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Conserved domains on  [gi|506598150|ref|WP_016062874|]
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VRR-NUC domain-containing protein [Candidatus Liberibacter asiaticus]

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 ...
 10-98 1.95e-17

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: 70.56  E-value: 1.95e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506598150  10 TEKDVEKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTG-RLSHQQMSEIEELRRRGQRVKVLISM 88
Cdd:cd22365    2 PEGEVQTYLKRRFKAQGGLIRKLSYEGRAGAPDLIIIIPRGHVLFVEVKKDENtKPEPHQLREHERMRKRGADVRVIGSI 81

                         90
                 ....*....|
gi 506598150  89 EEVDNFLEEL 98
Cdd:cd22365   82 DQVDSLIAEY 91
 
Name Accession Description Interval E-value
VRR-NUC-like cd22365
Virus-type replication repair nuclease; This model characterizes a set of nucleases that ...
 10-98 1.95e-17

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: 70.56  E-value: 1.95e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506598150  10 TEKDVEKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTG-RLSHQQMSEIEELRRRGQRVKVLISM 88
Cdd:cd22365    2 PEGEVQTYLKRRFKAQGGLIRKLSYEGRAGAPDLIIIIPRGHVLFVEVKKDENtKPEPHQLREHERMRKRGADVRVIGSI 81

                         90
                 ....*....|
gi 506598150  89 EEVDNFLEEL 98
Cdd:cd22365   82 DQVDSLIAEY 91
VRR_NUC smart00990
This model contains proteins with the VRR-NUC domain; It is associated with members of the PD- ...
 36-85 1.32e-07

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: 45.58  E-value: 1.32e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 506598150    36 GRRGCPDRLIITPNGGLW-WIEVKKPTGRLSHQQMSEIEELRRRGQRVKVL 85
Cdd:smart00990  54 LRGGVPDLILFLPQDGRYrFVEVKGPGDRLSPLQKRWIDRLAGLGFRVEVC 104
VRR_NUC pfam08774
VRR-NUC domain;
36-85 1.31e-06

VRR-NUC domain;


Pssm-ID: 430209  Cd Length: 115  Bit Score: 43.21  E-value: 1.31e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 506598150   36 GRRGCPDRLIITPNGGLW--WIEVKKPTGRLSHQQMSEIEELRRRGQRVKVL 85
Cdd:pfam08774  60 LGSGRPDLVLWNPEQKRVflLVEVKGPGDRLSDNQRAWIDELRRSGVRVEVC 111
 
Name Accession Description Interval E-value
VRR-NUC-like cd22365
Virus-type replication repair nuclease; This model characterizes a set of nucleases that ...
 10-98 1.95e-17

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: 70.56  E-value: 1.95e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506598150  10 TEKDVEKRLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGLWWIEVKKPTG-RLSHQQMSEIEELRRRGQRVKVLISM 88
Cdd:cd22365    2 PEGEVQTYLKRRFKAQGGLIRKLSYEGRAGAPDLIIIIPRGHVLFVEVKKDENtKPEPHQLREHERMRKRGADVRVIGSI 81

                         90
                 ....*....|
gi 506598150  89 EEVDNFLEEL 98
Cdd:cd22365   82 DQVDSLIAEY 91
VRR_NUC smart00990
This model contains proteins with the VRR-NUC domain; It is associated with members of the PD- ...
 36-85 1.32e-07

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: 45.58  E-value: 1.32e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 506598150    36 GRRGCPDRLIITPNGGLW-WIEVKKPTGRLSHQQMSEIEELRRRGQRVKVL 85
Cdd:smart00990  54 LRGGVPDLILFLPQDGRYrFVEVKGPGDRLSPLQKRWIDRLAGLGFRVEVC 104
VRR_NUC pfam08774
VRR-NUC domain;
36-85 1.31e-06

VRR-NUC domain;


Pssm-ID: 430209  Cd Length: 115  Bit Score: 43.21  E-value: 1.31e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 506598150   36 GRRGCPDRLIITPNGGLW--WIEVKKPTGRLSHQQMSEIEELRRRGQRVKVL 85
Cdd:pfam08774  60 LGSGRPDLVLWNPEQKRVflLVEVKGPGDRLSDNQRAWIDELRRSGVRVEVC 111
 
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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