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Conserved domains on  [gi|378976051|ref|YP_005229682|]
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hypothetical protein (plasmid) [Klebsiella pneumoniae subsp. pneumoniae HS11286]

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 ...
 65-178 2.36e-22

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 pfam10881:

Pssm-ID: 477358  Cd Length: 126  Bit Score: 87.76  E-value: 2.36e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378976051   65 TLMTPREQHFFRALLRhTSRTRWLLCPQVRVADIatLSPHIRPRSRTWWQLFRMASQWHCDVVIVDIHTFAIIGAVELDD 144
Cdd:pfam10881   3 PLFSPAERAFFHALKK-AVGDRYEIFAKVSLSDI--LSVTKGPGRSNWQRAFNRISAKRFDFLLCDKADLTPVLAIELDG 79

                          90       100       110
                  ....*....|....*....|....*....|....
gi 378976051  145 ASHQKKHRIRRDILLEEVLRQAGIPLLRDRDSES 178
Cdd:pfam10881  80 ASHYDAKAQKRDAFKNAACESAGIPLLRLSASKS 113
 
Name Accession Description Interval E-value
DUF2726 pfam10881
Protein of unknown function (DUF2726); This bacterial family of proteins has no known function.
 65-178 2.36e-22

Protein of unknown function (DUF2726); This bacterial family of proteins has no known function.


Pssm-ID: 431528  Cd Length: 126  Bit Score: 87.76  E-value: 2.36e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378976051   65 TLMTPREQHFFRALLRhTSRTRWLLCPQVRVADIatLSPHIRPRSRTWWQLFRMASQWHCDVVIVDIHTFAIIGAVELDD 144
Cdd:pfam10881   3 PLFSPAERAFFHALKK-AVGDRYEIFAKVSLSDI--LSVTKGPGRSNWQRAFNRISAKRFDFLLCDKADLTPVLAIELDG 79

                          90       100       110
                  ....*....|....*....|....*....|....
gi 378976051  145 ASHQKKHRIRRDILLEEVLRQAGIPLLRDRDSES 178
Cdd:pfam10881  80 ASHYDAKAQKRDAFKNAACESAGIPLLRLSASKS 113
 
Name Accession Description Interval E-value
DUF2726 pfam10881
Protein of unknown function (DUF2726); This bacterial family of proteins has no known function.
 65-178 2.36e-22

Protein of unknown function (DUF2726); This bacterial family of proteins has no known function.


Pssm-ID: 431528  Cd Length: 126  Bit Score: 87.76  E-value: 2.36e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 378976051   65 TLMTPREQHFFRALLRhTSRTRWLLCPQVRVADIatLSPHIRPRSRTWWQLFRMASQWHCDVVIVDIHTFAIIGAVELDD 144
Cdd:pfam10881   3 PLFSPAERAFFHALKK-AVGDRYEIFAKVSLSDI--LSVTKGPGRSNWQRAFNRISAKRFDFLLCDKADLTPVLAIELDG 79

                          90       100       110
                  ....*....|....*....|....*....|....
gi 378976051  145 ASHQKKHRIRRDILLEEVLRQAGIPLLRDRDSES 178
Cdd:pfam10881  80 ASHYDAKAQKRDAFKNAACESAGIPLLRLSASKS 113
 
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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