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Conserved domains on  [gi|422091051|gb|AFX77110|]
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NS3-4A protease, partial [Hepacivirus hominis]

Protein Classification

polyprotein( domain architecture ID 13683654)

partial polyprotein such as hepatitis C virus polyprotein, containing NS3 protease, helicase, and NS4

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Peptidase_S29 pfam02907
Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a ...
 30-178 6.25e-83

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: 258.90  E-value: 6.25e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422091051   30 EGEVQIVSTA*QTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDKDLVGWPAPQG*RSLTPCTCGSSDLYLVTR 109
Cdd:pfam02907   1 EGEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 422091051  110 HADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGIFRAAVCTRGVAKAVDFIPVENLETT 178
Cdd:pfam02907  81 DGDLIPGRRRGDPRVSLLSPRPLSYLKGSSGGPILCPSGHVVGMFRAAVHSGGVVKAVRFVPWETLPTT 149
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 197-340 6.46e-51

N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase superfamily is a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. The N-terminal domain contains the ATP-binding region.


The actual alignment was detected with superfamily member cd17931:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 151  Bit Score: 173.89  E-value: 6.46e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422091051 197 FQVAHLHAPTGSGKSTKVPAAYAAQGY----KVLVLNPSVAATLGFGAYMSKAhgiDPNIRTGVRTITTGS*--ITYSTY 270
Cdd:cd17931    1 GQLTVLDLHPGAGKTTRVLPQIIREAIkkrlRTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGGNeiVDYMCH 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 422091051 271 GKFLaDGGCSGGA---YDIIICDECHSTDATSILGIGTVLDQAETaGARLVVLATATPPGS*TVPH---PNIEEVA 340
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 ...
 336-457 3.55e-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: 166.28  E-value: 3.55e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422091051 336 IEEVALSTTGEIPFYGKAIPleVIKGGRHLIFCHSKKKCDELAAKLVALGVNAVAYYRGLDVSV---IPTSGDVVVVATD 412
Cdd:cd18806    1 IEDVALEIPGRIWFYGKAWI--TIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 422091051 413 ALMTGFTGDFDSVIDCNTCVTQTVDFSLDptFTIETT-TLPQDAVS 457
Cdd:cd18806   79 ISEMGANFDADRVIDCRTCVKPTILFSGD--FRVILTgPVPQTAAS 122
HCV_NS4a pfam01006
Hepatitis C virus non-structural protein NS4a; NS4a forms an integral part of the NS3 serine ...
 632-685 1.93e-20

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


:

Pssm-ID: 366414  Cd Length: 55  Bit Score: 85.21  E-value: 1.93e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 422091051  632 STWVLVGGVLAALAAYCLSTGCVVIVGRVVLSGKP-AIIPDKE*LYREFDEMEEC 685
Cdd:pfam01006   1 STWVLVGGALAAGAAYCLTTGSVVVVGRWSVNGKPpAVVPDREVLYQQGEEMEEC 55
 
Name Accession Description Interval E-value
Peptidase_S29 pfam02907
Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a ...
 30-178 6.25e-83

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: 258.90  E-value: 6.25e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422091051   30 EGEVQIVSTA*QTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDKDLVGWPAPQG*RSLTPCTCGSSDLYLVTR 109
Cdd:pfam02907   1 EGEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 422091051  110 HADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGIFRAAVCTRGVAKAVDFIPVENLETT 178
Cdd:pfam02907  81 DGDLIPGRRRGDPRVSLLSPRPLSYLKGSSGGPILCPSGHVVGMFRAAVHSGGVVKAVRFVPWETLPTT 149
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 197-340 6.46e-51

DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional protein found in pestiviruses that contains an N-terminal protease and a C-terminal helicase. The N-terminal domain is a chymotrypsin-like serine protease, which is responsible for most of the maturation cleavages of the polyprotein precursor in the cytosolic side of the endoplasmic reticulum membrane. The C-terminal domain, about two-thirds of NS3, is a helicase belonging to superfamily 2 (SF2) thought to be important for unwinding highly structured regions of the RNA genome during replication. NS3 plays an essential role in viral polyprotein processing and genome replication. NS3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350689 [Multi-domain]  Cd Length: 151  Bit Score: 173.89  E-value: 6.46e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422091051 197 FQVAHLHAPTGSGKSTKVPAAYAAQGY----KVLVLNPSVAATLGFGAYMSKAhgiDPNIRTGVRTITTGS*--ITYSTY 270
Cdd:cd17931    1 GQLTVLDLHPGAGKTTRVLPQIIREAIkkrlRTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGGNeiVDYMCH 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 422091051 271 GKFLaDGGCSGGA---YDIIICDECHSTDATSILGIGTVLDQAETaGARLVVLATATPPGS*TVPH---PNIEEVA 340
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 ...
 336-457 3.55e-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: 166.28  E-value: 3.55e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422091051 336 IEEVALSTTGEIPFYGKAIPleVIKGGRHLIFCHSKKKCDELAAKLVALGVNAVAYYRGLDVSV---IPTSGDVVVVATD 412
Cdd:cd18806    1 IEDVALEIPGRIWFYGKAWI--TIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 422091051 413 ALMTGFTGDFDSVIDCNTCVTQTVDFSLDptFTIETT-TLPQDAVS 457
Cdd:cd18806   79 ISEMGANFDADRVIDCRTCVKPTILFSGD--FRVILTgPVPQTAAS 122
HCV_NS4a pfam01006
Hepatitis C virus non-structural protein NS4a; NS4a forms an integral part of the NS3 serine ...
 632-685 1.93e-20

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


Pssm-ID: 366414  Cd Length: 55  Bit Score: 85.21  E-value: 1.93e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 422091051  632 STWVLVGGVLAALAAYCLSTGCVVIVGRVVLSGKP-AIIPDKE*LYREFDEMEEC 685
Cdd:pfam01006   1 STWVLVGGALAAGAAYCLTTGSVVVVGRWSVNGKPpAVVPDREVLYQQGEEMEEC 55
DEXDc smart00487
DEAD-like helicases superfamily;
202-327 8.56e-14

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 70.60  E-value: 8.56e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422091051   202 LHAPTGSGKSTKVPAAYAAQGY-----KVLVLNPSVAATLGFGAYMSKAHGIDPNIRTGVRT----------ITTGS*-I 265
Cdd:smart00487  29 LAAPTGSGKTLAALLPALEALKrgkggRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGgdskreqlrkLESGKTdI 108

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 422091051   266 TYSTYGKF---LADGGCSGGAYDIIICDECHSTD----ATSILGIGTVLdqaetAGARLVVLATATPPG 327
Cdd:smart00487 109 LVTTPGRLldlLENDKLSLSNVDLVILDEAHRLLdggfGDQLEKLLKLL-----PKNVQLLLLSATPPE 172
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
207-335 2.38e-05

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 44.63  E-value: 2.38e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422091051  207 GSGKSTKVPAAYAAQGY----KVLVLNPS--VAATlgfgayMSKA-HGIDPNIRTG--VRTITTGS*IT---YSTYGKFL 274
Cdd:pfam07652  12 GAGKTRKVLPELVRECIdrrlRTLVLAPTrvVLAE------MEEAlRGLPIRYHTPavSSEHTGREIVDvmcHATFTQRL 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 422091051  275 ADGGCSGGaYDIIICDECHSTDATSILGIGTVLDQAETAGARLVVLaTATPPGS*TVPHPN 335
Cdd:pfam07652  86 LSPVRVPN-YEVIIMDEAHFTDPASIAARGYISTLVELGEAAAIFM-TATPPGT-SDPFPE 143
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
202-325 4.17e-05

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 46.94  E-value: 4.17e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422091051 202 LHAPTGSGKST---KVpAAYAAQGYKVLVLNPSVAatLGFGAYmSKAHGIDPNIRTGVRTITTGS*ITYSTYGKFLADGG 278
Cdd:COG1061  105 VVAPTGTGKTVlalAL-AAELLRGKRVLVLVPRRE--LLEQWA-EELRRFLGDPLAGGGKKDSDAPITVATYQSLARRAH 180

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 422091051 279 CS--GGAYDIIICDECHSTDATSILGIgtvldqAETAGARLVVLATATP 325
Cdd:COG1061  181 LDelGDRFGLVIIDEAHHAGAPSYRRI------LEAFPAAYRLGLTATP 223
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
365-414 9.99e-04

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


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 42.05  E-value: 9.99e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 422091051 365 LIFCHSKKKCDELAAKLVALGVNAVAYYRGLDVSV--------IptSGDV-VVVATDAL 414
Cdd:COG0514  234 IVYCLSRKKVEELAEWLREAGIRAAAYHAGLDAEEreanqdrfL--RDEVdVIVATIAF 290
PRK11057 PRK11057
ATP-dependent DNA helicase RecQ; Provisional
 360-396 9.92e-03

ATP-dependent DNA helicase RecQ; Provisional


Pssm-ID: 182933 [Multi-domain]  Cd Length: 607  Bit Score: 39.31  E-value: 9.92e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 422091051 360 KGGRHLIFCHSKKKCDELAAKLVALGVNAVAYYRGLD 396
Cdd:PRK11057 235 RGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLD 271
 
Name Accession Description Interval E-value
Peptidase_S29 pfam02907
Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a ...
 30-178 6.25e-83

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: 258.90  E-value: 6.25e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422091051   30 EGEVQIVSTA*QTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDKDLVGWPAPQG*RSLTPCTCGSSDLYLVTR 109
Cdd:pfam02907   1 EGEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 422091051  110 HADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGIFRAAVCTRGVAKAVDFIPVENLETT 178
Cdd:pfam02907  81 DGDLIPGRRRGDPRVSLLSPRPLSYLKGSSGGPILCPSGHVVGMFRAAVHSGGVVKAVRFVPWETLPTT 149
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 197-340 6.46e-51

DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional protein found in pestiviruses that contains an N-terminal protease and a C-terminal helicase. The N-terminal domain is a chymotrypsin-like serine protease, which is responsible for most of the maturation cleavages of the polyprotein precursor in the cytosolic side of the endoplasmic reticulum membrane. The C-terminal domain, about two-thirds of NS3, is a helicase belonging to superfamily 2 (SF2) thought to be important for unwinding highly structured regions of the RNA genome during replication. NS3 plays an essential role in viral polyprotein processing and genome replication. NS3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350689 [Multi-domain]  Cd Length: 151  Bit Score: 173.89  E-value: 6.46e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422091051 197 FQVAHLHAPTGSGKSTKVPAAYAAQGY----KVLVLNPSVAATLGFGAYMSKAhgiDPNIRTGVRTITTGS*--ITYSTY 270
Cdd:cd17931    1 GQLTVLDLHPGAGKTTRVLPQIIREAIkkrlRTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGGNeiVDYMCH 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 422091051 271 GKFLaDGGCSGGA---YDIIICDECHSTDATSILGIGTVLDQAETaGARLVVLATATPPGS*TVPH---PNIEEVA 340
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 ...
 336-457 3.55e-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: 166.28  E-value: 3.55e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422091051 336 IEEVALSTTGEIPFYGKAIPleVIKGGRHLIFCHSKKKCDELAAKLVALGVNAVAYYRGLDVSV---IPTSGDVVVVATD 412
Cdd:cd18806    1 IEDVALEIPGRIWFYGKAWI--TIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 422091051 413 ALMTGFTGDFDSVIDCNTCVTQTVDFSLDptFTIETT-TLPQDAVS 457
Cdd:cd18806   79 ISEMGANFDADRVIDCRTCVKPTILFSGD--FRVILTgPVPQTAAS 122
HCV_NS4a pfam01006
Hepatitis C virus non-structural protein NS4a; NS4a forms an integral part of the NS3 serine ...
 632-685 1.93e-20

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


Pssm-ID: 366414  Cd Length: 55  Bit Score: 85.21  E-value: 1.93e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 422091051  632 STWVLVGGVLAALAAYCLSTGCVVIVGRVVLSGKP-AIIPDKE*LYREFDEMEEC 685
Cdd:pfam01006   1 STWVLVGGALAAGAAYCLTTGSVVVVGRWSVNGKPpAVVPDREVLYQQGEEMEEC 55
DEXDc smart00487
DEAD-like helicases superfamily;
202-327 8.56e-14

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 70.60  E-value: 8.56e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422091051   202 LHAPTGSGKSTKVPAAYAAQGY-----KVLVLNPSVAATLGFGAYMSKAHGIDPNIRTGVRT----------ITTGS*-I 265
Cdd:smart00487  29 LAAPTGSGKTLAALLPALEALKrgkggRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGgdskreqlrkLESGKTdI 108

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 422091051   266 TYSTYGKF---LADGGCSGGAYDIIICDECHSTD----ATSILGIGTVLdqaetAGARLVVLATATPPG 327
Cdd:smart00487 109 LVTTPGRLldlLENDKLSLSNVDLVILDEAHRLLdggfGDQLEKLLKLL-----PKNVQLLLLSATPPE 172
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
207-335 2.38e-05

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 44.63  E-value: 2.38e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422091051  207 GSGKSTKVPAAYAAQGY----KVLVLNPS--VAATlgfgayMSKA-HGIDPNIRTG--VRTITTGS*IT---YSTYGKFL 274
Cdd:pfam07652  12 GAGKTRKVLPELVRECIdrrlRTLVLAPTrvVLAE------MEEAlRGLPIRYHTPavSSEHTGREIVDvmcHATFTQRL 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 422091051  275 ADGGCSGGaYDIIICDECHSTDATSILGIGTVLDQAETAGARLVVLaTATPPGS*TVPHPN 335
Cdd:pfam07652  86 LSPVRVPN-YEVIIMDEAHFTDPASIAARGYISTLVELGEAAAIFM-TATPPGT-SDPFPE 143
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 360-413 3.27e-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: 3.27e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 422091051 360 KGGRHLIFCHSKKKCDELAAKLVALGVNAVAYYRGL----DVSVIP---TSGDVVVVATDA 413
Cdd:cd18794   29 LGGSGIIYCLSRKECEQVAARLQSKGISAAAYHAGLepsdRRDVQRkwlRDKIQVIVATVA 89
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
202-325 4.17e-05

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 46.94  E-value: 4.17e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422091051 202 LHAPTGSGKST---KVpAAYAAQGYKVLVLNPSVAatLGFGAYmSKAHGIDPNIRTGVRTITTGS*ITYSTYGKFLADGG 278
Cdd:COG1061  105 VVAPTGTGKTVlalAL-AAELLRGKRVLVLVPRRE--LLEQWA-EELRRFLGDPLAGGGKKDSDAPITVATYQSLARRAH 180

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 422091051 279 CS--GGAYDIIICDECHSTDATSILGIgtvldqAETAGARLVVLATATP 325
Cdd:COG1061  181 LDelGDRFGLVIIDEAHHAGAPSYRRI------LEAFPAAYRLGLTATP 223
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 356-396 1.82e-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: 1.82e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 422091051 356 LEVIKGGRHLIFCHSKKKCDELAAKLVALGVNAVAYYRGLD 396
Cdd:cd18787   22 LEKLKPGKAIIFVNTKKRVDRLAELLEELGIKVAALHGDLS 62
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 204-325 8.71e-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: 40.37  E-value: 8.71e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422091051 204 APTGSGKST---KVPAAYAAQgyKVLVLNPSVAatL------GFGAYMSKAHgiDPNIRTGVRTITTGS*ITYSTY---G 271
Cdd:cd17926   25 LPTGSGKTLtalALIAYLKEL--RTLIVVPTDA--LldqwkeRFEDFLGDSS--IGLIGGGKKKDFDDANVVVATYqslS 98

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 422091051 272 KFLADGGCSGGAYDIIICDECHSTDATSILGIgtvldqAETAGARLVVLATATP 325
Cdd:cd17926   99 NLAEEEKDLFDQFGLLIVDEAHHLPAKTFSEI------LKELNAKYRLGLTATP 146
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
365-414 9.99e-04

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


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 42.05  E-value: 9.99e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 422091051 365 LIFCHSKKKCDELAAKLVALGVNAVAYYRGLDVSV--------IptSGDV-VVVATDAL 414
Cdd:COG0514  234 IVYCLSRKKVEELAEWLREAGIRAAAYHAGLDAEEreanqdrfL--RDEVdVIVATIAF 290
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 198-318 1.02e-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: 40.63  E-value: 1.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422091051  198 QVAHLHAPTGSGKST---KVPAAYAAQGYKVLVLNPSVAATLGfgayMSKAHGIDpnirtgVRTIttgs*itystyGKFL 274
Cdd:pfam13604  19 RVAVLVGPAGTGKTTalkALREAWEAAGYRVIGLAPTGRAAKV----LGEELGIP------ADTI-----------AKLL 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 422091051  275 A--DGGCSGGAYDIIICDECHSTDATSILgigTVLDQAETAGARLV 318
Cdd:pfam13604  78 HrlGGRAGLDPGTLLIVDEAGMVGTRQMA---RLLKLAEDAGARVI 120
DEXHc_HrpB cd17990
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ...
 202-324 1.11e-03

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: 40.39  E-value: 1.11e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422091051 202 LHAPTGSGKSTKVPAAYAA----QGYKVLVLNPSVAATLGFGAYMSKAHGIDPNIRTGVR-----TITTGS*ITYSTYGK 272
Cdd:cd17990   22 LEAPPGAGKTTRVPLALLAelwiAGGKIIVLEPRRVAARAAARRLATLLGEAPGETVGYRvrgesRVGRRTRVEVVTEGV 101

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 422091051 273 FL----ADGGCSGgaYDIIICDECHSTDATSILGIGTVLD--QAETAGARLVVLaTAT 324
Cdd:cd17990  102 LLrrlqRDPELSG--VGAVILDEFHERSLDADLALALLLEvqQLLRDDLRLLAM-SAT 156
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
356-412 1.71e-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: 1.71e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 422091051 356 LEVIKGGRHLIFCHSKKKCDELAAKLVALGVNAVAYYRGLDVS----VIP--TSGDV-VVVATD 412
Cdd:COG0513  236 LRDEDPERAIVFCNTKRGADRLAEKLQKRGISAAALHGDLSQGqrerALDafRNGKIrVLVATD 299
ResIII pfam04851
Type III restriction enzyme, res subunit;
202-293 1.81e-03

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 39.58  E-value: 1.81e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422091051  202 LHAPTGSGK---STKVPAAYAAQGY--KVLVLNPSVA----ATLGFGAYMSKAHGIdPNIRTG--VRTITTGS*ITYSTY 270
Cdd:pfam04851  28 IVMATGSGKtltAAKLIARLFKKGPikKVLFLVPRKDlleqALEEFKKFLPNYVEI-GEIISGdkKDESVDDNKIVVTTI 106

                          90       100
                  ....*....|....*....|....*...
gi 422091051  271 GKF-----LADGGCSGGAYDIIICDECH 293
Cdd:pfam04851 107 QSLykaleLASLELLPDFFDVIIIDEAH 134
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 204-324 4.34e-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: 38.15  E-value: 4.34e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422091051 204 APTGSGKSTKV--PAAYAA--QGYKVLVLNPS------VAATLGFGAYMSKA-----HGIDPNIRTGVRTITtgS*ITYS 268
Cdd:cd00046    8 APTGSGKTLAAllAALLLLlkKGKKVLVLVPTkalalqTAERLRELFGPGIRvavlvGGSSAEEREKNKLGD--ADIIIA 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 422091051 269 TYGKF----LADGGCSGGAYDIIICDECHSTDATS--ILGIGTVLDQAETAGARlVVLATAT 324
Cdd:cd00046   86 TPDMLlnllLREDRLFLKDLKLIIVDEAHALLIDSrgALILDLAVRKAGLKNAQ-VILLSAT 146
DEXHc_DHX16 cd17974
DEXH-box helicase domain of DEAH-box helicase 16; DEAH-box helicase 16 (DHX16) is probably ...
 182-324 5.56e-03

DEXH-box helicase domain of DEAH-box helicase 16; DEAH-box helicase 16 (DHX16) is probably involved in pre-mRNA splicing. DHX16 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: 350732 [Multi-domain]  Cd Length: 174  Bit Score: 38.25  E-value: 5.56e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422091051 182 PVFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVP-----AAYAAQGYKVLVLNPSVAATLGFGAYMSKAHG------IDP 250
Cdd:cd17974    2 PVYPYRDDLLAAVKEHQVLIIVGETGSGKTTQIPqylheAGYTKGGGKIGCTQPRRVAAMSVAARVAEEMGvklgneVGY 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422091051 251 NIR----TGVRTIttgs*ITYSTYGKFLAD--GGCSGGAYDIIICDECHS-TDATSILgIGTVLDQAETAGARLVVLATA 323
Cdd:cd17974   82 SIRfedcTSEKTV-----LKYMTDGMLLREflTEPDLASYSVMIIDEAHErTLHTDIL-FGLVKDIARFRPDLKLLISSA 155


                 .
gi 422091051 324 T 324
Cdd:cd17974  156 T 156
PRK11057 PRK11057
ATP-dependent DNA helicase RecQ; Provisional
 360-396 9.92e-03

ATP-dependent DNA helicase RecQ; Provisional


Pssm-ID: 182933 [Multi-domain]  Cd Length: 607  Bit Score: 39.31  E-value: 9.92e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 422091051 360 KGGRHLIFCHSKKKCDELAAKLVALGVNAVAYYRGLD 396
Cdd:PRK11057 235 RGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLD 271
 
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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