NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|502951265|ref|WP_013186241|]
View 

very short patch repair endonuclease [Croceibacter atlanticus]

Protein Classification

very short patch repair endonuclease( domain architecture ID 10790390)

very short patch repair (VSR) endonuclease, recognizes damaged DNA and cleaves the backbone phosphodiester bond

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Vsr COG3727
G:T-mismatch repair DNA endonuclease Vsr, very short patch repair protein [Replication, ...
 14-137 1.85e-67

G:T-mismatch repair DNA endonuclease Vsr, very short patch repair protein [Replication, recombination and repair];


:

Pssm-ID: 442941  Cd Length: 141  Bit Score: 201.19  E-value: 1.85e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502951265  14 MRGNKSKHTKPELLLRKALWASGLRgYRLHFKKLAGSPDIVFSTKKIAIFVNGCFWHRCPKCNL-NLPKTNTEFWKDKFD 92
Cdd:COG3727   13 MSAIRGKDTKPELALRRALHALGLR-YRLHRKDLPGKPDIVFPKYRVAIFVHGCFWHGHPGCRLaTTPKTNTEFWRAKIE 91

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 502951265  93 TNMKRDQNNYVTLIRSNWTVLTIWECDIKKNLKEQVLKIESLIKD 137
Cdd:COG3727   92 RNVERDRRVNAALEAAGWRVLRVWECELKKKLALCVEALLERLEE 136
 
Name Accession Description Interval E-value
Vsr COG3727
G:T-mismatch repair DNA endonuclease Vsr, very short patch repair protein [Replication, ...
 14-137 1.85e-67

G:T-mismatch repair DNA endonuclease Vsr, very short patch repair protein [Replication, recombination and repair];


Pssm-ID: 442941  Cd Length: 141  Bit Score: 201.19  E-value: 1.85e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502951265  14 MRGNKSKHTKPELLLRKALWASGLRgYRLHFKKLAGSPDIVFSTKKIAIFVNGCFWHRCPKCNL-NLPKTNTEFWKDKFD 92
Cdd:COG3727   13 MSAIRGKDTKPELALRRALHALGLR-YRLHRKDLPGKPDIVFPKYRVAIFVHGCFWHGHPGCRLaTTPKTNTEFWRAKIE 91

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 502951265  93 TNMKRDQNNYVTLIRSNWTVLTIWECDIKKNLKEQVLKIESLIKD 137
Cdd:COG3727   92 RNVERDRRVNAALEAAGWRVLRVWECELKKKLALCVEALLERLEE 136
Vsr cd00221
Very short patch repair endonuclease; Very short patch repair (Vsr) is an endonuclease ...
 14-137 1.95e-55

Very short patch repair endonuclease; Very short patch repair (Vsr) is an endonuclease functioning in DNA repair that recognizes damaged DNA and cleaves the phosphodiester backbone. Vsr endonucleases have a common endonuclease topology that has been tailored for recognition of TG mismatches. It belongs to a superfamily of nucleases including 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: 411702  Cd Length: 133  Bit Score: 170.50  E-value: 1.95e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502951265  14 MRGNKSKHTKPELLLRKALWASGLRgYRLHFKKLAGSPDIVFSTKKIAIFVNGCFWHRCPKCNLNLPKTNTEFWKDKFDT 93
Cdd:cd00221   10 MSRIRSKNTKPELAVRKALWARGLR-YRLHVKKLPGKPDIVFPKYKVAVFVDGCFWHGCPCKKGKIPKSNREFWRAKIER 88

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 502951265  94 NMKRDQNNYVTLIRSNWTVLTIWECDIKKNLKEQVLKIESLIKD 137
Cdd:cd00221   89 NRERDRRVNAELRKLGWRVLRIWEHEIKKNPEKCARKILRALRK 132
vsr TIGR00632
DNA mismatch endonuclease Vsr; All proteins in this family for which functions are known are G: ...
 14-119 2.27e-35

DNA mismatch endonuclease Vsr; All proteins in this family for which functions are known are G:T mismatch endonucleases that function in a specialized mismatch repair process used usually to repair G:T mismatches in specific sections of the genome. This family was based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Members of this family typically are found near to a DNA cytosine methyltransferase. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 211591 [Multi-domain]  Cd Length: 117  Bit Score: 119.18  E-value: 2.27e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502951265   14 MRGNKSKHTKPELLLRKALWASGLRgYRLHFKKLAGSPDIVFSTKKIAIFVNGCFWHRCPKCNLNLPKTNTEFWKDKFDT 93
Cdd:TIGR00632  13 MQAIRTKGTKPEKALASLLTGLGLR-FRLQDASLPGTPDIVFDEYRCVIFIHGCFWHGHHCYLGKVPKTRTDFWSPKIEK 91

                          90       100
                  ....*....|....*....|....*.
gi 502951265   94 NMKRDQNNYVTLIRSNWTVLTIWECD 119
Cdd:TIGR00632  92 NVERDRRVNSRLQELGWRVLRVWECE 117
Vsr pfam03852
DNA mismatch endonuclease Vsr;
14-70 1.81e-22

DNA mismatch endonuclease Vsr;


Pssm-ID: 281799  Cd Length: 74  Bit Score: 84.87  E-value: 1.81e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 502951265   14 MRGNKSKHTKPELLLRKALWASGLRgYRLHFKKLAGSPDIVFSTKKIAIFVNGCFWH 70
Cdd:pfam03852  13 MQSIKSTDTKPELRLAKLLTGLGLR-YRKNDKSLPGKPDFVFPKYKVAVFVHGCFWH 68
 
Name Accession Description Interval E-value
Vsr COG3727
G:T-mismatch repair DNA endonuclease Vsr, very short patch repair protein [Replication, ...
 14-137 1.85e-67

G:T-mismatch repair DNA endonuclease Vsr, very short patch repair protein [Replication, recombination and repair];


Pssm-ID: 442941  Cd Length: 141  Bit Score: 201.19  E-value: 1.85e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502951265  14 MRGNKSKHTKPELLLRKALWASGLRgYRLHFKKLAGSPDIVFSTKKIAIFVNGCFWHRCPKCNL-NLPKTNTEFWKDKFD 92
Cdd:COG3727   13 MSAIRGKDTKPELALRRALHALGLR-YRLHRKDLPGKPDIVFPKYRVAIFVHGCFWHGHPGCRLaTTPKTNTEFWRAKIE 91

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 502951265  93 TNMKRDQNNYVTLIRSNWTVLTIWECDIKKNLKEQVLKIESLIKD 137
Cdd:COG3727   92 RNVERDRRVNAALEAAGWRVLRVWECELKKKLALCVEALLERLEE 136
Vsr cd00221
Very short patch repair endonuclease; Very short patch repair (Vsr) is an endonuclease ...
 14-137 1.95e-55

Very short patch repair endonuclease; Very short patch repair (Vsr) is an endonuclease functioning in DNA repair that recognizes damaged DNA and cleaves the phosphodiester backbone. Vsr endonucleases have a common endonuclease topology that has been tailored for recognition of TG mismatches. It belongs to a superfamily of nucleases including 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: 411702  Cd Length: 133  Bit Score: 170.50  E-value: 1.95e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502951265  14 MRGNKSKHTKPELLLRKALWASGLRgYRLHFKKLAGSPDIVFSTKKIAIFVNGCFWHRCPKCNLNLPKTNTEFWKDKFDT 93
Cdd:cd00221   10 MSRIRSKNTKPELAVRKALWARGLR-YRLHVKKLPGKPDIVFPKYKVAVFVDGCFWHGCPCKKGKIPKSNREFWRAKIER 88

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 502951265  94 NMKRDQNNYVTLIRSNWTVLTIWECDIKKNLKEQVLKIESLIKD 137
Cdd:cd00221   89 NRERDRRVNAELRKLGWRVLRIWEHEIKKNPEKCARKILRALRK 132
vsr TIGR00632
DNA mismatch endonuclease Vsr; All proteins in this family for which functions are known are G: ...
 14-119 2.27e-35

DNA mismatch endonuclease Vsr; All proteins in this family for which functions are known are G:T mismatch endonucleases that function in a specialized mismatch repair process used usually to repair G:T mismatches in specific sections of the genome. This family was based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Members of this family typically are found near to a DNA cytosine methyltransferase. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 211591 [Multi-domain]  Cd Length: 117  Bit Score: 119.18  E-value: 2.27e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502951265   14 MRGNKSKHTKPELLLRKALWASGLRgYRLHFKKLAGSPDIVFSTKKIAIFVNGCFWHRCPKCNLNLPKTNTEFWKDKFDT 93
Cdd:TIGR00632  13 MQAIRTKGTKPEKALASLLTGLGLR-FRLQDASLPGTPDIVFDEYRCVIFIHGCFWHGHHCYLGKVPKTRTDFWSPKIEK 91

                          90       100
                  ....*....|....*....|....*.
gi 502951265   94 NMKRDQNNYVTLIRSNWTVLTIWECD 119
Cdd:TIGR00632  92 NVERDRRVNSRLQELGWRVLRVWECE 117
Vsr pfam03852
DNA mismatch endonuclease Vsr;
14-70 1.81e-22

DNA mismatch endonuclease Vsr;


Pssm-ID: 281799  Cd Length: 74  Bit Score: 84.87  E-value: 1.81e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 502951265   14 MRGNKSKHTKPELLLRKALWASGLRgYRLHFKKLAGSPDIVFSTKKIAIFVNGCFWH 70
Cdd:pfam03852  13 MQSIKSTDTKPELRLAKLLTGLGLR-YRKNDKSLPGKPDFVFPKYKVAVFVHGCFWH 68
 
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