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Conserved domains on  [gi|1998001358|ref|WP_206423649|]
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hypothetical protein, partial [Gemmiger sp. An50]

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 ...
 114-182 1.62e-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: 38.15  E-value: 1.62e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1998001358 114 RVDV--VDKGGNgKCDIyELKTRKAEPKDLYQLRMY--WdglVLE--GIQPTRGILLTNGYSDRLQEMVRILNTL 182
Cdd:cd22341   159 RIDIlaKDKDGN-LVVI-ELKRGRADDRAVGQLLRYmgW---VKEelAGKNVRGILVAPDISEKARRALKEVGNL 228
 
Name Accession Description Interval E-value
NucS-like cd22341
Mismatch restriction endonuclease NucS and similar nucleases; Archaeal mismatch restriction ...
 114-182 1.62e-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: 38.15  E-value: 1.62e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1998001358 114 RVDV--VDKGGNgKCDIyELKTRKAEPKDLYQLRMY--WdglVLE--GIQPTRGILLTNGYSDRLQEMVRILNTL 182
Cdd:cd22341   159 RIDIlaKDKDGN-LVVI-ELKRGRADDRAVGQLLRYmgW---VKEelAGKNVRGILVAPDISEKARRALKEVGNL 228
PRK04247 PRK04247
endonuclease NucS;
110-177 3.52e-03

endonuclease NucS;


Pssm-ID: 235264  Cd Length: 238  Bit Score: 37.19  E-value: 3.52e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1998001358 110 PTGTrVDVVDKGGNGKCDIYELKTRKAEPKDLYQLRMYWDGLVLEGIQPTRGILLTNGYSDRLQEMVR 177
Cdd:PRK04247  158 PAGI-IDILGRDKDGNLVVLELKRRRAGLSAVSQLKRYVEALRELHGDKVRGILVAPSITDRARRLLE 224
 
Name Accession Description Interval E-value
NucS-like cd22341
Mismatch restriction endonuclease NucS and similar nucleases; Archaeal mismatch restriction ...
 114-182 1.62e-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: 38.15  E-value: 1.62e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1998001358 114 RVDV--VDKGGNgKCDIyELKTRKAEPKDLYQLRMY--WdglVLE--GIQPTRGILLTNGYSDRLQEMVRILNTL 182
Cdd:cd22341   159 RIDIlaKDKDGN-LVVI-ELKRGRADDRAVGQLLRYmgW---VKEelAGKNVRGILVAPDISEKARRALKEVGNL 228
PRK04247 PRK04247
endonuclease NucS;
110-177 3.52e-03

endonuclease NucS;


Pssm-ID: 235264  Cd Length: 238  Bit Score: 37.19  E-value: 3.52e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1998001358 110 PTGTrVDVVDKGGNGKCDIYELKTRKAEPKDLYQLRMYWDGLVLEGIQPTRGILLTNGYSDRLQEMVR 177
Cdd:PRK04247  158 PAGI-IDILGRDKDGNLVVLELKRRRAGLSAVSQLKRYVEALRELHGDKVRGILVAPSITDRARRLLE 224
 
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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