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Conserved domains on  [gi|212499740|ref|YP_002308548|]
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endonuclease [Bacteriophage APSE-2]

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 ...
 6-84 3.78e-18

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 cd22365:

Pssm-ID: 477358  Cd Length: 92  Bit Score: 72.10  E-value: 3.78e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212499740  6 EDSIEKHLVREVQKIGGIAYKFVSPGRRGVPDRLVALPNGKIIFVECKAPGE-KPTPYQLREHARLFALGHQVIVLDSQD 84
Cdd:cd22365   3 EGEVQTYLKRRFKAQGGLIRKLSYEGRAGAPDLIIIIPRGHVLFVEVKKDENtKPEPHQLREHERMRKRGADVRVIGSID 82
 
Name Accession Description Interval E-value
VRR-NUC-like cd22365
Virus-type replication repair nuclease; This model characterizes a set of nucleases that ...
 6-84 3.78e-18

Virus-type replication repair nuclease; This model characterizes a set of nucleases that resemble Holliday-junction resolving enzymes. They belong to a superfamily of 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: 411769  Cd Length: 92  Bit Score: 72.10  E-value: 3.78e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212499740  6 EDSIEKHLVREVQKIGGIAYKFVSPGRRGVPDRLVALPNGKIIFVECKAPGE-KPTPYQLREHARLFALGHQVIVLDSQD 84
Cdd:cd22365   3 EGEVQTYLKRRFKAQGGLIRKLSYEGRAGAPDLIIIIPRGHVLFVEVKKDENtKPEPHQLREHERMRKRGADVRVIGSID 82
VRR_NUC smart00990
This model contains proteins with the VRR-NUC domain; It is associated with members of the PD- ...
 16-84 3.19e-12

This model contains proteins with the VRR-NUC domain; It is associated with members of the PD-(D/E)XK nuclease superfamily, which include the type III restriction modification enzymes, for example StyLTI.


Pssm-ID: 214959  Cd Length: 108  Bit Score: 57.52  E-value: 3.19e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 212499740    16 EVQKIGGIAYKFVS--PGRR-GVPDRLVALP-NGKIIFVECKAPGEKPTPYQLREHARLFALGHQVIVLDSQD 84
Cdd:smart00990  36 PVKALKGIAGRFASdyPGLRgGVPDLILFLPqDGRYRFVEVKGPGDRLSPLQKRWIDRLAGLGFRVEVCDVVE 108
 
Name Accession Description Interval E-value
VRR-NUC-like cd22365
Virus-type replication repair nuclease; This model characterizes a set of nucleases that ...
 6-84 3.78e-18

Virus-type replication repair nuclease; This model characterizes a set of nucleases that resemble Holliday-junction resolving enzymes. They belong to a superfamily of 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: 411769  Cd Length: 92  Bit Score: 72.10  E-value: 3.78e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212499740  6 EDSIEKHLVREVQKIGGIAYKFVSPGRRGVPDRLVALPNGKIIFVECKAPGE-KPTPYQLREHARLFALGHQVIVLDSQD 84
Cdd:cd22365   3 EGEVQTYLKRRFKAQGGLIRKLSYEGRAGAPDLIIIIPRGHVLFVEVKKDENtKPEPHQLREHERMRKRGADVRVIGSID 82
VRR_NUC smart00990
This model contains proteins with the VRR-NUC domain; It is associated with members of the PD- ...
 16-84 3.19e-12

This model contains proteins with the VRR-NUC domain; It is associated with members of the PD-(D/E)XK nuclease superfamily, which include the type III restriction modification enzymes, for example StyLTI.


Pssm-ID: 214959  Cd Length: 108  Bit Score: 57.52  E-value: 3.19e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 212499740    16 EVQKIGGIAYKFVS--PGRR-GVPDRLVALP-NGKIIFVECKAPGEKPTPYQLREHARLFALGHQVIVLDSQD 84
Cdd:smart00990  36 PVKALKGIAGRFASdyPGLRgGVPDLILFLPqDGRYRFVEVKGPGDRLSPLQKRWIDRLAGLGFRVEVCDVVE 108
 
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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