NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1050193737|gb|ANY99143|]
View 

nonstructural protein 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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 2.45e-87

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: 270.07  E-value: 2.45e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050193737  30 EGEVQVVSTATQSFLASCINGVCWTVYHGAGSKTLAGPKGPITQMYTNVDQDLVGWQAPPGARSMTPCTCGSSDLYLVTR 109
Cdd:pfam02907   1 EGEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1050193737 110 HADVIPVRRRGDNRGSLLSPRPVSYLKGSSGGPLLCPSGHAVGIFRAAVCTRGVAKAVDFIPVESMETT 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 ...
 197-339 4.53e-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: 174.27  E-value: 4.53e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050193737 197 FQVAHLHAPTGSGKSTRVPAAYAAQGYQ----VLVLNPSVAATLGFGAYMSKAygiDPSIRTGVRTITTGA--PITYSTY 270
Cdd:cd17931     1 GQLTVLDLHPGAGKTTRVLPQIIREAIKkrlrTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGGneIVDYMCH 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1050193737 271 GKFLaDGGCAGGA---YDIIICDECHSTDSTTILGIGTVLDQAETaGARLVVLATATPPGSVTVPH---PNIEEV 339
Cdd:cd17931    78 GTFT-CRLLSPKRvpnYNLIIMDEAHFTDPASIAARGYIHTRVEM-GEAAVIFMTATPPGTVTPFPqsnHPIEDF 150
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 336-477 8.86e-51

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: 173.22  E-value: 8.86e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050193737 336 IEEVGLSNTGEIPFYGKAIPieTIKGGRHLIFCHSKKKCDELAAKLSNLGINAVAYYRGLDVSV---IPTSGDVVVVATD 412
Cdd:cd18806     1 IEDVALEIPGRIWFYGKAWI--TIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1050193737 413 ALMTGFTGDFDSVIDCNVCVIQTVDFSLDptFTIETT-TVPQDAVSRSQ---RRGRTGRGRTGIYRFVT 477
Cdd:cd18806    79 ISEMGANFDADRVIDCRTCVKPTILFSGD--FRVILTgPVPQTAASAAQrrgRTGRNPAQERDIYRFVG 145
HCV_NS4a pfam01006
Hepatitis C virus non-structural protein NS4a; NS4a forms an integral part of the NS3 serine ...
 632-685 1.39e-21

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


:

Pssm-ID: 366414  Cd Length: 55  Bit Score: 88.29  E-value: 1.39e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1050193737 632 STWVLVGGVLAALAAYCLTTGSVVIVGRIILSGRP-AVIPDREVLYREFDEMEEC 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 2.45e-87

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: 270.07  E-value: 2.45e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050193737  30 EGEVQVVSTATQSFLASCINGVCWTVYHGAGSKTLAGPKGPITQMYTNVDQDLVGWQAPPGARSMTPCTCGSSDLYLVTR 109
Cdd:pfam02907   1 EGEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1050193737 110 HADVIPVRRRGDNRGSLLSPRPVSYLKGSSGGPLLCPSGHAVGIFRAAVCTRGVAKAVDFIPVESMETT 178
Cdd:pfam02907  81 DGDLIPGRRRGDPRVSLLSPRPLSYLKGSSGGPILCPSGHVVGMFRAAVHSGGVVKAVRFVPWETLPTT 149
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 197-339 4.53e-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: 174.27  E-value: 4.53e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050193737 197 FQVAHLHAPTGSGKSTRVPAAYAAQGYQ----VLVLNPSVAATLGFGAYMSKAygiDPSIRTGVRTITTGA--PITYSTY 270
Cdd:cd17931     1 GQLTVLDLHPGAGKTTRVLPQIIREAIKkrlrTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGGneIVDYMCH 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1050193737 271 GKFLaDGGCAGGA---YDIIICDECHSTDSTTILGIGTVLDQAETaGARLVVLATATPPGSVTVPH---PNIEEV 339
Cdd:cd17931    78 GTFT-CRLLSPKRvpnYNLIIMDEAHFTDPASIAARGYIHTRVEM-GEAAVIFMTATPPGTVTPFPqsnHPIEDF 150
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 336-477 8.86e-51

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: 173.22  E-value: 8.86e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050193737 336 IEEVGLSNTGEIPFYGKAIPieTIKGGRHLIFCHSKKKCDELAAKLSNLGINAVAYYRGLDVSV---IPTSGDVVVVATD 412
Cdd:cd18806     1 IEDVALEIPGRIWFYGKAWI--TIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1050193737 413 ALMTGFTGDFDSVIDCNVCVIQTVDFSLDptFTIETT-TVPQDAVSRSQ---RRGRTGRGRTGIYRFVT 477
Cdd:cd18806    79 ISEMGANFDADRVIDCRTCVKPTILFSGD--FRVILTgPVPQTAASAAQrrgRTGRNPAQERDIYRFVG 145
HCV_NS4a pfam01006
Hepatitis C virus non-structural protein NS4a; NS4a forms an integral part of the NS3 serine ...
 632-685 1.39e-21

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


Pssm-ID: 366414  Cd Length: 55  Bit Score: 88.29  E-value: 1.39e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1050193737 632 STWVLVGGVLAALAAYCLTTGSVVIVGRIILSGRP-AVIPDREVLYREFDEMEEC 685
Cdd:pfam01006   1 STWVLVGGALAAGAAYCLTTGSVVVVGRWSVNGKPpAVVPDREVLYQQGEEMEEC 55
DEXDc smart00487
DEAD-like helicases superfamily;
202-329 3.53e-14

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 71.75  E-value: 3.53e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050193737  202 LHAPTGSGKSTRVPAAYAAQGY-----QVLVLNPSVAATLGFGAYMSKAYGIDPSIRTGVRT-----------ITTGAPI 265
Cdd:smart00487  29 LAAPTGSGKTLAALLPALEALKrgkggRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGgdskreqlrklESGKTDI 108

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1050193737  266 TYSTYGKF---LADGGCAGGAYDIIICDECHSTDS----TTILGIGTVLdqaetAGARLVVLATATPPGSV 329
Cdd:smart00487 109 LVTTPGRLldlLENDKLSLSNVDLVILDEAHRLLDggfgDQLEKLLKLL-----PKNVQLLLLSATPPEEI 174
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
202-325 2.78e-05

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 47.33  E-value: 2.78e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050193737 202 LHAPTGSGKsTRVPAAYAAQ---GYQVLVLNPSVAatLGFGAYmSKAYGIDPSIRTGVRTITTGAPITYSTYGKFLADGG 278
Cdd:COG1061   105 VVAPTGTGK-TVLALALAAEllrGKRVLVLVPRRE--LLEQWA-EELRRFLGDPLAGGGKKDSDAPITVATYQSLARRAH 180

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1050193737 279 CA--GGAYDIIICDECH--STDSTTILgigtvldqAETAGARLVVLATATP 325
Cdd:COG1061   181 LDelGDRFGLVIIDEAHhaGAPSYRRI--------LEAFPAAYRLGLTATP 223
PRK11057 PRK11057
ATP-dependent DNA helicase RecQ; Provisional
 356-396 3.12e-04

ATP-dependent DNA helicase RecQ; Provisional


Pssm-ID: 182933 [Multi-domain]  Cd Length: 607  Bit Score: 43.93  E-value: 3.12e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1050193737 356 IETIKGGRHLIFCHSKKKCDELAAKLSNLGINAVAYYRGLD 396
Cdd:PRK11057  231 VQEQRGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLD 271
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 198-318 3.40e-04

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: 42.17  E-value: 3.40e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050193737 198 QVAHLHAPTGSGKST---RVPAAYAAQGYQVLVLNPSVAATLGfgayMSKAYGIDpsirtgVRTIttgapitystyGKFL 274
Cdd:pfam13604  19 RVAVLVGPAGTGKTTalkALREAWEAAGYRVIGLAPTGRAAKV----LGEELGIP------ADTI-----------AKLL 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1050193737 275 A--DGGCAGGAYDIIICDECHSTDSTTILgigTVLDQAETAGARLV 318
Cdd:pfam13604  78 HrlGGRAGLDPGTLLIVDEAGMVGTRQMA---RLLKLAEDAGARVI 120
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
356-414 5.41e-04

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


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 43.21  E-value: 5.41e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1050193737 356 IETIKGGRHLIFCHSKKKCDELAAKLSNLGINAVAYYRGLDVSV--------IptSGDV-VVVATDAL 414
Cdd:COG0514   225 LKEHPGGSGIVYCLSRKKVEELAEWLREAGIRAAAYHAGLDAEEreanqdrfL--RDEVdVIVATIAF 290
 
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 2.45e-87

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: 270.07  E-value: 2.45e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050193737  30 EGEVQVVSTATQSFLASCINGVCWTVYHGAGSKTLAGPKGPITQMYTNVDQDLVGWQAPPGARSMTPCTCGSSDLYLVTR 109
Cdd:pfam02907   1 EGEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1050193737 110 HADVIPVRRRGDNRGSLLSPRPVSYLKGSSGGPLLCPSGHAVGIFRAAVCTRGVAKAVDFIPVESMETT 178
Cdd:pfam02907  81 DGDLIPGRRRGDPRVSLLSPRPLSYLKGSSGGPILCPSGHVVGMFRAAVHSGGVVKAVRFVPWETLPTT 149
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 197-339 4.53e-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: 174.27  E-value: 4.53e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050193737 197 FQVAHLHAPTGSGKSTRVPAAYAAQGYQ----VLVLNPSVAATLGFGAYMSKAygiDPSIRTGVRTITTGA--PITYSTY 270
Cdd:cd17931     1 GQLTVLDLHPGAGKTTRVLPQIIREAIKkrlrTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGGneIVDYMCH 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1050193737 271 GKFLaDGGCAGGA---YDIIICDECHSTDSTTILGIGTVLDQAETaGARLVVLATATPPGSVTVPH---PNIEEV 339
Cdd:cd17931    78 GTFT-CRLLSPKRvpnYNLIIMDEAHFTDPASIAARGYIHTRVEM-GEAAVIFMTATPPGTVTPFPqsnHPIEDF 150
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 336-477 8.86e-51

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: 173.22  E-value: 8.86e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050193737 336 IEEVGLSNTGEIPFYGKAIPieTIKGGRHLIFCHSKKKCDELAAKLSNLGINAVAYYRGLDVSV---IPTSGDVVVVATD 412
Cdd:cd18806     1 IEDVALEIPGRIWFYGKAWI--TIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1050193737 413 ALMTGFTGDFDSVIDCNVCVIQTVDFSLDptFTIETT-TVPQDAVSRSQ---RRGRTGRGRTGIYRFVT 477
Cdd:cd18806    79 ISEMGANFDADRVIDCRTCVKPTILFSGD--FRVILTgPVPQTAASAAQrrgRTGRNPAQERDIYRFVG 145
HCV_NS4a pfam01006
Hepatitis C virus non-structural protein NS4a; NS4a forms an integral part of the NS3 serine ...
 632-685 1.39e-21

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


Pssm-ID: 366414  Cd Length: 55  Bit Score: 88.29  E-value: 1.39e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1050193737 632 STWVLVGGVLAALAAYCLTTGSVVIVGRIILSGRP-AVIPDREVLYREFDEMEEC 685
Cdd:pfam01006   1 STWVLVGGALAAGAAYCLTTGSVVVVGRWSVNGKPpAVVPDREVLYQQGEEMEEC 55
DEXDc smart00487
DEAD-like helicases superfamily;
202-329 3.53e-14

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 71.75  E-value: 3.53e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050193737  202 LHAPTGSGKSTRVPAAYAAQGY-----QVLVLNPSVAATLGFGAYMSKAYGIDPSIRTGVRT-----------ITTGAPI 265
Cdd:smart00487  29 LAAPTGSGKTLAALLPALEALKrgkggRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGgdskreqlrklESGKTDI 108

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1050193737  266 TYSTYGKF---LADGGCAGGAYDIIICDECHSTDS----TTILGIGTVLdqaetAGARLVVLATATPPGSV 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 2.54e-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: 47.20  E-value: 2.54e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1050193737 360 KGGRHLIFCHSKKKCDELAAKLSNLGINAVAYYRGL----DVSVIP---TSGDVVVVATDA 413
Cdd:cd18794    29 LGGSGIIYCLSRKECEQVAARLQSKGISAAAYHAGLepsdRRDVQRkwlRDKIQVIVATVA 89
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
202-325 2.78e-05

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 47.33  E-value: 2.78e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050193737 202 LHAPTGSGKsTRVPAAYAAQ---GYQVLVLNPSVAatLGFGAYmSKAYGIDPSIRTGVRTITTGAPITYSTYGKFLADGG 278
Cdd:COG1061   105 VVAPTGTGK-TVLALALAAEllrGKRVLVLVPRRE--LLEQWA-EELRRFLGDPLAGGGKKDSDAPITVATYQSLARRAH 180

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1050193737 279 CA--GGAYDIIICDECH--STDSTTILgigtvldqAETAGARLVVLATATP 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 3.48e-05

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: 44.04  E-value: 3.48e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1050193737 356 IETIKGGRHLIFCHSKKKCDELAAKLSNLGINAVAYYRGLD 396
Cdd:cd18787    22 LEKLKPGKAIIFVNTKKRVDRLAELLEELGIKVAALHGDLS 62
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 204-324 2.95e-04

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: 41.62  E-value: 2.95e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050193737 204 APTGSGKSTRV--PAAYAA--QGYQVLVLNPSVAATLGFGAYMSKAYGIDPSIRT--------GVRTITTG-APITYSTY 270
Cdd:cd00046     8 APTGSGKTLAAllAALLLLlkKGKKVLVLVPTKALALQTAERLRELFGPGIRVAVlvggssaeEREKNKLGdADIIIATP 87

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050193737 271 GKFLADGGCAGG----AYDIIICDECHSTDSTT--ILGIGTVLDQAETAGARlVVLATAT 324
Cdd:cd00046    88 DMLLNLLLREDRlflkDLKLIIVDEAHALLIDSrgALILDLAVRKAGLKNAQ-VILLSAT 146
PRK11057 PRK11057
ATP-dependent DNA helicase RecQ; Provisional
 356-396 3.12e-04

ATP-dependent DNA helicase RecQ; Provisional


Pssm-ID: 182933 [Multi-domain]  Cd Length: 607  Bit Score: 43.93  E-value: 3.12e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1050193737 356 IETIKGGRHLIFCHSKKKCDELAAKLSNLGINAVAYYRGLD 396
Cdd:PRK11057  231 VQEQRGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLD 271
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 198-318 3.40e-04

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: 42.17  E-value: 3.40e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050193737 198 QVAHLHAPTGSGKST---RVPAAYAAQGYQVLVLNPSVAATLGfgayMSKAYGIDpsirtgVRTIttgapitystyGKFL 274
Cdd:pfam13604  19 RVAVLVGPAGTGKTTalkALREAWEAAGYRVIGLAPTGRAAKV----LGEELGIP------ADTI-----------AKLL 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1050193737 275 A--DGGCAGGAYDIIICDECHSTDSTTILgigTVLDQAETAGARLV 318
Cdd:pfam13604  78 HrlGGRAGLDPGTLLIVDEAGMVGTRQMA---RLLKLAEDAGARVI 120
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
284-335 3.96e-04

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 41.17  E-value: 3.96e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1050193737 284 YDIIICDECHSTDSTTILGIGTVLDQAETAGARLVVLaTATPPGSvTVPHPN 335
Cdd:pfam07652  94 YEVIIMDEAHFTDPASIAARGYISTLVELGEAAAIFM-TATPPGT-SDPFPE 143
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
356-414 5.41e-04

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


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 43.21  E-value: 5.41e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1050193737 356 IETIKGGRHLIFCHSKKKCDELAAKLSNLGINAVAYYRGLDVSV--------IptSGDV-VVVATDAL 414
Cdd:COG0514   225 LKEHPGGSGIVYCLSRKKVEELAEWLREAGIRAAAYHAGLDAEEreanqdrfL--RDEVdVIVATIAF 290
DEXHc_DHX16 cd17974
DEXH-box helicase domain of DEAH-box helicase 16; DEAH-box helicase 16 (DHX16) is probably ...
 182-324 9.36e-04

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: 40.56  E-value: 9.36e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050193737 182 PVFTDNSSPPAVPQTFQVAHLHAPTGSGKSTRVP-----AAYAAQGYQVLVLNPSVAATLGFGAYMSKAYG------IDP 250
Cdd:cd17974     2 PVYPYRDDLLAAVKEHQVLIIVGETGSGKTTQIPqylheAGYTKGGGKIGCTQPRRVAAMSVAARVAEEMGvklgneVGY 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050193737 251 SIR----TGVRTIttgapITYSTYG----KFLADGGCAGgaYDIIICDECHS-TDSTTILgIGTVLDQAETAGARLVVLA 321
Cdd:cd17974    82 SIRfedcTSEKTV-----LKYMTDGmllrEFLTEPDLAS--YSVMIIDEAHErTLHTDIL-FGLVKDIARFRPDLKLLIS 153


                  ...
gi 1050193737 322 TAT 324
Cdd:cd17974   154 SAT 156
DEXHc_HrpB cd17990
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ...
 202-324 1.12e-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: 1.12e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050193737 202 LHAPTGSGKSTRVPAAYAA----QGYQVLVLNPSVAATLGFGAYMSKAYGIDP--------------SIRTGVRTITTGA 263
Cdd:cd17990    22 LEAPPGAGKTTRVPLALLAelwiAGGKIIVLEPRRVAARAAARRLATLLGEAPgetvgyrvrgesrvGRRTRVEVVTEGV 101

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1050193737 264 PITystygKFLADGGCAGgaYDIIICDECHSTDSTTILGIGTVLD--QAETAGARLVVLaTAT 324
Cdd:cd17990   102 LLR-----RLQRDPELSG--VGAVILDEFHERSLDADLALALLLEvqQLLRDDLRLLAM-SAT 156
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 204-325 1.21e-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: 39.98  E-value: 1.21e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050193737 204 APTGSGKsTRVPAAYAAQGYQ--VLVLNPSVA---------ATLGFGAYMSKaygidpsIRTGVRTITTGAPITYSTY-- 270
Cdd:cd17926    25 LPTGSGK-TLTALALIAYLKElrTLIVVPTDAlldqwkerfEDFLGDSSIGL-------IGGGKKKDFDDANVVVATYqs 96

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1050193737 271 -GKFLADGGCAGGAYDIIICDECHSTDSTTILGIgtvldqAETAGARLVVLATATP 325
Cdd:cd17926    97 lSNLAEEEKDLFDQFGLLIVDEAHHLPAKTFSEI------LKELNAKYRLGLTATP 146
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
356-412 1.31e-03

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 41.67  E-value: 1.31e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1050193737 356 IETIKGGRHLIFCHSKKKCDELAAKLSNLGINAVAYYRGLDVS----VIP--TSGDV-VVVATD 412
Cdd:COG0513   236 LRDEDPERAIVFCNTKRGADRLAEKLQKRGISAAALHGDLSQGqrerALDafRNGKIrVLVATD 299
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 202-329 1.67e-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: 39.92  E-value: 1.67e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050193737 202 LHAPTGSGKST--RVPAAYAAQ----GYQVLVLNP---------SVAATLGFGAYMSKAYGIDPSIRTGVRTITTGAPIT 266
Cdd:pfam00270  19 VQAPTGSGKTLafLLPALEALDkldnGPQALVLAPtrelaeqiyEELKKLGKGLGLKVASLLGGDSRKEQLEKLKGPDIL 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050193737 267 YSTYGKFLADGGCAGGAYDI--IICDECHstdstTILGIGtVLDQAETAGARL-----VVLATATPPGSV 329
Cdd:pfam00270  99 VGTPGRLLDLLQERKLLKNLklLVLDEAH-----RLLDMG-FGPDLEEILRRLpkkrqILLLSATLPRNL 162
DEXHc_priA cd17929
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ...
 197-235 4.01e-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: 38.73  E-value: 4.01e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1050193737 197 FQVAHLHAPTGSGKS---TRVPAAYAAQGYQVLVLNPSVAAT 235
Cdd:cd17929    15 FKTFLLHGVTGSGKTevyIELIEKVLAKGKQVLVLVPEISLT 56
HrpA COG1643
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
198-234 7.35e-03

HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 39.68  E-value: 7.35e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1050193737 198 QVAHLHAPTGSGKSTRVPAAYAAQGY----QVLVLNP------SVAA 234
Cdd:COG1643    27 QVVVLAAPPGAGKTTQLPLALLELGWgaggRIGMLEPrrlaarAAAE 73
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH