+F Repair protein KO
#
DNA Repair and Recombination Proteins - Paraburkholderia phymatum
%
!
AEukaryotic type
B SSBR (single strand breaks repair)
C Direct repair
D Bphy_4268 methylated-DNA--protein-cysteine methyltransferase K00567 ogt; methylated-DNA-[protein]-cysteine S-methyltransferase [EC:2.1.1.63]
D Bphy_0522 methylated-DNA--protein-cysteine methyltransferase K00567 ogt; methylated-DNA-[protein]-cysteine S-methyltransferase [EC:2.1.1.63]
D Bphy_4409 Deoxyribodipyrimidine photo-lyase K01669 phr; deoxyribodipyrimidine photo-lyase [EC:4.1.99.3]
C BER (base exicision repair)
D DNA glycosylases
E Bphy_2703 uracil-DNA glycosylase K03648 UNG; uracil-DNA glycosylase [EC:3.2.2.27]
E Bphy_3243 DNA-3-methyladenine glycosylase K03652 MPG; DNA-3-methyladenine glycosylase [EC:3.2.2.21]
E Bphy_0320 A/G-specific adenine glycosylase K03575 mutY; A/G-specific adenine glycosylase [EC:3.2.2.31]
E Bphy_2097 endonuclease III 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 Bphy_5309 DEAD_2 domain protein 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 Bphy_2661 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Bphy_5852 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Bphy_5533 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Bphy_4759 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Bphy_6695 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Bphy_0570 deoxyuridine 5'-triphosphate nucleotidohydrolase Dut K01520 dut; dUTP diphosphatase [EC:3.6.1.23]
#
AProkaryotic type
B SSBR (single strand breaks repair)
C Direct repair
D Bphy_4268 methylated-DNA--protein-cysteine methyltransferase K00567 ogt; methylated-DNA-[protein]-cysteine S-methyltransferase [EC:2.1.1.63]
D Bphy_0522 methylated-DNA--protein-cysteine methyltransferase K00567 ogt; methylated-DNA-[protein]-cysteine S-methyltransferase [EC:2.1.1.63]
D Bphy_3088 transcriptional regulator, AraC family K10778 ada; AraC family transcriptional regulator, regulatory protein of adaptative response / methylated-DNA-[protein]-cysteine methyltransferase [EC:2.1.1.63]
D Bphy_4409 Deoxyribodipyrimidine photo-lyase K01669 phr; deoxyribodipyrimidine photo-lyase [EC:4.1.99.3]
C BER (base exicision repair)
D DNA glycosylases
E Bphy_2703 uracil-DNA glycosylase K03648 UNG; uracil-DNA glycosylase [EC:3.2.2.27]
E Bphy_5004 Uracil-DNA glycosylase superfamily K03649 mug; double-stranded uracil-DNA glycosylase [EC:3.2.2.28]
E Bphy_1363 phage SPO1 DNA polymerase-related protein K21929 udg; uracil-DNA glycosylase [EC:3.2.2.27]
E Bphy_5408 phage SPO1 DNA polymerase-related protein K21929 udg; uracil-DNA glycosylase [EC:3.2.2.27]
E Bphy_1310 phage SPO1 DNA polymerase-related protein K21929 udg; uracil-DNA glycosylase [EC:3.2.2.27]
E Bphy_3087 AlkA domain protein K01247 alkA; DNA-3-methyladenine glycosylase II [EC:3.2.2.21]
E Bphy_1389 HhH-GPD family protein K01247 alkA; DNA-3-methyladenine glycosylase II [EC:3.2.2.21]
E Bphy_3243 DNA-3-methyladenine glycosylase K03652 MPG; DNA-3-methyladenine glycosylase [EC:3.2.2.21]
E Bphy_0320 A/G-specific adenine glycosylase K03575 mutY; A/G-specific adenine glycosylase [EC:3.2.2.31]
E Bphy_2985 DNA-3-methyladenine glycosylase I K01246 tag; DNA-3-methyladenine glycosylase I [EC:3.2.2.20]
E Bphy_7198 DNA-3-methyladenine glycosylase I K01246 tag; DNA-3-methyladenine glycosylase I [EC:3.2.2.20]
E Bphy_0319 formamidopyrimidine-DNA glycosylase K10563 mutM; formamidopyrimidine-DNA glycosylase [EC:3.2.2.23 4.2.99.18]
E Bphy_2097 endonuclease III K10773 NTHL1; endonuclease III [EC:3.2.2.- 4.2.99.18]
D AP endonucleases
E Bphy_0057 exodeoxyribonuclease III Xth K01142 E3.1.11.2; exodeoxyribonuclease III [EC:3.1.11.2]
E Bphy_1478 exodeoxyribonuclease III Xth K01142 E3.1.11.2; exodeoxyribonuclease III [EC:3.1.11.2]
E Bphy_5537 exodeoxyribonuclease III Xth K01142 E3.1.11.2; exodeoxyribonuclease III [EC:3.1.11.2]
D RecJ
E Bphy_1448 single-stranded-DNA-specific exonuclease RecJ K07462 recJ; single-stranded-DNA-specific exonuclease [EC:3.1.-.-]
D DNA ligase
E Bphy_1343 DNA ligase, NAD-dependent K01972 E6.5.1.2; DNA ligase (NAD+) [EC:6.5.1.2]
D DNA polymerase I
E Bphy_4419 DNA polymerase I K02335 polA; DNA polymerase I [EC:2.7.7.7]
C NER (nucleotide excision repair)
D GGR (global genome repair) factors
E Bphy_1549 excinuclease ABC, A subunit K03701 uvrA; excinuclease ABC subunit A
E Bphy_0339 excinuclease ABC, A subunit K03701 uvrA; excinuclease ABC subunit A
E Bphy_6320 excinuclease ABC, A subunit K03701 uvrA; excinuclease ABC subunit A
E Bphy_1958 excinuclease ABC, B subunit K03702 uvrB; excinuclease ABC subunit B
E Bphy_0851 excinuclease ABC, C subunit K03703 uvrC; excinuclease ABC subunit C
E Bphy_1590 UvrD/REP helicase K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4]
E Bphy_0801 UvrD/REP helicase K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4]
E Bphy_4419 DNA polymerase I K02335 polA; DNA polymerase I [EC:2.7.7.7]
E Bphy_1343 DNA ligase, NAD-dependent 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 Bphy_2848 DNA-directed RNA polymerase, beta subunit K03043 rpoB; DNA-directed RNA polymerase subunit beta [EC:2.7.7.6]
F Bphy_2847 DNA-directed RNA polymerase, beta' subunit K03046 rpoC; DNA-directed RNA polymerase subunit beta' [EC:2.7.7.6]
F Bphy_2813 DNA-directed RNA polymerase, alpha subunit K03040 rpoA; DNA-directed RNA polymerase subunit alpha [EC:2.7.7.6]
F Bphy_0670 DNA-directed RNA polymerase, omega subunit K03060 rpoZ; DNA-directed RNA polymerase subunit omega [EC:2.7.7.6]
E TRCF (transcription-repair coupling factor)
F Bphy_0997 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 Bphy_1399 DNA mismatch repair protein MutS K03555 mutS; DNA mismatch repair protein MutS
D Molecular matchmaker
E Bphy_2485 DNA mismatch repair protein MutL K03572 mutL; DNA mismatch repair protein MutL
D Strand discrimination factor
D DNA exonucleases
E Bphy_0539 exodeoxyribonuclease VII, large subunit K03601 xseA; exodeoxyribonuclease VII large subunit [EC:3.1.11.6]
E Bphy_3950 exodeoxyribonuclease VII, small subunit K03602 xseB; exodeoxyribonuclease VII small subunit [EC:3.1.11.6]
D DNA polymerase III holoenzyme
E Bphy_2079 DNA polymerase III, alpha subunit K02337 dnaE; DNA polymerase III subunit alpha [EC:2.7.7.7]
E Bphy_0002 DNA polymerase III, beta subunit K02338 dnaN; DNA polymerase III subunit beta [EC:2.7.7.7]
E Bphy_2224 DNA polymerase III chi subunit HolC K02339 holC; DNA polymerase III subunit chi [EC:2.7.7.7]
E Bphy_2586 DNA polymerase III, delta subunit K02340 holA; DNA polymerase III subunit delta [EC:2.7.7.7]
E Bphy_1044 DNA polymerase III, delta prime subunit K02341 holB; DNA polymerase III subunit delta' [EC:2.7.7.7]
E Bphy_0677 DNA polymerase III, epsilon subunit K02342 dnaQ; DNA polymerase III subunit epsilon [EC:2.7.7.7]
E Bphy_0867 DNA polymerase III, epsilon subunit K02342 dnaQ; DNA polymerase III subunit epsilon [EC:2.7.7.7]
E Bphy_0951 DNA polymerase III, subunits gamma and tau K02343 dnaX; DNA polymerase III subunit gamma/tau [EC:2.7.7.7]
D DNA ligase
E Bphy_1343 DNA ligase, NAD-dependent K01972 E6.5.1.2; DNA ligase (NAD+) [EC:6.5.1.2]
D Other MMR factors
E Bphy_1590 UvrD/REP helicase K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4]
E Bphy_0801 UvrD/REP helicase K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4]
E Bphy_0341 single-strand binding protein K03111 ssb; single-strand DNA-binding protein
E Bphy_2141 DNA mismatch endonuclease Vsr K07458 vsr; DNA mismatch endonuclease, patch repair protein [EC:3.1.-.-]
B DSBR (double strand breaks repair)
C HR (homologous recombination)
D RecBC pathway proteins
E Bphy_1748 exodeoxyribonuclease V, beta subunit K03582 recB; exodeoxyribonuclease V beta subunit [EC:3.1.11.5]
E Bphy_1749 exodeoxyribonuclease V, gamma subunit K03583 recC; exodeoxyribonuclease V gamma subunit [EC:3.1.11.5]
E Bphy_1747 exodeoxyribonuclease V, alpha subunit K03581 recD; exodeoxyribonuclease V alpha subunit [EC:3.1.11.5]
E Bphy_0440 recA protein K03553 recA; recombination protein RecA
E Bphy_2556 Holliday junction DNA helicase RuvA K03550 ruvA; holliday junction DNA helicase RuvA
E Bphy_2557 Holliday junction DNA helicase RuvB K03551 ruvB; holliday junction DNA helicase RuvB [EC:5.6.2.4]
E Bphy_2554 crossover junction endodeoxyribonuclease RuvC K01159 ruvC; crossover junction endodeoxyribonuclease RuvC [EC:3.1.21.10]
E Bphy_3022 primosomal protein N' K04066 priA; primosomal protein N' (replication factor Y) (superfamily II helicase) [EC:5.6.2.4]
E Bphy_0912 putative primosomal replication protein N, PriB K02686 priB; primosomal replication protein N
D RecFOR pathway proteins
E Bphy_0440 recA protein K03553 recA; recombination protein RecA
E Bphy_1358 DNA repair protein RadA K04485 radA; DNA repair protein RadA/Sms
E Bphy_2523 ATP-dependent DNA helicase RecG K03655 recG; ATP-dependent DNA helicase RecG [EC:5.6.2.4]
E Bphy_1448 single-stranded-DNA-specific exonuclease RecJ K07462 recJ; single-stranded-DNA-specific exonuclease [EC:3.1.-.-]
E Bphy_0843 DNA repair protein RecO K03584 recO; DNA repair protein RecO (recombination protein O)
E Bphy_0953 recombination protein RecR K06187 recR; recombination protein RecR
E Bphy_2505 DNA repair protein RecN K03631 recN; DNA repair protein RecN (Recombination protein N)
E Bphy_4738 putative exonuclease RdgC K03554 rdgC; recombination associated protein RdgC
E Bphy_2556 Holliday junction DNA helicase RuvA K03550 ruvA; holliday junction DNA helicase RuvA
E Bphy_2557 Holliday junction DNA helicase RuvB K03551 ruvB; holliday junction DNA helicase RuvB [EC:5.6.2.4]
E Bphy_2554 crossover junction endodeoxyribonuclease RuvC K01159 ruvC; crossover junction endodeoxyribonuclease RuvC [EC:3.1.21.10]
D AddAB pathway proteins
D Other HR factor
D Archaeal homologous recombinant proteins
C NHEJ (non-homologous end-joining)
D Two-component NHEJ DNA repair complex
E Bphy_0980 Ku protein K10979 ku; DNA end-binding protein Ku
E Bphy_5208 Ku protein K10979 ku; DNA end-binding protein Ku
E Bphy_4772 DNA ligase D K01971 ligD; bifunctional non-homologous end joining protein LigD [EC:6.5.1.1]
E Bphy_7582 DNA ligase D K01971 ligD; bifunctional non-homologous end joining protein LigD [EC:6.5.1.1]
E Bphy_0981 DNA ligase D K01971 ligD; bifunctional non-homologous end joining protein LigD [EC:6.5.1.1]
D SHIIR (short-homology-independent illegitimate recombination)
E Facilitator
F Bphy_0738 DNA gyrase, A subunit K02469 gyrA; DNA gyrase subunit A [EC:5.6.2.2]
F Bphy_0003 DNA gyrase, B subunit K02470 gyrB; DNA gyrase subunit B [EC:5.6.2.2]
F Bphy_5297 DNA topoisomerase K03168 topA; DNA topoisomerase I [EC:5.6.2.1]
E Supressor
F Bphy_3067 histone family protein DNA-binding protein K03530 hupB; DNA-binding protein HU-beta
F Bphy_1014 histone family protein DNA-binding protein K03530 hupB; DNA-binding protein HU-beta
F Bphy_7326 histone family protein DNA-binding protein K03530 hupB; DNA-binding protein HU-beta
F Bphy_6261 histone family protein DNA-binding protein K03530 hupB; DNA-binding protein HU-beta
F Bphy_7592 DNA-binding protein HU-alpha K03530 hupB; DNA-binding protein HU-beta
D SHDIR (short-homology-dependent illegitimate recombination)
E RecET pathway
F Bphy_7123 RecT protein K07455 recT; recombination protein RecT
F Bphy_1448 single-stranded-DNA-specific exonuclease RecJ K07462 recJ; single-stranded-DNA-specific exonuclease [EC:3.1.-.-]
F Bphy_0843 DNA repair protein RecO K03584 recO; DNA repair protein RecO (recombination protein O)
F Bphy_0953 recombination protein RecR K06187 recR; recombination protein RecR
F Bphy_1343 DNA ligase, NAD-dependent K01972 E6.5.1.2; DNA ligase (NAD+) [EC:6.5.1.2]
E Facilitator
F Bphy_2552 transcriptional regulator, Fis family K03557 fis; Fis family transcriptional regulator, factor for inversion stimulation protein
F Bphy_1552 integration host factor, alpha subunit K04764 ihfA; integration host factor subunit alpha
F Bphy_0747 integration host factor, beta subunit K05788 ihfB; integration host factor subunit beta
E Supressor
F Bphy_4797 ATP-dependent DNA helicase, RecQ family K03654 recQ; ATP-dependent DNA helicase RecQ [EC:5.6.2.4]
F Bphy_2846 ATP-dependent DNA helicase RecQ K03654 recQ; ATP-dependent DNA helicase RecQ [EC:5.6.2.4]
F Bphy_1549 excinuclease ABC, A subunit K03701 uvrA; excinuclease ABC subunit A
F Bphy_0339 excinuclease ABC, A subunit K03701 uvrA; excinuclease ABC subunit A
F Bphy_6320 excinuclease ABC, A subunit K03701 uvrA; excinuclease ABC subunit A
F Bphy_1958 excinuclease ABC, B subunit K03702 uvrB; excinuclease ABC subunit B
F Bphy_0116 histone family protein nucleoid-structuring protein H-NS K03746 hns; DNA-binding protein H-NS
F Bphy_2981 histone family protein nucleoid-structuring protein H-NS K03746 hns; DNA-binding protein H-NS
F Bphy_4285 histone family protein nucleoid-structuring protein H-NS K03746 hns; DNA-binding protein H-NS
F Bphy_2172 histone family protein nucleoid-structuring protein H-NS K03746 hns; DNA-binding protein H-NS
F Bphy_3585 histone family protein nucleoid-structuring protein H-NS K03746 hns; DNA-binding protein H-NS
F Bphy_3892 conserved hypothetical protein K03746 hns; DNA-binding protein H-NS
F Bphy_4587 histone family protein nucleoid-structuring protein H-NS K03746 hns; DNA-binding protein H-NS
F Bphy_6773 histone family protein nucleoid-structuring protein H-NS K03746 hns; DNA-binding protein H-NS
F Bphy_3930 conserved hypothetical protein K03746 hns; DNA-binding protein H-NS
F Bphy_6195 hypothetical protein K03746 hns; DNA-binding protein H-NS
B TLS (translesion DNA synthesis) factors
C Y-family DNA polymerases
D Bphy_3123 DNA-directed DNA polymerase K02346 dinB; DNA polymerase IV [EC:2.7.7.7]
C Other SOS response factors
D Bphy_0440 recA protein K03553 recA; recombination protein RecA
D Bphy_1630 transcriptional repressor, LexA family K01356 lexA; repressor LexA [EC:3.4.21.88]
D Bphy_2505 DNA repair protein RecN K03631 recN; DNA repair protein RecN (Recombination protein N)
D Bphy_3658 DNA-directed DNA polymerase K02336 polB; DNA polymerase II [EC:2.7.7.7]
D Bphy_1972 conserved hypothetical protein K14160 imuA; protein ImuA
D Bphy_7576 conserved hypothetical protein K14160 imuA; protein ImuA
D Bphy_1971 conserved hypothetical protein K14161 imuB; protein ImuB
D Bphy_1970 DNA polymerase III, alpha subunit K14162 dnaE2; error-prone DNA polymerase [EC:2.7.7.7]
D Bphy_0341 single-strand binding protein K03111 ssb; single-strand DNA-binding protein
D Bphy_0441 regulatory protein RecX K03565 recX; regulatory protein
B Other factors with a suspected DNA repair function
C DNA polymerase
C DNA helicases
D Bphy_3000 UvrD/REP helicase K03656 rep; ATP-dependent DNA helicase Rep [EC:5.6.2.4]
D Bphy_1403 helicase c2 K03722 dinG; ATP-dependent DNA helicase DinG [EC:5.6.2.3]
D Bphy_5281 DEAD/H associated domain protein K03724 lhr; ATP-dependent helicase Lhr and Lhr-like helicase [EC:5.6.2.6 5.6.2.4]
D Bphy_6751 DEAD/H associated domain protein K03724 lhr; ATP-dependent helicase Lhr and Lhr-like helicase [EC:5.6.2.6 5.6.2.4]
D Bphy_1167 DEAD/DEAH box helicase domain protein 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 Bphy_2661 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Bphy_5852 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Bphy_5533 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Bphy_4759 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Bphy_6695 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Bphy_0570 deoxyuridine 5'-triphosphate nucleotidohydrolase Dut K01520 dut; dUTP diphosphatase [EC:3.6.1.23]
D Bphy_3305 ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent K00525 E1.17.4.1A; ribonucleoside-diphosphate reductase alpha chain [EC:1.17.4.1]
D Bphy_2639 ribonucleoside-diphosphate reductase, alpha subunit K00525 E1.17.4.1A; ribonucleoside-diphosphate reductase alpha chain [EC:1.17.4.1]
D Bphy_2638 Ribonucleoside-diphosphate reductase 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: August 19, 2024