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Conserved domains on  [gi|422094981|gb|AFX79075|]
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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 2.70e-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: 259.67  E-value: 2.70e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422094981   30 EGEVQIVSTAAQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDKDLVGWPAPQGSRSLTPCTCGSSDLYLVTR 109
Cdd:pfam02907   1 EGEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 422094981  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 2.17e-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: 175.05  E-value: 2.17e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422094981 197 FQVAHLHAPTGSGKSTKVPAAYAAQGYQ----VLVLNPSVAATLAFGAYMSKAhgvDPNIRTGVRTITTG--SPITYSTY 270
Cdd:cd17931    1 GQLTVLDLHPGAGKTTRVLPQIIREAIKkrlrTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGgnEIVDYMCH 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 422094981 271 GKFLaDGGCSGGA---YDIIICDECHSTDATSILGIGTVLDQAETaGARLVVLATATPPGSVTVPH---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 1.79e-49

P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.


The actual alignment was detected with superfamily member cd18806:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 145  Bit Score: 169.75  E-value: 1.79e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422094981 336 IEEVALSTTGEIPFYGKAIPleVIKGGRHLIFCHSKKKCDEVAAKLVKLGINAVAYYRGLDVSV---IPTSGDVVVVATD 412
Cdd:cd18806    1 IEDVALEIPGRIWFYGKAWI--TIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 422094981 413 ALMTGYTGDFDSVIDCNTCVTQTVDFSLDptFTIETT-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 1.13e-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: 85.59  E-value: 1.13e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 422094981  632 STWVLVGGVLAALAAYCLSTGCVVIVGRVVLSGKP-AVIPNREVLYREFDEMEEC 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 2.70e-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: 259.67  E-value: 2.70e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422094981   30 EGEVQIVSTAAQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDKDLVGWPAPQGSRSLTPCTCGSSDLYLVTR 109
Cdd:pfam02907   1 EGEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 422094981  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 2.17e-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: 175.05  E-value: 2.17e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422094981 197 FQVAHLHAPTGSGKSTKVPAAYAAQGYQ----VLVLNPSVAATLAFGAYMSKAhgvDPNIRTGVRTITTG--SPITYSTY 270
Cdd:cd17931    1 GQLTVLDLHPGAGKTTRVLPQIIREAIKkrlrTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGgnEIVDYMCH 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 422094981 271 GKFLaDGGCSGGA---YDIIICDECHSTDATSILGIGTVLDQAETaGARLVVLATATPPGSVTVPH---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 1.79e-49

C-terminal helicase domain of viral helicase; Viral helicases in this family here are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350193 [Multi-domain]  Cd Length: 145  Bit Score: 169.75  E-value: 1.79e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422094981 336 IEEVALSTTGEIPFYGKAIPleVIKGGRHLIFCHSKKKCDEVAAKLVKLGINAVAYYRGLDVSV---IPTSGDVVVVATD 412
Cdd:cd18806    1 IEDVALEIPGRIWFYGKAWI--TIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 422094981 413 ALMTGYTGDFDSVIDCNTCVTQTVDFSLDptFTIETT-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 1.13e-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: 85.59  E-value: 1.13e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 422094981  632 STWVLVGGVLAALAAYCLSTGCVVIVGRVVLSGKP-AVIPNREVLYREFDEMEEC 685
Cdd:pfam01006   1 STWVLVGGALAAGAAYCLTTGSVVVVGRWSVNGKPpAVVPDREVLYQQGEEMEEC 55
DEXDc smart00487
DEAD-like helicases superfamily;
202-329 1.41e-14

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 72.91  E-value: 1.41e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422094981   202 LHAPTGSGKSTKVPAAYAAQGY-----QVLVLNPSVAATLAFGAYMSKAHGVDPNIRTGVRT-----------ITTGSPI 265
Cdd:smart00487  29 LAAPTGSGKTLAALLPALEALKrgkggRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGgdskreqlrklESGKTDI 108

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 422094981   266 TYSTYGKF---LADGGCSGGAYDIIICDECHSTD----ATSILGIGTVLdqaetAGARLVVLATATPPGSV 329
Cdd:smart00487 109 LVTTPGRLldlLENDKLSLSNVDLVILDEAHRLLdggfGDQLEKLLKLL-----PKNVQLLLLSATPPEEI 174
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
202-325 1.09e-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: 1.09e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422094981 202 LHAPTGSGKST---KVpAAYAAQGYQVLVLNPSVAatLAFGAYmSKAHGVDPNIRTGVRTITTGSPITYSTYGKFLADGG 278
Cdd:COG1061  105 VVAPTGTGKTVlalAL-AAELLRGKRVLVLVPRRE--LLEQWA-EELRRFLGDPLAGGGKKDSDAPITVATYQSLARRAH 180

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 422094981 279 CS--GGAYDIIICDECHSTDATSILGIgtvldqAETAGARLVVLATATP 325
Cdd:COG1061  181 LDelGDRFGLVIIDEAHHAGAPSYRRI------LEAFPAAYRLGLTATP 223
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
207-335 2.75e-05

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 44.63  E-value: 2.75e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422094981  207 GSGKSTKVPAAYAAQGYQ----VLVLNPS--VAATlafgayMSKA-HGVDPNIRT-GVRTITTGSPIT----YSTYGKFL 274
Cdd:pfam07652  12 GAGKTRKVLPELVRECIDrrlrTLVLAPTrvVLAE------MEEAlRGLPIRYHTpAVSSEHTGREIVdvmcHATFTQRL 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 422094981  275 ADGGCSGGaYDIIICDECHSTDATSILGIGTVLDQAETAGARLVVLaTATPPGSvTVPHPN 335
Cdd:pfam07652  86 LSPVRVPN-YEVIIMDEAHFTDPASIAARGYISTLVELGEAAAIFM-TATPPGT-SDPFPE 143
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
365-414 5.05e-04

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


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 43.21  E-value: 5.05e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 422094981 365 LIFCHSKKKCDEVAAKLVKLGINAVAYYRGLDVSV--------IptSGDV-VVVATDAL 414
Cdd:COG0514  234 IVYCLSRKKVEELAEWLREAGIRAAAYHAGLDAEEreanqdrfL--RDEVdVIVATIAF 290
PRK11057 PRK11057
ATP-dependent DNA helicase RecQ; Provisional
 360-396 3.43e-03

ATP-dependent DNA helicase RecQ; Provisional


Pssm-ID: 182933 [Multi-domain]  Cd Length: 607  Bit Score: 40.47  E-value: 3.43e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 422094981 360 KGGRHLIFCHSKKKCDEVAAKLVKLGINAVAYYRGLD 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 2.70e-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: 259.67  E-value: 2.70e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422094981   30 EGEVQIVSTAAQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDKDLVGWPAPQGSRSLTPCTCGSSDLYLVTR 109
Cdd:pfam02907   1 EGEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 422094981  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 2.17e-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: 175.05  E-value: 2.17e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422094981 197 FQVAHLHAPTGSGKSTKVPAAYAAQGYQ----VLVLNPSVAATLAFGAYMSKAhgvDPNIRTGVRTITTG--SPITYSTY 270
Cdd:cd17931    1 GQLTVLDLHPGAGKTTRVLPQIIREAIKkrlrTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGgnEIVDYMCH 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 422094981 271 GKFLaDGGCSGGA---YDIIICDECHSTDATSILGIGTVLDQAETaGARLVVLATATPPGSVTVPH---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 1.79e-49

C-terminal helicase domain of viral helicase; Viral helicases in this family here are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350193 [Multi-domain]  Cd Length: 145  Bit Score: 169.75  E-value: 1.79e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422094981 336 IEEVALSTTGEIPFYGKAIPleVIKGGRHLIFCHSKKKCDEVAAKLVKLGINAVAYYRGLDVSV---IPTSGDVVVVATD 412
Cdd:cd18806    1 IEDVALEIPGRIWFYGKAWI--TIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 422094981 413 ALMTGYTGDFDSVIDCNTCVTQTVDFSLDptFTIETT-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 1.13e-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: 85.59  E-value: 1.13e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 422094981  632 STWVLVGGVLAALAAYCLSTGCVVIVGRVVLSGKP-AVIPNREVLYREFDEMEEC 685
Cdd:pfam01006   1 STWVLVGGALAAGAAYCLTTGSVVVVGRWSVNGKPpAVVPDREVLYQQGEEMEEC 55
DEXDc smart00487
DEAD-like helicases superfamily;
202-329 1.41e-14

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 72.91  E-value: 1.41e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422094981   202 LHAPTGSGKSTKVPAAYAAQGY-----QVLVLNPSVAATLAFGAYMSKAHGVDPNIRTGVRT-----------ITTGSPI 265
Cdd:smart00487  29 LAAPTGSGKTLAALLPALEALKrgkggRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGgdskreqlrklESGKTDI 108

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 422094981   266 TYSTYGKF---LADGGCSGGAYDIIICDECHSTD----ATSILGIGTVLdqaetAGARLVVLATATPPGSV 329
Cdd:smart00487 109 LVTTPGRLldlLENDKLSLSNVDLVILDEAHRLLdggfGDQLEKLLKLL-----PKNVQLLLLSATPPEEI 174
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 360-413 3.25e-06

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


Pssm-ID: 350181 [Multi-domain]  Cd Length: 134  Bit Score: 46.82  E-value: 3.25e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 422094981 360 KGGRHLIFCHSKKKCDEVAAKLVKLGINAVAYYRGL----DVSVIP---TSGDVVVVATDA 413
Cdd:cd18794   29 LGGSGIIYCLSRKECEQVAARLQSKGISAAAYHAGLepsdRRDVQRkwlRDKIQVIVATVA 89
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
202-325 1.09e-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: 1.09e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422094981 202 LHAPTGSGKST---KVpAAYAAQGYQVLVLNPSVAatLAFGAYmSKAHGVDPNIRTGVRTITTGSPITYSTYGKFLADGG 278
Cdd:COG1061  105 VVAPTGTGKTVlalAL-AAELLRGKRVLVLVPRRE--LLEQWA-EELRRFLGDPLAGGGKKDSDAPITVATYQSLARRAH 180

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 422094981 279 CS--GGAYDIIICDECHSTDATSILGIgtvldqAETAGARLVVLATATP 325
Cdd:COG1061  181 LDelGDRFGLVIIDEAHHAGAPSYRRI------LEAFPAAYRLGLTATP 223
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
207-335 2.75e-05

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 44.63  E-value: 2.75e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422094981  207 GSGKSTKVPAAYAAQGYQ----VLVLNPS--VAATlafgayMSKA-HGVDPNIRT-GVRTITTGSPIT----YSTYGKFL 274
Cdd:pfam07652  12 GAGKTRKVLPELVRECIDrrlrTLVLAPTrvVLAE------MEEAlRGLPIRYHTpAVSSEHTGREIVdvmcHATFTQRL 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 422094981  275 ADGGCSGGaYDIIICDECHSTDATSILGIGTVLDQAETAGARLVVLaTATPPGSvTVPHPN 335
Cdd:pfam07652  86 LSPVRVPN-YEVIIMDEAHFTDPASIAARGYISTLVELGEAAAIFM-TATPPGT-SDPFPE 143
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 204-324 7.30e-05

N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region.


Pssm-ID: 350668 [Multi-domain]  Cd Length: 146  Bit Score: 43.55  E-value: 7.30e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422094981 204 APTGSGKSTKV--PAAYAA--QGYQVLVLNPSVAATL----AFGAYMSKA-------HGVDPNIRTGVRTITtgSPITYS 268
Cdd:cd00046    8 APTGSGKTLAAllAALLLLlkKGKKVLVLVPTKALALqtaeRLRELFGPGirvavlvGGSSAEEREKNKLGD--ADIIIA 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 422094981 269 TYGKF----LADGGCSGGAYDIIICDECHSTDATS--ILGIGTVLDQAETAGARlVVLATAT 324
Cdd:cd00046   86 TPDMLlnllLREDRLFLKDLKLIIVDEAHALLIDSrgALILDLAVRKAGLKNAQ-VILLSAT 146
DEXHc_HrpB cd17990
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ...
 202-324 9.52e-05

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: 43.47  E-value: 9.52e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422094981 202 LHAPTGSGKSTKVPAAYAA----QGYQVLVLNPSVAATLAFGAYMSKAHGVDPNIRTG--VRTITTGSPIT---YSTYGK 272
Cdd:cd17990   22 LEAPPGAGKTTRVPLALLAelwiAGGKIIVLEPRRVAARAAARRLATLLGEAPGETVGyrVRGESRVGRRTrveVVTEGV 101

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 422094981 273 FL----ADGGCSGgaYDIIICDECHSTDATSILGIGTVLD--QAETAGARLVVLaTAT 324
Cdd:cd17990  102 LLrrlqRDPELSG--VGAVILDEFHERSLDADLALALLLEvqQLLRDDLRLLAM-SAT 156
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 356-396 1.09e-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: 42.49  E-value: 1.09e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 422094981 356 LEVIKGGRHLIFCHSKKKCDEVAAKLVKLGINAVAYYRGLD 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 4.78e-04

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


Pssm-ID: 350684 [Multi-domain]  Cd Length: 146  Bit Score: 41.14  E-value: 4.78e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422094981 204 APTGSGKST---KVPAAYAAQGyqVLVLNPSVAatLA------FGAYMSKAHgvDPNIRTGVRTITTGSPITYSTY---G 271
Cdd:cd17926   25 LPTGSGKTLtalALIAYLKELR--TLIVVPTDA--LLdqwkerFEDFLGDSS--IGLIGGGKKKDFDDANVVVATYqslS 98

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 422094981 272 KFLADGGCSGGAYDIIICDECHSTDATSILGIgtvldqAETAGARLVVLATATP 325
Cdd:cd17926   99 NLAEEEKDLFDQFGLLIVDEAHHLPAKTFSEI------LKELNAKYRLGLTATP 146
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
365-414 5.05e-04

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


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 43.21  E-value: 5.05e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 422094981 365 LIFCHSKKKCDEVAAKLVKLGINAVAYYRGLDVSV--------IptSGDV-VVVATDAL 414
Cdd:COG0514  234 IVYCLSRKKVEELAEWLREAGIRAAAYHAGLDAEEreanqdrfL--RDEVdVIVATIAF 290
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
356-412 6.00e-04

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 42.83  E-value: 6.00e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 422094981 356 LEVIKGGRHLIFCHSKKKCDEVAAKLVKLGINAVAYYRGLDVS----VIP--TSGDV-VVVATD 412
Cdd:COG0513  236 LRDEDPERAIVFCNTKRGADRLAEKLQKRGISAAALHGDLSQGqrerALDafRNGKIrVLVATD 299
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 198-318 3.32e-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: 39.08  E-value: 3.32e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422094981  198 QVAHLHAPTGSGKST---KVPAAYAAQGYQVLVLNPSVAATLAfgayMSKAHGVDpnirtgVRTIttgspitystyGKFL 274
Cdd:pfam13604  19 RVAVLVGPAGTGKTTalkALREAWEAAGYRVIGLAPTGRAAKV----LGEELGIP------ADTI-----------AKLL 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 422094981  275 A--DGGCSGGAYDIIICDECHSTDATSILgigTVLDQAETAGARLV 318
Cdd:pfam13604  78 HrlGGRAGLDPGTLLIVDEAGMVGTRQMA---RLLKLAEDAGARVI 120
PRK11057 PRK11057
ATP-dependent DNA helicase RecQ; Provisional
 360-396 3.43e-03

ATP-dependent DNA helicase RecQ; Provisional


Pssm-ID: 182933 [Multi-domain]  Cd Length: 607  Bit Score: 40.47  E-value: 3.43e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 422094981 360 KGGRHLIFCHSKKKCDEVAAKLVKLGINAVAYYRGLD 396
Cdd:PRK11057 235 RGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLD 271
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 202-329 3.82e-03

DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 38.76  E-value: 3.82e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422094981  202 LHAPTGSGKST--KVPAAYAAQ----GYQVLVLNPSVAatLA------FGAYMSKAHGVDPNIRTGV-----RTITTGSP 264
Cdd:pfam00270  19 VQAPTGSGKTLafLLPALEALDkldnGPQALVLAPTRE--LAeqiyeeLKKLGKGLGLKVASLLGGDsrkeqLEKLKGPD 96

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 422094981  265 ITYSTYGKFLADGGCSGGAYDI--IICDECH-STDATSILGIGTVLDQAETagARLVVLATATPPGSV 329
Cdd:pfam00270  97 ILVGTPGRLLDLLQERKLLKNLklLVLDEAHrLLDMGFGPDLEEILRRLPK--KRQILLLSATLPRNL 162
DEXHc_DHX16 cd17974
DEXH-box helicase domain of DEAH-box helicase 16; DEAH-box helicase 16 (DHX16) is probably ...
 182-324 3.90e-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: 39.02  E-value: 3.90e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422094981 182 PVFTDNSTPPAVPQSFQVAHLHAPTGSGKSTKVP-----AAYAAQGYQVLVLNP------SVAATLAFGAYMSKAHGVDP 250
Cdd:cd17974    2 PVYPYRDDLLAAVKEHQVLIIVGETGSGKTTQIPqylheAGYTKGGGKIGCTQPrrvaamSVAARVAEEMGVKLGNEVGY 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422094981 251 NIR----TGVRTIttgspITYSTYGKFLAD--GGCSGGAYDIIICDECHS-TDATSILgIGTVLDQAETAGARLVVLATA 323
Cdd:cd17974   82 SIRfedcTSEKTV-----LKYMTDGMLLREflTEPDLASYSVMIIDEAHErTLHTDIL-FGLVKDIARFRPDLKLLISSA 155


                 .
gi 422094981 324 T 324
Cdd:cd17974  156 T 156
ResIII pfam04851
Type III restriction enzyme, res subunit;
202-293 4.26e-03

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 38.42  E-value: 4.26e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 422094981  202 LHAPTGSGK---STKVPAAYAAQGYQ--VLVLNPSVA----ATLAFGAYMSKAHGVdPNIRTG--VRTITTGSPITYSTY 270
Cdd:pfam04851  28 IVMATGSGKtltAAKLIARLFKKGPIkkVLFLVPRKDlleqALEEFKKFLPNYVEI-GEIISGdkKDESVDDNKIVVTTI 106

                          90       100
                  ....*....|....*....|....*...
gi 422094981  271 GKF-----LADGGCSGGAYDIIICDECH 293
Cdd:pfam04851 107 QSLykaleLASLELLPDFFDVIIIDEAH 134
DEXHc_priA cd17929
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ...
 196-235 8.34e-03

DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' superfamily 2 DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA 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: 350687 [Multi-domain]  Cd Length: 178  Bit Score: 37.96  E-value: 8.34e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 422094981 196 SFQVAHLHAPTGSGKS---TKVPAAYAAQGYQVLVLNPSVAAT 235
Cdd:cd17929   14 GFKTFLLHGVTGSGKTevyIELIEKVLAKGKQVLVLVPEISLT 56
 
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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