+F	Repair protein	KO
#<h2><a href="/kegg/brite.html"><img src="/Fig/bget/kegg3.gif" align="middle" border=0></a>&nbsp; DNA Repair and Recombination Proteins - Subtercola endophyticus</h2>
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A<b>Eukaryotic type</b>
B  SSBR (single strand breaks repair)
C    Direct repair
D      LQ955_04600 methylated-DNA--[protein]-cysteine S-methyltransferase	K00567 ogt; methylated-DNA-[protein]-cysteine S-methyltransferase [EC:2.1.1.63] 
D      LQ955_17885 methylated-DNA--[protein]-cysteine S-methyltransferase	K00567 ogt; methylated-DNA-[protein]-cysteine S-methyltransferase [EC:2.1.1.63] 
D      LQ955_13635 DNA photolyase family protein	K01669 phr; deoxyribodipyrimidine photo-lyase [EC:4.1.99.3] 
C    BER (base exicision repair)
D      DNA glycosylases
E        LQ955_04370 uracil-DNA glycosylase	K03648 UNG; uracil-DNA glycosylase [EC:3.2.2.27] 
E        LQ955_08195 DNA-3-methyladenine glycosylase	K03652 MPG; DNA-3-methyladenine glycosylase [EC:3.2.2.21] 
E        LQ955_04785 A/G-specific adenine glycosylase	K03575 mutY; A/G-specific adenine glycosylase [EC:3.2.2.31] 
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        LQ955_02045 DEAD/DEAH box helicase	K10843 ERCC3; DNA excision repair protein ERCC-3 [EC:5.6.2.4] 
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      LQ955_04210 NUDIX hydrolase	K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55] 
D      LQ955_11060 (deoxy)nucleoside triphosphate pyrophosphohydrolase	K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55] 
D      LQ955_11125 (deoxy)nucleoside triphosphate pyrophosphohydrolase	K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55] 
D      LQ955_05580 dut; dUTP diphosphatase	K01520 dut; dUTP diphosphatase [EC:3.6.1.23] 
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A<b>Prokaryotic type</b>
B  SSBR (single strand breaks repair)
C    Direct repair
D      LQ955_04600 methylated-DNA--[protein]-cysteine S-methyltransferase	K00567 ogt; methylated-DNA-[protein]-cysteine S-methyltransferase [EC:2.1.1.63] 
D      LQ955_17885 methylated-DNA--[protein]-cysteine S-methyltransferase	K00567 ogt; methylated-DNA-[protein]-cysteine S-methyltransferase [EC:2.1.1.63] 
D      LQ955_13635 DNA photolyase family protein	K01669 phr; deoxyribodipyrimidine photo-lyase [EC:4.1.99.3] 
D      LQ955_07335 cryptochrome/photolyase family protein	K06876 phrB; (6-4)DNA photolyase [EC:4.1.99.13] 
C    BER (base exicision repair)
D      DNA glycosylases
E        LQ955_04370 uracil-DNA glycosylase	K03648 UNG; uracil-DNA glycosylase [EC:3.2.2.27] 
E        LQ955_17905 mismatch-specific DNA-glycosylase	K03649 mug; double-stranded uracil-DNA glycosylase [EC:3.2.2.28] 
E        LQ955_06710 hypothetical protein	K01247 alkA; DNA-3-methyladenine glycosylase II [EC:3.2.2.21] 
E        LQ955_06390 helix-turn-helix domain-containing protein	K13529 ada-alkA; AraC family transcriptional regulator, regulatory protein of adaptative response / DNA-3-methyladenine glycosylase II [EC:3.2.2.21] 
E        LQ955_08195 DNA-3-methyladenine glycosylase	K03652 MPG; DNA-3-methyladenine glycosylase [EC:3.2.2.21] 
E        LQ955_04785 A/G-specific adenine glycosylase	K03575 mutY; A/G-specific adenine glycosylase [EC:3.2.2.31] 
E        LQ955_04595 DNA-3-methyladenine glycosylase I	K01246 tag; DNA-3-methyladenine glycosylase I [EC:3.2.2.20] 
E        LQ955_02525 Fpg/Nei family DNA glycosylase	K10563 mutM; formamidopyrimidine-DNA glycosylase [EC:3.2.2.23 4.2.99.18] 
E        LQ955_10060 Fpg/Nei family DNA glycosylase	K10563 mutM; formamidopyrimidine-DNA glycosylase [EC:3.2.2.23 4.2.99.18] 
E        LQ955_00310 Fpg/Nei family DNA glycosylase	K05522 nei; endonuclease VIII [EC:3.2.2.- 4.2.99.18] 
E        LQ955_09180 Fpg/Nei family DNA glycosylase	K05522 nei; endonuclease VIII [EC:3.2.2.- 4.2.99.18] 
D      AP endonucleases
E        LQ955_12135 endonuclease/exonuclease/phosphatase family protein	K01142 E3.1.11.2; exodeoxyribonuclease III [EC:3.1.11.2] 
E        LQ955_18010 exodeoxyribonuclease III	K01142 E3.1.11.2; exodeoxyribonuclease III [EC:3.1.11.2] 
D      RecJ
D      DNA ligase
E        LQ955_09610 ligA; NAD-dependent DNA ligase LigA	K01972 E6.5.1.2; DNA ligase (NAD+) [EC:6.5.1.2] 
D      DNA polymerase I
E        LQ955_06105 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        LQ955_06165 uvrA; excinuclease ABC subunit UvrA	K03701 uvrA; excinuclease ABC subunit A 
E        LQ955_06155 uvrB; excinuclease ABC subunit UvrB	K03702 uvrB; excinuclease ABC subunit B 
E        LQ955_06170 uvrC; excinuclease ABC subunit UvrC	K03703 uvrC; excinuclease ABC subunit C 
E        LQ955_00900 UvrD-helicase domain-containing protein	K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4] 
E        LQ955_03825 ATP-dependent helicase	K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4] 
E        LQ955_06105 polA; DNA polymerase I	K02335 polA; DNA polymerase I [EC:2.7.7.7] 
E        LQ955_09610 ligA; NAD-dependent 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          LQ955_00380 rpoB; DNA-directed RNA polymerase subunit beta	K03043 rpoB; DNA-directed RNA polymerase subunit beta [EC:2.7.7.6] 
F          LQ955_00385 DNA-directed RNA polymerase subunit beta'	K03046 rpoC; DNA-directed RNA polymerase subunit beta' [EC:2.7.7.6] 
F          LQ955_00645 DNA-directed RNA polymerase subunit alpha	K03040 rpoA; DNA-directed RNA polymerase subunit alpha [EC:2.7.7.6] 
F          LQ955_05980 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          LQ955_02960 mfd; 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
D      Molecular matchmaker
D      Strand discrimination factor
D      DNA exonucleases
E        LQ955_03510 xseA; exodeoxyribonuclease VII large subunit	K03601 xseA; exodeoxyribonuclease VII large subunit [EC:3.1.11.6] 
E        LQ955_03505 exodeoxyribonuclease VII small subunit	K03602 xseB; exodeoxyribonuclease VII small subunit [EC:3.1.11.6] 
D      DNA polymerase III holoenzyme
E        LQ955_06905 dnaE; DNA polymerase III subunit alpha	K02337 dnaE; DNA polymerase III subunit alpha [EC:2.7.7.7] 
E        LQ955_15330 dnaN; DNA polymerase III subunit beta	K02338 dnaN; DNA polymerase III subunit beta [EC:2.7.7.7] 
E        LQ955_08480 DNA polymerase III subunit delta	K02340 holA; DNA polymerase III subunit delta [EC:2.7.7.7] 
E        LQ955_12245 DNA polymerase III subunit delta'	K02341 holB; DNA polymerase III subunit delta' [EC:2.7.7.7] 
E        LQ955_06350 3'-5' exonuclease	K02342 dnaQ; DNA polymerase III subunit epsilon [EC:2.7.7.7] 
D      DNA ligase
E        LQ955_09610 ligA; NAD-dependent DNA ligase LigA	K01972 E6.5.1.2; DNA ligase (NAD+) [EC:6.5.1.2] 
D      Other MMR factors
E        LQ955_00900 UvrD-helicase domain-containing protein	K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4] 
E        LQ955_03825 ATP-dependent helicase	K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4] 
E        LQ955_15960 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        LQ955_08335 recA; recombinase RecA	K03553 recA; recombination protein RecA 
E        LQ955_05820 ruvA; Holliday junction branch migration protein RuvA	K03550 ruvA; holliday junction DNA helicase RuvA 
E        LQ955_05825 ruvB; Holliday junction branch migration DNA helicase RuvB	K03551 ruvB; holliday junction DNA helicase RuvB [EC:5.6.2.4] 
E        LQ955_05815 ruvC; crossover junction endodeoxyribonuclease RuvC	K01159 ruvC; crossover junction endodeoxyribonuclease RuvC [EC:3.1.21.10] 
D      RecFOR pathway proteins
E        LQ955_08335 recA; recombinase RecA	K03553 recA; recombination protein RecA 
E        LQ955_15340 recF; DNA replication/repair protein RecF	K03629 recF; DNA replication and repair protein RecF 
E        LQ955_10165 ATP-dependent DNA helicase RecG	K03655 recG; ATP-dependent DNA helicase RecG [EC:5.6.2.4] 
E        LQ955_12745 recR; recombination mediator RecR	K06187 recR; recombination protein RecR 
E        LQ955_08140 DNA repair protein RecN	K03631 recN; DNA repair protein RecN (Recombination protein N) 
E        LQ955_05820 ruvA; Holliday junction branch migration protein RuvA	K03550 ruvA; holliday junction DNA helicase RuvA 
E        LQ955_05825 ruvB; Holliday junction branch migration DNA helicase RuvB	K03551 ruvB; holliday junction DNA helicase RuvB [EC:5.6.2.4] 
E        LQ955_05815 ruvC; 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
E        LQ955_09625 DUF853 domain-containing 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        LQ955_03955 Ku protein	K10979 ku; DNA end-binding protein Ku 
E        LQ955_03960 ATP-dependent DNA ligase	K01971 ligD; bifunctional non-homologous end joining protein LigD [EC:6.5.1.1] 
D      SHIIR (short-homology-independent illegitimate recombination)
E        Facilitator
F          LQ955_05545 DNA topoisomerase IV subunit A	K02469 gyrA; DNA gyrase subunit A [EC:5.6.2.2] 
F          LQ955_15355 gyrA; DNA gyrase subunit A	K02469 gyrA; DNA gyrase subunit A [EC:5.6.2.2] 
F          LQ955_05535 type IIA DNA topoisomerase subunit B	K02470 gyrB; DNA gyrase subunit B [EC:5.6.2.2] 
F          LQ955_15350 gyrB; DNA topoisomerase (ATP-hydrolyzing) subunit B	K02470 gyrB; DNA gyrase subunit B [EC:5.6.2.2] 
F          LQ955_00440 DNA topoisomerase IB	K03168 topA; DNA topoisomerase I [EC:5.6.2.1] 
F          LQ955_12255 topA; type I DNA topoisomerase	K03168 topA; DNA topoisomerase I [EC:5.6.2.1] 
E        Supressor
F          LQ955_16070 HU family DNA-binding protein	K03530 hupB; DNA-binding protein HU-beta 
D      SHDIR (short-homology-dependent illegitimate recombination)
E        RecET pathway
F          LQ955_12745 recR; recombination mediator RecR	K06187 recR; recombination protein RecR 
F          LQ955_09610 ligA; NAD-dependent DNA ligase LigA	K01972 E6.5.1.2; DNA ligase (NAD+) [EC:6.5.1.2] 
E        Facilitator
E        Supressor
F          LQ955_13715 RecQ family ATP-dependent DNA helicase	K03654 recQ; ATP-dependent DNA helicase RecQ [EC:5.6.2.4] 
F          LQ955_18590 recQ; DNA helicase RecQ	K03654 recQ; ATP-dependent DNA helicase RecQ [EC:5.6.2.4] 
F          LQ955_06165 uvrA; excinuclease ABC subunit UvrA	K03701 uvrA; excinuclease ABC subunit A 
F          LQ955_06155 uvrB; excinuclease ABC subunit UvrB	K03702 uvrB; excinuclease ABC subunit B 
B  TLS (translesion DNA synthesis) factors
C    Y-family DNA polymerases
D      LQ955_01740 dinB; DNA polymerase IV	K02346 dinB; DNA polymerase IV [EC:2.7.7.7] 
D      LQ955_09500 DNA polymerase IV	K02346 dinB; DNA polymerase IV [EC:2.7.7.7] 
C    Other SOS response factors
D      LQ955_08335 recA; recombinase RecA	K03553 recA; recombination protein RecA 
D      LQ955_08300 lexA; transcriptional repressor LexA	K01356 lexA; repressor LexA [EC:3.4.21.88] 
D      LQ955_08140 DNA repair protein RecN	K03631 recN; DNA repair protein RecN (Recombination protein N) 
D      LQ955_06110 error-prone DNA polymerase	K14162 dnaE2; error-prone DNA polymerase [EC:2.7.7.7] 
D      LQ955_15960 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      LQ955_00315 DEAD/DEAH box 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      LQ955_04210 NUDIX hydrolase	K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55] 
D      LQ955_11060 (deoxy)nucleoside triphosphate pyrophosphohydrolase	K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55] 
D      LQ955_11125 (deoxy)nucleoside triphosphate pyrophosphohydrolase	K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55] 
D      LQ955_01540 NUDIX domain-containing protein	K23258 mutT1; 8-oxo-(d)GTP phosphatase [EC:3.6.1.69] 
D      LQ955_08125 NUDIX hydrolase	K01554 K01554; 8-oxo-dGDP phosphatase [EC:3.6.1.58] 
D      LQ955_05580 dut; dUTP diphosphatase	K01520 dut; dUTP diphosphatase [EC:3.6.1.23] 
D      LQ955_12910 nrdE; class 1b ribonucleoside-diphosphate reductase subunit alpha	K00525 E1.17.4.1A; ribonucleoside-diphosphate reductase alpha chain [EC:1.17.4.1] 
D      LQ955_12905 nrdF; class 1b ribonucleoside-diphosphate reductase subunit beta	K00526 E1.17.4.1B; ribonucleoside-diphosphate reductase beta chain [EC:1.17.4.1] 
C    Others
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#Last updated: March 29, 2024