NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|728894627|gb|AIZ00649|]
View 

nonstructural protein 3, partial [Hepatitis C virus subtype 1b]

Protein Classification

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 4.80e-89

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: 273.15  E-value: 4.80e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894627   30 EGEVQVVSTATQSFLATCVNGVCWTVYHGAGSKTLAGPKGPVTQMYTNVDQDLVGWPAPPGARSLTPCTCGSSDLYLVTR 109
Cdd:pfam02907   1 EGEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 728894627  110 HADVIPVRRRGDSRGSLLSPRPVSYLKGSSGGPLLCPSGHAVGIFRAAVCTRGVAKAVDFVPVESMETT 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 8.73e-53

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: 178.13  E-value: 8.73e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894627 197 FQVAHLHAPTGSGKSTKVPAAYAAQGY----KVLVLNPSVAATLGFGAYMSKAhgtDPNIRTGVRTITTGA--PITYSTY 270
Cdd:cd17931    1 GQLTVLDLHPGAGKTTRVLPQIIREAIkkrlRTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGGneIVDYMCH 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 728894627 271 GKFLaDGGCSGGA---YDIIICDECHSTDSTTILGIGTVLDQAETaGARLVVLATATPPGSVTVPH---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 ...
 336-477 1.13e-52

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: 177.45  E-value: 1.13e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894627 336 IEEVALSNIGEIPFYGKAIPieTIKGGRHLIFCHSKKKCDELAAKLSGLGLNAVAYYRGLDVSV---IPTSGDVVVVATD 412
Cdd:cd18806    1 IEDVALEIPGRIWFYGKAWI--TIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 728894627 413 ALMTGFTGDFDSVIDCNTCVTQTVDFSLDptFTIETT-TVPQDAVSRSQ---RRGRTGRGRRGIYRFVT 477
Cdd:cd18806   79 ISEMGANFDADRVIDCRTCVKPTILFSGD--FRVILTgPVPQTAASAAQrrgRTGRNPAQERDIYRFVG 145
 
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 4.80e-89

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: 273.15  E-value: 4.80e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894627   30 EGEVQVVSTATQSFLATCVNGVCWTVYHGAGSKTLAGPKGPVTQMYTNVDQDLVGWPAPPGARSLTPCTCGSSDLYLVTR 109
Cdd:pfam02907   1 EGEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 728894627  110 HADVIPVRRRGDSRGSLLSPRPVSYLKGSSGGPLLCPSGHAVGIFRAAVCTRGVAKAVDFVPVESMETT 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 8.73e-53

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: 178.13  E-value: 8.73e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894627 197 FQVAHLHAPTGSGKSTKVPAAYAAQGY----KVLVLNPSVAATLGFGAYMSKAhgtDPNIRTGVRTITTGA--PITYSTY 270
Cdd:cd17931    1 GQLTVLDLHPGAGKTTRVLPQIIREAIkkrlRTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGGneIVDYMCH 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 728894627 271 GKFLaDGGCSGGA---YDIIICDECHSTDSTTILGIGTVLDQAETaGARLVVLATATPPGSVTVPH---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 ...
 336-477 1.13e-52

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: 177.45  E-value: 1.13e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894627 336 IEEVALSNIGEIPFYGKAIPieTIKGGRHLIFCHSKKKCDELAAKLSGLGLNAVAYYRGLDVSV---IPTSGDVVVVATD 412
Cdd:cd18806    1 IEDVALEIPGRIWFYGKAWI--TIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 728894627 413 ALMTGFTGDFDSVIDCNTCVTQTVDFSLDptFTIETT-TVPQDAVSRSQ---RRGRTGRGRRGIYRFVT 477
Cdd:cd18806   79 ISEMGANFDADRVIDCRTCVKPTILFSGD--FRVILTgPVPQTAASAAQrrgRTGRNPAQERDIYRFVG 145
DEXDc smart00487
DEAD-like helicases superfamily;
202-347 4.78e-15

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 74.07  E-value: 4.78e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894627   202 LHAPTGSGKSTKVPAAYAAQGY-----KVLVLNPSVAATLGFGAYMSKAHGTDPNIRTGVRT-----------ITTGAPI 265
Cdd:smart00487  29 LAAPTGSGKTLAALLPALEALKrgkggRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGgdskreqlrklESGKTDI 108

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894627   266 TYSTYGKF---LADGGCSGGAYDIIICDECHSTDS----TTILGIGTVLdqaetAGARLVVLATATPPGSVtvphPNIEE 338
Cdd:smart00487 109 LVTTPGRLldlLENDKLSLSNVDLVILDEAHRLLDggfgDQLEKLLKLL-----PKNVQLLLLSATPPEEI----ENLLE 179


                   ....*....
gi 728894627   339 VALSNIGEI 347
Cdd:smart00487 180 LFLNDPVFI 188
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
202-325 3.27e-05

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 46.94  E-value: 3.27e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894627 202 LHAPTGSGKST---KVpAAYAAQGYKVLVLNPSVAatLGFGAYmSKAHGTDPNIRTGVRTITTGAPITYSTYGKFLADGG 278
Cdd:COG1061  105 VVAPTGTGKTVlalAL-AAELLRGKRVLVLVPRRE--LLEQWA-EELRRFLGDPLAGGGKKDSDAPITVATYQSLARRAH 180

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 728894627 279 CS--GGAYDIIICDECH--STDSTTILgigtvldqAETAGARLVVLATATP 325
Cdd:COG1061  181 LDelGDRFGLVIIDEAHhaGAPSYRRI--------LEAFPAAYRLGLTATP 223
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
207-335 2.81e-04

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 41.55  E-value: 2.81e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894627  207 GSGKSTKVPAAYAAQGY----KVLVLNPS--VAATlgfgayMSKA-HGTDPNIRTG--VRTITTGAPIT---YSTYGKFL 274
Cdd:pfam07652  12 GAGKTRKVLPELVRECIdrrlRTLVLAPTrvVLAE------MEEAlRGLPIRYHTPavSSEHTGREIVDvmcHATFTQRL 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 728894627  275 ADGGCSGGaYDIIICDECHSTDSTTILGIGTVLDQAETAGARLVVLaTATPPGSvTVPHPN 335
Cdd:pfam07652  86 LSPVRVPN-YEVIIMDEAHFTDPASIAARGYISTLVELGEAAAIFM-TATPPGT-SDPFPE 143
PRK11057 PRK11057
ATP-dependent DNA helicase RecQ; Provisional
 356-396 9.73e-04

ATP-dependent DNA helicase RecQ; Provisional


Pssm-ID: 182933 [Multi-domain]  Cd Length: 607  Bit Score: 42.39  E-value: 9.73e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 728894627 356 IETIKGGRHLIFCHSKKKCDELAAKLSGLGLNAVAYYRGLD 396
Cdd:PRK11057 231 VQEQRGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLD 271
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
356-414 1.40e-03

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


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 41.67  E-value: 1.40e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 728894627 356 IETIKGGRHLIFCHSKKKCDELAAKLSGLGLNAVAYYRGLDVSV--------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 4.80e-89

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: 273.15  E-value: 4.80e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894627   30 EGEVQVVSTATQSFLATCVNGVCWTVYHGAGSKTLAGPKGPVTQMYTNVDQDLVGWPAPPGARSLTPCTCGSSDLYLVTR 109
Cdd:pfam02907   1 EGEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 728894627  110 HADVIPVRRRGDSRGSLLSPRPVSYLKGSSGGPLLCPSGHAVGIFRAAVCTRGVAKAVDFVPVESMETT 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 8.73e-53

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: 178.13  E-value: 8.73e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894627 197 FQVAHLHAPTGSGKSTKVPAAYAAQGY----KVLVLNPSVAATLGFGAYMSKAhgtDPNIRTGVRTITTGA--PITYSTY 270
Cdd:cd17931    1 GQLTVLDLHPGAGKTTRVLPQIIREAIkkrlRTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGGneIVDYMCH 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 728894627 271 GKFLaDGGCSGGA---YDIIICDECHSTDSTTILGIGTVLDQAETaGARLVVLATATPPGSVTVPH---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 ...
 336-477 1.13e-52

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: 177.45  E-value: 1.13e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894627 336 IEEVALSNIGEIPFYGKAIPieTIKGGRHLIFCHSKKKCDELAAKLSGLGLNAVAYYRGLDVSV---IPTSGDVVVVATD 412
Cdd:cd18806    1 IEDVALEIPGRIWFYGKAWI--TIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 728894627 413 ALMTGFTGDFDSVIDCNTCVTQTVDFSLDptFTIETT-TVPQDAVSRSQ---RRGRTGRGRRGIYRFVT 477
Cdd:cd18806   79 ISEMGANFDADRVIDCRTCVKPTILFSGD--FRVILTgPVPQTAASAAQrrgRTGRNPAQERDIYRFVG 145
DEXDc smart00487
DEAD-like helicases superfamily;
202-347 4.78e-15

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 74.07  E-value: 4.78e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894627   202 LHAPTGSGKSTKVPAAYAAQGY-----KVLVLNPSVAATLGFGAYMSKAHGTDPNIRTGVRT-----------ITTGAPI 265
Cdd:smart00487  29 LAAPTGSGKTLAALLPALEALKrgkggRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGgdskreqlrklESGKTDI 108

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894627   266 TYSTYGKF---LADGGCSGGAYDIIICDECHSTDS----TTILGIGTVLdqaetAGARLVVLATATPPGSVtvphPNIEE 338
Cdd:smart00487 109 LVTTPGRLldlLENDKLSLSNVDLVILDEAHRLLDggfgDQLEKLLKLL-----PKNVQLLLLSATPPEEI----ENLLE 179


                   ....*....
gi 728894627   339 VALSNIGEI 347
Cdd:smart00487 180 LFLNDPVFI 188
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 360-413 2.20e-05

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


Pssm-ID: 350181 [Multi-domain]  Cd Length: 134  Bit Score: 44.51  E-value: 2.20e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 728894627 360 KGGRHLIFCHSKKKCDELAAKLSGLGLNAVAYYRGL----DVSVIP---TSGDVVVVATDA 413
Cdd:cd18794   29 LGGSGIIYCLSRKECEQVAARLQSKGISAAAYHAGLepsdRRDVQRkwlRDKIQVIVATVA 89
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
202-325 3.27e-05

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 46.94  E-value: 3.27e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894627 202 LHAPTGSGKST---KVpAAYAAQGYKVLVLNPSVAatLGFGAYmSKAHGTDPNIRTGVRTITTGAPITYSTYGKFLADGG 278
Cdd:COG1061  105 VVAPTGTGKTVlalAL-AAELLRGKRVLVLVPRRE--LLEQWA-EELRRFLGDPLAGGGKKDSDAPITVATYQSLARRAH 180

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 728894627 279 CS--GGAYDIIICDECH--STDSTTILgigtvldqAETAGARLVVLATATP 325
Cdd:COG1061  181 LDelGDRFGLVIIDEAHhaGAPSYRRI--------LEAFPAAYRLGLTATP 223
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 204-324 3.87e-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: 43.93  E-value: 3.87e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894627 204 APTGSGKSTKV--PAAYAA--QGYKVLVLNPS------VAATLGFGAYMSKA-----HGTDPNIRTGVRTITtgAPITYS 268
Cdd:cd00046    8 APTGSGKTLAAllAALLLLlkKGKKVLVLVPTkalalqTAERLRELFGPGIRvavlvGGSSAEEREKNKLGD--ADIIIA 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 728894627 269 TYGKF----LADGGCSGGAYDIIICDECHSTDSTT--ILGIGTVLDQAETAGARlVVLATAT 324
Cdd:cd00046   86 TPDMLlnllLREDRLFLKDLKLIIVDEAHALLIDSrgALILDLAVRKAGLKNAQ-VILLSAT 146
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 204-325 1.29e-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: 42.68  E-value: 1.29e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894627 204 APTGSGKST---KVPAAYAAQgyKVLVLNPSVAatL------GFGAYMSKAHgtDPNIRTGVRTITTGAPITYSTY---G 271
Cdd:cd17926   25 LPTGSGKTLtalALIAYLKEL--RTLIVVPTDA--LldqwkeRFEDFLGDSS--IGLIGGGKKKDFDDANVVVATYqslS 98

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 728894627 272 KFLADGGCSGGAYDIIICDECHSTDSTTILGIgtvldqAETAGARLVVLATATP 325
Cdd:cd17926   99 NLAEEEKDLFDQFGLLIVDEAHHLPAKTFSEI------LKELNAKYRLGLTATP 146
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
207-335 2.81e-04

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 41.55  E-value: 2.81e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894627  207 GSGKSTKVPAAYAAQGY----KVLVLNPS--VAATlgfgayMSKA-HGTDPNIRTG--VRTITTGAPIT---YSTYGKFL 274
Cdd:pfam07652  12 GAGKTRKVLPELVRECIdrrlRTLVLAPTrvVLAE------MEEAlRGLPIRYHTPavSSEHTGREIVDvmcHATFTQRL 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 728894627  275 ADGGCSGGaYDIIICDECHSTDSTTILGIGTVLDQAETAGARLVVLaTATPPGSvTVPHPN 335
Cdd:pfam07652  86 LSPVRVPN-YEVIIMDEAHFTDPASIAARGYISTLVELGEAAAIFM-TATPPGT-SDPFPE 143
DEXHc_HrpB cd17990
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ...
 202-324 3.20e-04

DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA two-partner secretion (TPS) system, a secretion pathway important to the secretion of large virulence-associated proteins. HrpB belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438711 [Multi-domain]  Cd Length: 174  Bit Score: 41.93  E-value: 3.20e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894627 202 LHAPTGSGKSTKVPAAYAA----QGYKVLVLNPSVAATLGFGAYMSKAHGTDPNIRTG--VRTITTGAPIT---YSTYGK 272
Cdd:cd17990   22 LEAPPGAGKTTRVPLALLAelwiAGGKIIVLEPRRVAARAAARRLATLLGEAPGETVGyrVRGESRVGRRTrveVVTEGV 101

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 728894627 273 FL----ADGGCSGgaYDIIICDECHSTDSTTILGIGTVLD--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 3.98e-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: 40.57  E-value: 3.98e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 728894627 356 IETIKGGRHLIFCHSKKKCDELAAKLSGLGLNAVAYYRGLD 396
Cdd:cd18787   22 LEKLKPGKAIIFVNTKKRVDRLAELLEELGIKVAALHGDLS 62
PRK11057 PRK11057
ATP-dependent DNA helicase RecQ; Provisional
 356-396 9.73e-04

ATP-dependent DNA helicase RecQ; Provisional


Pssm-ID: 182933 [Multi-domain]  Cd Length: 607  Bit Score: 42.39  E-value: 9.73e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 728894627 356 IETIKGGRHLIFCHSKKKCDELAAKLSGLGLNAVAYYRGLD 396
Cdd:PRK11057 231 VQEQRGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLD 271
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
356-414 1.40e-03

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


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 41.67  E-value: 1.40e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 728894627 356 IETIKGGRHLIFCHSKKKCDELAAKLSGLGLNAVAYYRGLDVSV--------IptSGDV-VVVATDAL 414
Cdd:COG0514  225 LKEHPGGSGIVYCLSRKKVEELAEWLREAGIRAAAYHAGLDAEEreanqdrfL--RDEVdVIVATIAF 290
ResIII pfam04851
Type III restriction enzyme, res subunit;
202-293 2.36e-03

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 39.19  E-value: 2.36e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894627  202 LHAPTGSGK---STKVPAAYAAQGY--KVLVLNPSVA----ATLGFGAYMSKAHGTdPNIRTG--VRTITTGAPITYSTY 270
Cdd:pfam04851  28 IVMATGSGKtltAAKLIARLFKKGPikKVLFLVPRKDlleqALEEFKKFLPNYVEI-GEIISGdkKDESVDDNKIVVTTI 106

                          90       100
                  ....*....|....*....|....*...
gi 728894627  271 GKF-----LADGGCSGGAYDIIICDECH 293
Cdd:pfam04851 107 QSLykaleLASLELLPDFFDVIIIDEAH 134
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 198-318 2.86e-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: 39.47  E-value: 2.86e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894627  198 QVAHLHAPTGSGKST---KVPAAYAAQGYKVLVLNPS--VAATLGFGaymskahgtdpnirTGVRTittgapitySTYGK 272
Cdd:pfam13604  19 RVAVLVGPAGTGKTTalkALREAWEAAGYRVIGLAPTgrAAKVLGEE--------------LGIPA---------DTIAK 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 728894627  273 FLA--DGGCSGGAYDIIICDECHSTDSTTILgigTVLDQAETAGARLV 318
Cdd:pfam13604  76 LLHrlGGRAGLDPGTLLIVDEAGMVGTRQMA---RLLKLAEDAGARVI 120
SF2_C_Ski2 cd18795
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ...
 356-385 5.43e-03

C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. This family includes spliceosomal Brr2 RNA helicase, ASCC3 (involved in the repair of N-alkylated nucleotides), Mtr4 (involved in processing of structured RNAs), DDX60 (involved in viral RNA degradation), and other proteins. Ski2-like RNA helicases 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: 350182 [Multi-domain]  Cd Length: 154  Bit Score: 37.92  E-value: 5.43e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 728894627 356 IETIKGGRH-LIFCHSKKKCDELAAKLSGLG 385
Cdd:cd18795   37 IETVSEGKPvLVFCSSRKECEKTAKDLAGIA 67
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
356-412 5.85e-03

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 39.36  E-value: 5.85e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 728894627 356 IETIKGGRHLIFCHSKKKCDELAAKLSGLGLNAVAYYRGLDVS----VIP--TSGDV-VVVATD 412
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