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Conserved domains on  [gi|52355542|gb|AAU44924|]
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NS3, partial (endogenous virus) [Hepacivirus hominis]

Protein Classification

DEAD/DEAH box-containing ATP-dependent helicase( domain architecture ID 1565721)

DEAD/DEAH box-containing ATP-dependent helicase catalyzes the unwinding of DNA or RNA, similar to mitochondrial ATP-dependent RNA helicase MRH4

CATH:  1.10.820.10
EC:  3.6.4.13|3.6.4.12
Gene Ontology:  GO:0005524|GO:0016887|GO:0004386
PubMed:  21779027|20225155

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 56-134 1.89e-31

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: 109.27  E-value: 1.89e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52355542  56 IEEVGLSNIGEIPFYGKAIPieTIKGGRHLIFCHSKKKCDEFAAKLSGLGINAVAYYRGLDVSV---IPTSGDVVVVATD 132
Cdd:cd18806   1 IEDVALEIPGRIWFYGKAWI--TIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78


                ..
gi 52355542 133 AL 134
Cdd:cd18806  79 IS 80
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 4-59 8.38e-22

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: 84.52  E-value: 8.38e-22
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 52355542   4 YDIIICDECHSTDSTTILGIGTVLDQAETaGARLVVLATATPPGSVTVPH---PNIEEV 59
Cdd:cd17931  93 YNLIIMDEAHFTDPASIAARGYIHTRVEM-GEAAVIFMTATPPGTVTPFPqsnHPIEDF 150
 
Name Accession Description Interval E-value
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 56-134 1.89e-31

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: 109.27  E-value: 1.89e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52355542  56 IEEVGLSNIGEIPFYGKAIPieTIKGGRHLIFCHSKKKCDEFAAKLSGLGINAVAYYRGLDVSV---IPTSGDVVVVATD 132
Cdd:cd18806   1 IEDVALEIPGRIWFYGKAWI--TIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78


                ..
gi 52355542 133 AL 134
Cdd:cd18806  79 IS 80
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 4-59 8.38e-22

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: 84.52  E-value: 8.38e-22
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 52355542   4 YDIIICDECHSTDSTTILGIGTVLDQAETaGARLVVLATATPPGSVTVPH---PNIEEV 59
Cdd:cd17931  93 YNLIIMDEAHFTDPASIAARGYIHTRVEM-GEAAVIFMTATPPGTVTPFPqsnHPIEDF 150
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
4-55 1.98e-05

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 41.55  E-value: 1.98e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 52355542     4 YDIIICDECHSTDSTTILGIGTVLDQAETAGARLVVLaTATPPGSvTVPHPN 55
Cdd:pfam07652  94 YEVIIMDEAHFTDPASIAARGYISTLVELGEAAAIFM-TATPPGT-SDPFPE 143
PRK11057 PRK11057
ATP-dependent DNA helicase RecQ; Provisional
 76-116 8.43e-05

ATP-dependent DNA helicase RecQ; Provisional


Pssm-ID: 182933 [Multi-domain]  Cd Length: 607  Bit Score: 40.85  E-value: 8.43e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 52355542   76 IETIKGGRHLIFCHSKKKCDEFAAKLSGLGINAVAYYRGLD 116
Cdd:PRK11057 231 VQEQRGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLD 271
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
76-134 1.07e-04

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


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 40.51  E-value: 1.07e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 52355542  76 IETIKGGRHLIFCHSKKKCDEFAAKLSGLGINAVAYYRGLDVSV--------IptSGDV-VVVATDAL 134
Cdd:COG0514 225 LKEHPGGSGIVYCLSRKKVEELAEWLREAGIRAAAYHAGLDAEEreanqdrfL--RDEVdVIVATIAF 290
DEXDc smart00487
DEAD-like helicases superfamily;
4-67 2.21e-03

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 36.32  E-value: 2.21e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 52355542      4 YDIIICDECHSTDS----TTILGIGTVLdqaetAGARLVVLATATPPGSVtvphPNIEEVGLSNIGEI 67
Cdd:smart00487 130 VDLVILDEAHRLLDggfgDQLEKLLKLL-----PKNVQLLLLSATPPEEI----ENLLELFLNDPVFI 188
 
Name Accession Description Interval E-value
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 56-134 1.89e-31

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: 109.27  E-value: 1.89e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52355542  56 IEEVGLSNIGEIPFYGKAIPieTIKGGRHLIFCHSKKKCDEFAAKLSGLGINAVAYYRGLDVSV---IPTSGDVVVVATD 132
Cdd:cd18806   1 IEDVALEIPGRIWFYGKAWI--TIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78


                ..
gi 52355542 133 AL 134
Cdd:cd18806  79 IS 80
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 4-59 8.38e-22

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: 84.52  E-value: 8.38e-22
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 52355542   4 YDIIICDECHSTDSTTILGIGTVLDQAETaGARLVVLATATPPGSVTVPH---PNIEEV 59
Cdd:cd17931  93 YNLIIMDEAHFTDPASIAARGYIHTRVEM-GEAAVIFMTATPPGTVTPFPqsnHPIEDF 150
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 80-133 4.21e-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: 42.97  E-value: 4.21e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 52355542  80 KGGRHLIFCHSKKKCDEFAAKLSGLGINAVAYYRGL----DVSVIP---TSGDVVVVATDA 133
Cdd:cd18794  29 LGGSGIIYCLSRKECEQVAARLQSKGISAAAYHAGLepsdRRDVQRkwlRDKIQVIVATVA 89
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
4-55 1.98e-05

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 41.55  E-value: 1.98e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 52355542     4 YDIIICDECHSTDSTTILGIGTVLDQAETAGARLVVLaTATPPGSvTVPHPN 55
Cdd:pfam07652  94 YEVIIMDEAHFTDPASIAARGYISTLVELGEAAAIFM-TATPPGT-SDPFPE 143
PRK11057 PRK11057
ATP-dependent DNA helicase RecQ; Provisional
 76-116 8.43e-05

ATP-dependent DNA helicase RecQ; Provisional


Pssm-ID: 182933 [Multi-domain]  Cd Length: 607  Bit Score: 40.85  E-value: 8.43e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 52355542   76 IETIKGGRHLIFCHSKKKCDEFAAKLSGLGINAVAYYRGLD 116
Cdd:PRK11057 231 VQEQRGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLD 271
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 76-116 9.91e-05

C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350174 [Multi-domain]  Cd Length: 131  Bit Score: 39.41  E-value: 9.91e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 52355542  76 IETIKGGRHLIFCHSKKKCDEFAAKLSGLGINAVAYYRGLD 116
Cdd:cd18787  22 LEKLKPGKAIIFVNTKKRVDRLAELLEELGIKVAALHGDLS 62
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
76-134 1.07e-04

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


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 40.51  E-value: 1.07e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 52355542  76 IETIKGGRHLIFCHSKKKCDEFAAKLSGLGINAVAYYRGLDVSV--------IptSGDV-VVVATDAL 134
Cdd:COG0514 225 LKEHPGGSGIVYCLSRKKVEELAEWLREAGIRAAAYHAGLDAEEreanqdrfL--RDEVdVIVATIAF 290
SF2_C_Ski2 cd18795
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ...
 76-106 3.47e-04

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: 38.30  E-value: 3.47e-04
                        10        20        30
                ....*....|....*....|....*....|..
gi 52355542  76 IETIKGGRH-LIFCHSKKKCDEFAAKLSGLGI 106
Cdd:cd18795  37 IETVSEGKPvLVFCSSRKECEKTAKDLAGIAF 68
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
76-132 1.66e-03

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 37.05  E-value: 1.66e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 52355542  76 IETIKGGRHLIFCHSKKKCDEFAAKLSGLGINAVAYYRGLDVS----VIP--TSGDV-VVVATD 132
Cdd:COG0513 236 LRDEDPERAIVFCNTKRGADRLAEKLQKRGISAAALHGDLSQGqrerALDafRNGKIrVLVATD 299
DEXDc smart00487
DEAD-like helicases superfamily;
4-67 2.21e-03

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 36.32  E-value: 2.21e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 52355542      4 YDIIICDECHSTDS----TTILGIGTVLdqaetAGARLVVLATATPPGSVtvphPNIEEVGLSNIGEI 67
Cdd:smart00487 130 VDLVILDEAHRLLDggfgDQLEKLLKLL-----PKNVQLLLLSATPPEEI----ENLLELFLNDPVFI 188
 
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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