFAWYLKGKWVPGAVYALYGMWPLLLLLLALP 787
Cdd:cd20903 1 ALENLVVLNAASAAGTHGLLWFLLFFCAAWYIKGRLVPAATYALLGLWPLLLLLLALP 58
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
1211-1338 |
2.85e-14 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 73.30 E-value: 2.85e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 1211 LHAPTGSGKSTKVPAAYAAQGY-----KVLVLNPSVAATLGFGAYMSKAHGIDPNIRTGVRTITTS-----------SPI 1274
Cdd:smart00487 29 LAAPTGSGKTLAALLPALEALKrgkggRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKreqlrklesgkTDI 108
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1839358633 1275 TYSTYGKF---LADGGCSGGAYDIIICDECHSTD----ATSILGIGTVLdqaetAGARLVVLATATPPGSI 1338
Cdd:smart00487 109 LVTTPGRLldlLENDKLSLSNVDLVILDEAHRLLdggfGDQLEKLLKLL-----PKNVQLLLLSATPPEEI 174
|
|
| Flavi_DEAD |
pfam07652 |
Flavivirus DEAD domain; |
1216-1344 |
2.16e-05 |
|
Flavivirus DEAD domain;
Pssm-ID: 400138 [Multi-domain] Cd Length: 146 Bit Score: 46.17 E-value: 2.16e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 1216 GSGKSTKVPAAYAAQGY----KVLVLNPS--VAATlgfgayMSKA-HGIdpnirtGVRTITTSSPITYS----------- 1277
Cdd:pfam07652 12 GAGKTRKVLPELVRECIdrrlRTLVLAPTrvVLAE------MEEAlRGL------PIRYHTPAVSSEHTgreivdvmcha 79
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1839358633 1278 TYGKFLADGGCSGGaYDIIICDECHSTDATSILGIGTVLDQAETAGARLVVLaTATPPGSIT-VPHSN 1344
Cdd:pfam07652 80 TFTQRLLSPVRVPN-YEVIIMDEAHFTDPASIAARGYISTLVELGEAAAIFM-TATPPGTSDpFPESN 145
|
|
| SF2_C_RecQ |
cd18794 |
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ... |
1369-1422 |
3.07e-05 |
|
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: 45.28 E-value: 3.07e-05
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1839358633 1369 RGGRHLIFCHSRKKCDELAAKLVALGVNAVAYYRGL----DVSVIP---TSGDVVVVATDA 1422
Cdd:cd18794 29 LGGSGIIYCLSRKECEQVAARLQSKGISAAAYHAGLepsdRRDVQRkwlRDKIQVIVATVA 89
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
1211-1334 |
4.41e-05 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 48.10 E-value: 4.41e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 1211 LHAPTGSGKST---KVpAAYAAQGYKVLVLNPSVAatLGFGAYmSKAHGIDPNIRTGVRTITTSSPITYSTYGKFLADGG 1287
Cdd:COG1061 105 VVAPTGTGKTVlalAL-AAELLRGKRVLVLVPRRE--LLEQWA-EELRRFLGDPLAGGGKKDSDAPITVATYQSLARRAH 180
|
90 100 110 120
....*....|....*....|....*....|....*....|....*....
gi 1839358633 1288 CS--GGAYDIIICDECHSTDATSILGIgtvldqAETAGARLVVLATATP 1334
Cdd:COG1061 181 LDelGDRFGLVIIDEAHHAGAPSYRRI------LEAFPAAYRLGLTATP 223
|
|
| RecQ |
COG0514 |
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
1365-1423 |
1.58e-04 |
|
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 46.29 E-value: 1.58e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1839358633 1365 LEAIRGGRHLIFCHSRKKCDELAAKLVALGVNAVAYYRGLDVSV--------IptSGDV-VVVATDAL 1423
Cdd:COG0514 225 LKEHPGGSGIVYCLSRKKVEELAEWLREAGIRAAAYHAGLDAEEreanqdrfL--RDEVdVIVATIAF 290
|
|
| DEXHc_HrpB |
cd17990 |
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ... |
1211-1333 |
5.69e-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: 42.32 E-value: 5.69e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 1211 LHAPTGSGKSTKVPAAYAA----QGYKVLVLNPSVAATLGFGAYMSKAHGIDPNIRTG--VRTITTSSPIT---YSTYGK 1281
Cdd:cd17990 22 LEAPPGAGKTTRVPLALLAelwiAGGKIIVLEPRRVAARAAARRLATLLGEAPGETVGyrVRGESRVGRRTrveVVTEGV 101
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*...
gi 1839358633 1282 FL----ADGGCSGgaYDIIICDECHSTDATSILGIGTVLD--QAETAGARLVVLaTAT 1333
Cdd:cd17990 102 LLrrlqRDPELSG--VGAVILDEFHERSLDADLALALLLEvqQLLRDDLRLLAM-SAT 156
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
1213-1334 |
8.31e-04 |
|
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350684 [Multi-domain] Cd Length: 146 Bit Score: 41.52 E-value: 8.31e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 1213 APTGSGKST---KVPAAYAAQgyKVLVLNPSVAatL------GFGAYMSKAHgiDPNIRTGVRTITTSSPITYSTY---G 1280
Cdd:cd17926 25 LPTGSGKTLtalALIAYLKEL--RTLIVVPTDA--LldqwkeRFEDFLGDSS--IGLIGGGKKKDFDDANVVVATYqslS 98
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....
gi 1839358633 1281 KFLADGGCSGGAYDIIICDECHSTDATSILGIgtvldqAETAGARLVVLATATP 1334
Cdd:cd17926 99 NLAEEEKDLFDQFGLLIVDEAHHLPAKTFSEI------LKELNAKYRLGLTATP 146
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
1213-1333 |
1.22e-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: 40.85 E-value: 1.22e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 1213 APTGSGKSTKV--PAAYAA--QGYKVLVLNPSVAATLGFGAYMSKAhgIDPNIRTGVRTITTSS-----------PITYS 1277
Cdd:cd00046 8 APTGSGKTLAAllAALLLLlkKGKKVLVLVPTKALALQTAERLREL--FGPGIRVAVLVGGSSAeereknklgdaDIIIA 85
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1839358633 1278 TYGKF----LADGGCSGGAYDIIICDECHSTDATS--ILGIGTVLDQAETAGARlVVLATAT 1333
Cdd:cd00046 86 TPDMLlnllLREDRLFLKDLKLIIVDEAHALLIDSrgALILDLAVRKAGLKNAQ-VILLSAT 146
|
|
| AAA_30 |
pfam13604 |
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
1207-1327 |
1.53e-03 |
|
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.
Pssm-ID: 433343 [Multi-domain] Cd Length: 191 Bit Score: 41.40 E-value: 1.53e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 1207 QVAHLHAPTGSGKST---KVPAAYAAQGYKVLVLNPSVAATLGfgayMSKAHGIDpnirtgVRTIttsspitystyGKFL 1283
Cdd:pfam13604 19 RVAVLVGPAGTGKTTalkALREAWEAAGYRVIGLAPTGRAAKV----LGEELGIP------ADTI-----------AKLL 77
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 1839358633 1284 A--DGGCSGGAYDIIICDECHSTDATSILgigTVLDQAETAGARLV 1327
Cdd:pfam13604 78 HrlGGRAGLDPGTLLIVDEAGMVGTRQMA---RLLKLAEDAGARVI 120
|
|
| PRK11057 |
PRK11057 |
ATP-dependent DNA helicase RecQ; Provisional |
1365-1405 |
1.83e-03 |
|
ATP-dependent DNA helicase RecQ; Provisional
Pssm-ID: 182933 [Multi-domain] Cd Length: 607 Bit Score: 42.78 E-value: 1.83e-03
10 20 30 40
....*....|....*....|....*....|....*....|.
gi 1839358633 1365 LEAIRGGRHLIFCHSRKKCDELAAKLVALGVNAVAYYRGLD 1405
Cdd:PRK11057 231 VQEQRGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLD 271
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
1211-1302 |
2.45e-03 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 40.35 E-value: 2.45e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 1211 LHAPTGSGK---STKVPAAYAAQGY--KVLVLNPSVA----ATLGFGAYMSKAHGIdPNIRTG--VRTITTSSPITYSTY 1279
Cdd:pfam04851 28 IVMATGSGKtltAAKLIARLFKKGPikKVLFLVPRKDlleqALEEFKKFLPNYVEI-GEIISGdkKDESVDDNKIVVTTI 106
|
90 100
....*....|....*....|....*...
gi 1839358633 1280 GKF-----LADGGCSGGAYDIIICDECH 1302
Cdd:pfam04851 107 QSLykaleLASLELLPDFFDVIIIDEAH 134
|
|
| SF2_C_DEAD |
cd18787 |
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
1365-1405 |
2.65e-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: 39.80 E-value: 2.65e-03
10 20 30 40
....*....|....*....|....*....|....*....|.
gi 1839358633 1365 LEAIRGGRHLIFCHSRKKCDELAAKLVALGVNAVAYYRGLD 1405
Cdd:cd18787 22 LEKLKPGKAIIFVNTKKRVDRLAELLEELGIKVAALHGDLS 62
|
|
| uvsW |
PHA02558 |
UvsW helicase; Provisional |
1211-1320 |
5.69e-03 |
|
UvsW helicase; Provisional
Pssm-ID: 222875 [Multi-domain] Cd Length: 501 Bit Score: 41.15 E-value: 5.69e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1839358633 1211 LHAPTGSGKS--TKVPAAYAAQGY--KVLVLNPSVAATL----GFGAYMSKAHGIDPNIRTGvRTITTSSPITYSTY--- 1279
Cdd:PHA02558 134 LNLPTSAGKSliQYLLSRYYLENYegKVLIIVPTTSLVTqmidDFVDYRLFPREAMHKIYSG-TAKDTDAPIVVSTWqsa 212
|
90 100 110 120
....*....|....*....|....*....|....*....|....*
gi 1839358633 1280 ----GKFLADGGCsggaydiIICDECHSTDATSILGIGTVLDQAE 1320
Cdd:PHA02558 213 vkqpKEWFDQFGM-------VIVDECHLFTGKSLTSIITKLDNCK 250
|
|
| |
