NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1518638728|ref|WP_123486327|]
View 

MULTISPECIES: very short patch repair endonuclease [Bacteroidales]

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, ...
 2-142 8.26e-82

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


:

Pssm-ID: 442941  Cd Length: 141  Bit Score: 238.17  E-value: 8.26e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1518638728   2 ADVMTPEQRSRCMAAIKGKDTKPELIVRKYLFSRGLRFRVQVRKLSGNPDIVLPKYKTVIFVNGCFWHGHEGCKYFRLPK 81
Cdd:COG3727     1 ADVLTPETRSRNMSAIRGKDTKPELALRRALHALGLRYRLHRKDLPGKPDIVFPKYRVAIFVHGCFWHGHPGCRLATTPK 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1518638728  82 SNVEFWEAKIERNVARDVRNEAELKALGWRVVRVWECEIKtvAERKEYLKRLYDRIVNLVQ 142
Cdd:COG3727    81 TNTEFWRAKIERNVERDRRVNAALEAAGWRVLRVWECELK--KKLALCVEALLERLEEWLR 139
 
Name Accession Description Interval E-value
Vsr COG3727
G:T-mismatch repair DNA endonuclease Vsr, very short patch repair protein [Replication, ...
 2-142 8.26e-82

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


Pssm-ID: 442941  Cd Length: 141  Bit Score: 238.17  E-value: 8.26e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1518638728   2 ADVMTPEQRSRCMAAIKGKDTKPELIVRKYLFSRGLRFRVQVRKLSGNPDIVLPKYKTVIFVNGCFWHGHEGCKYFRLPK 81
Cdd:COG3727     1 ADVLTPETRSRNMSAIRGKDTKPELALRRALHALGLRYRLHRKDLPGKPDIVFPKYRVAIFVHGCFWHGHPGCRLATTPK 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1518638728  82 SNVEFWEAKIERNVARDVRNEAELKALGWRVVRVWECEIKtvAERKEYLKRLYDRIVNLVQ 142
Cdd:COG3727    81 TNTEFWRAKIERNVERDRRVNAALEAAGWRVLRVWECELK--KKLALCVEALLERLEEWLR 139
Vsr cd00221
Very short patch repair endonuclease; Very short patch repair (Vsr) is an endonuclease ...
 5-126 1.42e-67

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: 201.70  E-value: 1.42e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1518638728   5 MTPEQRSRCMAAIKGKDTKPELIVRKYLFSRGLRFRVQVRKLSGNPDIVLPKYKTVIFVNGCFWHGHEgCKYFRLPKSNV 84
Cdd:cd00221     1 FTPEKRSRIMSRIRSKNTKPELAVRKALWARGLRYRLHVKKLPGKPDIVFPKYKVAVFVDGCFWHGCP-CKKGKIPKSNR 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1518638728  85 EFWEAKIERNVARDVRNEAELKALGWRVVRVWECEIKTVAER 126
Cdd:cd00221    80 EFWRAKIERNRERDRRVNAELRKLGWRVLRIWEHEIKKNPEK 121
vsr TIGR00632
DNA mismatch endonuclease Vsr; All proteins in this family for which functions are known are G: ...
 2-119 9.51e-53

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: 163.87  E-value: 9.51e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1518638728   2 ADVMTPEQRSRCMAAIKGKDTKPELIVRKYLFSRGLRFRVQVRKLSGNPDIVLPKYKTVIFVNGCFWHGHeGCKYFRLPK 81
Cdd:TIGR00632   1 ADKLSPATRSKNMQAIRTKGTKPEKALASLLTGLGLRFRLQDASLPGTPDIVFDEYRCVIFIHGCFWHGH-HCYLGKVPK 79

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1518638728  82 SNVEFWEAKIERNVARDVRNEAELKALGWRVVRVWECE 119
Cdd:TIGR00632  80 TRTDFWSPKIEKNVERDRRVNSRLQELGWRVLRVWECE 117
Vsr pfam03852
DNA mismatch endonuclease Vsr;
2-72 8.52e-33

DNA mismatch endonuclease Vsr;


Pssm-ID: 281799  Cd Length: 74  Bit Score: 111.45  E-value: 8.52e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1518638728   2 ADVMTPEQRSRCMAAIKGKDTKPELIVRKYLFSRGLRFRVQVRKLSGNPDIVLPKYKTVIFVNGCFWHGHE 72
Cdd:pfam03852   1 MDVLTPAKRSKVMQSIKSTDTKPELRLAKLLTGLGLRYRKNDKSLPGKPDFVFPKYKVAVFVHGCFWHGHD 71
 
Name Accession Description Interval E-value
Vsr COG3727
G:T-mismatch repair DNA endonuclease Vsr, very short patch repair protein [Replication, ...
 2-142 8.26e-82

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


Pssm-ID: 442941  Cd Length: 141  Bit Score: 238.17  E-value: 8.26e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1518638728   2 ADVMTPEQRSRCMAAIKGKDTKPELIVRKYLFSRGLRFRVQVRKLSGNPDIVLPKYKTVIFVNGCFWHGHEGCKYFRLPK 81
Cdd:COG3727     1 ADVLTPETRSRNMSAIRGKDTKPELALRRALHALGLRYRLHRKDLPGKPDIVFPKYRVAIFVHGCFWHGHPGCRLATTPK 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1518638728  82 SNVEFWEAKIERNVARDVRNEAELKALGWRVVRVWECEIKtvAERKEYLKRLYDRIVNLVQ 142
Cdd:COG3727    81 TNTEFWRAKIERNVERDRRVNAALEAAGWRVLRVWECELK--KKLALCVEALLERLEEWLR 139
Vsr cd00221
Very short patch repair endonuclease; Very short patch repair (Vsr) is an endonuclease ...
 5-126 1.42e-67

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: 201.70  E-value: 1.42e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1518638728   5 MTPEQRSRCMAAIKGKDTKPELIVRKYLFSRGLRFRVQVRKLSGNPDIVLPKYKTVIFVNGCFWHGHEgCKYFRLPKSNV 84
Cdd:cd00221     1 FTPEKRSRIMSRIRSKNTKPELAVRKALWARGLRYRLHVKKLPGKPDIVFPKYKVAVFVDGCFWHGCP-CKKGKIPKSNR 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1518638728  85 EFWEAKIERNVARDVRNEAELKALGWRVVRVWECEIKTVAER 126
Cdd:cd00221    80 EFWRAKIERNRERDRRVNAELRKLGWRVLRIWEHEIKKNPEK 121
vsr TIGR00632
DNA mismatch endonuclease Vsr; All proteins in this family for which functions are known are G: ...
 2-119 9.51e-53

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: 163.87  E-value: 9.51e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1518638728   2 ADVMTPEQRSRCMAAIKGKDTKPELIVRKYLFSRGLRFRVQVRKLSGNPDIVLPKYKTVIFVNGCFWHGHeGCKYFRLPK 81
Cdd:TIGR00632   1 ADKLSPATRSKNMQAIRTKGTKPEKALASLLTGLGLRFRLQDASLPGTPDIVFDEYRCVIFIHGCFWHGH-HCYLGKVPK 79

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1518638728  82 SNVEFWEAKIERNVARDVRNEAELKALGWRVVRVWECE 119
Cdd:TIGR00632  80 TRTDFWSPKIEKNVERDRRVNSRLQELGWRVLRVWECE 117
Vsr pfam03852
DNA mismatch endonuclease Vsr;
2-72 8.52e-33

DNA mismatch endonuclease Vsr;


Pssm-ID: 281799  Cd Length: 74  Bit Score: 111.45  E-value: 8.52e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1518638728   2 ADVMTPEQRSRCMAAIKGKDTKPELIVRKYLFSRGLRFRVQVRKLSGNPDIVLPKYKTVIFVNGCFWHGHE 72
Cdd:pfam03852   1 MDVLTPAKRSKVMQSIKSTDTKPELRLAKLLTGLGLRYRKNDKSLPGKPDFVFPKYKVAVFVHGCFWHGHD 71
YcjD COG2852
Very-short-patch-repair endonuclease [Replication, recombination and repair];
21-120 1.14e-07

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


Pssm-ID: 442100  Cd Length: 104  Bit Score: 47.55  E-value: 1.14e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1518638728  21 DTKPELIVRKYLFSR---GLRFRVQVRKLSGNPDIVLPKYKTVIFVNGcFWHGHEGckyfrlpksnvefweakierNVAR 97
Cdd:COG2852     5 DTPAERRLWQRLRNRqlrGLKFRRQVPIGGYIVDFYCPEARLAIEVDG-GYHGSPE--------------------QRER 63

                          90       100
                  ....*....|....*....|...
gi 1518638728  98 DVRNEAELKALGWRVVRVWECEI 120
Cdd:COG2852    64 DRRRDAYLERLGWRVLRFWNEDV 86
Hef-like cd22328
Hef-like homing endonuclease and similar nucleases; Hef-like homing endonuclease such as ...
 22-69 3.38e-04

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: 38.00  E-value: 3.38e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1518638728  22 TKPELIVRKYLFSRGLRFRVQVRKLSG--NPDIVLPKYKTVIFVNGCFWH 69
Cdd:cd22328     2 SKPEKEIKDFLKELGIIYETRKRIILNgkELDIYIPEKKLAIEYNGLYWH 51
Endonuclease_DUF559 cd01038
Putative endonuclease; Domain of unknown function 559 (DUF559) is a putative endonuclease of ...
 22-120 1.14e-03

Putative endonuclease; Domain of unknown function 559 (DUF559) is a putative endonuclease of unknown function, belongs 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: 411708  Cd Length: 97  Bit Score: 36.41  E-value: 1.14e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1518638728  22 TKPELIVRKYLFSR---GLRFRVQVRKLSGNPDIVLPKYKTVIFVNGCFWHGhegckyfrlpksnvefweakiERNVARD 98
Cdd:cd01038     2 TEAERKLWQHLRNRqflGLKFRRQKPIGFYIVDFYCAEKKLVIEIDGGQHHE---------------------KKAEEYD 60

                          90       100
                  ....*....|....*....|..
gi 1518638728  99 VRNEAELKALGWRVVRVWECEI 120
Cdd:cd01038    61 ARRDKYLESLGYTVLRFWNEEV 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