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Conserved domains on  [gi|446866353|ref|WP_000943609|]
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MULTISPECIES: VRR-NUC domain-containing protein [Enterobacteriaceae]

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 ...
 91-171 2.57e-08

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: 49.38  E-value: 2.57e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446866353  91 KRSKATAG---KMKAEGqKKGYPDMSLDKACGiyHGMRIELKEPNGKAPTKEQIAWMRRLREEGYYVVLAYGAEQAITAI 167
Cdd:cd22365   12 RRFKAQGGlirKLSYEG-RAGAPDLIIIIPRG--HVLFVEVKKDENTKPEPHQLREHERMRKRGADVRVIGSIDQVDSLI 88


                 ....
gi 446866353 168 LEYI 171
Cdd:cd22365   89 AEYI 92
 
Name Accession Description Interval E-value
VRR-NUC-like cd22365
Virus-type replication repair nuclease; This model characterizes a set of nucleases that ...
 91-171 2.57e-08

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: 49.38  E-value: 2.57e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446866353  91 KRSKATAG---KMKAEGqKKGYPDMSLDKACGiyHGMRIELKEPNGKAPTKEQIAWMRRLREEGYYVVLAYGAEQAITAI 167
Cdd:cd22365   12 RRFKAQGGlirKLSYEG-RAGAPDLIIIIPRG--HVLFVEVKKDENTKPEPHQLREHERMRKRGADVRVIGSIDQVDSLI 88


                 ....
gi 446866353 168 LEYI 171
Cdd:cd22365   89 AEYI 92
VRR_NUC smart00990
This model contains proteins with the VRR-NUC domain; It is associated with members of the PD- ...
 88-161 1.41e-05

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: 42.50  E-value: 1.41e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446866353    88 NGGKRSKATAGKMKAE--GQKKGYPDMSLDKAC-GIYHGmrIELKEPNGKaPTKEQIAWMRRLREEGYYVVLAYGAE 161
Cdd:smart00990  35 LPVKALKGIAGRFASDypGLRGGVPDLILFLPQdGRYRF--VEVKGPGDR-LSPLQKRWIDRLAGLGFRVEVCDVVE 108
VRR_NUC pfam08774
VRR-NUC domain;
104-160 1.31e-03

VRR-NUC domain;


Pssm-ID: 430209  Cd Length: 115  Bit Score: 37.05  E-value: 1.31e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 446866353  104 GQKKGYPDMSLDKACGIYHGMRIELKEPNGKApTKEQIAWMRRLREEGYYVVLAYGA 160
Cdd:pfam08774  59 GLGSGRPDLVLWNPEQKRVFLLVEVKGPGDRL-SDNQRAWIDELRRSGVRVEVCRVA 114
 
Name Accession Description Interval E-value
VRR-NUC-like cd22365
Virus-type replication repair nuclease; This model characterizes a set of nucleases that ...
 91-171 2.57e-08

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: 49.38  E-value: 2.57e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446866353  91 KRSKATAG---KMKAEGqKKGYPDMSLDKACGiyHGMRIELKEPNGKAPTKEQIAWMRRLREEGYYVVLAYGAEQAITAI 167
Cdd:cd22365   12 RRFKAQGGlirKLSYEG-RAGAPDLIIIIPRG--HVLFVEVKKDENTKPEPHQLREHERMRKRGADVRVIGSIDQVDSLI 88


                 ....
gi 446866353 168 LEYI 171
Cdd:cd22365   89 AEYI 92
VRR_NUC smart00990
This model contains proteins with the VRR-NUC domain; It is associated with members of the PD- ...
 88-161 1.41e-05

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: 42.50  E-value: 1.41e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446866353    88 NGGKRSKATAGKMKAE--GQKKGYPDMSLDKAC-GIYHGmrIELKEPNGKaPTKEQIAWMRRLREEGYYVVLAYGAE 161
Cdd:smart00990  35 LPVKALKGIAGRFASDypGLRGGVPDLILFLPQdGRYRF--VEVKGPGDR-LSPLQKRWIDRLAGLGFRVEVCDVVE 108
VRR_NUC pfam08774
VRR-NUC domain;
104-160 1.31e-03

VRR-NUC domain;


Pssm-ID: 430209  Cd Length: 115  Bit Score: 37.05  E-value: 1.31e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 446866353  104 GQKKGYPDMSLDKACGIYHGMRIELKEPNGKApTKEQIAWMRRLREEGYYVVLAYGA 160
Cdd:pfam08774  59 GLGSGRPDLVLWNPEQKRVFLLVEVKGPGDRL-SDNQRAWIDELRRSGVRVEVCRVA 114
 
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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