+F Repair protein KO
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DNA Repair and Recombination Proteins - Sinorhizobium fredii USDA 257
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AEukaryotic type
B SSBR (single strand breaks repair)
C Direct repair
D USDA257_c30080 methylated-DNA-[protein]-cysteine S-methyltransferase protein K00567 ogt; methylated-DNA-[protein]-cysteine S-methyltransferase [EC:2.1.1.63]
C BER (base exicision repair)
D DNA glycosylases
E USDA257_c53990 ung; uracil-DNA glycosylase Ung K03648 UNG; uracil-DNA glycosylase [EC:3.2.2.27]
E USDA257_c30370 putative 3-methyladenine DNA glycosylase K03652 MPG; DNA-3-methyladenine glycosylase [EC:3.2.2.21]
E USDA257_c06540 mutY; A/G-specific adenine glycosylase MutY K03575 mutY; A/G-specific adenine glycosylase [EC:3.2.2.31]
E USDA257_c59920 nth; 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
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 USDA257_c50320 mutT; putative mutator protein MutT K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D USDA257_c08310 ADP-ribose pyrophosphatase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D USDA257_c61980 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 USDA257_c30080 methylated-DNA-[protein]-cysteine S-methyltransferase protein K00567 ogt; methylated-DNA-[protein]-cysteine S-methyltransferase [EC:2.1.1.63]
D USDA257_c00720 ada1; bifunctional transcriptional activator/DNA repair enzyme Ada K10778 ada; AraC family transcriptional regulator, regulatory protein of adaptative response / methylated-DNA-[protein]-cysteine methyltransferase [EC:2.1.1.63]
D USDA257_c59900 ada2; regulatory protein Ada K10778 ada; AraC family transcriptional regulator, regulatory protein of adaptative response / methylated-DNA-[protein]-cysteine methyltransferase [EC:2.1.1.63]
D USDA257_c59110 alkB; alpha-ketoglutarate-dependent dioxygenase AlkB K03919 alkB; DNA oxidative demethylase [EC:1.14.11.33]
C BER (base exicision repair)
D DNA glycosylases
E USDA257_c53990 ung; uracil-DNA glycosylase Ung K03648 UNG; uracil-DNA glycosylase [EC:3.2.2.27]
E USDA257_c07640 DNA polymerase K21929 udg; uracil-DNA glycosylase [EC:3.2.2.27]
E USDA257_c30450 putative DNA-directed DNA polymerase protein K21929 udg; uracil-DNA glycosylase [EC:3.2.2.27]
E USDA257_c50450 DNA-3-methyladenine glycosidase K01247 alkA; DNA-3-methyladenine glycosylase II [EC:3.2.2.21]
E USDA257_c30370 putative 3-methyladenine DNA glycosylase K03652 MPG; DNA-3-methyladenine glycosylase [EC:3.2.2.21]
E USDA257_c06540 mutY; A/G-specific adenine glycosylase MutY K03575 mutY; A/G-specific adenine glycosylase [EC:3.2.2.31]
E USDA257_c04960 guaA1; putative GMP synthase K01246 tag; DNA-3-methyladenine glycosylase I [EC:3.2.2.20]
E USDA257_c62200 mutM; formamidopyrimidine-DNA glycosylase MutM K10563 mutM; formamidopyrimidine-DNA glycosylase [EC:3.2.2.23 4.2.99.18]
E USDA257_c59920 nth; endonuclease III K10773 NTHL1; endonuclease III [EC:3.2.2.- 4.2.99.18]
D AP endonucleases
E USDA257_c15200 xthA1; exodeoxyribonuclease III K01142 E3.1.11.2; exodeoxyribonuclease III [EC:3.1.11.2]
E USDA257_c35580 xthA2; exodeoxyribonuclease III K01142 E3.1.11.2; exodeoxyribonuclease III [EC:3.1.11.2]
E USDA257_c57810 xthA3; exodeoxyribonuclease III K01142 E3.1.11.2; exodeoxyribonuclease III [EC:3.1.11.2]
D RecJ
E USDA257_c35970 recJ; single-stranded-DNA-specific exonuclease RecJ K07462 recJ; single-stranded-DNA-specific exonuclease [EC:3.1.-.-]
D DNA ligase
E USDA257_c44900 ligA; DNA ligase LigA K01972 E6.5.1.2; DNA ligase (NAD+) [EC:6.5.1.2]
D DNA polymerase I
E USDA257_c60150 polA; 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 USDA257_c39890 uvrA; UvrABC system protein A K03701 uvrA; excinuclease ABC subunit A
E USDA257_c41710 uvrB; UvrABC system protein B K03702 uvrB; excinuclease ABC subunit B
E USDA257_c08930 uvrC; UvrABC system protein C K03703 uvrC; excinuclease ABC subunit C
E USDA257_c11300 pcrA; ATP-dependent DNA helicase PcrA K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4]
E USDA257_c44690 uvrD; putative DNA helicase II K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4]
E USDA257_c60150 polA; DNA polymerase I K02335 polA; DNA polymerase I [EC:2.7.7.7]
E USDA257_c44900 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 USDA257_c33820 rpoB; DNA-directed RNA polymerase subunit beta K03043 rpoB; DNA-directed RNA polymerase subunit beta [EC:2.7.7.6]
F USDA257_c33830 rpoC; DNA-directed RNA polymerase subunit beta' K03046 rpoC; DNA-directed RNA polymerase subunit beta' [EC:2.7.7.6]
F USDA257_c34140 rpoA; DNA-directed RNA polymerase subunit alpha K03040 rpoA; DNA-directed RNA polymerase subunit alpha [EC:2.7.7.6]
F USDA257_c07940 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 USDA257_c36860 mfd; transcription-repair-coupling factor Mfd 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 USDA257_c00320 mutS; DNA mismatch repair protein MutS K03555 mutS; DNA mismatch repair protein MutS
D Molecular matchmaker
E USDA257_c05270 mutL; DNA mismatch repair protein MutL K03572 mutL; DNA mismatch repair protein MutL
D Strand discrimination factor
D DNA exonucleases
E USDA257_c61470 xseA; exodeoxyribonuclease 7 large subunit XseA K03601 xseA; exodeoxyribonuclease VII large subunit [EC:3.1.11.6]
E USDA257_c05960 xseB; exodeoxyribonuclease 7 small subunit XseB K03602 xseB; exodeoxyribonuclease VII small subunit [EC:3.1.11.6]
D DNA polymerase III holoenzyme
E USDA257_c33230 dnaE1; DNA polymerase III subunit alpha K02337 dnaE; DNA polymerase III subunit alpha [EC:2.7.7.7]
E USDA257_c61810 dnaN; DNA polymerase III subunit beta K02338 dnaN; DNA polymerase III subunit beta [EC:2.7.7.7]
E USDA257_c08780 DNA polymerase III chi subunit HolC K02339 holC; DNA polymerase III subunit chi [EC:2.7.7.7]
E USDA257_c58510 DNA polymerase III, delta subunit protein K02340 holA; DNA polymerase III subunit delta [EC:2.7.7.7]
E USDA257_c40400 DNA polymerase III, delta prime subunit K02341 holB; DNA polymerase III subunit delta' [EC:2.7.7.7]
E USDA257_c24920 exonuclease RNase T and DNA polymerase K02342 dnaQ; DNA polymerase III subunit epsilon [EC:2.7.7.7]
E USDA257_c24350 exonuclease RNase T and DNA polymerase III K02342 dnaQ; DNA polymerase III subunit epsilon [EC:2.7.7.7]
E USDA257_c58640 dnaQ; DNA polymerase III subunit epsilon K02342 dnaQ; DNA polymerase III subunit epsilon [EC:2.7.7.7]
E USDA257_c60550 dnaX; DNA polymerase III subunit tau K02343 dnaX; DNA polymerase III subunit gamma/tau [EC:2.7.7.7]
D DNA ligase
E USDA257_c44900 ligA; DNA ligase LigA K01972 E6.5.1.2; DNA ligase (NAD+) [EC:6.5.1.2]
D Other MMR factors
E USDA257_c11300 pcrA; ATP-dependent DNA helicase PcrA K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4]
E USDA257_c44690 uvrD; putative DNA helicase II K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4]
E USDA257_c39900 ssb; single-stranded DNA-binding protein K03111 ssb; single-strand DNA-binding protein
B DSBR (double strand breaks repair)
C HR (homologous recombination)
D RecBC pathway proteins
E USDA257_c40730 recA; protein RecA K03553 recA; recombination protein RecA
E USDA257_c52130 ruvA; holliday junction ATP-dependent DNA helicase RuvA K03550 ruvA; holliday junction DNA helicase RuvA
E USDA257_c52120 ruvB; holliday junction ATP-dependent DNA helicase RuvB K03551 ruvB; holliday junction DNA helicase RuvB [EC:5.6.2.4]
E USDA257_c52140 ruvC; crossover junction endodeoxyribonuclease RuvC K01159 ruvC; crossover junction endodeoxyribonuclease RuvC [EC:3.1.21.10]
E USDA257_c55650 priA; primosomal protein N' K04066 priA; primosomal protein N' (replication factor Y) (superfamily II helicase) [EC:5.6.2.4]
D RecFOR pathway proteins
E USDA257_c40730 recA; protein RecA K03553 recA; recombination protein RecA
E USDA257_c08520 radA; DNA repair protein RadA K04485 radA; DNA repair protein RadA/Sms
E USDA257_c60010 recF; DNA replication and repair protein RecF K03629 recF; DNA replication and repair protein RecF
E USDA257_c36850 recG; ATP-dependent DNA helicase RecG K03655 recG; ATP-dependent DNA helicase RecG [EC:5.6.2.4]
E USDA257_c35970 recJ; single-stranded-DNA-specific exonuclease RecJ K07462 recJ; single-stranded-DNA-specific exonuclease [EC:3.1.-.-]
E USDA257_c08130 recO; DNA repair protein RecO K03584 recO; DNA repair protein RecO (recombination protein O)
E USDA257_c60580 recR; recombination protein RecR K06187 recR; recombination protein RecR
E USDA257_c44910 recN; DNA repair protein RecN K03631 recN; DNA repair protein RecN (Recombination protein N)
E USDA257_c52130 ruvA; holliday junction ATP-dependent DNA helicase RuvA K03550 ruvA; holliday junction DNA helicase RuvA
E USDA257_c52120 ruvB; holliday junction ATP-dependent DNA helicase RuvB K03551 ruvB; holliday junction DNA helicase RuvB [EC:5.6.2.4]
E USDA257_c52140 ruvC; crossover junction endodeoxyribonuclease RuvC K01159 ruvC; crossover junction endodeoxyribonuclease RuvC [EC:3.1.21.10]
D AddAB pathway proteins
E USDA257_c58950 addA; ATP-dependent helicase/nuclease subunit A K16898 addA; ATP-dependent helicase/nuclease subunit A [EC:5.6.2.4 3.1.-.-]
E USDA257_c58960 uncharacterized 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 USDA257_c06930 yjgR; uncharacterized protein YjgR K06915 herA; DNA double-strand break repair helicase HerA and related ATPase
E USDA257_c39860 putative ski2-type helicase K03726 helS; ATP-dependent DNA helicase [EC:5.6.2.4]
C NHEJ (non-homologous end-joining)
D Two-component NHEJ DNA repair complex
E USDA257_c16560 putative DNA repair protein K10979 ku; DNA end-binding protein Ku
E USDA257_c16590 putative DNA repair protein K10979 ku; DNA end-binding protein Ku
E USDA257_c15170 putative DNA repair protein K10979 ku; DNA end-binding protein Ku
E USDA257_c52050 putative DNA repair protein K10979 ku; DNA end-binding protein Ku
E USDA257_c28000 putative DNA ligase-like protein K01971 ligD; bifunctional non-homologous end joining protein LigD [EC:6.5.1.1]
E USDA257_c29030 putative DNA ligase-like protein K01971 ligD; bifunctional non-homologous end joining protein LigD [EC:6.5.1.1]
E USDA257_c41770 ligD; DNA polymerase LigD ligase region K01971 ligD; bifunctional non-homologous end joining protein LigD [EC:6.5.1.1]
E USDA257_c52060 ykoU3; putative ATP-dependent DNA ligase YkoU K01971 ligD; bifunctional non-homologous end joining protein LigD [EC:6.5.1.1]
E USDA257_c16580 ykoU2; putative ATP-dependent DNA ligase YkoU K01971 ligD; bifunctional non-homologous end joining protein LigD [EC:6.5.1.1]
D SHIIR (short-homology-independent illegitimate recombination)
E Facilitator
F USDA257_c39920 gyrA; DNA gyrase subunit A K02469 gyrA; DNA gyrase subunit A [EC:5.6.2.2]
F USDA257_c58710 gyrB2; DNA gyrase subunit B K02470 gyrB; DNA gyrase subunit B [EC:5.6.2.2]
F USDA257_c33360 topA; DNA topoisomerase 1 K03168 topA; DNA topoisomerase I [EC:5.6.2.1]
F USDA257_c54950 TOP1E: DNA topoisomerase 1B K03168 topA; DNA topoisomerase I [EC:5.6.2.1]
E Supressor
F USDA257_c32890 hupB; DNA-binding protein HRm K03530 hupB; DNA-binding protein HU-beta
D SHDIR (short-homology-dependent illegitimate recombination)
E RecET pathway
F USDA257_c35970 recJ; single-stranded-DNA-specific exonuclease RecJ K07462 recJ; single-stranded-DNA-specific exonuclease [EC:3.1.-.-]
F USDA257_c08130 recO; DNA repair protein RecO K03584 recO; DNA repair protein RecO (recombination protein O)
F USDA257_c60580 recR; recombination protein RecR K06187 recR; recombination protein RecR
F USDA257_c44900 ligA; DNA ligase LigA K01972 E6.5.1.2; DNA ligase (NAD+) [EC:6.5.1.2]
E Facilitator
F USDA257_c09480 ihfA; integration host factor subunit alpha K04764 ihfA; integration host factor subunit alpha
F USDA257_c00230 ihfB; integration host factor subunit beta K05788 ihfB; integration host factor subunit beta
E Supressor
F USDA257_c04340 helicase-like protein K03654 recQ; ATP-dependent DNA helicase RecQ [EC:5.6.2.4]
F USDA257_c46450 recQ; ATP-dependent DNA helicase RecQ K03654 recQ; ATP-dependent DNA helicase RecQ [EC:5.6.2.4]
F USDA257_c39290 recS; putative ATP-dependent DNA helicase RecS K03654 recQ; ATP-dependent DNA helicase RecQ [EC:5.6.2.4]
F USDA257_c39890 uvrA; UvrABC system protein A K03701 uvrA; excinuclease ABC subunit A
F USDA257_c41710 uvrB; UvrABC system protein B K03702 uvrB; excinuclease ABC subunit B
B TLS (translesion DNA synthesis) factors
C Y-family DNA polymerases
D USDA257_c24380 dinB1; DNA polymerase IV K02346 dinB; DNA polymerase IV [EC:2.7.7.7]
D USDA257_c33250 dinB2; DNA polymerase IV K02346 dinB; DNA polymerase IV [EC:2.7.7.7]
D USDA257_c39250 dinB3; DNA polymerase IV K02346 dinB; DNA polymerase IV [EC:2.7.7.7]
C Other SOS response factors
D USDA257_c40730 recA; protein RecA K03553 recA; recombination protein RecA
D USDA257_c37610 lexA; LexA repressor K01356 lexA; repressor LexA [EC:3.4.21.88]
D USDA257_c44910 recN; DNA repair protein RecN K03631 recN; DNA repair protein RecN (Recombination protein N)
D USDA257_c56910 imuB; protein ImuB K14161 imuB; protein ImuB
D USDA257_c56900 dnaE2; error-prone DNA polymerase DnaE K14162 dnaE2; error-prone DNA polymerase [EC:2.7.7.7]
D USDA257_c39900 ssb; single-stranded DNA-binding protein K03111 ssb; single-strand DNA-binding protein
B Other factors with a suspected DNA repair function
C DNA polymerase
C DNA helicases
D USDA257_c01550 putative ATP-dependent 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 USDA257_c50320 mutT; putative mutator protein MutT K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D USDA257_c08310 ADP-ribose pyrophosphatase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D USDA257_c61980 dut; deoxyuridine 5'-triphosphate nucleotidohydrolase Dut K01520 dut; dUTP diphosphatase [EC:3.6.1.23]
D USDA257_c39870 nrdJ; vitamin B12-dependent ribonucleotide reductase NrdJ K00525 E1.17.4.1A; ribonucleoside-diphosphate reductase alpha chain [EC:1.17.4.1]
C Others
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#[ BRITE | KEGG2 | KEGG ]
#Last updated: March 29, 2024