+F Repair protein KO
#
DNA Repair and Recombination Proteins - Hyphomicrobium sp. MC1
%
!
AEukaryotic type
B SSBR (single strand breaks repair)
C Direct repair
D HYPMC_1296 DNA photolyase FAD-binding protein K01669 phr; deoxyribodipyrimidine photo-lyase [EC:4.1.99.3]
C BER (base exicision repair)
D DNA glycosylases
E HYPMC_0460 putative 3-methyladenine DNA glycosylase K03652 MPG; DNA-3-methyladenine glycosylase [EC:3.2.2.21]
E HYPMC_4156 mutY; A/G-specific adenine glycosylase K03575 mutY; A/G-specific adenine glycosylase [EC:3.2.2.31]
E HYPMC_4674 nth; endonuclease III; DNA glycosylase/apyrimidinic lyase 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 HYPMC_4430 nudG; NUDIX hydrolase (nudG), putative dihydroneopterin triphosphate pyrophosphatase (ntpA-like) K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D HYPMC_4747 dut; Deoxyuridine 5'-triphosphate nucleotidohydrolase K01520 dut; dUTP diphosphatase [EC:3.6.1.23]
#
AProkaryotic type
B SSBR (single strand breaks repair)
C Direct repair
D HYPMC_3803 ada; fused DNA-binding transcriptional dual regulator; O6-methylguanine-DNA methyltransferase K10778 ada; AraC family transcriptional regulator, regulatory protein of adaptative response / methylated-DNA-[protein]-cysteine methyltransferase [EC:2.1.1.63]
D HYPMC_1296 DNA photolyase FAD-binding protein K01669 phr; deoxyribodipyrimidine photo-lyase [EC:4.1.99.3]
C BER (base exicision repair)
D DNA glycosylases
E HYPMC_1169 Uracil-DNA glycosylase superfamily K21929 udg; uracil-DNA glycosylase [EC:3.2.2.27]
E HYPMC_2455 Uracil-DNA glycosylase superfamily protein (DNA replication, recombination and repair) (fragment) K21929 udg; uracil-DNA glycosylase [EC:3.2.2.27]
E HYPMC_4149 putative phage DNA polymerase K21929 udg; uracil-DNA glycosylase [EC:3.2.2.27]
E HYPMC_4713 HhH-GPD family protein K01247 alkA; DNA-3-methyladenine glycosylase II [EC:3.2.2.21]
E HYPMC_0460 putative 3-methyladenine DNA glycosylase K03652 MPG; DNA-3-methyladenine glycosylase [EC:3.2.2.21]
E HYPMC_4156 mutY; A/G-specific adenine glycosylase K03575 mutY; A/G-specific adenine glycosylase [EC:3.2.2.31]
E HYPMC_2971 tag; 3-methyl-adenine DNA glycosylase I K01246 tag; DNA-3-methyladenine glycosylase I [EC:3.2.2.20]
E HYPMC_4947 mutM; Formamidopyrimidine-DNA glycosylase (Fapy-DNA glycosylase) (DNA-(apurinic or apyrimidinic site) lyase mutM) (AP lyase mutM) K10563 mutM; formamidopyrimidine-DNA glycosylase [EC:3.2.2.23 4.2.99.18]
E HYPMC_4674 nth; endonuclease III; DNA glycosylase/apyrimidinic lyase K10773 NTHL1; endonuclease III [EC:3.2.2.- 4.2.99.18]
D AP endonucleases
E HYPMC_2696 xthA; Exodeoxyribonuclease III (Exonuclease III) (EXO III) (AP endonuclease VI) K01142 E3.1.11.2; exodeoxyribonuclease III [EC:3.1.11.2]
D RecJ
E HYPMC_2497 recJ; putative single-strand DNA-specific exonuclease RecJ K07462 recJ; single-stranded-DNA-specific exonuclease [EC:3.1.-.-]
D DNA ligase
E HYPMC_0346 ligA; DNA ligase K01972 E6.5.1.2; DNA ligase (NAD+) [EC:6.5.1.2]
D DNA polymerase I
E HYPMC_3913 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 HYPMC_1339 uvrA; excinuclease ABC, subunit A K03701 uvrA; excinuclease ABC subunit A
E HYPMC_0965 uvrB; excinuclease ABC, subunit B K03702 uvrB; excinuclease ABC subunit B
E HYPMC_2989 uvrC; excinuclease ABC, subunit C K03703 uvrC; excinuclease ABC subunit C
E HYPMC_0352 uvrD; DNA-dependent ATPase I and helicase II K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4]
E HYPMC_3913 polA; DNA polymerase I K02335 polA; DNA polymerase I [EC:2.7.7.7]
E HYPMC_0346 ligA; DNA ligase 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 HYPMC_2583 rpoB; RNA polymerase, beta subunit K03043 rpoB; DNA-directed RNA polymerase subunit beta [EC:2.7.7.6]
F HYPMC_2582 rpoC; RNA polymerase, beta prime subunit K03046 rpoC; DNA-directed RNA polymerase subunit beta' [EC:2.7.7.6]
F HYPMC_2549 rpoA; DNA-directed RNA polymerase, alpha subunit K03040 rpoA; DNA-directed RNA polymerase subunit alpha [EC:2.7.7.6]
F HYPMC_1172 rpoZ; DNA-directed RNA polymerase omega chain (RNAP omega subunit) (Transcriptase omega chain) (RNA polymerase omega subunit) K03060 rpoZ; DNA-directed RNA polymerase subunit omega [EC:2.7.7.6]
E TRCF (transcription-repair coupling factor)
F HYPMC_1936 mfd; transcription repair coupling protein, ATP-dependent helicase 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 HYPMC_4786 mutS; DNA mismatch repair protein mutS K03555 mutS; DNA mismatch repair protein MutS
D Molecular matchmaker
E HYPMC_3841 mutL; DNA mismatch repair protein mutL K03572 mutL; DNA mismatch repair protein MutL
D Strand discrimination factor
D DNA exonucleases
E HYPMC_3829 xseA; putative exonuclease VII, large subunit OB-fold nucleic acid binding domain K03601 xseA; exodeoxyribonuclease VII large subunit [EC:3.1.11.6]
E HYPMC_2955 xseB; exodeoxyribonuclease VII small subunit (exonuclease VII small subunit) K03602 xseB; exodeoxyribonuclease VII small subunit [EC:3.1.11.6]
D DNA polymerase III holoenzyme
E HYPMC_2877 dnaE; DNA polymerase III, alpha subunit K02337 dnaE; DNA polymerase III subunit alpha [EC:2.7.7.7]
E HYPMC_0002 dnaN; DNA polymerase III, beta-subunit K02338 dnaN; DNA polymerase III subunit beta [EC:2.7.7.7]
E HYPMC_3178 DNA polymerase III chi subunit HolC K02339 holC; DNA polymerase III subunit chi [EC:2.7.7.7]
E HYPMC_4541 DNA polymerase III, delta subunit K02340 holA; DNA polymerase III subunit delta [EC:2.7.7.7]
E HYPMC_2030 AAA ATPase K02341 holB; DNA polymerase III subunit delta' [EC:2.7.7.7]
E HYPMC_4563 dnaQ; DNA polymerase III epsilon subunit K02342 dnaQ; DNA polymerase III subunit epsilon [EC:2.7.7.7]
E HYPMC_0633 dnaX; DNA polymerase III, tau and gamma subunits K02343 dnaX; DNA polymerase III subunit gamma/tau [EC:2.7.7.7]
D DNA ligase
E HYPMC_0346 ligA; DNA ligase K01972 E6.5.1.2; DNA ligase (NAD+) [EC:6.5.1.2]
D Other MMR factors
E HYPMC_0352 uvrD; DNA-dependent ATPase I and helicase II K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4]
E HYPMC_1346 ssb; Single-stranded DNA-binding protein K03111 ssb; single-strand DNA-binding protein
E HYPMC_2022 putative 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 HYPMC_1399 recA; recombinase A K03553 recA; recombination protein RecA
E HYPMC_1004 ruvA; Holliday junction ATP-dependent DNA helicase ruvA K03550 ruvA; holliday junction DNA helicase RuvA
E HYPMC_1006 ruvB; Holliday junction ATP-dependent DNA helicase K03551 ruvB; holliday junction DNA helicase RuvB [EC:5.6.2.4]
E HYPMC_1003 ruvC; Crossover junction endodeoxyribonuclease ruvC (Holliday junction nuclease ruvC) (Holliday juction resolvase ruvC) K01159 ruvC; crossover junction endodeoxyribonuclease RuvC [EC:3.1.21.10]
E HYPMC_4512 priA; Primosome factor N' (replication factor Y) K04066 priA; primosomal protein N' (replication factor Y) (superfamily II helicase) [EC:5.6.2.4]
E HYPMC_3349 Serine/threonine protein kinase K04067 priC; primosomal replication protein N''
D RecFOR pathway proteins
E HYPMC_1399 recA; recombinase A K03553 recA; recombination protein RecA
E HYPMC_2038 radA; DNA repair protein RadA K04485 radA; DNA repair protein RadA/Sms
E HYPMC_0005 recF; putative RecF protein K03629 recF; DNA replication and repair protein RecF
E HYPMC_1934 recG; DNA helicase, ATP-dependent resolution of Holliday junctions, branch migration K03655 recG; ATP-dependent DNA helicase RecG [EC:5.6.2.4]
E HYPMC_2497 recJ; putative single-strand DNA-specific exonuclease RecJ K07462 recJ; single-stranded-DNA-specific exonuclease [EC:3.1.-.-]
E HYPMC_1180 recO; DNA repair protein RecO K03584 recO; DNA repair protein RecO (recombination protein O)
E HYPMC_0635 recR; recombination protein recR K06187 recR; recombination protein RecR
E HYPMC_1004 ruvA; Holliday junction ATP-dependent DNA helicase ruvA K03550 ruvA; holliday junction DNA helicase RuvA
E HYPMC_1006 ruvB; Holliday junction ATP-dependent DNA helicase K03551 ruvB; holliday junction DNA helicase RuvB [EC:5.6.2.4]
E HYPMC_1003 ruvC; Crossover junction endodeoxyribonuclease ruvC (Holliday junction nuclease ruvC) (Holliday juction resolvase ruvC) K01159 ruvC; crossover junction endodeoxyribonuclease RuvC [EC:3.1.21.10]
D AddAB pathway proteins
E HYPMC_0554 Double-strand break repair helicase AddA K16898 addA; ATP-dependent helicase/nuclease subunit A [EC:5.6.2.4 3.1.-.-]
E HYPMC_0555 Double-strand break repair protein AddB 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 HYPMC_0887 putative ATPase 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 HYPMC_2435 putative DNA repair protein Hden_1068 K10979 ku; DNA end-binding protein Ku
E HYPMC_2434 DNA polymerase LigD, ligase domain protein K01971 ligD; bifunctional non-homologous end joining protein LigD [EC:6.5.1.1]
E HYPMC_2433 DNA polymerase LigD, polymerase domain protein K01971 ligD; bifunctional non-homologous end joining protein LigD [EC:6.5.1.1]
D SHIIR (short-homology-independent illegitimate recombination)
E Facilitator
F HYPMC_1352 gyrA; DNA gyrase, subunit A K02469 gyrA; DNA gyrase subunit A [EC:5.6.2.2]
F HYPMC_0006 gyrB; DNA gyrase, subunit B K02470 gyrB; DNA gyrase subunit B [EC:5.6.2.2]
F HYPMC_1126 TopA; DNA topoisomerase I K03168 topA; DNA topoisomerase I [EC:5.6.2.1]
E Supressor
F HYPMC_0038 Histone family protein DNA-binding protein K03530 hupB; DNA-binding protein HU-beta
F HYPMC_2915 hupB; DNA-binding protein HU-beta (NS1) (HU-1) K03530 hupB; DNA-binding protein HU-beta
D SHDIR (short-homology-dependent illegitimate recombination)
E RecET pathway
F HYPMC_2497 recJ; putative single-strand DNA-specific exonuclease RecJ K07462 recJ; single-stranded-DNA-specific exonuclease [EC:3.1.-.-]
F HYPMC_1180 recO; DNA repair protein RecO K03584 recO; DNA repair protein RecO (recombination protein O)
F HYPMC_0635 recR; recombination protein recR K06187 recR; recombination protein RecR
F HYPMC_0346 ligA; DNA ligase K01972 E6.5.1.2; DNA ligase (NAD+) [EC:6.5.1.2]
E Facilitator
F HYPMC_2656 ihfA; integration host factor, alpha subunit K04764 ihfA; integration host factor subunit alpha
F HYPMC_0542 ihfB; integration host factor, beta subunit K05788 ihfB; integration host factor subunit beta
E Supressor
F HYPMC_3807 recQ; ATP-dependent DNA helicase RecQ K03654 recQ; ATP-dependent DNA helicase RecQ [EC:5.6.2.4]
F HYPMC_1339 uvrA; excinuclease ABC, subunit A K03701 uvrA; excinuclease ABC subunit A
F HYPMC_0965 uvrB; excinuclease ABC, subunit B K03702 uvrB; excinuclease ABC subunit B
F HYPMC_0891 Histone family protein nucleoid-structuring protein H-NS K03746 hns; DNA-binding protein H-NS
F HYPMC_3268 Trans-acting regulatory protein hvrA (modular protein) K03746 hns; DNA-binding protein H-NS
B TLS (translesion DNA synthesis) factors
C Y-family DNA polymerases
D HYPMC_3535 dinB; DNA polymerase IV 2 K02346 dinB; DNA polymerase IV [EC:2.7.7.7]
C Other SOS response factors
D HYPMC_1399 recA; recombinase A K03553 recA; recombination protein RecA
D HYPMC_2855 lexA; SOS response transcriptional repressor, lexA K01356 lexA; repressor LexA [EC:3.4.21.88]
D HYPMC_2300 Transcriptional repressor (LexA family) K01356 lexA; repressor LexA [EC:3.4.21.88]
D HYPMC_3993 conserved protein of unknown function K14160 imuA; protein ImuA
D HYPMC_3992 conserved protein of unknown function K14161 imuB; protein ImuB
D HYPMC_3991 dnaE; DNA polymerase III, alpha subunit K14162 dnaE2; error-prone DNA polymerase [EC:2.7.7.7]
D HYPMC_1346 ssb; Single-stranded DNA-binding protein K03111 ssb; single-strand DNA-binding protein
D HYPMC_2022 putative 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 HYPMC_0814 ATP-dependent DNA 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 HYPMC_4430 nudG; NUDIX hydrolase (nudG), putative dihydroneopterin triphosphate pyrophosphatase (ntpA-like) K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D HYPMC_4747 dut; Deoxyuridine 5'-triphosphate nucleotidohydrolase K01520 dut; dUTP diphosphatase [EC:3.6.1.23]
D HYPMC_4069 Ribonucleoside-diphosphate reductase K00525 E1.17.4.1A; ribonucleoside-diphosphate reductase alpha chain [EC:1.17.4.1]
D HYPMC_2785 nrd; ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent, large subunit K00525 E1.17.4.1A; ribonucleoside-diphosphate reductase alpha chain [EC:1.17.4.1]
C Others
!
#
#[ BRITE | KEGG2 | KEGG ]
#Last updated: March 29, 2024