NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|447132049|ref|WP_001209305|]
View 

MULTISPECIES: VRR-NUC domain-containing protein [Acinetobacter calcoaceticus/baumannii complex]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 3-86 2.11e-14

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: 62.09  E-value: 2.11e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447132049  3 ESVIEKYLVDKVKALGGEVRKVKWISRNSAPDRLVMLPDNTFW-AELKAPKE-KPTAAQAREHERMRKMGQRVEVIDSLE 80
Cdd:cd22365   3 EGEVQTYLKRRFKAQGGLIRKLSYEGRAGAPDLIIIIPRGHVLfVEVKKDENtKPEPHQLREHERMRKRGADVRVIGSID 82


                ....*.
gi 447132049 81 RIEELL 86
Cdd:cd22365  83 QVDSLI 88
 
Name Accession Description Interval E-value
VRR-NUC-like cd22365
Virus-type replication repair nuclease; This model characterizes a set of nucleases that ...
 3-86 2.11e-14

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: 62.09  E-value: 2.11e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447132049  3 ESVIEKYLVDKVKALGGEVRKVKWISRNSAPDRLVMLPDNTFW-AELKAPKE-KPTAAQAREHERMRKMGQRVEVIDSLE 80
Cdd:cd22365   3 EGEVQTYLKRRFKAQGGLIRKLSYEGRAGAPDLIIIIPRGHVLfVEVKKDENtKPEPHQLREHERMRKRGADVRVIGSID 82


                ....*.
gi 447132049 81 RIEELL 86
Cdd:cd22365  83 QVDSLI 88
VRR_NUC smart00990
This model contains proteins with the VRR-NUC domain; It is associated with members of the PD- ...
 14-80 2.52e-08

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: 47.12  E-value: 2.52e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 447132049    14 VKALGGEVRKVKWISRNSA---PDRLVMLPDN--TFWAELKAPKEKPTAAQAREHERMRKMGQRVEVIDSLE 80
Cdd:smart00990  37 VKALKGIAGRFASDYPGLRggvPDLILFLPQDgrYRFVEVKGPGDRLSPLQKRWIDRLAGLGFRVEVCDVVE 108
 
Name Accession Description Interval E-value
VRR-NUC-like cd22365
Virus-type replication repair nuclease; This model characterizes a set of nucleases that ...
 3-86 2.11e-14

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: 62.09  E-value: 2.11e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447132049  3 ESVIEKYLVDKVKALGGEVRKVKWISRNSAPDRLVMLPDNTFW-AELKAPKE-KPTAAQAREHERMRKMGQRVEVIDSLE 80
Cdd:cd22365   3 EGEVQTYLKRRFKAQGGLIRKLSYEGRAGAPDLIIIIPRGHVLfVEVKKDENtKPEPHQLREHERMRKRGADVRVIGSID 82


                ....*.
gi 447132049 81 RIEELL 86
Cdd:cd22365  83 QVDSLI 88
VRR_NUC smart00990
This model contains proteins with the VRR-NUC domain; It is associated with members of the PD- ...
 14-80 2.52e-08

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: 47.12  E-value: 2.52e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 447132049    14 VKALGGEVRKVKWISRNSA---PDRLVMLPDN--TFWAELKAPKEKPTAAQAREHERMRKMGQRVEVIDSLE 80
Cdd:smart00990  37 VKALKGIAGRFASDYPGLRggvPDLILFLPQDgrYRFVEVKGPGDRLSPLQKRWIDRLAGLGFRVEVCDVVE 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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH