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Conserved domains on  [gi|728894647|gb|AIZ00659|]
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nonstructural protein 3, partial [Hepatitis C virus subtype 1b]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Peptidase_S29 pfam02907
Hepatitis C virus NS3 protease; Hepatitis C virus NS3 protein is a serine protease which has a ...
 30-178 1.07e-88

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: 271.99  E-value: 1.07e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894647   30 EGEVQVVSTATQSFLATCVNGVCWTVYHGAGSKTLAGPKGPITQMYTNVDQDLVGWPAPPGARSLTPCTCGGSDLYLVTR 109
Cdd:pfam02907   1 EGEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 728894647  110 HADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPSGHVVGIFRAAVCTRGVAKAVDFVPVESMETT 178
Cdd:pfam02907  81 DGDLIPGRRRGDPRVSLLSPRPLSYLKGSSGGPILCPSGHVVGMFRAAVHSGGVVKAVRFVPWETLPTT 149
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 336-477 8.82e-53

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: 177.84  E-value: 8.82e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894647 336 IEEIALSNTGEIPFYGKAIPieTIKGGRHLIFCHSKKKCDELAAKLSGLGLNAVAYYRGLDVSV---IPASGDVVVVATD 412
Cdd:cd18806    1 IEDVALEIPGRIWFYGKAWI--TIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 728894647 413 ALMTGFTGDFDSVIDCNTCVTQTVDFSLDptFTIETT-TVPQDAVSRSQ---RRGRTGRGRRGIYRFVT 477
Cdd:cd18806   79 ISEMGANFDADRVIDCRTCVKPTILFSGD--FRVILTgPVPQTAASAAQrrgRTGRNPAQERDIYRFVG 145
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 197-340 5.57e-52

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


The actual alignment was detected with superfamily member cd17931:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 151  Bit Score: 175.82  E-value: 5.57e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894647 197 FQVAHLHAPTGSGKSTKVPAAYAAQGY----KVLVLNPSVTATLGFGAYMSKAhgvDPNIRTGVRTITTGA--PITYSTY 270
Cdd:cd17931    1 GQLTVLDLHPGAGKTTRVLPQIIREAIkkrlRTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGGneIVDYMCH 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 728894647 271 GKFLaDGGCSGGA---YDIIMCDECHSIDSTSILGIGTVLDQAETaGARLVVLATATPPGSVTVPH---PNIEEIA 340
Cdd:cd17931   78 GTFT-CRLLSPKRvpnYNLIIMDEAHFTDPASIAARGYIHTRVEM-GEAAVIFMTATPPGTVTPFPqsnHPIEDFE 151
 
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 1.07e-88

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: 271.99  E-value: 1.07e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894647   30 EGEVQVVSTATQSFLATCVNGVCWTVYHGAGSKTLAGPKGPITQMYTNVDQDLVGWPAPPGARSLTPCTCGGSDLYLVTR 109
Cdd:pfam02907   1 EGEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 728894647  110 HADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPSGHVVGIFRAAVCTRGVAKAVDFVPVESMETT 178
Cdd:pfam02907  81 DGDLIPGRRRGDPRVSLLSPRPLSYLKGSSGGPILCPSGHVVGMFRAAVHSGGVVKAVRFVPWETLPTT 149
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 336-477 8.82e-53

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: 177.84  E-value: 8.82e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894647 336 IEEIALSNTGEIPFYGKAIPieTIKGGRHLIFCHSKKKCDELAAKLSGLGLNAVAYYRGLDVSV---IPASGDVVVVATD 412
Cdd:cd18806    1 IEDVALEIPGRIWFYGKAWI--TIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 728894647 413 ALMTGFTGDFDSVIDCNTCVTQTVDFSLDptFTIETT-TVPQDAVSRSQ---RRGRTGRGRRGIYRFVT 477
Cdd:cd18806   79 ISEMGANFDADRVIDCRTCVKPTILFSGD--FRVILTgPVPQTAASAAQrrgRTGRNPAQERDIYRFVG 145
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 197-340 5.57e-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: 175.82  E-value: 5.57e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894647 197 FQVAHLHAPTGSGKSTKVPAAYAAQGY----KVLVLNPSVTATLGFGAYMSKAhgvDPNIRTGVRTITTGA--PITYSTY 270
Cdd:cd17931    1 GQLTVLDLHPGAGKTTRVLPQIIREAIkkrlRTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGGneIVDYMCH 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 728894647 271 GKFLaDGGCSGGA---YDIIMCDECHSIDSTSILGIGTVLDQAETaGARLVVLATATPPGSVTVPH---PNIEEIA 340
Cdd:cd17931   78 GTFT-CRLLSPKRvpnYNLIIMDEAHFTDPASIAARGYIHTRVEM-GEAAVIFMTATPPGTVTPFPqsnHPIEDFE 151
DEXDc smart00487
DEAD-like helicases superfamily;
202-329 7.45e-14

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 70.60  E-value: 7.45e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894647   202 LHAPTGSGKSTKVPAAYAAQGY-----KVLVLNPSVTATLGFGAYMSKAHGVDPNIRTGVRT-----------ITTGAPI 265
Cdd:smart00487  29 LAAPTGSGKTLAALLPALEALKrgkggRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGgdskreqlrklESGKTDI 108

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 728894647   266 TYSTYGKF---LADGGCSGGAYDIIMCDECHSIDSTS----ILGIGTVLdqaetAGARLVVLATATPPGSV 329
Cdd:smart00487 109 LVTTPGRLldlLENDKLSLSNVDLVILDEAHRLLDGGfgdqLEKLLKLL-----PKNVQLLLLSATPPEEI 174
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
202-325 2.98e-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: 2.98e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894647 202 LHAPTGSGKST---KVpAAYAAQGYKVLVLNPsvTATLGFGAYmSKAHGVDPNIRTGVRTITTGAPITYSTYGKFLADGG 278
Cdd:COG1061  105 VVAPTGTGKTVlalAL-AAELLRGKRVLVLVP--RRELLEQWA-EELRRFLGDPLAGGGKKDSDAPITVATYQSLARRAH 180

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 728894647 279 CS--GGAYDIIMCDECHSIDSTSILGIgtvldqAETAGARLVVLATATP 325
Cdd:COG1061  181 LDelGDRFGLVIIDEAHHAGAPSYRRI------LEAFPAAYRLGLTATP 223
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
207-335 5.03e-04

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 40.78  E-value: 5.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894647  207 GSGKSTKVPAAYAAQGY----KVLVLNPS-VTAtlgfgAYMSKA-HGVDPNIRTG--VRTITTGAPIT---YSTYGKFLA 275
Cdd:pfam07652  12 GAGKTRKVLPELVRECIdrrlRTLVLAPTrVVL-----AEMEEAlRGLPIRYHTPavSSEHTGREIVDvmcHATFTQRLL 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894647  276 DGGCSGGAYDIIMcDECHSIDSTSILGIGTVLDQAETAGARLVVLaTATPPGSvTVPHPN 335
Cdd:pfam07652  87 SPVRVPNYEVIIM-DEAHFTDPASIAARGYISTLVELGEAAAIFM-TATPPGT-SDPFPE 143
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
356-414 7.88e-04

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


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 42.44  E-value: 7.88e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894647 356 IETIKGGRHLIFCHSKKKCDELAAKLSGLGLNAVAYYRGLDvsviPA----------SGDV-VVVATDAL 414
Cdd:COG0514  225 LKEHPGGSGIVYCLSRKKVEELAEWLREAGIRAAAYHAGLD----AEereanqdrflRDEVdVIVATIAF 290
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 728894647 356 IETIKGGRHLIFCHSKKKCDELAAKLSGLGLNAVAYYRGLD 396
Cdd:PRK11057 231 VQEQRGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLD 271
uvsW PHA02558
UvsW helicase; Provisional
 202-311 7.94e-03

UvsW helicase; Provisional


Pssm-ID: 222875 [Multi-domain]  Cd Length: 501  Bit Score: 39.22  E-value: 7.94e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894647 202 LHAPTGSGKS--TKVPAAYAAQGY--KVLVLNPS---VTATLG-FGAYMSKAHGVDPNIRTGvRTITTGAPITYSTY--- 270
Cdd:PHA02558 134 LNLPTSAGKSliQYLLSRYYLENYegKVLIIVPTtslVTQMIDdFVDYRLFPREAMHKIYSG-TAKDTDAPIVVSTWqsa 212

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 728894647 271 ----GKFLADGGCsggaydiIMCDECHSIDSTSILGIGTVLDQAE 311
Cdd:PHA02558 213 vkqpKEWFDQFGM-------VIVDECHLFTGKSLTSIITKLDNCK 250
 
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 1.07e-88

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: 271.99  E-value: 1.07e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894647   30 EGEVQVVSTATQSFLATCVNGVCWTVYHGAGSKTLAGPKGPITQMYTNVDQDLVGWPAPPGARSLTPCTCGGSDLYLVTR 109
Cdd:pfam02907   1 EGEVQVLGTATQRFMGTCVNGVLWTTFHGAGSRTLAGPKGPVNQMYWSASDDVVGYPLPPGAGSLTPCTCGATDLYLVTR 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 728894647  110 HADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPSGHVVGIFRAAVCTRGVAKAVDFVPVESMETT 178
Cdd:pfam02907  81 DGDLIPGRRRGDPRVSLLSPRPLSYLKGSSGGPILCPSGHVVGMFRAAVHSGGVVKAVRFVPWETLPTT 149
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 336-477 8.82e-53

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: 177.84  E-value: 8.82e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894647 336 IEEIALSNTGEIPFYGKAIPieTIKGGRHLIFCHSKKKCDELAAKLSGLGLNAVAYYRGLDVSV---IPASGDVVVVATD 412
Cdd:cd18806    1 IEDVALEIPGRIWFYGKAWI--TIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 728894647 413 ALMTGFTGDFDSVIDCNTCVTQTVDFSLDptFTIETT-TVPQDAVSRSQ---RRGRTGRGRRGIYRFVT 477
Cdd:cd18806   79 ISEMGANFDADRVIDCRTCVKPTILFSGD--FRVILTgPVPQTAASAAQrrgRTGRNPAQERDIYRFVG 145
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 197-340 5.57e-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: 175.82  E-value: 5.57e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894647 197 FQVAHLHAPTGSGKSTKVPAAYAAQGY----KVLVLNPSVTATLGFGAYMSKAhgvDPNIRTGVRTITTGA--PITYSTY 270
Cdd:cd17931    1 GQLTVLDLHPGAGKTTRVLPQIIREAIkkrlRTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGGneIVDYMCH 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 728894647 271 GKFLaDGGCSGGA---YDIIMCDECHSIDSTSILGIGTVLDQAETaGARLVVLATATPPGSVTVPH---PNIEEIA 340
Cdd:cd17931   78 GTFT-CRLLSPKRvpnYNLIIMDEAHFTDPASIAARGYIHTRVEM-GEAAVIFMTATPPGTVTPFPqsnHPIEDFE 151
DEXDc smart00487
DEAD-like helicases superfamily;
202-329 7.45e-14

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 70.60  E-value: 7.45e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894647   202 LHAPTGSGKSTKVPAAYAAQGY-----KVLVLNPSVTATLGFGAYMSKAHGVDPNIRTGVRT-----------ITTGAPI 265
Cdd:smart00487  29 LAAPTGSGKTLAALLPALEALKrgkggRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGgdskreqlrklESGKTDI 108

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 728894647   266 TYSTYGKF---LADGGCSGGAYDIIMCDECHSIDSTS----ILGIGTVLdqaetAGARLVVLATATPPGSV 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 1.05e-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: 45.28  E-value: 1.05e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 728894647 360 KGGRHLIFCHSKKKCDELAAKLSGLGLNAVAYYRGL----DVSVIPA--SGDV-VVVATDA 413
Cdd:cd18794   29 LGGSGIIYCLSRKECEQVAARLQSKGISAAAYHAGLepsdRRDVQRKwlRDKIqVIVATVA 89
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
202-325 2.98e-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: 2.98e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894647 202 LHAPTGSGKST---KVpAAYAAQGYKVLVLNPsvTATLGFGAYmSKAHGVDPNIRTGVRTITTGAPITYSTYGKFLADGG 278
Cdd:COG1061  105 VVAPTGTGKTVlalAL-AAELLRGKRVLVLVP--RRELLEQWA-EELRRFLGDPLAGGGKKDSDAPITVATYQSLARRAH 180

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 728894647 279 CS--GGAYDIIMCDECHSIDSTSILGIgtvldqAETAGARLVVLATATP 325
Cdd:COG1061  181 LDelGDRFGLVIIDEAHHAGAPSYRRI------LEAFPAAYRLGLTATP 223
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 204-325 2.28e-04

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


Pssm-ID: 350684 [Multi-domain]  Cd Length: 146  Bit Score: 41.91  E-value: 2.28e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894647 204 APTGSGKST---KVPAAYAAQgyKVLVLNPS---VTATLG-FGAYMSKAHgvDPNIRTGVRTITTGAPITYSTY---GKF 273
Cdd:cd17926   25 LPTGSGKTLtalALIAYLKEL--RTLIVVPTdalLDQWKErFEDFLGDSS--IGLIGGGKKKDFDDANVVVATYqslSNL 100

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 728894647 274 LADGGCSGGAYDIIMCDECHSIDSTSILGIgtvldqAETAGARLVVLATATP 325
Cdd:cd17926  101 AEEEKDLFDQFGLLIVDEAHHLPAKTFSEI------LKELNAKYRLGLTATP 146
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 728894647 356 IETIKGGRHLIFCHSKKKCDELAAKLSGLGLNAVAYYRGLD 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 4.08e-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: 4.08e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894647 204 APTGSGKSTKV--PAAYAA--QGYKVLVLNPSVTAT----------LGFG---AYMSkaHGVDPNIRTGVRTITtgAPIT 266
Cdd:cd00046    8 APTGSGKTLAAllAALLLLlkKGKKVLVLVPTKALAlqtaerlrelFGPGirvAVLV--GGSSAEEREKNKLGD--ADII 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 728894647 267 YSTYGKF----LADGGCSGGAYDIIMCDECHSIDSTS--ILGIGTVLDQAETAGARlVVLATAT 324
Cdd:cd00046   84 IATPDMLlnllLREDRLFLKDLKLIIVDEAHALLIDSrgALILDLAVRKAGLKNAQ-VILLSAT 146
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
207-335 5.03e-04

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 40.78  E-value: 5.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894647  207 GSGKSTKVPAAYAAQGY----KVLVLNPS-VTAtlgfgAYMSKA-HGVDPNIRTG--VRTITTGAPIT---YSTYGKFLA 275
Cdd:pfam07652  12 GAGKTRKVLPELVRECIdrrlRTLVLAPTrVVL-----AEMEEAlRGLPIRYHTPavSSEHTGREIVDvmcHATFTQRLL 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894647  276 DGGCSGGAYDIIMcDECHSIDSTSILGIGTVLDQAETAGARLVVLaTATPPGSvTVPHPN 335
Cdd:pfam07652  87 SPVRVPNYEVIIM-DEAHFTDPASIAARGYISTLVELGEAAAIFM-TATPPGT-SDPFPE 143
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
356-414 7.88e-04

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


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 42.44  E-value: 7.88e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894647 356 IETIKGGRHLIFCHSKKKCDELAAKLSGLGLNAVAYYRGLDvsviPA----------SGDV-VVVATDAL 414
Cdd:COG0514  225 LKEHPGGSGIVYCLSRKKVEELAEWLREAGIRAAAYHAGLD----AEereanqdrflRDEVdVIVATIAF 290
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 728894647 356 IETIKGGRHLIFCHSKKKCDELAAKLSGLGLNAVAYYRGLD 396
Cdd:PRK11057 231 VQEQRGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLD 271
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
356-412 1.81e-03

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 41.29  E-value: 1.81e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 728894647 356 IETIKGGRHLIFCHSKKKCDELAAKLSGLGLNAVAYYRGLDVS----VIPA--SGDV-VVVATD 412
Cdd:COG0513  236 LRDEDPERAIVFCNTKRGADRLAEKLQKRGISAAALHGDLSQGqrerALDAfrNGKIrVLVATD 299
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 198-318 3.73e-03

AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.


Pssm-ID: 433343 [Multi-domain]  Cd Length: 191  Bit Score: 39.08  E-value: 3.73e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894647  198 QVAHLHAPTGSGKST---KVPAAYAAQGYKVLVLNPSVTATLGfgayMSKAHGVDpnirtgVRTIttgapitystyGKFL 274
Cdd:pfam13604  19 RVAVLVGPAGTGKTTalkALREAWEAAGYRVIGLAPTGRAAKV----LGEELGIP------ADTI-----------AKLL 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 728894647  275 A--DGGCSGGAYDIIMCDECHSIDSTSILgigTVLDQAETAGARLV 318
Cdd:pfam13604  78 HrlGGRAGLDPGTLLIVDEAGMVGTRQMA---RLLKLAEDAGARVI 120
SF2_C_Ski2 cd18795
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ...
 356-385 5.64e-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: 5.64e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 728894647 356 IETIKGGRH-LIFCHSKKKCDELAAKLSGLG 385
Cdd:cd18795   37 IETVSEGKPvLVFCSSRKECEKTAKDLAGIA 67
DEXHc_RHA-like cd17917
DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) ...
 198-325 6.07e-03

DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) family includes RHA, also called DEAH-box helicase 9 (DHX9), DHX8, DHX15-16, DHX32-38, and many others. The RHA family 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: 438707 [Multi-domain]  Cd Length: 159  Bit Score: 37.82  E-value: 6.07e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894647 198 QVAHLHAPTGSGKSTKVP-----AAYAAQGY-KVLVLNPSVTATLGFGAYMSKAHGVDP------NIRtGVRTITTGAPI 265
Cdd:cd17917    2 QVVVIVGETGSGKTTQVPqflleDGLAKGGKgRIVCTQPRRIAAISVAERVAEERGEKLgeevgyQIR-FESKTSSKTRI 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 728894647 266 TYSTYGKFL----ADGGCSGgaYDIIMCDECH--SIDSTSILGigtVLDQAETAGARL-VVLATATP 325
Cdd:cd17917   81 KFCTDGILLrellSDPLLSG--YSHVILDEAHerSLDTDFLLG---LLKDLLRKRPDLkVILMSATL 142
uvsW PHA02558
UvsW helicase; Provisional
 202-311 7.94e-03

UvsW helicase; Provisional


Pssm-ID: 222875 [Multi-domain]  Cd Length: 501  Bit Score: 39.22  E-value: 7.94e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 728894647 202 LHAPTGSGKS--TKVPAAYAAQGY--KVLVLNPS---VTATLG-FGAYMSKAHGVDPNIRTGvRTITTGAPITYSTY--- 270
Cdd:PHA02558 134 LNLPTSAGKSliQYLLSRYYLENYegKVLIIVPTtslVTQMIDdFVDYRLFPREAMHKIYSG-TAKDTDAPIVVSTWqsa 212

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 728894647 271 ----GKFLADGGCsggaydiIMCDECHSIDSTSILGIGTVLDQAE 311
Cdd:PHA02558 213 vkqpKEWFDQFGM-------VIVDECHLFTGKSLTSIITKLDNCK 250
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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