NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1203926852|gb|OVU56340|]
View 

very short patch repair endonuclease [Klebsiella pneumoniae]

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, ...
 2-141 7.75e-73

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


:

Pssm-ID: 442941  Cd Length: 141  Bit Score: 215.06  E-value: 7.75e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1203926852   2 ADVHDKATRSKNMRAIATRDTAIEKRIAALLTGAGFTFVAQDRALPGRPDFALPDYRCVIFTHGCFWHHHD-CYLFKVPA 80
Cdd:COG3727     1 ADVLTPETRSRNMSAIRGKDTKPELALRRALHALGLRYRLHRKDLPGKPDIVFPKYRVAIFVHGCFWHGHPgCRLATTPK 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1203926852  81 TRTAFWLDKIAGNVARDARDRQKLAEEGWRVLIIWECALRGRLRLSDAALTERLEEWICGA 141
Cdd:COG3727    81 TNTEFWRAKIERNVERDRRVNAALEAAGWRVLRVWECELKKKLALCVEALLERLEEWLRSR 141
 
Name Accession Description Interval E-value
Vsr COG3727
G:T-mismatch repair DNA endonuclease Vsr, very short patch repair protein [Replication, ...
 2-141 7.75e-73

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


Pssm-ID: 442941  Cd Length: 141  Bit Score: 215.06  E-value: 7.75e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1203926852   2 ADVHDKATRSKNMRAIATRDTAIEKRIAALLTGAGFTFVAQDRALPGRPDFALPDYRCVIFTHGCFWHHHD-CYLFKVPA 80
Cdd:COG3727     1 ADVLTPETRSRNMSAIRGKDTKPELALRRALHALGLRYRLHRKDLPGKPDIVFPKYRVAIFVHGCFWHGHPgCRLATTPK 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1203926852  81 TRTAFWLDKIAGNVARDARDRQKLAEEGWRVLIIWECALRGRLRLSDAALTERLEEWICGA 141
Cdd:COG3727    81 TNTEFWRAKIERNVERDRRVNAALEAAGWRVLRVWECELKKKLALCVEALLERLEEWLRSR 141
vsr TIGR00632
DNA mismatch endonuclease Vsr; All proteins in this family for which functions are known are G: ...
 2-118 9.99e-56

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: 170.80  E-value: 9.99e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1203926852   2 ADVHDKATRSKNMRAIATRDTAIEKRIAALLTGAGFTFVAQDRALPGRPDFALPDYRCVIFTHGCFWHHHDCYLFKVPAT 81
Cdd:TIGR00632   1 ADKLSPATRSKNMQAIRTKGTKPEKALASLLTGLGLRFRLQDASLPGTPDIVFDEYRCVIFIHGCFWHGHHCYLGKVPKT 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1203926852  82 RTAFWLDKIAGNVARDARDRQKLAEEGWRVLIIWECA 118
Cdd:TIGR00632  81 RTDFWSPKIEKNVERDRRVNSRLQELGWRVLRVWECE 117
Vsr cd00221
Very short patch repair endonuclease; Very short patch repair (Vsr) is an endonuclease ...
 5-137 5.88e-52

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: 162.02  E-value: 5.88e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1203926852   5 HDKATRSKNMRAIATRDTAIEKRIAALLTGAGFTFVAQDRALPGRPDFALPDYRCVIFTHGCFWHHHDCYLFKVPATRTA 84
Cdd:cd00221     1 FTPEKRSRIMSRIRSKNTKPELAVRKALWARGLRYRLHVKKLPGKPDIVFPKYKVAVFVDGCFWHGCPCKKGKIPKSNRE 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1203926852  85 FWLDKIAGNVARDARDRQKLAEEGWRVLIIWECALRGRLRLSDAALTERLEEW 137
Cdd:cd00221    81 FWRAKIERNRERDRRVNAELRKLGWRVLRIWEHEIKKNPEKCARKILRALRKR 133
Vsr pfam03852
DNA mismatch endonuclease Vsr;
2-75 2.85e-36

DNA mismatch endonuclease Vsr;


Pssm-ID: 281799  Cd Length: 74  Bit Score: 120.31  E-value: 2.85e-36
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1203926852   2 ADVHDKATRSKNMRAIATRDTAIEKRIAALLTGAGFTFVAQDRALPGRPDFALPDYRCVIFTHGCFWHHHDCYL 75
Cdd:pfam03852   1 ADVHDKAKRSKVMRAIASRDTKPELRLAKLLTGQGLRYRKNDKSLPGKPDFVVPKYRCVVFVHGCFWHGHDCYL 74
 
Name Accession Description Interval E-value
Vsr COG3727
G:T-mismatch repair DNA endonuclease Vsr, very short patch repair protein [Replication, ...
 2-141 7.75e-73

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


Pssm-ID: 442941  Cd Length: 141  Bit Score: 215.06  E-value: 7.75e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1203926852   2 ADVHDKATRSKNMRAIATRDTAIEKRIAALLTGAGFTFVAQDRALPGRPDFALPDYRCVIFTHGCFWHHHD-CYLFKVPA 80
Cdd:COG3727     1 ADVLTPETRSRNMSAIRGKDTKPELALRRALHALGLRYRLHRKDLPGKPDIVFPKYRVAIFVHGCFWHGHPgCRLATTPK 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1203926852  81 TRTAFWLDKIAGNVARDARDRQKLAEEGWRVLIIWECALRGRLRLSDAALTERLEEWICGA 141
Cdd:COG3727    81 TNTEFWRAKIERNVERDRRVNAALEAAGWRVLRVWECELKKKLALCVEALLERLEEWLRSR 141
vsr TIGR00632
DNA mismatch endonuclease Vsr; All proteins in this family for which functions are known are G: ...
 2-118 9.99e-56

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: 170.80  E-value: 9.99e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1203926852   2 ADVHDKATRSKNMRAIATRDTAIEKRIAALLTGAGFTFVAQDRALPGRPDFALPDYRCVIFTHGCFWHHHDCYLFKVPAT 81
Cdd:TIGR00632   1 ADKLSPATRSKNMQAIRTKGTKPEKALASLLTGLGLRFRLQDASLPGTPDIVFDEYRCVIFIHGCFWHGHHCYLGKVPKT 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1203926852  82 RTAFWLDKIAGNVARDARDRQKLAEEGWRVLIIWECA 118
Cdd:TIGR00632  81 RTDFWSPKIEKNVERDRRVNSRLQELGWRVLRVWECE 117
Vsr cd00221
Very short patch repair endonuclease; Very short patch repair (Vsr) is an endonuclease ...
 5-137 5.88e-52

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: 162.02  E-value: 5.88e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1203926852   5 HDKATRSKNMRAIATRDTAIEKRIAALLTGAGFTFVAQDRALPGRPDFALPDYRCVIFTHGCFWHHHDCYLFKVPATRTA 84
Cdd:cd00221     1 FTPEKRSRIMSRIRSKNTKPELAVRKALWARGLRYRLHVKKLPGKPDIVFPKYKVAVFVDGCFWHGCPCKKGKIPKSNRE 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1203926852  85 FWLDKIAGNVARDARDRQKLAEEGWRVLIIWECALRGRLRLSDAALTERLEEW 137
Cdd:cd00221    81 FWRAKIERNRERDRRVNAELRKLGWRVLRIWEHEIKKNPEKCARKILRALRKR 133
Vsr pfam03852
DNA mismatch endonuclease Vsr;
2-75 2.85e-36

DNA mismatch endonuclease Vsr;


Pssm-ID: 281799  Cd Length: 74  Bit Score: 120.31  E-value: 2.85e-36
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1203926852   2 ADVHDKATRSKNMRAIATRDTAIEKRIAALLTGAGFTFVAQDRALPGRPDFALPDYRCVIFTHGCFWHHHDCYL 75
Cdd:pfam03852   1 ADVHDKAKRSKVMRAIASRDTKPELRLAKLLTGQGLRYRKNDKSLPGKPDFVVPKYRCVVFVHGCFWHGHDCYL 74
YcjD COG2852
Very-short-patch-repair endonuclease [Replication, recombination and repair];
21-115 1.72e-03

Very-short-patch-repair endonuclease [Replication, recombination and repair];


Pssm-ID: 442100  Cd Length: 104  Bit Score: 35.99  E-value: 1.72e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1203926852  21 DTAIEKRIAALLTG---AGFTFVAQDRALPGRPDFALPDYRCVIFTHGcfwHHHDCylfkvpatrtafwldkiAGNVARD 97
Cdd:COG2852     5 DTPAERRLWQRLRNrqlRGLKFRRQVPIGGYIVDFYCPEARLAIEVDG---GYHGS-----------------PEQRERD 64

                          90
                  ....*....|....*...
gi 1203926852  98 ARDRQKLAEEGWRVLIIW 115
Cdd:COG2852    65 RRRDAYLERLGWRVLRFW 82
 
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