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Conserved domains on  [gi|51979470|gb|AAU20355|]
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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 ...
 1-110 1.32e-48

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: 153.19  E-value: 1.32e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51979470   1 PFYGKAIPIeaIKGGRHLIFCHSKKKCDELAAKLSSLGLNAVAYYRGLDVSV---IPASGDVVVVATDALMTGYTGDFDS 77
Cdd:cd18806  13 WFYGKAWIT--IYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTDISEMGANFDADR 90

                        90       100       110
                ....*....|....*....|....*....|....
gi 51979470  78 VIDCNTCVTQTVDFSLDptFTIETT-TVPQDAVS 110
Cdd:cd18806  91 VIDCRTCVKPTILFSGD--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 ...
 1-110 1.32e-48

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: 153.19  E-value: 1.32e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51979470   1 PFYGKAIPIeaIKGGRHLIFCHSKKKCDELAAKLSSLGLNAVAYYRGLDVSV---IPASGDVVVVATDALMTGYTGDFDS 77
Cdd:cd18806  13 WFYGKAWIT--IYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTDISEMGANFDADR 90

                        90       100       110
                ....*....|....*....|....*....|....
gi 51979470  78 VIDCNTCVTQTVDFSLDptFTIETT-TVPQDAVS 110
Cdd:cd18806  91 VIDCRTCVKPTILFSGD--FRVILTgPVPQTAAS 122
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
9-67 9.68e-06

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


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 43.98  E-value: 9.68e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51979470   9 IEAIKGGRHLIFCHSKKKCDELAAKLSSLGLNAVAYYRGLDvsviPA----------SGDV-VVVATDAL 67
Cdd:COG0514 225 LKEHPGGSGIVYCLSRKKVEELAEWLREAGIRAAAYHAGLD----AEereanqdrflRDEVdVIVATIAF 290
PRK11057 PRK11057
ATP-dependent DNA helicase RecQ; Provisional
 9-49 2.71e-05

ATP-dependent DNA helicase RecQ; Provisional


Pssm-ID: 182933 [Multi-domain]  Cd Length: 607  Bit Score: 42.78  E-value: 2.71e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 51979470    9 IEAIKGGRHLIFCHSKKKCDELAAKLSSLGLNAVAYYRGLD 49
Cdd:PRK11057 231 VQEQRGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLD 271
 
Name Accession Description Interval E-value
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 1-110 1.32e-48

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: 153.19  E-value: 1.32e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51979470   1 PFYGKAIPIeaIKGGRHLIFCHSKKKCDELAAKLSSLGLNAVAYYRGLDVSV---IPASGDVVVVATDALMTGYTGDFDS 77
Cdd:cd18806  13 WFYGKAWIT--IYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTDISEMGANFDADR 90

                        90       100       110
                ....*....|....*....|....*....|....
gi 51979470  78 VIDCNTCVTQTVDFSLDptFTIETT-TVPQDAVS 110
Cdd:cd18806  91 VIDCRTCVKPTILFSGD--FRVILTgPVPQTAAS 122
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 13-66 1.35e-07

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: 47.59  E-value: 1.35e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 51979470  13 KGGRHLIFCHSKKKCDELAAKLSSLGLNAVAYYRGL----DVSVIPA--SGDV-VVVATDA 66
Cdd:cd18794  29 LGGSGIIYCLSRKECEQVAARLQSKGISAAAYHAGLepsdRRDVQRKwlRDKIqVIVATVA 89
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
9-67 9.68e-06

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


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 43.98  E-value: 9.68e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51979470   9 IEAIKGGRHLIFCHSKKKCDELAAKLSSLGLNAVAYYRGLDvsviPA----------SGDV-VVVATDAL 67
Cdd:COG0514 225 LKEHPGGSGIVYCLSRKKVEELAEWLREAGIRAAAYHAGLD----AEereanqdrflRDEVdVIVATIAF 290
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 9-49 2.69e-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: 41.34  E-value: 2.69e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 51979470   9 IEAIKGGRHLIFCHSKKKCDELAAKLSSLGLNAVAYYRGLD 49
Cdd:cd18787  22 LEKLKPGKAIIFVNTKKRVDRLAELLEELGIKVAALHGDLS 62
PRK11057 PRK11057
ATP-dependent DNA helicase RecQ; Provisional
 9-49 2.71e-05

ATP-dependent DNA helicase RecQ; Provisional


Pssm-ID: 182933 [Multi-domain]  Cd Length: 607  Bit Score: 42.78  E-value: 2.71e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 51979470    9 IEAIKGGRHLIFCHSKKKCDELAAKLSSLGLNAVAYYRGLD 49
Cdd:PRK11057 231 VQEQRGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLD 271
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
9-65 4.82e-05

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 41.67  E-value: 4.82e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 51979470   9 IEAIKGGRHLIFCHSKKKCDELAAKLSSLGLNAVAYYRGLDVS----VIPA--SGDV-VVVATD 65
Cdd:COG0513 236 LRDEDPERAIVFCNTKRGADRLAEKLQKRGISAAALHGDLSQGqrerALDAfrNGKIrVLVATD 299
COG1202 COG1202
Superfamily II helicase, archaea-specific [Replication, recombination and repair];
13-75 3.48e-03

Superfamily II helicase, archaea-specific [Replication, recombination and repair];


Pssm-ID: 440815 [Multi-domain]  Cd Length: 790  Bit Score: 36.41  E-value: 3.48e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 51979470  13 KG--GRHLIFCHSKKKCDELAAKlssLGLNAVAYYRGLD------VSVIPASGDV-VVVATDALMTGYtgDF 75
Cdd:COG1202 424 KGyrGQTIIFTNSRRRCHEIARA---LGYKAAPYHAGLDygerkkVERRFADQELaAVVTTAALAAGV--DF 490
 
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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