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Conserved domains on  [gi|499986138|ref|WP_011666856|]
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hypothetical protein [Levilactobacillus brevis]

Protein Classification

PDDEXK family nuclease( domain architecture ID 1750065)

PDDEXK family nuclease similar to Halobacterium salinarum endonuclease NucS 1 that cleaves both 3' and 5' ssDNA extremities of branched DNA structures

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PDDEXK_nuclease-like super family cl40440
PDDEXK family nucleases; Superfamily of PDDEXK nucleases including very short patch repair ...
 10-94 4.76e-03

PDDEXK family nucleases; Superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.


The actual alignment was detected with superfamily member cd22341:

Pssm-ID: 477358 [Multi-domain]  Cd Length: 237  Bit Score: 34.69  E-value: 4.76e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499986138  10 NWGGSNVKLYKVKPDSTDQLLLSEIDSIGFTK------------EKRLQNLIEDNISLT-LGINFIASEFTVGKYRMDTI 76
Cdd:cd22341   84 DEGRLVLRSYRRKPREELEILLDEVELLTAEDledeeelelgglEKDLEDYLARNPELIeEGLRIIGREYPTPVGRIDIL 163

                         90       100
                 ....*....|....*....|....*....
gi 499986138  77 GYDTEvQSFIIIE-----------WQIAR 94
Cdd:cd22341  164 AKDKD-GNLVVIElkrgraddravGQLLR 191
 
Name Accession Description Interval E-value
NucS-like cd22341
Mismatch restriction endonuclease NucS and similar nucleases; Archaeal mismatch restriction ...
 10-94 4.76e-03

Mismatch restriction endonuclease NucS and similar nucleases; Archaeal mismatch restriction endonuclease NucS and its ortholog EndoMS specifically cleave dsDNA containing mismatched bases. They belong to a superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.


Pssm-ID: 411745 [Multi-domain]  Cd Length: 237  Bit Score: 34.69  E-value: 4.76e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499986138  10 NWGGSNVKLYKVKPDSTDQLLLSEIDSIGFTK------------EKRLQNLIEDNISLT-LGINFIASEFTVGKYRMDTI 76
Cdd:cd22341   84 DEGRLVLRSYRRKPREELEILLDEVELLTAEDledeeelelgglEKDLEDYLARNPELIeEGLRIIGREYPTPVGRIDIL 163

                         90       100
                 ....*....|....*....|....*....
gi 499986138  77 GYDTEvQSFIIIE-----------WQIAR 94
Cdd:cd22341  164 AKDKD-GNLVVIElkrgraddravGQLLR 191
 
Name Accession Description Interval E-value
NucS-like cd22341
Mismatch restriction endonuclease NucS and similar nucleases; Archaeal mismatch restriction ...
 10-94 4.76e-03

Mismatch restriction endonuclease NucS and similar nucleases; Archaeal mismatch restriction endonuclease NucS and its ortholog EndoMS specifically cleave dsDNA containing mismatched bases. They belong to a superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.


Pssm-ID: 411745 [Multi-domain]  Cd Length: 237  Bit Score: 34.69  E-value: 4.76e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499986138  10 NWGGSNVKLYKVKPDSTDQLLLSEIDSIGFTK------------EKRLQNLIEDNISLT-LGINFIASEFTVGKYRMDTI 76
Cdd:cd22341   84 DEGRLVLRSYRRKPREELEILLDEVELLTAEDledeeelelgglEKDLEDYLARNPELIeEGLRIIGREYPTPVGRIDIL 163

                         90       100
                 ....*....|....*....|....*....
gi 499986138  77 GYDTEvQSFIIIE-----------WQIAR 94
Cdd:cd22341  164 AKDKD-GNLVVIElkrgraddravGQLLR 191
 
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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