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Conserved domains on  [gi|2124349269|gb|UDM57142|]
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polyprotein, partial [Hepacivirus hominis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HCV_NS1 super family cl03263
Hepatitis C virus non-structural protein E2/NS1; The hypervariable region of the E2/NS1 region ...
 374-716 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: 705.46  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269  374 VTGGVAARGAARIAGIFSPGARQNIQLINTNGSWHINRTALNCNDSLTTGWVAGLFYHHKFNSSGCPERLASCRPLTYFA 453
Cdd:pfam01560    2 VTGGSAARTTRGLVSLFSPGAKQNIQLINTNGSWHINRTALNCNDSLQTGFLASLFYTHRFNSSGCPERLASCRSIDDFR 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269  454 QGWGPIRHTNGSGPDQRPYCWHYPPKPCGIVPAKSVCGPVYCFTPSPVVVGTTDRLGVPTYNWGGNDTDVFVLNNTRPPL 533
Cdd:pfam01560   82 QGWGPITYEETNPEDQRPYCWHYPPRPCGIVPASSVCGPVYCFTPSPVVVGTTDRSGAPTYSWGENETDVFLLNNTRPPQ 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269  534 GNWFGCTWMNSTGFTKVCGAPPCDIGGEGNNTLLCPTDCFRKHPEATYSRCGSGPWITPRCLVNYPYRLWHYPCTINYTI 613
Cdd:pfam01560  162 GNWFGCTWMNSTGFTKTCGAPPCRIGGDGNNTLLCPTDCFRKHPDATYTKCGSGPWLTPRCMVDYPYRLWHYPCTVNFTI 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269  614 FKVRMYVGGVEHRLEAACNWTRGERCRLDDRDRSELSPLLLSTTQWQVLPCSFTTLPALSTGLIHLHQNIVDVQYLYGVG 693
Cdd:pfam01560  242 FKVRMYVGGVEHRLNAACNWTRGERCDLEDRDRSELSPLLLSTTEWQVLPCSFTTLPALSTGLIHLHQNIVDVQYLYGLG 321

                          330       340
                   ....*....|....*....|...
gi 2124349269  694 SSITSWAIKWEYVVLLFLLLADA 716
Cdd:pfam01560  322 SAVTSFAIKWEYVVLLFLLLADA 344
HCV_env super family cl03255
Hepatitis C virus envelope glycoprotein E1;
180-369 6.86e-115

Hepatitis C virus envelope glycoprotein E1;


The actual alignment was detected with superfamily member pfam01539:

Pssm-ID: 110536  Cd Length: 190  Bit Score: 360.35  E-value: 6.86e-115
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269  180 QVRNSTGLYHVTNDCPNSSIVYEAADAILHTPGCVPCVQEGNVSRCWVAVTPTVATRDGKLPTTQLRRHIDLLVGSATLC 259
Cdd:pfam01539    1 EVRNISGSYHVTNDCSNSSITWQLADAVLHTPGCVPCEREGNTSRCWIAVTPNVAVRHRGALTTSLRTHVDMLVMAATLC 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269  260 SALYVGDLCGSVFLVGQLFTFSPRRHRTTQDCNCSIYPGHITGHRMAWDMMMNWSPTAALVVAQVLRIPQAILDMIAGAH 339
Cdd:pfam01539   81 SALYVGDLCGSVMLVSQLFTVSPQRHWFTQDCNCSIYPGHITGHRMAWDMMMNWSPTATMILAYALRVPEAVLDIIAGAH 160

                          170       180       190
                   ....*....|....*....|....*....|
gi 2124349269  340 WGVLAGIAYFSMVGNWAKVVVVLLLFAGVD 369
Cdd:pfam01539  161 WGVLFGLAYFSMQGAWAKVLVILLLFAGVD 190
HCV_NS2 pfam01538
Hepatitis C virus non-structural protein NS2; The viral genome is translated into a single ...
 799-992 6.73e-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: 329.63  E-value: 6.73e-104
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269  799 TEVAASCGGVVLVGLMALTLSPYYKRYICWCLWWLQYFLTRIEALLHVWVPPLNVRGGRDAVILLMCAIHPALIFDITKL 878
Cdd:pfam01538    2 TEDAGWLGAAVLSWITLFTLTPTYKGLLAKLLWWLQYCIARQEARLHVWVPPLGVRGGRDAVILLWCLAHPDLVFDVTKI 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269  879 LLAVFGPLWILQASLLKVPYFVRVQGLLRICALARKMAGGHYVQMVIIKLGALTGTYVYNHLTPLRDWAHNGLRDLAVAV 958
Cdd:pfam01538   82 LLAILGPLYLLQASLLRVPYFVRAARLLRSCVLVRHLAGGKYVQMALLKLGRWTGTYLYDHLGPLSDWAAEGLRDLAVAL 161

                          170       180       190
                   ....*....|....*....|....*....|....
gi 2124349269  959 EPVVFSRMETKLITWGADTAACGDIINGLPVSAR 992
Cdd:pfam01538  162 EPVVFSPMECKIITWGADTAACGDIVHGLPVSAR 195
Peptidase_S29 pfam02907
Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a ...
 1043-1191 1.90e-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: 1.90e-80
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269 1043 EGEVQIVSTAAQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGTRSLTPCTCGASDLYLVTR 1122
Cdd:pfam02907    1 EGEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTR 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2124349269 1123 HADVVPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGIFRAAVCTRGVAKAVDFIPVESLETT 1191
Cdd:pfam02907   81 DGDLIPGRRRGDPRVSLLSPRPLSYLKGSSGGPILCPSGHVVGMFRAAVHSGGVVKAVRFVPWETLPTT 149
HCV_capsid pfam01543
Hepatitis C virus capsid protein;
1-102 6.51e-64

Hepatitis C virus capsid protein;


:

Pssm-ID: 144947  Cd Length: 121  Bit Score: 212.63  E-value: 6.51e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269    1 NTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARRPEGRTWAQPGYPWP------LYG 74
Cdd:pfam01543   13 NTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARPPEGRSWLSPGTLGPstamraLYG 92

                           90       100
                   ....*....|....*....|....*....
gi 2124349269   75 NEG-CGWAGWLLSPRGSRPSWGPSDPRRR 102
Cdd:pfam01543   93 NDGsCGWAGWLLPPRGSRPSWGQNDPRRR 121
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 1210-1353 2.06e-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: 181.21  E-value: 2.06e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269 1210 FQVAHLHAPTGSGKSTKVPAAYAAQGY----KVLVLNPSVAATLGFGAYMSKAhgvDPNIRTGVRTITTG--SPITYSTY 1283
Cdd:cd17931      1 GQLTVLDLHPGAGKTTRVLPQIIREAIkkrlRTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGgnEIVDYMCH 77

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2124349269 1284 GKFLaDGGCSGGA---YDIIICDECHSTDATSVLGIGTVLDQAETaGARLVVLATATPPGSITVPH---PNIEEVA 1353
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 ...
 1349-1470 2.57e-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: 168.98  E-value: 2.57e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269 1349 IEEVALSTTGEIPFYGKAIPleVIKGGRHLIFCHSKKKCDELAAKLVALGVNAVAYYRGLDVSV---IPTSGDVVVVATD 1425
Cdd:cd18806      1 IEDVALEIPGRIWFYGKAWI--TIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 2124349269 1426 ALMTGYTGDFDSVIDCNTCVTQTVDFSLDptFTIETT-TLPQDAVS 1470
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 ...
 103-177 1.96e-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: 1.96e-31
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2124349269  103 SRNLGKVIDTLTCGFADLMGYIPLVGAPLGGAARALAHGVRVLEDGVNYATGNLPGCSFSIFLLALLSCLTVPAS 177
Cdd:pfam01542    1 MRNLGKPIDKLKCGFADLMGDIKFPGAGLGGAARALAHGRGPLEDGRATAKGNEPGCPFGIFLLALKACLPEGAS 75
HCV_p7 cd20903
Hepatitis C virus p7 protein; Hepatitis C virus (HCV) p7 protein is a viroporin essential for ...
 734-782 4.38e-23

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: 93.83  E-value: 4.38e-23
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 2124349269  734 ALENLVVLNAASLAGTHGLASFLVFFCFAWYLKGRWVPGAVYTFYGMWP 782
Cdd:cd20903      1 ALENLVVLNAASAAGTHGLLWFLLFFCAAWYIKGRLVPAATYALLGLWP 49
 
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 ...
 374-716 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: 705.46  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269  374 VTGGVAARGAARIAGIFSPGARQNIQLINTNGSWHINRTALNCNDSLTTGWVAGLFYHHKFNSSGCPERLASCRPLTYFA 453
Cdd:pfam01560    2 VTGGSAARTTRGLVSLFSPGAKQNIQLINTNGSWHINRTALNCNDSLQTGFLASLFYTHRFNSSGCPERLASCRSIDDFR 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269  454 QGWGPIRHTNGSGPDQRPYCWHYPPKPCGIVPAKSVCGPVYCFTPSPVVVGTTDRLGVPTYNWGGNDTDVFVLNNTRPPL 533
Cdd:pfam01560   82 QGWGPITYEETNPEDQRPYCWHYPPRPCGIVPASSVCGPVYCFTPSPVVVGTTDRSGAPTYSWGENETDVFLLNNTRPPQ 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269  534 GNWFGCTWMNSTGFTKVCGAPPCDIGGEGNNTLLCPTDCFRKHPEATYSRCGSGPWITPRCLVNYPYRLWHYPCTINYTI 613
Cdd:pfam01560  162 GNWFGCTWMNSTGFTKTCGAPPCRIGGDGNNTLLCPTDCFRKHPDATYTKCGSGPWLTPRCMVDYPYRLWHYPCTVNFTI 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269  614 FKVRMYVGGVEHRLEAACNWTRGERCRLDDRDRSELSPLLLSTTQWQVLPCSFTTLPALSTGLIHLHQNIVDVQYLYGVG 693
Cdd:pfam01560  242 FKVRMYVGGVEHRLNAACNWTRGERCDLEDRDRSELSPLLLSTTEWQVLPCSFTTLPALSTGLIHLHQNIVDVQYLYGLG 321

                          330       340
                   ....*....|....*....|...
gi 2124349269  694 SSITSWAIKWEYVVLLFLLLADA 716
Cdd:pfam01560  322 SAVTSFAIKWEYVVLLFLLLADA 344
HCV_env pfam01539
Hepatitis C virus envelope glycoprotein E1;
180-369 6.86e-115

Hepatitis C virus envelope glycoprotein E1;


Pssm-ID: 110536  Cd Length: 190  Bit Score: 360.35  E-value: 6.86e-115
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269  180 QVRNSTGLYHVTNDCPNSSIVYEAADAILHTPGCVPCVQEGNVSRCWVAVTPTVATRDGKLPTTQLRRHIDLLVGSATLC 259
Cdd:pfam01539    1 EVRNISGSYHVTNDCSNSSITWQLADAVLHTPGCVPCEREGNTSRCWIAVTPNVAVRHRGALTTSLRTHVDMLVMAATLC 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269  260 SALYVGDLCGSVFLVGQLFTFSPRRHRTTQDCNCSIYPGHITGHRMAWDMMMNWSPTAALVVAQVLRIPQAILDMIAGAH 339
Cdd:pfam01539   81 SALYVGDLCGSVMLVSQLFTVSPQRHWFTQDCNCSIYPGHITGHRMAWDMMMNWSPTATMILAYALRVPEAVLDIIAGAH 160

                          170       180       190
                   ....*....|....*....|....*....|
gi 2124349269  340 WGVLAGIAYFSMVGNWAKVVVVLLLFAGVD 369
Cdd:pfam01539  161 WGVLFGLAYFSMQGAWAKVLVILLLFAGVD 190
HCV_NS2 pfam01538
Hepatitis C virus non-structural protein NS2; The viral genome is translated into a single ...
 799-992 6.73e-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: 329.63  E-value: 6.73e-104
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269  799 TEVAASCGGVVLVGLMALTLSPYYKRYICWCLWWLQYFLTRIEALLHVWVPPLNVRGGRDAVILLMCAIHPALIFDITKL 878
Cdd:pfam01538    2 TEDAGWLGAAVLSWITLFTLTPTYKGLLAKLLWWLQYCIARQEARLHVWVPPLGVRGGRDAVILLWCLAHPDLVFDVTKI 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269  879 LLAVFGPLWILQASLLKVPYFVRVQGLLRICALARKMAGGHYVQMVIIKLGALTGTYVYNHLTPLRDWAHNGLRDLAVAV 958
Cdd:pfam01538   82 LLAILGPLYLLQASLLRVPYFVRAARLLRSCVLVRHLAGGKYVQMALLKLGRWTGTYLYDHLGPLSDWAAEGLRDLAVAL 161

                          170       180       190
                   ....*....|....*....|....*....|....
gi 2124349269  959 EPVVFSRMETKLITWGADTAACGDIINGLPVSAR 992
Cdd:pfam01538  162 EPVVFSPMECKIITWGADTAACGDIVHGLPVSAR 195
Peptidase_S29 pfam02907
Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a ...
 1043-1191 1.90e-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: 1.90e-80
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269 1043 EGEVQIVSTAAQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGTRSLTPCTCGASDLYLVTR 1122
Cdd:pfam02907    1 EGEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTR 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2124349269 1123 HADVVPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGIFRAAVCTRGVAKAVDFIPVESLETT 1191
Cdd:pfam02907   81 DGDLIPGRRRGDPRVSLLSPRPLSYLKGSSGGPILCPSGHVVGMFRAAVHSGGVVKAVRFVPWETLPTT 149
HCV_capsid pfam01543
Hepatitis C virus capsid protein;
1-102 6.51e-64

Hepatitis C virus capsid protein;


Pssm-ID: 144947  Cd Length: 121  Bit Score: 212.63  E-value: 6.51e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269    1 NTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARRPEGRTWAQPGYPWP------LYG 74
Cdd:pfam01543   13 NTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARPPEGRSWLSPGTLGPstamraLYG 92

                           90       100
                   ....*....|....*....|....*....
gi 2124349269   75 NEG-CGWAGWLLSPRGSRPSWGPSDPRRR 102
Cdd:pfam01543   93 NDGsCGWAGWLLPPRGSRPSWGQNDPRRR 121
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 1210-1353 2.06e-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: 181.21  E-value: 2.06e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269 1210 FQVAHLHAPTGSGKSTKVPAAYAAQGY----KVLVLNPSVAATLGFGAYMSKAhgvDPNIRTGVRTITTG--SPITYSTY 1283
Cdd:cd17931      1 GQLTVLDLHPGAGKTTRVLPQIIREAIkkrlRTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGgnEIVDYMCH 77

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2124349269 1284 GKFLaDGGCSGGA---YDIIICDECHSTDATSVLGIGTVLDQAETaGARLVVLATATPPGSITVPH---PNIEEVA 1353
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 ...
 1349-1470 2.57e-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: 168.98  E-value: 2.57e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269 1349 IEEVALSTTGEIPFYGKAIPleVIKGGRHLIFCHSKKKCDELAAKLVALGVNAVAYYRGLDVSV---IPTSGDVVVVATD 1425
Cdd:cd18806      1 IEDVALEIPGRIWFYGKAWI--TIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 2124349269 1426 ALMTGYTGDFDSVIDCNTCVTQTVDFSLDptFTIETT-TLPQDAVS 1470
Cdd:cd18806     79 ISEMGANFDADRVIDCRTCVKPTILFSGD--FRVILTgPVPQTAAS 122
HCV_core pfam01542
Hepatitis C virus core protein; The viral core protein forms the internal viral coat that ...
 103-177 1.96e-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: 1.96e-31
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2124349269  103 SRNLGKVIDTLTCGFADLMGYIPLVGAPLGGAARALAHGVRVLEDGVNYATGNLPGCSFSIFLLALLSCLTVPAS 177
Cdd:pfam01542    1 MRNLGKPIDKLKCGFADLMGDIKFPGAGLGGAARALAHGRGPLEDGRATAKGNEPGCPFGIFLLALKACLPEGAS 75
HCV_p7 cd20903
Hepatitis C virus p7 protein; Hepatitis C virus (HCV) p7 protein is a viroporin essential for ...
 734-782 4.38e-23

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: 93.83  E-value: 4.38e-23
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 2124349269  734 ALENLVVLNAASLAGTHGLASFLVFFCFAWYLKGRWVPGAVYTFYGMWP 782
Cdd:cd20903      1 ALENLVVLNAASAAGTHGLLWFLLFFCAAWYIKGRLVPAATYALLGLWP 49
DEXDc smart00487
DEAD-like helicases superfamily;
1215-1342 9.37e-14

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 71.75  E-value: 9.37e-14
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269  1215 LHAPTGSGKSTKVPAAYAAQGY-----KVLVLNPSVAATLGFGAYMSKAHGVDPNIRTGVRT-----------ITTGSPI 1278
Cdd:smart00487   29 LAAPTGSGKTLAALLPALEALKrgkggRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGgdskreqlrklESGKTDI 108

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2124349269  1279 TYSTYGKF---LADGGCSGGAYDIIICDECHSTD----ATSVLGIGTVLdqaetAGARLVVLATATPPGSI 1342
Cdd:smart00487  109 LVTTPGRLldlLENDKLSLSNVDLVILDEAHRLLdggfGDQLEKLLKLL-----PKNVQLLLLSATPPEEI 174
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
1215-1338 3.29e-05

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 48.48  E-value: 3.29e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269 1215 LHAPTGSGKST---KVpAAYAAQGYKVLVLNPSVAatLGFGAYmSKAHGVDPNIRTGVRTITTGSPITYSTYGKFLADGG 1291
Cdd:COG1061    105 VVAPTGTGKTVlalAL-AAELLRGKRVLVLVPRRE--LLEQWA-EELRRFLGDPLAGGGKKDSDAPITVATYQSLARRAH 180

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 2124349269 1292 CS--GGAYDIIICDECHSTDATSVLGIgtvldqAETAGARLVVLATATP 1338
Cdd:COG1061    181 LDelGDRFGLVIIDEAHHAGAPSYRRI------LEAFPAAYRLGLTATP 223
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
1220-1348 1.29e-04

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 43.86  E-value: 1.29e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269 1220 GSGKSTKVPAAYAAQGY----KVLVLNPS--VAATlgfgayMSKA-HGVDPNIRT-GVRTITTGSPIT----YSTYGKFL 1287
Cdd:pfam07652   12 GAGKTRKVLPELVRECIdrrlRTLVLAPTrvVLAE------MEEAlRGLPIRYHTpAVSSEHTGREIVdvmcHATFTQRL 85

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2124349269 1288 ADGGCSGGaYDIIICDECHSTDATSVLGIGTVLDQAETAGARLVVLaTATPPGSiTVPHPN 1348
Cdd:pfam07652   86 LSPVRVPN-YEVIIMDEAHFTDPASIAARGYISTLVELGEAAAIFM-TATPPGT-SDPFPE 143
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
1378-1427 2.75e-03

Superfamily II DNA helicase RecQ [Replication, recombination and repair];


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 42.05  E-value: 2.75e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2124349269 1378 LIFCHSKKKCDELAAKLVALGVNAVAYYRGLDVSV--------IptSGDV-VVVATDAL 1427
Cdd:COG0514    234 IVYCLSRKKVEELAEWLREAGIRAAAYHAGLDAEEreanqdrfL--RDEVdVIVATIAF 290
 
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 ...
 374-716 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: 705.46  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269  374 VTGGVAARGAARIAGIFSPGARQNIQLINTNGSWHINRTALNCNDSLTTGWVAGLFYHHKFNSSGCPERLASCRPLTYFA 453
Cdd:pfam01560    2 VTGGSAARTTRGLVSLFSPGAKQNIQLINTNGSWHINRTALNCNDSLQTGFLASLFYTHRFNSSGCPERLASCRSIDDFR 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269  454 QGWGPIRHTNGSGPDQRPYCWHYPPKPCGIVPAKSVCGPVYCFTPSPVVVGTTDRLGVPTYNWGGNDTDVFVLNNTRPPL 533
Cdd:pfam01560   82 QGWGPITYEETNPEDQRPYCWHYPPRPCGIVPASSVCGPVYCFTPSPVVVGTTDRSGAPTYSWGENETDVFLLNNTRPPQ 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269  534 GNWFGCTWMNSTGFTKVCGAPPCDIGGEGNNTLLCPTDCFRKHPEATYSRCGSGPWITPRCLVNYPYRLWHYPCTINYTI 613
Cdd:pfam01560  162 GNWFGCTWMNSTGFTKTCGAPPCRIGGDGNNTLLCPTDCFRKHPDATYTKCGSGPWLTPRCMVDYPYRLWHYPCTVNFTI 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269  614 FKVRMYVGGVEHRLEAACNWTRGERCRLDDRDRSELSPLLLSTTQWQVLPCSFTTLPALSTGLIHLHQNIVDVQYLYGVG 693
Cdd:pfam01560  242 FKVRMYVGGVEHRLNAACNWTRGERCDLEDRDRSELSPLLLSTTEWQVLPCSFTTLPALSTGLIHLHQNIVDVQYLYGLG 321

                          330       340
                   ....*....|....*....|...
gi 2124349269  694 SSITSWAIKWEYVVLLFLLLADA 716
Cdd:pfam01560  322 SAVTSFAIKWEYVVLLFLLLADA 344
HCV_env pfam01539
Hepatitis C virus envelope glycoprotein E1;
180-369 6.86e-115

Hepatitis C virus envelope glycoprotein E1;


Pssm-ID: 110536  Cd Length: 190  Bit Score: 360.35  E-value: 6.86e-115
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269  180 QVRNSTGLYHVTNDCPNSSIVYEAADAILHTPGCVPCVQEGNVSRCWVAVTPTVATRDGKLPTTQLRRHIDLLVGSATLC 259
Cdd:pfam01539    1 EVRNISGSYHVTNDCSNSSITWQLADAVLHTPGCVPCEREGNTSRCWIAVTPNVAVRHRGALTTSLRTHVDMLVMAATLC 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269  260 SALYVGDLCGSVFLVGQLFTFSPRRHRTTQDCNCSIYPGHITGHRMAWDMMMNWSPTAALVVAQVLRIPQAILDMIAGAH 339
Cdd:pfam01539   81 SALYVGDLCGSVMLVSQLFTVSPQRHWFTQDCNCSIYPGHITGHRMAWDMMMNWSPTATMILAYALRVPEAVLDIIAGAH 160

                          170       180       190
                   ....*....|....*....|....*....|
gi 2124349269  340 WGVLAGIAYFSMVGNWAKVVVVLLLFAGVD 369
Cdd:pfam01539  161 WGVLFGLAYFSMQGAWAKVLVILLLFAGVD 190
HCV_NS2 pfam01538
Hepatitis C virus non-structural protein NS2; The viral genome is translated into a single ...
 799-992 6.73e-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: 329.63  E-value: 6.73e-104
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269  799 TEVAASCGGVVLVGLMALTLSPYYKRYICWCLWWLQYFLTRIEALLHVWVPPLNVRGGRDAVILLMCAIHPALIFDITKL 878
Cdd:pfam01538    2 TEDAGWLGAAVLSWITLFTLTPTYKGLLAKLLWWLQYCIARQEARLHVWVPPLGVRGGRDAVILLWCLAHPDLVFDVTKI 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269  879 LLAVFGPLWILQASLLKVPYFVRVQGLLRICALARKMAGGHYVQMVIIKLGALTGTYVYNHLTPLRDWAHNGLRDLAVAV 958
Cdd:pfam01538   82 LLAILGPLYLLQASLLRVPYFVRAARLLRSCVLVRHLAGGKYVQMALLKLGRWTGTYLYDHLGPLSDWAAEGLRDLAVAL 161

                          170       180       190
                   ....*....|....*....|....*....|....
gi 2124349269  959 EPVVFSRMETKLITWGADTAACGDIINGLPVSAR 992
Cdd:pfam01538  162 EPVVFSPMECKIITWGADTAACGDIVHGLPVSAR 195
Peptidase_S29 pfam02907
Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a ...
 1043-1191 1.90e-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: 1.90e-80
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269 1043 EGEVQIVSTAAQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGTRSLTPCTCGASDLYLVTR 1122
Cdd:pfam02907    1 EGEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTR 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2124349269 1123 HADVVPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGIFRAAVCTRGVAKAVDFIPVESLETT 1191
Cdd:pfam02907   81 DGDLIPGRRRGDPRVSLLSPRPLSYLKGSSGGPILCPSGHVVGMFRAAVHSGGVVKAVRFVPWETLPTT 149
HCV_capsid pfam01543
Hepatitis C virus capsid protein;
1-102 6.51e-64

Hepatitis C virus capsid protein;


Pssm-ID: 144947  Cd Length: 121  Bit Score: 212.63  E-value: 6.51e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269    1 NTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARRPEGRTWAQPGYPWP------LYG 74
Cdd:pfam01543   13 NTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARPPEGRSWLSPGTLGPstamraLYG 92

                           90       100
                   ....*....|....*....|....*....
gi 2124349269   75 NEG-CGWAGWLLSPRGSRPSWGPSDPRRR 102
Cdd:pfam01543   93 NDGsCGWAGWLLPPRGSRPSWGQNDPRRR 121
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 1210-1353 2.06e-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: 181.21  E-value: 2.06e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269 1210 FQVAHLHAPTGSGKSTKVPAAYAAQGY----KVLVLNPSVAATLGFGAYMSKAhgvDPNIRTGVRTITTG--SPITYSTY 1283
Cdd:cd17931      1 GQLTVLDLHPGAGKTTRVLPQIIREAIkkrlRTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGgnEIVDYMCH 77

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2124349269 1284 GKFLaDGGCSGGA---YDIIICDECHSTDATSVLGIGTVLDQAETaGARLVVLATATPPGSITVPH---PNIEEVA 1353
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 ...
 1349-1470 2.57e-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: 168.98  E-value: 2.57e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269 1349 IEEVALSTTGEIPFYGKAIPleVIKGGRHLIFCHSKKKCDELAAKLVALGVNAVAYYRGLDVSV---IPTSGDVVVVATD 1425
Cdd:cd18806      1 IEDVALEIPGRIWFYGKAWI--TIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 2124349269 1426 ALMTGYTGDFDSVIDCNTCVTQTVDFSLDptFTIETT-TLPQDAVS 1470
Cdd:cd18806     79 ISEMGANFDADRVIDCRTCVKPTILFSGD--FRVILTgPVPQTAAS 122
HCV_core pfam01542
Hepatitis C virus core protein; The viral core protein forms the internal viral coat that ...
 103-177 1.96e-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: 1.96e-31
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2124349269  103 SRNLGKVIDTLTCGFADLMGYIPLVGAPLGGAARALAHGVRVLEDGVNYATGNLPGCSFSIFLLALLSCLTVPAS 177
Cdd:pfam01542    1 MRNLGKPIDKLKCGFADLMGDIKFPGAGLGGAARALAHGRGPLEDGRATAKGNEPGCPFGIFLLALKACLPEGAS 75
HCV_core pfam01542
Hepatitis C virus core protein; The viral core protein forms the internal viral coat that ...
 1-62 1.24e-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: 1.24e-26
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2124349269    1 NTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARRPEGRT 62
Cdd:pfam01542   14 GFADLMGDIKFPGAGLGGAARALAHGRGPLEDGRATAKGNEPGCPFGIFLLALKACLPEGAS 75
HCV_p7 cd20903
Hepatitis C virus p7 protein; Hepatitis C virus (HCV) p7 protein is a viroporin essential for ...
 734-782 4.38e-23

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: 93.83  E-value: 4.38e-23
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 2124349269  734 ALENLVVLNAASLAGTHGLASFLVFFCFAWYLKGRWVPGAVYTFYGMWP 782
Cdd:cd20903      1 ALENLVVLNAASAAGTHGLLWFLLFFCAAWYIKGRLVPAATYALLGLWP 49
DEXDc smart00487
DEAD-like helicases superfamily;
1215-1342 9.37e-14

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 71.75  E-value: 9.37e-14
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269  1215 LHAPTGSGKSTKVPAAYAAQGY-----KVLVLNPSVAATLGFGAYMSKAHGVDPNIRTGVRT-----------ITTGSPI 1278
Cdd:smart00487   29 LAAPTGSGKTLAALLPALEALKrgkggRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGgdskreqlrklESGKTDI 108

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2124349269  1279 TYSTYGKF---LADGGCSGGAYDIIICDECHSTD----ATSVLGIGTVLdqaetAGARLVVLATATPPGSI 1342
Cdd:smart00487  109 LVTTPGRLldlLENDKLSLSNVDLVILDEAHRLLdggfGDQLEKLLKLL-----PKNVQLLLLSATPPEEI 174
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
1215-1338 3.29e-05

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 48.48  E-value: 3.29e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269 1215 LHAPTGSGKST---KVpAAYAAQGYKVLVLNPSVAatLGFGAYmSKAHGVDPNIRTGVRTITTGSPITYSTYGKFLADGG 1291
Cdd:COG1061    105 VVAPTGTGKTVlalAL-AAELLRGKRVLVLVPRRE--LLEQWA-EELRRFLGDPLAGGGKKDSDAPITVATYQSLARRAH 180

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 2124349269 1292 CS--GGAYDIIICDECHSTDATSVLGIgtvldqAETAGARLVVLATATP 1338
Cdd:COG1061    181 LDelGDRFGLVIIDEAHHAGAPSYRRI------LEAFPAAYRLGLTATP 223
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 1373-1426 9.26e-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: 44.12  E-value: 9.26e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2124349269 1373 KGGRHLIFCHSKKKCDELAAKLVALGVNAVAYYRGL----DVSVIP---TSGDVVVVATDA 1426
Cdd:cd18794     29 LGGSGIIYCLSRKECEQVAARLQSKGISAAAYHAGLepsdRRDVQRkwlRDKIQVIVATVA 89
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
1220-1348 1.29e-04

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 43.86  E-value: 1.29e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269 1220 GSGKSTKVPAAYAAQGY----KVLVLNPS--VAATlgfgayMSKA-HGVDPNIRT-GVRTITTGSPIT----YSTYGKFL 1287
Cdd:pfam07652   12 GAGKTRKVLPELVRECIdrrlRTLVLAPTrvVLAE------MEEAlRGLPIRYHTpAVSSEHTGREIVdvmcHATFTQRL 85

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2124349269 1288 ADGGCSGGaYDIIICDECHSTDATSVLGIGTVLDQAETAGARLVVLaTATPPGSiTVPHPN 1348
Cdd:pfam07652   86 LSPVRVPN-YEVIIMDEAHFTDPASIAARGYISTLVELGEAAAIFM-TATPPGT-SDPFPE 143
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 1369-1409 4.57e-04

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: 41.72  E-value: 4.57e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 2124349269 1369 LEVIKGGRHLIFCHSKKKCDELAAKLVALGVNAVAYYRGLD 1409
Cdd:cd18787     22 LEKLKPGKAIIFVNTKKRVDRLAELLEELGIKVAALHGDLS 62
DEXHc_HrpB cd17990
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ...
 1215-1337 6.35e-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: 6.35e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269 1215 LHAPTGSGKSTKVPAAYAA----QGYKVLVLNPSVAATLGFGAYMSKAHGVDPNIRTG--VRTITTGSPIT---YSTYGK 1285
Cdd:cd17990     22 LEAPPGAGKTTRVPLALLAelwiAGGKIIVLEPRRVAARAAARRLATLLGEAPGETVGyrVRGESRVGRRTrveVVTEGV 101

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2124349269 1286 FL----ADGGCSGgaYDIIICDECHSTDATSVLGIGTVLD--QAETAGARLVVLaTAT 1337
Cdd:cd17990    102 LLrrlqRDPELSG--VGAVILDEFHERSLDADLALALLLEvqQLLRDDLRLLAM-SAT 156
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 1217-1338 1.19e-03

DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350684 [Multi-domain]  Cd Length: 146  Bit Score: 41.14  E-value: 1.19e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269 1217 APTGSGKST---KVPAAYAAQgyKVLVLNPSVAatL------GFGAYMSKAHgvDPNIRTGVRTITTGSPITYSTY---G 1284
Cdd:cd17926     25 LPTGSGKTLtalALIAYLKEL--RTLIVVPTDA--LldqwkeRFEDFLGDSS--IGLIGGGKKKDFDDANVVVATYqslS 98

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2124349269 1285 KFLADGGCSGGAYDIIICDECHSTDATSvlgIGTVLDQAEtagARLVVLATATP 1338
Cdd:cd17926     99 NLAEEEKDLFDQFGLLIVDEAHHLPAKT---FSEILKELN---AKYRLGLTATP 146
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 1217-1337 1.20e-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: 1.20e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269 1217 APTGSGKSTKV--PAAYAA--QGYKVLVLNPS------VAATLGFGAYMSKA-----HGVDPNIRTGVRTITtgSPITYS 1281
Cdd:cd00046      8 APTGSGKTLAAllAALLLLlkKGKKVLVLVPTkalalqTAERLRELFGPGIRvavlvGGSSAEEREKNKLGD--ADIIIA 85

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2124349269 1282 TYGKF----LADGGCSGGAYDIIICDECHSTDATSV--LGIGTVLDQAETAGARlVVLATAT 1337
Cdd:cd00046     86 TPDMLlnllLREDRLFLKDLKLIIVDEAHALLIDSRgaLILDLAVRKAGLKNAQ-VILLSAT 146
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
1378-1427 2.75e-03

Superfamily II DNA helicase RecQ [Replication, recombination and repair];


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 42.05  E-value: 2.75e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2124349269 1378 LIFCHSKKKCDELAAKLVALGVNAVAYYRGLDVSV--------IptSGDV-VVVATDAL 1427
Cdd:COG0514    234 IVYCLSRKKVEELAEWLREAGIRAAAYHAGLDAEEreanqdrfL--RDEVdVIVATIAF 290
ResIII pfam04851
Type III restriction enzyme, res subunit;
1215-1306 3.80e-03

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 39.96  E-value: 3.80e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269 1215 LHAPTGSGK---STKVPAAYAAQGY--KVLVLNPSVA----ATLGFGAYMSKAHGVdPNIRTG--VRTITTGSPITYSTY 1283
Cdd:pfam04851   28 IVMATGSGKtltAAKLIARLFKKGPikKVLFLVPRKDlleqALEEFKKFLPNYVEI-GEIISGdkKDESVDDNKIVVTTI 106

                           90       100
                   ....*....|....*....|....*...
gi 2124349269 1284 GKF-----LADGGCSGGAYDIIICDECH 1306
Cdd:pfam04851  107 QSLykaleLASLELLPDFFDVIIIDEAH 134
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 1211-1331 3.82e-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: 40.24  E-value: 3.82e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124349269 1211 QVAHLHAPTGSGKST---KVPAAYAAQGYKVLVLNPSVAATLGfgayMSKAHGVDpnirtgVRTIttgspitystyGKFL 1287
Cdd:pfam13604   19 RVAVLVGPAGTGKTTalkALREAWEAAGYRVIGLAPTGRAAKV----LGEELGIP------ADTI-----------AKLL 77

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 2124349269 1288 A--DGGCSGGAYDIIICDEchstdaTSVLGI---GTVLDQAETAGARLV 1331
Cdd:pfam13604   78 HrlGGRAGLDPGTLLIVDE------AGMVGTrqmARLLKLAEDAGARVI 120
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
1369-1425 4.68e-03

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 41.29  E-value: 4.68e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2124349269 1369 LEVIKGGRHLIFCHSKKKCDELAAKLVALGVNAVAYYRGLDVS----VIP--TSGDV-VVVATD 1425
Cdd:COG0513    236 LRDEDPERAIVFCNTKRGADRLAEKLQKRGISAAALHGDLSQGqrerALDafRNGKIrVLVATD 299
 
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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