+F Repair protein KO
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DNA Repair and Recombination Proteins - Ruegeria sp. TM1040
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AEukaryotic type
B SSBR (single strand breaks repair)
C Direct repair
D TM1040_1441 phrB; Deoxyribodipyrimidine photo-lyase type I K01669 phr; deoxyribodipyrimidine photo-lyase [EC:4.1.99.3]
D TM1040_3370 Deoxyribodipyrimidine photo-lyase family protein K01669 phr; deoxyribodipyrimidine photo-lyase [EC:4.1.99.3]
C BER (base exicision repair)
D DNA glycosylases
E TM1040_1139 Uracil-DNA glycosylase K03648 UNG; uracil-DNA glycosylase [EC:3.2.2.27]
E TM1040_2645 A/G-specific DNA-adenine glycosylase K03575 mutY; A/G-specific adenine glycosylase [EC:3.2.2.31]
E TM1040_2451 DNA-(apurinic or apyrimidinic site) lyase / 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 TM1040_2914 mutator mutT protein K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D TM1040_2888 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D TM1040_0128 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D TM1040_3067 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D TM1040_0461 deoxyuridine 5'-triphosphate nucleotidohydrolase 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 TM1040_2450 transcriptional regulator, AraC family / DNA-O6-methylguanine--protein-cysteine S-methyltransferase / Transcriptional regulator Ada K10778 ada; AraC family transcriptional regulator, regulatory protein of adaptative response / methylated-DNA-[protein]-cysteine methyltransferase [EC:2.1.1.63]
D TM1040_2682 DNA-O6-methylguanine--protein-cysteine S-methyltransferase / Transcriptional regulator Ada K10778 ada; AraC family transcriptional regulator, regulatory protein of adaptative response / methylated-DNA-[protein]-cysteine methyltransferase [EC:2.1.1.63]
D TM1040_1441 phrB; Deoxyribodipyrimidine photo-lyase type I K01669 phr; deoxyribodipyrimidine photo-lyase [EC:4.1.99.3]
D TM1040_3370 Deoxyribodipyrimidine photo-lyase family protein K01669 phr; deoxyribodipyrimidine photo-lyase [EC:4.1.99.3]
D TM1040_2281 deoxyribodipyrimidine photolyase-related protein K06876 phrB; (6-4)DNA photolyase [EC:4.1.99.13]
D TM1040_0011 DNA-N1-methyladenine dioxygenase K03919 alkB; DNA oxidative demethylase [EC:1.14.11.33]
C BER (base exicision repair)
D DNA glycosylases
E TM1040_1139 Uracil-DNA glycosylase K03648 UNG; uracil-DNA glycosylase [EC:3.2.2.27]
E TM1040_3061 phage SPO1 DNA polymerase-related protein K21929 udg; uracil-DNA glycosylase [EC:3.2.2.27]
E TM1040_1157 HhH-GPD K01247 alkA; DNA-3-methyladenine glycosylase II [EC:3.2.2.21]
E TM1040_2645 A/G-specific DNA-adenine glycosylase K03575 mutY; A/G-specific adenine glycosylase [EC:3.2.2.31]
E TM1040_1922 DNA-3-methyladenine glycosylase I K01246 tag; DNA-3-methyladenine glycosylase I [EC:3.2.2.20]
E TM1040_3029 mutM; Formamidopyrimidine-DNA glycosylase / DNA-(apurinic or apyrimidinic site) lyase K10563 mutM; formamidopyrimidine-DNA glycosylase [EC:3.2.2.23 4.2.99.18]
E TM1040_2451 DNA-(apurinic or apyrimidinic site) lyase / endonuclease III K10773 NTHL1; endonuclease III [EC:3.2.2.- 4.2.99.18]
D AP endonucleases
E TM1040_0897 xth; Exodeoxyribonuclease III K01142 E3.1.11.2; exodeoxyribonuclease III [EC:3.1.11.2]
E TM1040_0053 exodeoxyribonuclease III K01142 E3.1.11.2; exodeoxyribonuclease III [EC:3.1.11.2]
D RecJ
E TM1040_2166 single-stranded-DNA-specific exonuclease RecJ K07462 recJ; single-stranded-DNA-specific exonuclease [EC:3.1.-.-]
D DNA ligase
E TM1040_1398 DNA ligase NAD-dependent K01972 E6.5.1.2; DNA ligase (NAD+) [EC:6.5.1.2]
D DNA polymerase I
E TM1040_2764 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 TM1040_1098 Excinuclease ABC subunit A K03701 uvrA; excinuclease ABC subunit A
E TM1040_0144 Excinuclease ABC subunit B K03702 uvrB; excinuclease ABC subunit B
E TM1040_2520 Excinuclease ABC subunit C K03703 uvrC; excinuclease ABC subunit C
E TM1040_2024 ATP-dependent DNA helicase, Rep family K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4]
E TM1040_2764 DNA polymerase I K02335 polA; DNA polymerase I [EC:2.7.7.7]
E TM1040_1398 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 TM1040_0234 DNA-directed RNA polymerase beta subunit K03043 rpoB; DNA-directed RNA polymerase subunit beta [EC:2.7.7.6]
F TM1040_0235 DNA-directed RNA polymerase subunit beta-prime K03046 rpoC; DNA-directed RNA polymerase subunit beta' [EC:2.7.7.6]
F TM1040_0279 DNA-directed RNA polymerase alpha subunit K03040 rpoA; DNA-directed RNA polymerase subunit alpha [EC:2.7.7.6]
F TM1040_2566 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 TM1040_1349 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 TM1040_2875 DNA mismatch repair protein MutS K03555 mutS; DNA mismatch repair protein MutS
D Molecular matchmaker
E TM1040_0102 DNA mismatch repair protein MutL K03572 mutL; DNA mismatch repair protein MutL
D Strand discrimination factor
D DNA exonucleases
E TM1040_1945 Exodeoxyribonuclease VII large subunit K03601 xseA; exodeoxyribonuclease VII large subunit [EC:3.1.11.6]
E TM1040_2922 Exodeoxyribonuclease VII small subunit K03602 xseB; exodeoxyribonuclease VII small subunit [EC:3.1.11.6]
D DNA polymerase III holoenzyme
E TM1040_0500 DNA polymerase III alpha subunit K02337 dnaE; DNA polymerase III subunit alpha [EC:2.7.7.7]
E TM1040_0002 DNA polymerase III, beta subunit K02338 dnaN; DNA polymerase III subunit beta [EC:2.7.7.7]
E TM1040_0951 DNA polymerase III chi subunit HolC K02339 holC; DNA polymerase III subunit chi [EC:2.7.7.7]
E TM1040_0043 DNA polymerase III, delta subunit K02340 holA; DNA polymerase III subunit delta [EC:2.7.7.7]
E TM1040_3592 DNA polymerase III, delta prime subunit K02341 holB; DNA polymerase III subunit delta' [EC:2.7.7.7]
E TM1040_3669 DNA polymerase III epsilon subunit K02342 dnaQ; DNA polymerase III subunit epsilon [EC:2.7.7.7]
E TM1040_2858 DNA polymerase III epsilon subunit K02342 dnaQ; DNA polymerase III subunit epsilon [EC:2.7.7.7]
E TM1040_0166 DNA polymerase III subunits gamma and tau K02343 dnaX; DNA polymerase III subunit gamma/tau [EC:2.7.7.7]
D DNA ligase
E TM1040_1398 DNA ligase NAD-dependent K01972 E6.5.1.2; DNA ligase (NAD+) [EC:6.5.1.2]
D Other MMR factors
E TM1040_2024 ATP-dependent DNA helicase, Rep family K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4]
E TM1040_1425 single-strand binding protein K03111 ssb; single-strand DNA-binding protein
E TM1040_1676 ssb; Single-strand binding protein K03111 ssb; single-strand DNA-binding protein
E TM1040_0796 ssb; Single-strand binding protein K03111 ssb; single-strand DNA-binding protein
E TM1040_1587 DNA adenine methylase Dam K06223 dam; DNA adenine methylase [EC:2.1.1.72]
B DSBR (double strand breaks repair)
C HR (homologous recombination)
D RecBC pathway proteins
E TM1040_1230 recA protein K03553 recA; recombination protein RecA
E TM1040_2372 Holliday junction DNA helicase RuvA K03550 ruvA; holliday junction DNA helicase RuvA
E TM1040_2371 Holliday junction DNA helicase RuvB K03551 ruvB; holliday junction DNA helicase RuvB [EC:5.6.2.4]
E TM1040_2373 crossover junction endodeoxyribonuclease RuvC K01159 ruvC; crossover junction endodeoxyribonuclease RuvC [EC:3.1.21.10]
E TM1040_0793 Hypothetical protein PD1345 K01160 rusA; crossover junction endodeoxyribonuclease RusA [EC:3.1.21.10]
E TM1040_1678 Hypothetical protein PD1345 K01160 rusA; crossover junction endodeoxyribonuclease RusA [EC:3.1.21.10]
E TM1040_2378 primosomal protein N' K04066 priA; primosomal protein N' (replication factor Y) (superfamily II helicase) [EC:5.6.2.4]
D RecFOR pathway proteins
E TM1040_1230 recA protein K03553 recA; recombination protein RecA
E TM1040_1784 DNA repair protein RadA K04485 radA; DNA repair protein RadA/Sms
E TM1040_0003 DNA replication and repair protein RecF K03629 recF; DNA replication and repair protein RecF
E TM1040_1397 DEAD/DEAH box helicase-like protein K03655 recG; ATP-dependent DNA helicase RecG [EC:5.6.2.4]
E TM1040_2166 single-stranded-DNA-specific exonuclease RecJ K07462 recJ; single-stranded-DNA-specific exonuclease [EC:3.1.-.-]
E TM1040_2556 DNA repair protein RecO K03584 recO; DNA repair protein RecO (recombination protein O)
E TM1040_0164 recombination protein RecR K06187 recR; recombination protein RecR
E TM1040_0692 DNA repair protein RecN K03631 recN; DNA repair protein RecN (Recombination protein N)
E TM1040_2372 Holliday junction DNA helicase RuvA K03550 ruvA; holliday junction DNA helicase RuvA
E TM1040_2371 Holliday junction DNA helicase RuvB K03551 ruvB; holliday junction DNA helicase RuvB [EC:5.6.2.4]
E TM1040_2373 crossover junction endodeoxyribonuclease RuvC K01159 ruvC; crossover junction endodeoxyribonuclease RuvC [EC:3.1.21.10]
D AddAB pathway proteins
E TM1040_2846 uvrD; ATP-dependent nuclease subunit A K16898 addA; ATP-dependent helicase/nuclease subunit A [EC:5.6.2.4 3.1.-.-]
D Other HR factor
D Archaeal homologous recombinant proteins
E TM1040_1223 protein of unknown function DUF853 NPT hydrolase putative 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
D SHIIR (short-homology-independent illegitimate recombination)
E Facilitator
F TM1040_1332 DNA gyrase A subunit K02469 gyrA; DNA gyrase subunit A [EC:5.6.2.2]
F TM1040_0007 DNA gyrase subunit B K02470 gyrB; DNA gyrase subunit B [EC:5.6.2.2]
F TM1040_2339 DNA topoisomerase I K03168 topA; DNA topoisomerase I [EC:5.6.2.1]
E Supressor
F TM1040_2801 histone-like DNA-binding protein K03530 hupB; DNA-binding protein HU-beta
D SHDIR (short-homology-dependent illegitimate recombination)
E RecET pathway
F TM1040_2166 single-stranded-DNA-specific exonuclease RecJ K07462 recJ; single-stranded-DNA-specific exonuclease [EC:3.1.-.-]
F TM1040_2556 DNA repair protein RecO K03584 recO; DNA repair protein RecO (recombination protein O)
F TM1040_0164 recombination protein RecR K06187 recR; recombination protein RecR
F TM1040_1398 DNA ligase NAD-dependent K01972 E6.5.1.2; DNA ligase (NAD+) [EC:6.5.1.2]
E Facilitator
F TM1040_0913 integration host factor alpha subunit K04764 ihfA; integration host factor subunit alpha
F TM1040_0202 integration host factor beta subunit K05788 ihfB; integration host factor subunit beta
E Supressor
F TM1040_2659 ATP-dependent DNA helicase RecQ K03654 recQ; ATP-dependent DNA helicase RecQ [EC:5.6.2.4]
F TM1040_1098 Excinuclease ABC subunit A K03701 uvrA; excinuclease ABC subunit A
F TM1040_0144 Excinuclease ABC subunit B K03702 uvrB; excinuclease ABC subunit B
F TM1040_3107 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 TM1040_0127 DNA polymerase IV; putative K02346 dinB; DNA polymerase IV [EC:2.7.7.7]
C Other SOS response factors
D TM1040_1230 recA protein K03553 recA; recombination protein RecA
D TM1040_1135 SOS-response transcriptional repressor, LexA K01356 lexA; repressor LexA [EC:3.4.21.88]
D TM1040_0692 DNA repair protein RecN K03631 recN; DNA repair protein RecN (Recombination protein N)
D TM1040_0177 hypothetical protein K14160 imuA; protein ImuA
D TM1040_0176 hypothetical protein K14161 imuB; protein ImuB
D TM1040_0175 DNA polymerase III alpha subunit K14162 dnaE2; error-prone DNA polymerase [EC:2.7.7.7]
D TM1040_1425 single-strand binding protein K03111 ssb; single-strand DNA-binding protein
D TM1040_1676 ssb; Single-strand binding protein K03111 ssb; single-strand DNA-binding protein
D TM1040_0796 ssb; Single-strand binding protein K03111 ssb; single-strand DNA-binding protein
B Other factors with a suspected DNA repair function
C DNA polymerase
C DNA helicases
C Modulation of nucleotide pools
D TM1040_2914 mutator mutT protein K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D TM1040_2888 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D TM1040_0128 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D TM1040_3067 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D TM1040_0461 deoxyuridine 5'-triphosphate nucleotidohydrolase K01520 dut; dUTP diphosphatase [EC:3.6.1.23]
D TM1040_1151 ribonucleoside-diphosphate reductase class II K00525 E1.17.4.1A; ribonucleoside-diphosphate reductase alpha chain [EC:1.17.4.1]
D TM1040_0519 ribonucleoside-diphosphate reductase class Ib alpha subunit K00525 E1.17.4.1A; ribonucleoside-diphosphate reductase alpha chain [EC:1.17.4.1]
D TM1040_0518 ribonucleoside-diphosphate reductase class Ib beta subunit 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