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Conserved domains on  [gi|446708659|ref|WP_000786005|]
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MULTISPECIES: VSPR family DNA mismatch endonuclease [Enterobacteriaceae]

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

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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 6.68e-75

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


:

Pssm-ID: 442941  Cd Length: 141  Bit Score: 220.07  E-value: 6.68e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446708659   2 ADVHDKATRSKNMRAIATRDTAIEKRLASLLTGQGLAFRVQDASLPGRPDFVVDEYRCVIFTHGCFWHHHH-CYLFKVPA 80
Cdd:COG3727    1 ADVLTPETRSRNMSAIRGKDTKPELALRRALHALGLRYRLHRKDLPGKPDIVFPKYRVAIFVHGCFWHGHPgCRLATTPK 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446708659  81 TRTEFWLEKIGKNVERDRRDISRLQELGWRVLIVWECALRGREKLTDEALTERLEEWICGE 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 6.68e-75

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


Pssm-ID: 442941  Cd Length: 141  Bit Score: 220.07  E-value: 6.68e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446708659   2 ADVHDKATRSKNMRAIATRDTAIEKRLASLLTGQGLAFRVQDASLPGRPDFVVDEYRCVIFTHGCFWHHHH-CYLFKVPA 80
Cdd:COG3727    1 ADVLTPETRSRNMSAIRGKDTKPELALRRALHALGLRYRLHRKDLPGKPDIVFPKYRVAIFVHGCFWHGHPgCRLATTPK 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446708659  81 TRTEFWLEKIGKNVERDRRDISRLQELGWRVLIVWECALRGREKLTDEALTERLEEWICGE 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 5.15e-68

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: 201.62  E-value: 5.15e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446708659    2 ADVHDKATRSKNMRAIATRDTAIEKRLASLLTGQGLAFRVQDASLPGRPDFVVDEYRCVIFTHGCFWHHHHCYLFKVPAT 81
Cdd:TIGR00632   1 ADKLSPATRSKNMQAIRTKGTKPEKALASLLTGLGLRFRLQDASLPGTPDIVFDEYRCVIFIHGCFWHGHHCYLGKVPKT 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 446708659   82 RTEFWLEKIGKNVERDRRDISRLQELGWRVLIVWECA 118
Cdd:TIGR00632  81 RTDFWSPKIEKNVERDRRVNSRLQELGWRVLRVWECE 117
Vsr cd00221
Very short patch repair endonuclease; Very short patch repair (Vsr) is an endonuclease ...
 5-137 1.64e-53

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: 165.49  E-value: 1.64e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446708659   5 HDKATRSKNMRAIATRDTAIEKRLASLLTGQGLAFRVQDASLPGRPDFVVDEYRCVIFTHGCFWHHHHCYLFKVPATRTE 84
Cdd:cd00221    1 FTPEKRSRIMSRIRSKNTKPELAVRKALWARGLRYRLHVKKLPGKPDIVFPKYKVAVFVDGCFWHGCPCKKGKIPKSNRE 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446708659  85 FWLEKIGKNVERDRRDISRLQELGWRVLIVWECALRGREKLTDEALTERLEEW 137
Cdd:cd00221   81 FWRAKIERNRERDRRVNAELRKLGWRVLRIWEHEIKKNPEKCARKILRALRKR 133
Vsr pfam03852
DNA mismatch endonuclease Vsr;
2-75 7.54e-43

DNA mismatch endonuclease Vsr;


Pssm-ID: 281799  Cd Length: 74  Bit Score: 136.49  E-value: 7.54e-43
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446708659    2 ADVHDKATRSKNMRAIATRDTAIEKRLASLLTGQGLAFRVQDASLPGRPDFVVDEYRCVIFTHGCFWHHHHCYL 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 6.68e-75

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


Pssm-ID: 442941  Cd Length: 141  Bit Score: 220.07  E-value: 6.68e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446708659   2 ADVHDKATRSKNMRAIATRDTAIEKRLASLLTGQGLAFRVQDASLPGRPDFVVDEYRCVIFTHGCFWHHHH-CYLFKVPA 80
Cdd:COG3727    1 ADVLTPETRSRNMSAIRGKDTKPELALRRALHALGLRYRLHRKDLPGKPDIVFPKYRVAIFVHGCFWHGHPgCRLATTPK 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446708659  81 TRTEFWLEKIGKNVERDRRDISRLQELGWRVLIVWECALRGREKLTDEALTERLEEWICGE 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 5.15e-68

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: 201.62  E-value: 5.15e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446708659    2 ADVHDKATRSKNMRAIATRDTAIEKRLASLLTGQGLAFRVQDASLPGRPDFVVDEYRCVIFTHGCFWHHHHCYLFKVPAT 81
Cdd:TIGR00632   1 ADKLSPATRSKNMQAIRTKGTKPEKALASLLTGLGLRFRLQDASLPGTPDIVFDEYRCVIFIHGCFWHGHHCYLGKVPKT 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 446708659   82 RTEFWLEKIGKNVERDRRDISRLQELGWRVLIVWECA 118
Cdd:TIGR00632  81 RTDFWSPKIEKNVERDRRVNSRLQELGWRVLRVWECE 117
Vsr cd00221
Very short patch repair endonuclease; Very short patch repair (Vsr) is an endonuclease ...
 5-137 1.64e-53

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: 165.49  E-value: 1.64e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446708659   5 HDKATRSKNMRAIATRDTAIEKRLASLLTGQGLAFRVQDASLPGRPDFVVDEYRCVIFTHGCFWHHHHCYLFKVPATRTE 84
Cdd:cd00221    1 FTPEKRSRIMSRIRSKNTKPELAVRKALWARGLRYRLHVKKLPGKPDIVFPKYKVAVFVDGCFWHGCPCKKGKIPKSNRE 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446708659  85 FWLEKIGKNVERDRRDISRLQELGWRVLIVWECALRGREKLTDEALTERLEEW 137
Cdd:cd00221   81 FWRAKIERNRERDRRVNAELRKLGWRVLRIWEHEIKKNPEKCARKILRALRKR 133
Vsr pfam03852
DNA mismatch endonuclease Vsr;
2-75 7.54e-43

DNA mismatch endonuclease Vsr;


Pssm-ID: 281799  Cd Length: 74  Bit Score: 136.49  E-value: 7.54e-43
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446708659    2 ADVHDKATRSKNMRAIATRDTAIEKRLASLLTGQGLAFRVQDASLPGRPDFVVDEYRCVIFTHGCFWHHHHCYL 75
Cdd:pfam03852   1 ADVHDKAKRSKVMRAIASRDTKPELRLAKLLTGQGLRYRKNDKSLPGKPDFVVPKYRCVVFVHGCFWHGHDCYL 74
YcjD COG2852
Very-short-patch-repair endonuclease [Replication, recombination and repair];
21-115 1.80e-03

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


Pssm-ID: 442100  Cd Length: 104  Bit Score: 35.99  E-value: 1.80e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446708659  21 DTAIEKRLASLLTG---QGLAFRVQDASLPGRPDFVVDEYRCVIFTHGcfwHHHHCylfkvpatrtefwlekiGKNVERD 97
Cdd:COG2852    5 DTPAERRLWQRLRNrqlRGLKFRRQVPIGGYIVDFYCPEARLAIEVDG---GYHGS-----------------PEQRERD 64

                         90
                 ....*....|....*...
gi 446708659  98 RRDISRLQELGWRVLIVW 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.
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