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Conserved domains on  [gi|959976045|gb|KSV85552|]
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DNA glycosylase [Sinorhizobium fredii USDA 205]

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, ...
 3-141 2.95e-66

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


:

Pssm-ID: 442941  Cd Length: 141  Bit Score: 197.34  E-value: 2.95e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 959976045   3 DTLDPQARSERMSRIRGKDSKAEVTVRRLVHGMGFRYRLHRKELPGKPDLVFGKRKKVIFVHGCFWHRHsdSDCKLARLP 82
Cdd:COG3727    2 DVLTPETRSRNMSAIRGKDTKPELALRRALHALGLRYRLHRKDLPGKPDIVFPKYRVAIFVHGCFWHGH--PGCRLATTP 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 959976045  83 KSRLDFWLPKLERNAARDAESSARLKVLGWDVMAVWECEV---SRSNLPLLGEKIRKFLCDE 141
Cdd:COG3727   80 KTNTEFWRAKIERNVERDRRVNAALEAAGWRVLRVWECELkkkLALCVEALLERLEEWLRSR 141
 
Name Accession Description Interval E-value
Vsr COG3727
G:T-mismatch repair DNA endonuclease Vsr, very short patch repair protein [Replication, ...
 3-141 2.95e-66

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


Pssm-ID: 442941  Cd Length: 141  Bit Score: 197.34  E-value: 2.95e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 959976045   3 DTLDPQARSERMSRIRGKDSKAEVTVRRLVHGMGFRYRLHRKELPGKPDLVFGKRKKVIFVHGCFWHRHsdSDCKLARLP 82
Cdd:COG3727    2 DVLTPETRSRNMSAIRGKDTKPELALRRALHALGLRYRLHRKDLPGKPDIVFPKYRVAIFVHGCFWHGH--PGCRLATTP 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 959976045  83 KSRLDFWLPKLERNAARDAESSARLKVLGWDVMAVWECEV---SRSNLPLLGEKIRKFLCDE 141
Cdd:COG3727   80 KTNTEFWRAKIERNVERDRRVNAALEAAGWRVLRVWECELkkkLALCVEALLERLEEWLRSR 141
Vsr cd00221
Very short patch repair endonuclease; Very short patch repair (Vsr) is an endonuclease ...
 5-141 1.69e-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: 165.10  E-value: 1.69e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 959976045   5 LDPQARSERMSRIRGKDSKAEVTVRRLVHGMGFRYRLHRKELPGKPDLVFGKRKKVIFVHGCFWHRHsdsDCKLARLPKS 84
Cdd:cd00221    1 FTPEKRSRIMSRIRSKNTKPELAVRKALWARGLRYRLHVKKLPGKPDIVFPKYKVAVFVDGCFWHGC---PCKKGKIPKS 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 959976045  85 RLDFWLPKLERNAARDAESSARLKVLGWDVMAVWECEVsRSNLPLLGEKIRKFLCDE 141
Cdd:cd00221   78 NREFWRAKIERNRERDRRVNAELRKLGWRVLRIWEHEI-KKNPEKCARKILRALRKR 133
vsr TIGR00632
DNA mismatch endonuclease Vsr; All proteins in this family for which functions are known are G: ...
 3-121 4.04e-43

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: 138.06  E-value: 4.04e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 959976045    3 DTLDPQARSERMSRIRGKDSKAEVTVRRLVHGMGFRYRLHRKELPGKPDLVFGKRKKVIFVHGCFWHRHsdsDCKLARLP 82
Cdd:TIGR00632   2 DKLSPATRSKNMQAIRTKGTKPEKALASLLTGLGLRFRLQDASLPGTPDIVFDEYRCVIFIHGCFWHGH---HCYLGKVP 78

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 959976045   83 KSRLDFWLPKLERNAARDAESSARLKVLGWDVMAVWECE 121
Cdd:TIGR00632  79 KTRTDFWSPKIEKNVERDRRVNSRLQELGWRVLRVWECE 117
Vsr pfam03852
DNA mismatch endonuclease Vsr;
3-72 3.66e-26

DNA mismatch endonuclease Vsr;


Pssm-ID: 281799  Cd Length: 74  Bit Score: 93.73  E-value: 3.66e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 959976045    3 DTLDPQARSERMSRIRGKDSKAEVTVRRLVHGMGFRYRLHRKELPGKPDLVFGKRKKVIFVHGCFWHRHS 72
Cdd:pfam03852   2 DVLTPAKRSKVMQSIKSTDTKPELRLAKLLTGLGLRYRKNDKSLPGKPDFVFPKYKVAVFVHGCFWHGHD 71
 
Name Accession Description Interval E-value
Vsr COG3727
G:T-mismatch repair DNA endonuclease Vsr, very short patch repair protein [Replication, ...
 3-141 2.95e-66

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


Pssm-ID: 442941  Cd Length: 141  Bit Score: 197.34  E-value: 2.95e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 959976045   3 DTLDPQARSERMSRIRGKDSKAEVTVRRLVHGMGFRYRLHRKELPGKPDLVFGKRKKVIFVHGCFWHRHsdSDCKLARLP 82
Cdd:COG3727    2 DVLTPETRSRNMSAIRGKDTKPELALRRALHALGLRYRLHRKDLPGKPDIVFPKYRVAIFVHGCFWHGH--PGCRLATTP 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 959976045  83 KSRLDFWLPKLERNAARDAESSARLKVLGWDVMAVWECEV---SRSNLPLLGEKIRKFLCDE 141
Cdd:COG3727   80 KTNTEFWRAKIERNVERDRRVNAALEAAGWRVLRVWECELkkkLALCVEALLERLEEWLRSR 141
Vsr cd00221
Very short patch repair endonuclease; Very short patch repair (Vsr) is an endonuclease ...
 5-141 1.69e-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: 165.10  E-value: 1.69e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 959976045   5 LDPQARSERMSRIRGKDSKAEVTVRRLVHGMGFRYRLHRKELPGKPDLVFGKRKKVIFVHGCFWHRHsdsDCKLARLPKS 84
Cdd:cd00221    1 FTPEKRSRIMSRIRSKNTKPELAVRKALWARGLRYRLHVKKLPGKPDIVFPKYKVAVFVDGCFWHGC---PCKKGKIPKS 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 959976045  85 RLDFWLPKLERNAARDAESSARLKVLGWDVMAVWECEVsRSNLPLLGEKIRKFLCDE 141
Cdd:cd00221   78 NREFWRAKIERNRERDRRVNAELRKLGWRVLRIWEHEI-KKNPEKCARKILRALRKR 133
vsr TIGR00632
DNA mismatch endonuclease Vsr; All proteins in this family for which functions are known are G: ...
 3-121 4.04e-43

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: 138.06  E-value: 4.04e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 959976045    3 DTLDPQARSERMSRIRGKDSKAEVTVRRLVHGMGFRYRLHRKELPGKPDLVFGKRKKVIFVHGCFWHRHsdsDCKLARLP 82
Cdd:TIGR00632   2 DKLSPATRSKNMQAIRTKGTKPEKALASLLTGLGLRFRLQDASLPGTPDIVFDEYRCVIFIHGCFWHGH---HCYLGKVP 78

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 959976045   83 KSRLDFWLPKLERNAARDAESSARLKVLGWDVMAVWECE 121
Cdd:TIGR00632  79 KTRTDFWSPKIEKNVERDRRVNSRLQELGWRVLRVWECE 117
Vsr pfam03852
DNA mismatch endonuclease Vsr;
3-72 3.66e-26

DNA mismatch endonuclease Vsr;


Pssm-ID: 281799  Cd Length: 74  Bit Score: 93.73  E-value: 3.66e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 959976045    3 DTLDPQARSERMSRIRGKDSKAEVTVRRLVHGMGFRYRLHRKELPGKPDLVFGKRKKVIFVHGCFWHRHS 72
Cdd:pfam03852   2 DVLTPAKRSKVMQSIKSTDTKPELRLAKLLTGLGLRYRKNDKSLPGKPDFVFPKYKVAVFVHGCFWHGHD 71
 
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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