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Conserved domains on  [gi|553951725|ref|WP_023150684|]
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MULTISPECIES: very short patch repair endonuclease [Enterobacteriaceae]

Protein Classification

very short patch repair endonuclease( domain architecture ID 10083058)

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 cd00221
Very short patch repair endonuclease; Very short patch repair (Vsr) is an endonuclease ...
 4-136 9.31e-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: 163.56  E-value: 9.31e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553951725   4 ISQEKRSHIMRSIHSKNTKPEIIVDGILSNLDINYMAHCHSLYGKPDFLCEAYKAAIFVNGCFWHGHQCHMFRTPDSTNK 83
Cdd:cd00221    1 FTPEKRSRIMSRIRSKNTKPELAVRKALWARGLRYRLHVKKLPGKPDIVFPKYKVAVFVDGCFWHGCPCKKGKIPKSNRE 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 553951725  84 YWVSKLQKNSERDIRVVSILNNLGYKVIVVWECALIGKRKLDTLVLQDCLEEW 136
Cdd:cd00221   81 FWRAKIERNRERDRRVNAELRKLGWRVLRIWEHEIKKNPEKCARKILRALRKR 133
 
Name Accession Description Interval E-value
Vsr cd00221
Very short patch repair endonuclease; Very short patch repair (Vsr) is an endonuclease ...
 4-136 9.31e-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: 163.56  E-value: 9.31e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553951725   4 ISQEKRSHIMRSIHSKNTKPEIIVDGILSNLDINYMAHCHSLYGKPDFLCEAYKAAIFVNGCFWHGHQCHMFRTPDSTNK 83
Cdd:cd00221    1 FTPEKRSRIMSRIRSKNTKPELAVRKALWARGLRYRLHVKKLPGKPDIVFPKYKVAVFVDGCFWHGCPCKKGKIPKSNRE 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 553951725  84 YWVSKLQKNSERDIRVVSILNNLGYKVIVVWECALIGKRKLDTLVLQDCLEEW 136
Cdd:cd00221   81 FWRAKIERNRERDRRVNAELRKLGWRVLRIWEHEIKKNPEKCARKILRALRKR 133
Vsr COG3727
G:T-mismatch repair DNA endonuclease Vsr, very short patch repair protein [Replication, ...
 1-140 1.43e-50

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


Pssm-ID: 442941  Cd Length: 141  Bit Score: 158.44  E-value: 1.43e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553951725   1 MMRISQEKRSHIMRSIHSKNTKPEIIVDGILSNLDINYMAHCHSLYGKPDFLCEAYKAAIFVNGCFWHGH-QCHMFRTPd 79
Cdd:COG3727    1 ADVLTPETRSRNMSAIRGKDTKPELALRRALHALGLRYRLHRKDLPGKPDIVFPKYRVAIFVHGCFWHGHpGCRLATTP- 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 553951725  80 STNK-YWVSKLQKNSERDIRVVSILNNLGYKVIVVWECALIGKRKLDTLVLQDCLEEWLLAG 140
Cdd:COG3727   80 KTNTeFWRAKIERNVERDRRVNAALEAAGWRVLRVWECELKKKLALCVEALLERLEEWLRSR 141
vsr TIGR00632
DNA mismatch endonuclease Vsr; All proteins in this family for which functions are known are G: ...
 1-117 7.43e-38

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: 125.35  E-value: 7.43e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553951725    1 MMRISQEKRSHIMRSIHSKNTKPEIIVDGILSNLDINYMAHCHSLYGKPDFLCEAYKAAIFVNGCFWHGHQCHMFRTPDS 80
Cdd:TIGR00632   1 ADKLSPATRSKNMQAIRTKGTKPEKALASLLTGLGLRFRLQDASLPGTPDIVFDEYRCVIFIHGCFWHGHHCYLGKVPKT 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 553951725   81 TNKYWVSKLQKNSERDIRVVSILNNLGYKVIVVWECA 117
Cdd:TIGR00632  81 RTDFWSPKIEKNVERDRRVNSRLQELGWRVLRVWECE 117
Vsr pfam03852
DNA mismatch endonuclease Vsr;
7-72 3.43e-22

DNA mismatch endonuclease Vsr;


Pssm-ID: 281799  Cd Length: 74  Bit Score: 84.10  E-value: 3.43e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 553951725    7 EKRSHIMRSIHSKNTKPEIIVDGILSNLDINYMAHCHSLYGKPDFLCEAYKAAIFVNGCFWHGHQC 72
Cdd:pfam03852   7 AKRSKVMQSIKSTDTKPELRLAKLLTGLGLRYRKNDKSLPGKPDFVFPKYKVAVFVHGCFWHGHDC 72
 
Name Accession Description Interval E-value
Vsr cd00221
Very short patch repair endonuclease; Very short patch repair (Vsr) is an endonuclease ...
 4-136 9.31e-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: 163.56  E-value: 9.31e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553951725   4 ISQEKRSHIMRSIHSKNTKPEIIVDGILSNLDINYMAHCHSLYGKPDFLCEAYKAAIFVNGCFWHGHQCHMFRTPDSTNK 83
Cdd:cd00221    1 FTPEKRSRIMSRIRSKNTKPELAVRKALWARGLRYRLHVKKLPGKPDIVFPKYKVAVFVDGCFWHGCPCKKGKIPKSNRE 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 553951725  84 YWVSKLQKNSERDIRVVSILNNLGYKVIVVWECALIGKRKLDTLVLQDCLEEW 136
Cdd:cd00221   81 FWRAKIERNRERDRRVNAELRKLGWRVLRIWEHEIKKNPEKCARKILRALRKR 133
Vsr COG3727
G:T-mismatch repair DNA endonuclease Vsr, very short patch repair protein [Replication, ...
 1-140 1.43e-50

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


Pssm-ID: 442941  Cd Length: 141  Bit Score: 158.44  E-value: 1.43e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553951725   1 MMRISQEKRSHIMRSIHSKNTKPEIIVDGILSNLDINYMAHCHSLYGKPDFLCEAYKAAIFVNGCFWHGH-QCHMFRTPd 79
Cdd:COG3727    1 ADVLTPETRSRNMSAIRGKDTKPELALRRALHALGLRYRLHRKDLPGKPDIVFPKYRVAIFVHGCFWHGHpGCRLATTP- 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 553951725  80 STNK-YWVSKLQKNSERDIRVVSILNNLGYKVIVVWECALIGKRKLDTLVLQDCLEEWLLAG 140
Cdd:COG3727   80 KTNTeFWRAKIERNVERDRRVNAALEAAGWRVLRVWECELKKKLALCVEALLERLEEWLRSR 141
vsr TIGR00632
DNA mismatch endonuclease Vsr; All proteins in this family for which functions are known are G: ...
 1-117 7.43e-38

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: 125.35  E-value: 7.43e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553951725    1 MMRISQEKRSHIMRSIHSKNTKPEIIVDGILSNLDINYMAHCHSLYGKPDFLCEAYKAAIFVNGCFWHGHQCHMFRTPDS 80
Cdd:TIGR00632   1 ADKLSPATRSKNMQAIRTKGTKPEKALASLLTGLGLRFRLQDASLPGTPDIVFDEYRCVIFIHGCFWHGHHCYLGKVPKT 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 553951725   81 TNKYWVSKLQKNSERDIRVVSILNNLGYKVIVVWECA 117
Cdd:TIGR00632  81 RTDFWSPKIEKNVERDRRVNSRLQELGWRVLRVWECE 117
Vsr pfam03852
DNA mismatch endonuclease Vsr;
7-72 3.43e-22

DNA mismatch endonuclease Vsr;


Pssm-ID: 281799  Cd Length: 74  Bit Score: 84.10  E-value: 3.43e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 553951725    7 EKRSHIMRSIHSKNTKPEIIVDGILSNLDINYMAHCHSLYGKPDFLCEAYKAAIFVNGCFWHGHQC 72
Cdd:pfam03852   7 AKRSKVMQSIKSTDTKPELRLAKLLTGLGLRYRKNDKSLPGKPDFVFPKYKVAVFVHGCFWHGHDC 72
Hef-like cd22328
Hef-like homing endonuclease and similar nucleases; Hef-like homing endonuclease such as ...
 20-102 8.39e-03

Hef-like homing endonuclease and similar nucleases; Hef-like homing endonuclease such as I-Bth0305I, which is encoded within a group I intron in the recA gene of a Bacillus thuringiensis bacteriophage and cleaves a DNA target in the uninterrupted recA gene at a position immediately adjacent to the intron insertion site. It belongs to a 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.


Pssm-ID: 411732  Cd Length: 99  Bit Score: 34.15  E-value: 8.39e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553951725  20 NTKPEIIVDGILSNLDINYMAH-CHSLYGKP-DFLCEAYKAAIFVNGCFWHGHQCHMFRTpdstnkYWVSKLQKNSERDI 97
Cdd:cd22328    1 SSKPEKEIKDFLKELGIIYETRkRIILNGKElDIYIPEKKLAIEYNGLYWHSEKYKKDKN------YHLNKTEECESKGI 74


                 ....*
gi 553951725  98 RVVSI 102
Cdd:cd22328   75 RLLHI 79
 
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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