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Conserved domains on  [gi|52355534|gb|AAU44920|]
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NS3, partial (endogenous virus) [Hepacivirus hominis]

Protein Classification

P-loop NTPase family protein( domain architecture ID 1562424)

P-loop NTPase (nucleoside triphosphate hydrolase) family protein contains two conserved sequence signatures, the Walker A motif (the P-loop proper) and Walker B motif which bind, respectively, the beta and gamma phosphate moieties of the bound nucleotide (typically ATP or GTP), and a Mg(2+) cation

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 ...
 1-107 2.97e-46

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: 148.18  E-value: 2.97e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52355534   1 GKAIPieTIKGGRHLIFCHSKKKCDEFAAKLSGLGINAVAYYRGLDVSV---IPTSGDVVVVATDALMTGFTGDFDSVID 77
Cdd:cd18806  16 GKAWI--TIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTDISEMGANFDADRVID 93

                        90       100       110
                ....*....|....*....|....*....|.
gi 52355534  78 CNTCVTQTVDFSLDptFTIETT-TVPQDAVS 107
Cdd:cd18806  94 CRTCVKPTILFSGD--FRVILTgPVPQTAAS 122
 
Name Accession Description Interval E-value
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 1-107 2.97e-46

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: 148.18  E-value: 2.97e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52355534   1 GKAIPieTIKGGRHLIFCHSKKKCDEFAAKLSGLGINAVAYYRGLDVSV---IPTSGDVVVVATDALMTGFTGDFDSVID 77
Cdd:cd18806  16 GKAWI--TIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTDISEMGANFDADRVID 93

                        90       100       110
                ....*....|....*....|....*....|.
gi 52355534  78 CNTCVTQTVDFSLDptFTIETT-TVPQDAVS 107
Cdd:cd18806  94 CRTCVKPTILFSGD--FRVILTgPVPQTAAS 122
PRK11057 PRK11057
ATP-dependent DNA helicase RecQ; Provisional
 6-46 1.75e-04

ATP-dependent DNA helicase RecQ; Provisional


Pssm-ID: 182933 [Multi-domain]  Cd Length: 607  Bit Score: 40.85  E-value: 1.75e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 52355534    6 IETIKGGRHLIFCHSKKKCDEFAAKLSGLGINAVAYYRGLD 46
Cdd:PRK11057 231 VQEQRGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLD 271
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
6-64 2.18e-04

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


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 40.51  E-value: 2.18e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 52355534   6 IETIKGGRHLIFCHSKKKCDEFAAKLSGLGINAVAYYRGLDVSV--------IptSGDV-VVVATDAL 64
Cdd:COG0514 225 LKEHPGGSGIVYCLSRKKVEELAEWLREAGIRAAAYHAGLDAEEreanqdrfL--RDEVdVIVATIAF 290
 
Name Accession Description Interval E-value
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 1-107 2.97e-46

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: 148.18  E-value: 2.97e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52355534   1 GKAIPieTIKGGRHLIFCHSKKKCDEFAAKLSGLGINAVAYYRGLDVSV---IPTSGDVVVVATDALMTGFTGDFDSVID 77
Cdd:cd18806  16 GKAWI--TIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTDISEMGANFDADRVID 93

                        90       100       110
                ....*....|....*....|....*....|.
gi 52355534  78 CNTCVTQTVDFSLDptFTIETT-TVPQDAVS 107
Cdd:cd18806  94 CRTCVKPTILFSGD--FRVILTgPVPQTAAS 122
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 10-63 8.86e-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: 8.86e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 52355534  10 KGGRHLIFCHSKKKCDEFAAKLSGLGINAVAYYRGL----DVSVIP---TSGDVVVVATDA 63
Cdd:cd18794  29 LGGSGIIYCLSRKECEQVAARLQSKGISAAAYHAGLepsdRRDVQRkwlRDKIQVIVATVA 89
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 6-46 1.10e-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: 39.80  E-value: 1.10e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 52355534   6 IETIKGGRHLIFCHSKKKCDEFAAKLSGLGINAVAYYRGLD 46
Cdd:cd18787  22 LEKLKPGKAIIFVNTKKRVDRLAELLEELGIKVAALHGDLS 62
PRK11057 PRK11057
ATP-dependent DNA helicase RecQ; Provisional
 6-46 1.75e-04

ATP-dependent DNA helicase RecQ; Provisional


Pssm-ID: 182933 [Multi-domain]  Cd Length: 607  Bit Score: 40.85  E-value: 1.75e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 52355534    6 IETIKGGRHLIFCHSKKKCDEFAAKLSGLGINAVAYYRGLD 46
Cdd:PRK11057 231 VQEQRGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLD 271
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
6-64 2.18e-04

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


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 40.51  E-value: 2.18e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 52355534   6 IETIKGGRHLIFCHSKKKCDEFAAKLSGLGINAVAYYRGLDVSV--------IptSGDV-VVVATDAL 64
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 ...
 6-36 3.34e-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: 39.07  E-value: 3.34e-04
                        10        20        30
                ....*....|....*....|....*....|..
gi 52355534   6 IETIKGGRH-LIFCHSKKKCDEFAAKLSGLGI 36
Cdd:cd18795  37 IETVSEGKPvLVFCSSRKECEKTAKDLAGIAF 68
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
6-62 2.64e-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: 2.64e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 52355534   6 IETIKGGRHLIFCHSKKKCDEFAAKLSGLGINAVAYYRGLDVS----VIP--TSGDV-VVVATD 62
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.
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