NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1228349757|gb|ASS33640|]
View 

polyprotein, partial [Hepatitis C virus subtype 1b]

Protein Classification

polyprotein( domain architecture ID 13683648)

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 ...
 67-215 6.68e-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: 6.68e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228349757  67 EGEVQVVSTATQSFLATCVNGVCWTVYHGAGPKTLAGPKGPITQMYTNVDQDLVGWQAPPGARSMTPCTCGSSDLYLVTR 146
Cdd:pfam02907   1 EGEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1228349757 147 HADVIPVRRRGDSRGSLLSPRPVSYLKGSSGGPLLCPSGHVVGIFRAAVCTRGVAKAVDFVPVESMETT 215
Cdd:pfam02907  81 DGDLIPGRRRGDPRVSLLSPRPLSYLKGSSGGPILCPSGHVVGMFRAAVHSGGVVKAVRFVPWETLPTT 149
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 234-377 4.42e-52

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


:

Pssm-ID: 350689 [Multi-domain]  Cd Length: 151  Bit Score: 177.74  E-value: 4.42e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228349757 234 FQVAHLHAPTGSGKSTKVPAAYAAQGY----KVLVLNPSVAATLGFGAYMSKAhgiDPNIRTGVRTITTGAS--ITYSTY 307
Cdd:cd17931     1 GQLTVLDLHPGAGKTTRVLPQIIREAIkkrlRTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGGNeiVDYMCH 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1228349757 308 GKFLaDGGCSGGA---YDIIICDECHSTDSTSILGIGTVLDQAETaGARLVVLATATPPGSVTVPH---PNIEEVA 377
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 ...
 373-494 3.10e-50

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: 172.45  E-value: 3.10e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228349757 373 IEEVALSNTGEIPFYGKAIPieTIKGGRHLIFCHSKKKCDELAAKLSSLGLNAVAYYRGLDVSV---IPTSGDVVVVATD 449
Cdd:cd18806     1 IEDVALEIPGRIWFYGKAWI--TIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1228349757 450 ALMTGFTGDFDSVIDCNTCVTQTVDFSLDptFTIETT-TVPQDAVS 494
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 ...
 669-722 4.97e-22

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: 89.83  E-value: 4.97e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1228349757 669 STWVLVGGVLAALAAYCLTTGSVVIVGRIILSGRP-AVIPDREVLYQEFDEMEEC 722
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 ...
 67-215 6.68e-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: 6.68e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228349757  67 EGEVQVVSTATQSFLATCVNGVCWTVYHGAGPKTLAGPKGPITQMYTNVDQDLVGWQAPPGARSMTPCTCGSSDLYLVTR 146
Cdd:pfam02907   1 EGEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1228349757 147 HADVIPVRRRGDSRGSLLSPRPVSYLKGSSGGPLLCPSGHVVGIFRAAVCTRGVAKAVDFVPVESMETT 215
Cdd:pfam02907  81 DGDLIPGRRRGDPRVSLLSPRPLSYLKGSSGGPILCPSGHVVGMFRAAVHSGGVVKAVRFVPWETLPTT 149
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 234-377 4.42e-52

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


Pssm-ID: 350689 [Multi-domain]  Cd Length: 151  Bit Score: 177.74  E-value: 4.42e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228349757 234 FQVAHLHAPTGSGKSTKVPAAYAAQGY----KVLVLNPSVAATLGFGAYMSKAhgiDPNIRTGVRTITTGAS--ITYSTY 307
Cdd:cd17931     1 GQLTVLDLHPGAGKTTRVLPQIIREAIkkrlRTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGGNeiVDYMCH 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1228349757 308 GKFLaDGGCSGGA---YDIIICDECHSTDSTSILGIGTVLDQAETaGARLVVLATATPPGSVTVPH---PNIEEVA 377
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 ...
 373-494 3.10e-50

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: 172.45  E-value: 3.10e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228349757 373 IEEVALSNTGEIPFYGKAIPieTIKGGRHLIFCHSKKKCDELAAKLSSLGLNAVAYYRGLDVSV---IPTSGDVVVVATD 449
Cdd:cd18806     1 IEDVALEIPGRIWFYGKAWI--TIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1228349757 450 ALMTGFTGDFDSVIDCNTCVTQTVDFSLDptFTIETT-TVPQDAVS 494
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 ...
 669-722 4.97e-22

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: 89.83  E-value: 4.97e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1228349757 669 STWVLVGGVLAALAAYCLTTGSVVIVGRIILSGRP-AVIPDREVLYQEFDEMEEC 722
Cdd:pfam01006   1 STWVLVGGALAAGAAYCLTTGSVVVVGRWSVNGKPpAVVPDREVLYQQGEEMEEC 55
DEXDc smart00487
DEAD-like helicases superfamily;
239-366 2.31e-14

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 72.52  E-value: 2.31e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228349757  239 LHAPTGSGKSTKVPAAYAAQGY-----KVLVLNPSVAATLGFGAYMSKAHGIDPNIRTGVRT----------ITTGAS-I 302
Cdd:smart00487  29 LAAPTGSGKTLAALLPALEALKrgkggRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGgdskreqlrkLESGKTdI 108

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1228349757  303 TYSTYGKF---LADGGCSGGAYDIIICDECHSTDSTS----ILGIGTVLdqaetAGARLVVLATATPPGSV 366
Cdd:smart00487 109 LVTTPGRLldlLENDKLSLSNVDLVILDEAHRLLDGGfgdqLEKLLKLL-----PKNVQLLLLSATPPEEI 174
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
244-372 2.16e-05

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 45.02  E-value: 2.16e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228349757 244 GSGKSTKVPAAYAAQGY----KVLVLNPS--VAATlgfgayMSKA-HGIDPNIRTG--VRTITTGASIT---YSTYGKFL 311
Cdd:pfam07652  12 GAGKTRKVLPELVRECIdrrlRTLVLAPTrvVLAE------MEEAlRGLPIRYHTPavSSEHTGREIVDvmcHATFTQRL 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1228349757 312 ADGGCSGGaYDIIICDECHSTDSTSILGIGTVLDQAETAGARLVVLaTATPPGSvTVPHPN 372
Cdd:pfam07652  86 LSPVRVPN-YEVIIMDEAHFTDPASIAARGYISTLVELGEAAAIFM-TATPPGT-SDPFPE 143
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
239-362 8.15e-05

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 45.79  E-value: 8.15e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228349757 239 LHAPTGSGKST---KVpAAYAAQGYKVLVLNPSVAatLGFGAYmSKAHGIDPNIRTGVRTITTGASITYSTYGKFLADGG 315
Cdd:COG1061   105 VVAPTGTGKTVlalAL-AAELLRGKRVLVLVPRRE--LLEQWA-EELRRFLGDPLAGGGKKDSDAPITVATYQSLARRAH 180

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1228349757 316 CS--GGAYDIIICDECHSTDSTSILGIgtvldqAETAGARLVVLATATP 362
Cdd:COG1061   181 LDelGDRFGLVIIDEAHHAGAPSYRRI------LEAFPAAYRLGLTATP 223
PRK11057 PRK11057
ATP-dependent DNA helicase RecQ; Provisional
 393-433 4.29e-04

ATP-dependent DNA helicase RecQ; Provisional


Pssm-ID: 182933 [Multi-domain]  Cd Length: 607  Bit Score: 43.55  E-value: 4.29e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1228349757 393 IETIKGGRHLIFCHSKKKCDELAAKLSSLGLNAVAYYRGLD 433
Cdd:PRK11057  231 VQEQRGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLD 271
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
393-451 1.26e-03

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


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 42.05  E-value: 1.26e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1228349757 393 IETIKGGRHLIFCHSKKKCDELAAKLSSLGLNAVAYYRGLDVSV--------IptSGDV-VVVATDAL 451
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 ...
 67-215 6.68e-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: 6.68e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228349757  67 EGEVQVVSTATQSFLATCVNGVCWTVYHGAGPKTLAGPKGPITQMYTNVDQDLVGWQAPPGARSMTPCTCGSSDLYLVTR 146
Cdd:pfam02907   1 EGEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1228349757 147 HADVIPVRRRGDSRGSLLSPRPVSYLKGSSGGPLLCPSGHVVGIFRAAVCTRGVAKAVDFVPVESMETT 215
Cdd:pfam02907  81 DGDLIPGRRRGDPRVSLLSPRPLSYLKGSSGGPILCPSGHVVGMFRAAVHSGGVVKAVRFVPWETLPTT 149
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 234-377 4.42e-52

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


Pssm-ID: 350689 [Multi-domain]  Cd Length: 151  Bit Score: 177.74  E-value: 4.42e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228349757 234 FQVAHLHAPTGSGKSTKVPAAYAAQGY----KVLVLNPSVAATLGFGAYMSKAhgiDPNIRTGVRTITTGAS--ITYSTY 307
Cdd:cd17931     1 GQLTVLDLHPGAGKTTRVLPQIIREAIkkrlRTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGGNeiVDYMCH 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1228349757 308 GKFLaDGGCSGGA---YDIIICDECHSTDSTSILGIGTVLDQAETaGARLVVLATATPPGSVTVPH---PNIEEVA 377
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 ...
 373-494 3.10e-50

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: 172.45  E-value: 3.10e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228349757 373 IEEVALSNTGEIPFYGKAIPieTIKGGRHLIFCHSKKKCDELAAKLSSLGLNAVAYYRGLDVSV---IPTSGDVVVVATD 449
Cdd:cd18806     1 IEDVALEIPGRIWFYGKAWI--TIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1228349757 450 ALMTGFTGDFDSVIDCNTCVTQTVDFSLDptFTIETT-TVPQDAVS 494
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 ...
 669-722 4.97e-22

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: 89.83  E-value: 4.97e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1228349757 669 STWVLVGGVLAALAAYCLTTGSVVIVGRIILSGRP-AVIPDREVLYQEFDEMEEC 722
Cdd:pfam01006   1 STWVLVGGALAAGAAYCLTTGSVVVVGRWSVNGKPpAVVPDREVLYQQGEEMEEC 55
DEXDc smart00487
DEAD-like helicases superfamily;
239-366 2.31e-14

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 72.52  E-value: 2.31e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228349757  239 LHAPTGSGKSTKVPAAYAAQGY-----KVLVLNPSVAATLGFGAYMSKAHGIDPNIRTGVRT----------ITTGAS-I 302
Cdd:smart00487  29 LAAPTGSGKTLAALLPALEALKrgkggRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGgdskreqlrkLESGKTdI 108

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1228349757  303 TYSTYGKF---LADGGCSGGAYDIIICDECHSTDSTS----ILGIGTVLdqaetAGARLVVLATATPPGSV 366
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 ...
 397-450 3.71e-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: 3.71e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1228349757 397 KGGRHLIFCHSKKKCDELAAKLSSLGLNAVAYYRGL----DVSVIP---TSGDVVVVATDA 450
Cdd:cd18794    29 LGGSGIIYCLSRKECEQVAARLQSKGISAAAYHAGLepsdRRDVQRkwlRDKIQVIVATVA 89
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
244-372 2.16e-05

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 45.02  E-value: 2.16e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228349757 244 GSGKSTKVPAAYAAQGY----KVLVLNPS--VAATlgfgayMSKA-HGIDPNIRTG--VRTITTGASIT---YSTYGKFL 311
Cdd:pfam07652  12 GAGKTRKVLPELVRECIdrrlRTLVLAPTrvVLAE------MEEAlRGLPIRYHTPavSSEHTGREIVDvmcHATFTQRL 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1228349757 312 ADGGCSGGaYDIIICDECHSTDSTSILGIGTVLDQAETAGARLVVLaTATPPGSvTVPHPN 372
Cdd:pfam07652  86 LSPVRVPN-YEVIIMDEAHFTDPASIAARGYISTLVELGEAAAIFM-TATPPGT-SDPFPE 143
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
239-362 8.15e-05

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 45.79  E-value: 8.15e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228349757 239 LHAPTGSGKST---KVpAAYAAQGYKVLVLNPSVAatLGFGAYmSKAHGIDPNIRTGVRTITTGASITYSTYGKFLADGG 315
Cdd:COG1061   105 VVAPTGTGKTVlalAL-AAELLRGKRVLVLVPRRE--LLEQWA-EELRRFLGDPLAGGGKKDSDAPITVATYQSLARRAH 180

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1228349757 316 CS--GGAYDIIICDECHSTDSTSILGIgtvldqAETAGARLVVLATATP 362
Cdd:COG1061   181 LDelGDRFGLVIIDEAHHAGAPSYRRI------LEAFPAAYRLGLTATP 223
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 235-355 1.06e-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: 43.71  E-value: 1.06e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228349757 235 QVAHLHAPTGSGKST---KVPAAYAAQGYKVLVLNPSVAATLGfgayMSKAHGIDpnirtgVRTIttgASITYSTYGKFL 311
Cdd:pfam13604  19 RVAVLVGPAGTGKTTalkALREAWEAAGYRVIGLAPTGRAAKV----LGEELGIP------ADTI---AKLLHRLGGRAG 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1228349757 312 ADGGcsggayDIIICDECHSTDSTSILgigTVLDQAETAGARLV 355
Cdd:pfam13604  86 LDPG------TLLIVDEAGMVGTRQMA---RLLKLAEDAGARVI 120
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 393-433 1.68e-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: 42.11  E-value: 1.68e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1228349757 393 IETIKGGRHLIFCHSKKKCDELAAKLSSLGLNAVAYYRGLD 433
Cdd:cd18787    22 LEKLKPGKAIIFVNTKKRVDRLAELLEELGIKVAALHGDLS 62
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 241-361 3.80e-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: 41.23  E-value: 3.80e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228349757 241 APTGSGKSTKV--PAAYAA--QGYKVLVLNPS------VAATLGFGAYMSKA-----HGIDPNIRTGVRTITtgASITYS 305
Cdd:cd00046     8 APTGSGKTLAAllAALLLLlkKGKKVLVLVPTkalalqTAERLRELFGPGIRvavlvGGSSAEEREKNKLGD--ADIIIA 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1228349757 306 TYGKF----LADGGCSGGAYDIIICDECHSTDSTS--ILGIGTVLDQAETAGARlVVLATAT 361
Cdd:cd00046    86 TPDMLlnllLREDRLFLKDLKLIIVDEAHALLIDSrgALILDLAVRKAGLKNAQ-VILLSAT 146
PRK11057 PRK11057
ATP-dependent DNA helicase RecQ; Provisional
 393-433 4.29e-04

ATP-dependent DNA helicase RecQ; Provisional


Pssm-ID: 182933 [Multi-domain]  Cd Length: 607  Bit Score: 43.55  E-value: 4.29e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1228349757 393 IETIKGGRHLIFCHSKKKCDELAAKLSSLGLNAVAYYRGLD 433
Cdd:PRK11057  231 VQEQRGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLD 271
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 241-362 5.89e-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: 40.75  E-value: 5.89e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228349757 241 APTGSGKST---KVPAAYAAQgyKVLVLNPSVAatL------GFGAYMSKAHgiDPNIRTGVRTITTGASITYSTY---G 308
Cdd:cd17926    25 LPTGSGKTLtalALIAYLKEL--RTLIVVPTDA--LldqwkeRFEDFLGDSS--IGLIGGGKKKDFDDANVVVATYqslS 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1228349757 309 KFLADGGCSGGAYDIIICDECHSTDSTSILGIgtvldqAETAGARLVVLATATP 362
Cdd:cd17926    99 NLAEEEKDLFDQFGLLIVDEAHHLPAKTFSEI------LKELNAKYRLGLTATP 146
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
393-451 1.26e-03

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


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 42.05  E-value: 1.26e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1228349757 393 IETIKGGRHLIFCHSKKKCDELAAKLSSLGLNAVAYYRGLDVSV--------IptSGDV-VVVATDAL 451
Cdd:COG0514   225 LKEHPGGSGIVYCLSRKKVEELAEWLREAGIRAAAYHAGLDAEEreanqdrfL--RDEVdVIVATIAF 290
ResIII pfam04851
Type III restriction enzyme, res subunit;
239-330 1.83e-03

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 39.58  E-value: 1.83e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228349757 239 LHAPTGSGK---STKVPAAYAAQGY--KVLVLNPSVA----ATLGFGAYMSKAHGIdPNIRTG--VRTITTGASITYSTY 307
Cdd:pfam04851  28 IVMATGSGKtltAAKLIARLFKKGPikKVLFLVPRKDlleqALEEFKKFLPNYVEI-GEIISGdkKDESVDDNKIVVTTI 106

                          90       100
                  ....*....|....*....|....*...
gi 1228349757 308 GKF-----LADGGCSGGAYDIIICDECH 330
Cdd:pfam04851 107 QSLykaleLASLELLPDFFDVIIIDEAH 134
DEXHc_HrpB cd17990
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ...
 239-361 2.63e-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: 39.24  E-value: 2.63e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228349757 239 LHAPTGSGKSTKVPAAYAA----QGYKVLVLNPSVAATLGFGAYMSKAHGIDPNIRTGVR-----TITTGASITYSTYGK 309
Cdd:cd17990    22 LEAPPGAGKTTRVPLALLAelwiAGGKIIVLEPRRVAARAAARRLATLLGEAPGETVGYRvrgesRVGRRTRVEVVTEGV 101

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1228349757 310 FL----ADGGCSGgaYDIIICDECHSTDSTSILGIGTVLD--QAETAGARLVVLaTAT 361
Cdd:cd17990   102 LLrrlqRDPELSG--VGAVILDEFHERSLDADLALALLLEvqQLLRDDLRLLAM-SAT 156
DEXHc_DHX16 cd17974
DEXH-box helicase domain of DEAH-box helicase 16; DEAH-box helicase 16 (DHX16) is probably ...
 219-361 3.59e-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: 3.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228349757 219 PVFTDNSSPPAVPQTFQVAHLHAPTGSGKSTKVP-----AAYAAQGYKVLVLNPSVAATLGFGAYMSKAHG------IDP 287
Cdd:cd17974     2 PVYPYRDDLLAAVKEHQVLIIVGETGSGKTTQIPqylheAGYTKGGGKIGCTQPRRVAAMSVAARVAEEMGvklgneVGY 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228349757 288 NIR----TGVRTIttgasITYSTYGKFLAD--GGCSGGAYDIIICDECHS-TDSTSILgIGTVLDQAETAGARLVVLATA 360
Cdd:cd17974    82 SIRfedcTSEKTV-----LKYMTDGMLLREflTEPDLASYSVMIIDEAHErTLHTDIL-FGLVKDIARFRPDLKLLISSA 155


                  .
gi 1228349757 361 T 361
Cdd:cd17974   156 T 156
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
393-449 5.12e-03

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 39.75  E-value: 5.12e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1228349757 393 IETIKGGRHLIFCHSKKKCDELAAKLSSLGLNAVAYYRGLDVS----VIP--TSGDV-VVVATD 449
Cdd:COG0513   236 LRDEDPERAIVFCNTKRGADRLAEKLQKRGISAAALHGDLSQGqrerALDafRNGKIrVLVATD 299
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH