+F Repair protein KO
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DNA Repair and Recombination Proteins - Variovorax paradoxus B4
%
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AEukaryotic type
B SSBR (single strand breaks repair)
C Direct repair
D VAPA_1c26510 putative methylated-DNA-[protein]-cysteine S-methyltransferase K00567 ogt; methylated-DNA-[protein]-cysteine S-methyltransferase [EC:2.1.1.63]
D VAPA_1c38520 methylated-DNA--protein-cysteine methyltransferase K00567 ogt; methylated-DNA-[protein]-cysteine S-methyltransferase [EC:2.1.1.63]
D VAPA_1c47590 phrA; deoxyribodipyrimidine photo-lyase PhrA K01669 phr; deoxyribodipyrimidine photo-lyase [EC:4.1.99.3]
C BER (base exicision repair)
D DNA glycosylases
E VAPA_1c07300 ung; uracil-DNA glycosylase Ung K03648 UNG; uracil-DNA glycosylase [EC:3.2.2.27]
E VAPA_1c45080 mutY; A/G-specific adenine glycosylase MutY K03575 mutY; A/G-specific adenine glycosylase [EC:3.2.2.31]
E VAPA_1c29820 nth; endonuclease 3 Nth K10773 NTHL1; endonuclease III [EC:3.2.2.- 4.2.99.18]
D AP endonucleases
D Long Patch-BER factors
E DNA polymerase delta complex
E DNA polymerase epsilon complex
D Short Patch-BER factors
D Other BER factors
C NER (nucleotide excision repair)
D GGR (global genome repair) factors
E XPC-HR23B-CETN2 complex
E Cul4-DDB2 complex
E NER4 complex
D TCR (transcription coupled repair) factors
E DNA-directed RNA polymerase II complex
E Cul4-CSA complex
E Other TCR factor
D TFIIH complex
E VAPA_1c27470 putative helicase K10844 ERCC2; DNA excision repair protein ERCC-2 [EC:5.6.2.3]
D RPA (replication factor A)
D Other NER factors
C MMR (mismatch excision repair)
D Mismatch and loop recognition factors
D MutL homologs
D DNA polymerase delta complex
D RPA (replication factor A)
D RFC (replication factor C)
D Other MMR factors
B DSBR (double strand breaks repair)
C HR (homologous recombination)
D MRN(MRX) complex
D BRCA1-core complex
D BRCA1-A complex
D BRCA1-B complex
D BRCA1-C complex
D BRCA complex
D RecA family proteins
D Rad52 family proteins
D Rad54 family proteins
D RecQ family DNA helicases
D Bloom's syndrome complex (BTR)
D RPA (replication factor A)
D Protein phosphatase 4
D AP-5 complex
D SMC5-SMC6 complex
D Other HR factors
C NHEJ (non-homologous end-joining)
D DNA-PK complex
D MRX complex
D DNA Ligase 4 complex
D X-family DNA polymerases
D Other NHEJ factors
C FA (Fanconi anemia) pathway
D FA core complex
D FA core complex binding factors
D Bloom's syndrome complex (BTR)
D FANCD2-I complex
D Downstream FA components
D Other FA pathway factors
C Other DSBR factors
D Protein phosphatase 6
D Ubiquitin ligases
D Others
B TLS (translesion DNA synthesis) factors
C Y-family DNA polymerases
C B-family DNA polymerases
C A-family DNA polymerase
C Rad6 epistasis group
C Other TLS factors
B Check point factors
C Rad9-Hus1-Rad1 complex
C HRAD17(Rad24)-RFC complex
C Rad17-Mec3-Ddc1 complex
C FPC (fork protection complex)
C Triple T complex
C BAG6-UBL4A-GET4 complex
C Other check point factors
B Other factors with a suspected DNA repair function
C DNA polymerases
C Nucleases
C Helicases
C PSO4 complex
C Modulation of nucleotide pools
D VAPA_1c43870 putative hydrolase, NUDIX family K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D VAPA_2c00560 NUDIX domain-containing protein K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D VAPA_2c08300 putative hydrolase, NUDIX family K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D VAPA_1c35470 dut; deoxyuridine 5'-triphosphate nucleotidohydrolase Dut K01520 dut; dUTP diphosphatase [EC:3.6.1.23]
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AProkaryotic type
B SSBR (single strand breaks repair)
C Direct repair
D VAPA_1c26510 putative methylated-DNA-[protein]-cysteine S-methyltransferase K00567 ogt; methylated-DNA-[protein]-cysteine S-methyltransferase [EC:2.1.1.63]
D VAPA_1c38520 methylated-DNA--protein-cysteine methyltransferase K00567 ogt; methylated-DNA-[protein]-cysteine S-methyltransferase [EC:2.1.1.63]
D VAPA_1c47590 phrA; deoxyribodipyrimidine photo-lyase PhrA K01669 phr; deoxyribodipyrimidine photo-lyase [EC:4.1.99.3]
D VAPA_1c47940 alkB; putative alpha-ketoglutarate-dependent dioxygenase AlkB K03919 alkB; DNA oxidative demethylase [EC:1.14.11.33]
C BER (base exicision repair)
D DNA glycosylases
E VAPA_1c07300 ung; uracil-DNA glycosylase Ung K03648 UNG; uracil-DNA glycosylase [EC:3.2.2.27]
E VAPA_1c52740 uracil-DNA glycosylase superfamily protein K21929 udg; uracil-DNA glycosylase [EC:3.2.2.27]
E VAPA_1c27450 uracil-DNA glycosylase family protein K21929 udg; uracil-DNA glycosylase [EC:3.2.2.27]
E VAPA_1c31570 HhH-GPD superfamily protein K01247 alkA; DNA-3-methyladenine glycosylase II [EC:3.2.2.21]
E VAPA_1c38510 putative bifunctional transcriptional regulator, AraC family K13529 ada-alkA; AraC family transcriptional regulator, regulatory protein of adaptative response / DNA-3-methyladenine glycosylase II [EC:3.2.2.21]
E VAPA_1c45080 mutY; A/G-specific adenine glycosylase MutY K03575 mutY; A/G-specific adenine glycosylase [EC:3.2.2.31]
E VAPA_2c10000 DNA-3-methyladenine glycosylase K01246 tag; DNA-3-methyladenine glycosylase I [EC:3.2.2.20]
E VAPA_1c33500 tag; DNA-3-methyladenine glycosylase 1 K01246 tag; DNA-3-methyladenine glycosylase I [EC:3.2.2.20]
E VAPA_1c45100 mutM; formamidopyrimidine-DNA glycosylase MutM K10563 mutM; formamidopyrimidine-DNA glycosylase [EC:3.2.2.23 4.2.99.18]
E VAPA_1c29820 nth; endonuclease 3 Nth K10773 NTHL1; endonuclease III [EC:3.2.2.- 4.2.99.18]
D AP endonucleases
E VAPA_1c20980 putative exodeoxyribonuclease III K01142 E3.1.11.2; exodeoxyribonuclease III [EC:3.1.11.2]
E VAPA_1c17430 exodeoxyribonuclease III K01142 E3.1.11.2; exodeoxyribonuclease III [EC:3.1.11.2]
E VAPA_1c03400 xth; exodeoxyribonuclease III Xth K01142 E3.1.11.2; exodeoxyribonuclease III [EC:3.1.11.2]
D RecJ
E VAPA_1c12680 single-stranded-DNA-specific exonuclease K07462 recJ; single-stranded-DNA-specific exonuclease [EC:3.1.-.-]
D DNA ligase
E VAPA_1c26020 ligA; DNA ligase LigA K01972 E6.5.1.2; DNA ligase (NAD+) [EC:6.5.1.2]
D DNA polymerase I
E VAPA_1c16370 polA; DNA polymerase I PolA K02335 polA; DNA polymerase I [EC:2.7.7.7]
C NER (nucleotide excision repair)
D GGR (global genome repair) factors
E VAPA_1c04560 uvrA1; UvrABC system protein A UvrA K03701 uvrA; excinuclease ABC subunit A
E VAPA_1c48560 uvrA2; UvrABC system protein A K03701 uvrA; excinuclease ABC subunit A
E VAPA_1c23100 uvrB; uvrABC system protein B UvrB K03702 uvrB; excinuclease ABC subunit B
E VAPA_1c18680 uvrC; UvrABC system protein C Uvrc K03703 uvrC; excinuclease ABC subunit C
E VAPA_1c04800 pcrA; putative ATP-dependent DNA helicase PcrA K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4]
E VAPA_1c16330 DNA helicase II K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4]
E VAPA_1c16370 polA; DNA polymerase I PolA K02335 polA; DNA polymerase I [EC:2.7.7.7]
E VAPA_1c26020 ligA; DNA ligase LigA K01972 E6.5.1.2; DNA ligase (NAD+) [EC:6.5.1.2]
D TCR (transcription coupled repair) factors
E DNA-directed RNA polymerase complex (RNAP)
F VAPA_1c07420 rpoB; DNA-directed RNA polymerase, subunit beta RpoB K03043 rpoB; DNA-directed RNA polymerase subunit beta [EC:2.7.7.6]
F VAPA_1c07430 rpoC; DNA-directed RNA polymerase, subunit beta' RpoC K03046 rpoC; DNA-directed RNA polymerase subunit beta' [EC:2.7.7.6]
F VAPA_1c52370 rpoA; DNA-directed RNA polymerase subunit alpha K03040 rpoA; DNA-directed RNA polymerase subunit alpha [EC:2.7.7.6]
F VAPA_1c44970 rpoZ; DNA-directed RNA polymerase subunit omega K03060 rpoZ; DNA-directed RNA polymerase subunit omega [EC:2.7.7.6]
E TRCF (transcription-repair coupling factor)
F VAPA_1c29760 transcription-repair-coupling factor K03723 mfd; transcription-repair coupling factor (superfamily II helicase) [EC:5.6.2.4]
C MMR (mismatch excision repair)
D Mismatch and loop recognition factors
E VAPA_1c37070 mutS; DNA mismatch repair protein MutS K03555 mutS; DNA mismatch repair protein MutS
D Molecular matchmaker
E VAPA_1c35740 mutL; DNA mismatch repair protein MutL K03572 mutL; DNA mismatch repair protein MutL
D Strand discrimination factor
D DNA exonucleases
E VAPA_1c28990 exodeoxyribonuclease 1 K01141 sbcB; exodeoxyribonuclease I [EC:3.1.11.1]
E VAPA_1c29080 xseA; exodeoxyribonuclease 7, large subunit XseA K03601 xseA; exodeoxyribonuclease VII large subunit [EC:3.1.11.6]
E VAPA_1c16640 putative exodeoxyribonuclease 7, small subunit K03602 xseB; exodeoxyribonuclease VII small subunit [EC:3.1.11.6]
D DNA polymerase III holoenzyme
E VAPA_1c31860 dnaE1; DNA polymerase 3, subunit alpha K02337 dnaE; DNA polymerase III subunit alpha [EC:2.7.7.7]
E VAPA_1c00020 dnaN; DNA polymerase III, subunit beta K02338 dnaN; DNA polymerase III subunit beta [EC:2.7.7.7]
E VAPA_1c28280 putative DNA polymerase III, subunit chi K02339 holC; DNA polymerase III subunit chi [EC:2.7.7.7]
E VAPA_1c05040 holA; DNA polymerase III, delta subunit HolA K02340 holA; DNA polymerase III subunit delta [EC:2.7.7.7]
E VAPA_1c26980 putative DNA polymerase III, subunit delta' K02341 holB; DNA polymerase III subunit delta' [EC:2.7.7.7]
E VAPA_1c23180 dnaQ; DNA polymerase 3, subunit epsilon DnaQ K02342 dnaQ; DNA polymerase III subunit epsilon [EC:2.7.7.7]
E VAPA_1c24690 dnaX; DNA polymerase III DnaX K02343 dnaX; DNA polymerase III subunit gamma/tau [EC:2.7.7.7]
D DNA ligase
E VAPA_1c26020 ligA; DNA ligase LigA K01972 E6.5.1.2; DNA ligase (NAD+) [EC:6.5.1.2]
D Other MMR factors
E VAPA_1c04800 pcrA; putative ATP-dependent DNA helicase PcrA K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4]
E VAPA_1c16330 DNA helicase II K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4]
E VAPA_1c04570 ssb; single-stranded DNA-binding protein Ssb K03111 ssb; single-strand DNA-binding protein
B DSBR (double strand breaks repair)
C HR (homologous recombination)
D RecBC pathway proteins
E VAPA_1c54030 recA; protein RecA K03553 recA; recombination protein RecA
E VAPA_1c48170 ruvA; holliday junction ATP-dependent DNA helicase RuvA K03550 ruvA; holliday junction DNA helicase RuvA
E VAPA_1c48010 ruvB; holliday junction ATP-dependent DNA helicase RuvB K03551 ruvB; holliday junction DNA helicase RuvB [EC:5.6.2.4]
E VAPA_1c09820 ruvC; crossover junction endodeoxyribonuclease RuvC K01159 ruvC; crossover junction endodeoxyribonuclease RuvC [EC:3.1.21.10]
E VAPA_1c07810 priA; primosomal protein N' PriA K04066 priA; primosomal protein N' (replication factor Y) (superfamily II helicase) [EC:5.6.2.4]
E VAPA_1c19040 priB; putative primosomal replication protein PriB K02686 priB; primosomal replication protein N
E VAPA_1c28990 exodeoxyribonuclease 1 K01141 sbcB; exodeoxyribonuclease I [EC:3.1.11.1]
D RecFOR pathway proteins
E VAPA_1c54030 recA; protein RecA K03553 recA; recombination protein RecA
E VAPA_1c03050 radA; DNA repair protein RadA K04485 radA; DNA repair protein RadA/Sms
E VAPA_1c52590 recG; ATP-dependent DNA helicase RecG K03655 recG; ATP-dependent DNA helicase RecG [EC:5.6.2.4]
E VAPA_1c12680 single-stranded-DNA-specific exonuclease K07462 recJ; single-stranded-DNA-specific exonuclease [EC:3.1.-.-]
E VAPA_1c14970 recO; DNA repair protein recO K03584 recO; DNA repair protein RecO (recombination protein O)
E VAPA_1c24710 recR; recombination protein RecR K06187 recR; recombination protein RecR
E VAPA_1c45060 recN; DNA repair protein RecN K03631 recN; DNA repair protein RecN (Recombination protein N)
E VAPA_1c03100 rdgC; putative recombination-associated protein RdgC K03554 rdgC; recombination associated protein RdgC
E VAPA_1c48170 ruvA; holliday junction ATP-dependent DNA helicase RuvA K03550 ruvA; holliday junction DNA helicase RuvA
E VAPA_1c48010 ruvB; holliday junction ATP-dependent DNA helicase RuvB K03551 ruvB; holliday junction DNA helicase RuvB [EC:5.6.2.4]
E VAPA_1c09820 ruvC; crossover junction endodeoxyribonuclease RuvC K01159 ruvC; crossover junction endodeoxyribonuclease RuvC [EC:3.1.21.10]
D AddAB pathway proteins
E VAPA_1c24650 putative DNA helicase, UvrD/REP-type K16898 addA; ATP-dependent helicase/nuclease subunit A [EC:5.6.2.4 3.1.-.-]
E VAPA_1c24640 PD-(D/E)XK nuclease superfamily domain-containing protein K16899 addB; ATP-dependent helicase/nuclease subunit B [EC:5.6.2.4 3.1.-.-]
D Other HR factor
D Archaeal homologous recombinant proteins
E VAPA_1c28780 hypothetical protein K06915 herA; DNA double-strand break repair helicase HerA and related ATPase
C NHEJ (non-homologous end-joining)
D Two-component NHEJ DNA repair complex
E VAPA_1c05780 putative DNA repair protein Ku K10979 ku; DNA end-binding protein Ku
E VAPA_1c17500 putative DNA ligase D K01971 ligD; bifunctional non-homologous end joining protein LigD [EC:6.5.1.1]
E VAPA_1c05790 ligD; putative DNA polymerase LigD K01971 ligD; bifunctional non-homologous end joining protein LigD [EC:6.5.1.1]
D SHIIR (short-homology-independent illegitimate recombination)
E Facilitator
F VAPA_1c17150 gyrA; DNA gyrase, subunit A GyrA K02469 gyrA; DNA gyrase subunit A [EC:5.6.2.2]
F VAPA_1c00030 gyrB; DNA gyrase, subunit B GyrB K02470 gyrB; DNA gyrase subunit B [EC:5.6.2.2]
F VAPA_1c13920 putative DNA topoisomerase 1B K03168 topA; DNA topoisomerase I [EC:5.6.2.1]
E Supressor
F VAPA_1c07670 putative DNA-binding protein K03530 hupB; DNA-binding protein HU-beta
F VAPA_1c18740 putative DNA-binding protein HU-beta K03530 hupB; DNA-binding protein HU-beta
F VAPA_1c44260 DNA-binding protein K03530 hupB; DNA-binding protein HU-beta
D SHDIR (short-homology-dependent illegitimate recombination)
E RecET pathway
F VAPA_1c09360 putative hydrolase K07455 recT; recombination protein RecT
F VAPA_1c12680 single-stranded-DNA-specific exonuclease K07462 recJ; single-stranded-DNA-specific exonuclease [EC:3.1.-.-]
F VAPA_1c14970 recO; DNA repair protein recO K03584 recO; DNA repair protein RecO (recombination protein O)
F VAPA_1c24710 recR; recombination protein RecR K06187 recR; recombination protein RecR
F VAPA_1c26020 ligA; DNA ligase LigA K01972 E6.5.1.2; DNA ligase (NAD+) [EC:6.5.1.2]
E Facilitator
F VAPA_1c47740 transcriptional regulator, Fis family K03557 fis; Fis family transcriptional regulator, factor for inversion stimulation protein
F VAPA_1c19710 ihfA; integration host factor, subunit alpha K04764 ihfA; integration host factor subunit alpha
F VAPA_1c17080 putative integration host factor, subunit beta K05788 ihfB; integration host factor subunit beta
E Supressor
F VAPA_1c28990 exodeoxyribonuclease 1 K01141 sbcB; exodeoxyribonuclease I [EC:3.1.11.1]
F VAPA_1c01860 recQ; ATP-dependent DNA helicase RecQ K03654 recQ; ATP-dependent DNA helicase RecQ [EC:5.6.2.4]
F VAPA_1c47280 putative ATP-dependent DNA helicase, RecQ family K03654 recQ; ATP-dependent DNA helicase RecQ [EC:5.6.2.4]
F VAPA_1c04560 uvrA1; UvrABC system protein A UvrA K03701 uvrA; excinuclease ABC subunit A
F VAPA_1c48560 uvrA2; UvrABC system protein A K03701 uvrA; excinuclease ABC subunit A
F VAPA_1c23100 uvrB; uvrABC system protein B UvrB K03702 uvrB; excinuclease ABC subunit B
F VAPA_1c18820 putative histone-like nucleoid-structuring protein H-NS K03746 hns; DNA-binding protein H-NS
B TLS (translesion DNA synthesis) factors
C Y-family DNA polymerases
D VAPA_1c13950 putative DNA polymerase IV K02346 dinB; DNA polymerase IV [EC:2.7.7.7]
C Other SOS response factors
D VAPA_1c54030 recA; protein RecA K03553 recA; recombination protein RecA
D VAPA_1c29160 lexA; repressor LexA K01356 lexA; repressor LexA [EC:3.4.21.88]
D VAPA_1c45060 recN; DNA repair protein RecN K03631 recN; DNA repair protein RecN (Recombination protein N)
D VAPA_2c10720 polB; DNA polymerase II K02336 polB; DNA polymerase II [EC:2.7.7.7]
D VAPA_1c33060 hypothetical protein K14160 imuA; protein ImuA
D VAPA_1c33050 hypothetical protein K14161 imuB; protein ImuB
D VAPA_1c33040 dnaE2; error-prone DNA polymerase DnaE K14162 dnaE2; error-prone DNA polymerase [EC:2.7.7.7]
D VAPA_1c04570 ssb; single-stranded DNA-binding protein Ssb K03111 ssb; single-strand DNA-binding protein
D VAPA_1c54020 recX; regulatory protein RecX K03565 recX; regulatory protein
B Other factors with a suspected DNA repair function
C DNA polymerase
D VAPA_2c04110 polX; putative DNA polymerase/3'-5' exonuclease PolX K02347 polX; DNA polymerase (family X)
C DNA helicases
D VAPA_1c07770 rep; ATP-dependent DNA helicase Rep K03656 rep; ATP-dependent DNA helicase Rep [EC:5.6.2.4]
D VAPA_1c23580 putative ATP-dependent helicase K03722 dinG; ATP-dependent DNA helicase DinG [EC:5.6.2.3]
D VAPA_1c50330 putative helicase K03724 lhr; ATP-dependent helicase Lhr and Lhr-like helicase [EC:5.6.2.6 5.6.2.4]
C Modulation of nucleotide pools
D VAPA_1c43870 putative hydrolase, NUDIX family K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D VAPA_2c00560 NUDIX domain-containing protein K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D VAPA_2c08300 putative hydrolase, NUDIX family K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D VAPA_1c35470 dut; deoxyuridine 5'-triphosphate nucleotidohydrolase Dut K01520 dut; dUTP diphosphatase [EC:3.6.1.23]
D VAPA_2c04470 putative ribonucleotide reductase K00525 E1.17.4.1A; ribonucleoside-diphosphate reductase alpha chain [EC:1.17.4.1]
D VAPA_1c10080 nrdA; ribonucleoside-diphosphate reductase, subunit alpha NrdA K00525 E1.17.4.1A; ribonucleoside-diphosphate reductase alpha chain [EC:1.17.4.1]
D VAPA_1c10070 nrdB; ribonucleoside-diphosphate reductase, subunit beta NrdB K00526 E1.17.4.1B; ribonucleoside-diphosphate reductase beta chain [EC:1.17.4.1]
C Others
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#[ BRITE | KEGG2 | KEGG ]
#Last updated: March 29, 2024