+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 - Polaromonas naphthalenivorans</h2>
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A<b>Eukaryotic type</b>
B  SSBR (single strand breaks repair)
C    Direct repair
D      Pnap_1100 methylated-DNA--protein-cysteine methyltransferase	K00567 ogt; methylated-DNA-[protein]-cysteine S-methyltransferase [EC:2.1.1.63] 
D      Pnap_3349 deoxyribodipyrimidine photo-lyase type I	K01669 phr; deoxyribodipyrimidine photo-lyase [EC:4.1.99.3] 
C    BER (base exicision repair)
D      DNA glycosylases
E        Pnap_3648 Uracil-DNA glycosylase	K03648 UNG; uracil-DNA glycosylase [EC:3.2.2.27] 
E        Pnap_0905 A/G-specific DNA-adenine glycosylase	K03575 mutY; A/G-specific adenine glycosylase [EC:3.2.2.31] 
E        Pnap_2079 endonuclease III / DNA-(apurinic or apyrimidinic site) 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
E        Pnap_0984 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      Pnap_0741 8-oxo-dGTPase	K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55] 
D      Pnap_3721 NUDIX hydrolase	K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55] 
D      Pnap_1188 deoxyuridine 5'-triphosphate nucleotidohydrolase	K01520 dut; dUTP diphosphatase [EC:3.6.1.23] 
#
A<b>Prokaryotic type</b>
B  SSBR (single strand breaks repair)
C    Direct repair
D      Pnap_1100 methylated-DNA--protein-cysteine methyltransferase	K00567 ogt; methylated-DNA-[protein]-cysteine S-methyltransferase [EC:2.1.1.63] 
D      Pnap_3349 deoxyribodipyrimidine photo-lyase type I	K01669 phr; deoxyribodipyrimidine photo-lyase [EC:4.1.99.3] 
D      Pnap_4097 DNA-N1-methyladenine dioxygenase	K03919 alkB; DNA oxidative demethylase [EC:1.14.11.33] 
C    BER (base exicision repair)
D      DNA glycosylases
E        Pnap_3648 Uracil-DNA glycosylase	K03648 UNG; uracil-DNA glycosylase [EC:3.2.2.27] 
E        Pnap_3844 phage SPO1 DNA polymerase-related protein	K21929 udg; uracil-DNA glycosylase [EC:3.2.2.27] 
E        Pnap_2892 HhH-GPD family protein	K01247 alkA; DNA-3-methyladenine glycosylase II [EC:3.2.2.21] 
E        Pnap_1101 DNA-3-methyladenine glycosylase II	K13529 ada-alkA; AraC family transcriptional regulator, regulatory protein of adaptative response / DNA-3-methyladenine glycosylase II [EC:3.2.2.21] 
E        Pnap_0905 A/G-specific DNA-adenine glycosylase	K03575 mutY; A/G-specific adenine glycosylase [EC:3.2.2.31] 
E        Pnap_0903 DNA-(apurinic or apyrimidinic site) lyase / Formamidopyrimidine-DNA glycosylase	K10563 mutM; formamidopyrimidine-DNA glycosylase [EC:3.2.2.23 4.2.99.18] 
E        Pnap_2079 endonuclease III / DNA-(apurinic or apyrimidinic site) lyase	K10773 NTHL1; endonuclease III [EC:3.2.2.- 4.2.99.18] 
D      AP endonucleases
E        Pnap_2776 Exodeoxyribonuclease III	K01142 E3.1.11.2; exodeoxyribonuclease III [EC:3.1.11.2] 
E        Pnap_0167 exodeoxyribonuclease III Xth	K01142 E3.1.11.2; exodeoxyribonuclease III [EC:3.1.11.2] 
D      RecJ
E        Pnap_3258 exonuclease RecJ	K07462 recJ; single-stranded-DNA-specific exonuclease [EC:3.1.-.-] 
D      DNA ligase
E        Pnap_1816 DNA ligase, NAD-dependent	K01972 E6.5.1.2; DNA ligase (NAD+) [EC:6.5.1.2] 
D      DNA polymerase I
E        Pnap_1478 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        Pnap_0488 UvrA family protein	K03701 uvrA; excinuclease ABC subunit A 
E        Pnap_3827 Excinuclease ABC subunit A	K03701 uvrA; excinuclease ABC subunit A 
E        Pnap_4737 excinuclease ABC, A subunit	K03701 uvrA; excinuclease ABC subunit A 
E        Pnap_1563 Excinuclease ABC subunit B	K03702 uvrB; excinuclease ABC subunit B 
E        Pnap_1627 Excinuclease ABC subunit C	K03703 uvrC; excinuclease ABC subunit C 
E        Pnap_1474 ATP-dependent DNA helicase UvrD	K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4] 
E        Pnap_4906 pathogenesis-related protein	K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4] 
E        Pnap_4315 UvrD/REP helicase	K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4] 
E        Pnap_0995 conserved hypothetical protein	K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4] 
E        Pnap_1478 DNA polymerase I	K02335 polA; DNA polymerase I [EC:2.7.7.7] 
E        Pnap_1816 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          Pnap_3640 DNA-directed RNA polymerase subunit beta	K03043 rpoB; DNA-directed RNA polymerase subunit beta [EC:2.7.7.6] 
F          Pnap_3639 DNA-directed RNA polymerase subunit beta'	K03046 rpoC; DNA-directed RNA polymerase subunit beta' [EC:2.7.7.6] 
F          Pnap_0345 DNA-directed RNA polymerase subunit alpha	K03040 rpoA; DNA-directed RNA polymerase subunit alpha [EC:2.7.7.6] 
F          Pnap_0810 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          Pnap_2550 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        Pnap_1359 DNA mismatch repair protein MutS	K03555 mutS; DNA mismatch repair protein MutS 
D      Molecular matchmaker
E        Pnap_1157 DNA mismatch repair protein MutL	K03572 mutL; DNA mismatch repair protein MutL 
D      Strand discrimination factor
D      DNA exonucleases
E        Pnap_1935 Exodeoxyribonuclease I subunit C	K01141 sbcB; exodeoxyribonuclease I [EC:3.1.11.1] 
E        Pnap_1926 Exodeoxyribonuclease VII large subunit	K03601 xseA; exodeoxyribonuclease VII large subunit [EC:3.1.11.6] 
E        Pnap_4878 Exodeoxyribonuclease VII large subunit	K03601 xseA; exodeoxyribonuclease VII large subunit [EC:3.1.11.6] 
E        Pnap_4879 hypothetical protein	K03602 xseB; exodeoxyribonuclease VII small subunit [EC:3.1.11.6] 
E        Pnap_1499 exodeoxyribonuclease VII, small subunit	K03602 xseB; exodeoxyribonuclease VII small subunit [EC:3.1.11.6] 
D      DNA polymerase III holoenzyme
E        Pnap_2925 DNA polymerase III, alpha subunit	K02337 dnaE; DNA polymerase III subunit alpha [EC:2.7.7.7] 
E        Pnap_4118 DNA polymerase III, beta subunit	K02338 dnaN; DNA polymerase III subunit beta [EC:2.7.7.7] 
E        Pnap_4305 DNA polymerase III beta subunit family protein	K02338 dnaN; DNA polymerase III subunit beta [EC:2.7.7.7] 
E        Pnap_2168 DNA polymerase III, chi subunit	K02339 holC; DNA polymerase III subunit chi [EC:2.7.7.7] 
E        Pnap_3769 DNA polymerase III, delta subunit	K02340 holA; DNA polymerase III subunit delta [EC:2.7.7.7] 
E        Pnap_1949 DNA-directed DNA polymerase	K02341 holB; DNA polymerase III subunit delta' [EC:2.7.7.7] 
E        Pnap_4120 DNA-directed DNA polymerase	K02342 dnaQ; DNA polymerase III subunit epsilon [EC:2.7.7.7] 
E        Pnap_0481 Exonuclease, RNase T and DNA polymerase III	K02342 dnaQ; DNA polymerase III subunit epsilon [EC:2.7.7.7] 
E        Pnap_2284 DNA polymerase III, epsilon subunit	K02342 dnaQ; DNA polymerase III subunit epsilon [EC:2.7.7.7] 
E        Pnap_1670 DNA polymerase III, subunits gamma and tau	K02343 dnaX; DNA polymerase III subunit gamma/tau [EC:2.7.7.7] 
D      DNA ligase
E        Pnap_1816 DNA ligase, NAD-dependent	K01972 E6.5.1.2; DNA ligase (NAD+) [EC:6.5.1.2] 
D      Other MMR factors
E        Pnap_1474 ATP-dependent DNA helicase UvrD	K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4] 
E        Pnap_4906 pathogenesis-related protein	K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4] 
E        Pnap_4315 UvrD/REP helicase	K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4] 
E        Pnap_0995 conserved hypothetical protein	K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4] 
E        Pnap_3819 single-strand binding protein	K03111 ssb; single-strand DNA-binding protein 
E        Pnap_4323 single-strand binding protein	K03111 ssb; single-strand DNA-binding protein 
B  DSBR (double strand breaks repair)
C    HR (homologous recombination)
D      RecBC pathway proteins
E        Pnap_3956 recA protein	K03553 recA; recombination protein RecA 
E        Pnap_0510 Holliday junction DNA helicase RuvA	K03550 ruvA; holliday junction DNA helicase RuvA 
E        Pnap_0512 Holliday junction DNA helicase RuvB	K03551 ruvB; holliday junction DNA helicase RuvB [EC:5.6.2.4] 
E        Pnap_3409 crossover junction endodeoxyribonuclease RuvC	K01159 ruvC; crossover junction endodeoxyribonuclease RuvC [EC:3.1.21.10] 
E        Pnap_0362 primosomal protein N'	K04066 priA; primosomal protein N' (replication factor Y) (superfamily II helicase) [EC:5.6.2.4] 
E        Pnap_2394 putative primosomal replication protein	K02686 priB; primosomal replication protein N 
E        Pnap_1935 Exodeoxyribonuclease I subunit C	K01141 sbcB; exodeoxyribonuclease I [EC:3.1.11.1] 
E        Pnap_4320 putative ATPase involved in DNA repair	K03546 sbcC; DNA repair protein SbcC/Rad50 
E        Pnap_1663 conserved hypothetical protein	K03546 sbcC; DNA repair protein SbcC/Rad50 
E        Pnap_4318 DNA repair exonuclease-like protein	K03547 sbcD; DNA repair protein SbcD/Mre11 
D      RecFOR pathway proteins
E        Pnap_3956 recA protein	K03553 recA; recombination protein RecA 
E        Pnap_0138 DNA replication and repair protein RadA	K04485 radA; DNA repair protein RadA/Sms 
E        Pnap_0322 ATP-dependent DNA helicase RecG	K03655 recG; ATP-dependent DNA helicase RecG [EC:5.6.2.4] 
E        Pnap_3258 exonuclease RecJ	K07462 recJ; single-stranded-DNA-specific exonuclease [EC:3.1.-.-] 
E        Pnap_3059 DNA repair protein RecO	K03584 recO; DNA repair protein RecO (recombination protein O) 
E        Pnap_1672 DNA replication and repair protein RecR	K06187 recR; recombination protein RecR 
E        Pnap_0907 DNA replication and repair protein RecN	K03631 recN; DNA repair protein RecN (Recombination protein N) 
E        Pnap_2818 putative exonuclease, RdgC	K03554 rdgC; recombination associated protein RdgC 
E        Pnap_0510 Holliday junction DNA helicase RuvA	K03550 ruvA; holliday junction DNA helicase RuvA 
E        Pnap_0512 Holliday junction DNA helicase RuvB	K03551 ruvB; holliday junction DNA helicase RuvB [EC:5.6.2.4] 
E        Pnap_3409 crossover junction endodeoxyribonuclease RuvC	K01159 ruvC; crossover junction endodeoxyribonuclease RuvC [EC:3.1.21.10] 
D      AddAB pathway proteins
E        Pnap_2193 DNA helicase/exodeoxyribonuclease V, subunit A	K16898 addA; ATP-dependent helicase/nuclease subunit A [EC:5.6.2.4 3.1.-.-] 
E        Pnap_2194 DNA helicase/exodeoxyribonuclease V, subunit B	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        Pnap_4320 putative ATPase involved in DNA repair	K03546 sbcC; DNA repair protein SbcC/Rad50 
E        Pnap_1663 conserved hypothetical protein	K03546 sbcC; DNA repair protein SbcC/Rad50 
E        Pnap_4318 DNA repair exonuclease-like protein	K03547 sbcD; DNA repair protein SbcD/Mre11 
E        Pnap_1727 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
E        Pnap_1894 Ku domain protein	K10979 ku; DNA end-binding protein Ku 
D      SHIIR (short-homology-independent illegitimate recombination)
E        Facilitator
F          Pnap_2790 DNA gyrase subunit A	K02469 gyrA; DNA gyrase subunit A [EC:5.6.2.2] 
F          Pnap_4119 DNA gyrase subunit B	K02470 gyrB; DNA gyrase subunit B [EC:5.6.2.2] 
E        Supressor
F          Pnap_1633 histone family protein DNA-binding protein	K03530 hupB; DNA-binding protein HU-beta 
D      SHDIR (short-homology-dependent illegitimate recombination)
E        RecET pathway
F          Pnap_3441 beta-lactamase domain protein	K07455 recT; recombination protein RecT 
F          Pnap_3258 exonuclease RecJ	K07462 recJ; single-stranded-DNA-specific exonuclease [EC:3.1.-.-] 
F          Pnap_3059 DNA repair protein RecO	K03584 recO; DNA repair protein RecO (recombination protein O) 
F          Pnap_1672 DNA replication and repair protein RecR	K06187 recR; recombination protein RecR 
F          Pnap_1816 DNA ligase, NAD-dependent	K01972 E6.5.1.2; DNA ligase (NAD+) [EC:6.5.1.2] 
E        Facilitator
F          Pnap_3359 DNA-binding protein Fis	K03557 fis; Fis family transcriptional regulator, factor for inversion stimulation protein 
F          Pnap_2848 integration host factor, alpha subunit	K04764 ihfA; integration host factor subunit alpha 
F          Pnap_2797 integration host factor, beta subunit	K05788 ihfB; integration host factor subunit beta 
E        Supressor
F          Pnap_1935 Exodeoxyribonuclease I subunit C	K01141 sbcB; exodeoxyribonuclease I [EC:3.1.11.1] 
F          Pnap_0114 ATP-dependent DNA helicase RecQ	K03654 recQ; ATP-dependent DNA helicase RecQ [EC:5.6.2.4] 
F          Pnap_2963 ATP-dependent DNA helicase, RecQ-like protein	K03654 recQ; ATP-dependent DNA helicase RecQ [EC:5.6.2.4] 
F          Pnap_0488 UvrA family protein	K03701 uvrA; excinuclease ABC subunit A 
F          Pnap_3827 Excinuclease ABC subunit A	K03701 uvrA; excinuclease ABC subunit A 
F          Pnap_4737 excinuclease ABC, A subunit	K03701 uvrA; excinuclease ABC subunit A 
F          Pnap_1563 Excinuclease ABC subunit B	K03702 uvrB; excinuclease ABC subunit B 
F          Pnap_4578 nucleoid protein H-NS	K03746 hns; DNA-binding protein H-NS 
F          Pnap_4886 nucleoid protein H-NS	K03746 hns; DNA-binding protein H-NS 
F          Pnap_3939 histone-like nucleoid-structuring protein H-NS	K03746 hns; DNA-binding protein H-NS 
F          Pnap_4715 hypothetical protein	K03746 hns; DNA-binding protein H-NS 
F          Pnap_4730 histone family protein nucleoid-structuring protein H-NS	K03746 hns; DNA-binding protein H-NS 
F          Pnap_4220 histone family protein nucleoid-structuring protein H-NS	K03746 hns; DNA-binding protein H-NS 
F          Pnap_3493 histone family protein nucleoid-structuring protein H-NS	K03746 hns; DNA-binding protein H-NS 
B  TLS (translesion DNA synthesis) factors
C    Y-family DNA polymerases
D      Pnap_3159 DNA-directed DNA polymerase	K02346 dinB; DNA polymerase IV [EC:2.7.7.7] 
D      Pnap_4268 UMUC domain protein DNA-repair protein	K03502 umuC; DNA polymerase V 
C    Other SOS response factors
D      Pnap_3956 recA protein	K03553 recA; recombination protein RecA 
D      Pnap_1918 SOS-response transcriptional repressor, LexA	K01356 lexA; repressor LexA [EC:3.4.21.88] 
D      Pnap_0907 DNA replication and repair protein RecN	K03631 recN; DNA repair protein RecN (Recombination protein N) 
D      Pnap_4894 conserved hypothetical protein	K14160 imuA; protein ImuA 
D      Pnap_4895 conserved hypothetical protein	K14161 imuB; protein ImuB 
D      Pnap_4896 DNA polymerase III, alpha subunit	K14162 dnaE2; error-prone DNA polymerase [EC:2.7.7.7] 
D      Pnap_3819 single-strand binding protein	K03111 ssb; single-strand DNA-binding protein 
D      Pnap_4323 single-strand binding protein	K03111 ssb; single-strand DNA-binding protein 
D      Pnap_3955 regulatory protein RecX	K03565 recX; regulatory protein 
B  Other factors with a suspected DNA repair function
C    DNA polymerase
D      Pnap_0820 PHP C-terminal domain protein	K02347 polX; DNA polymerase (family X) 
C    DNA helicases
D      Pnap_0352 UvrD/REP helicase	K03656 rep; ATP-dependent DNA helicase Rep [EC:5.6.2.4] 
D      Pnap_4961 UvrD/REP helicase	K03658 helD; DNA helicase IV [EC:5.6.2.4] 
D      Pnap_0503 helicase c2	K03722 dinG; ATP-dependent DNA helicase DinG [EC:5.6.2.3] 
D      Pnap_1863 helicase c2	K03722 dinG; ATP-dependent DNA helicase DinG [EC:5.6.2.3] 
D      Pnap_4469 Rad3-related DNA helicases-like protein	K03722 dinG; ATP-dependent DNA helicase DinG [EC:5.6.2.3] 
D      Pnap_4277 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      Pnap_0741 8-oxo-dGTPase	K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55] 
D      Pnap_3721 NUDIX hydrolase	K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55] 
D      Pnap_1188 deoxyuridine 5'-triphosphate nucleotidohydrolase	K01520 dut; dUTP diphosphatase [EC:3.6.1.23] 
D      Pnap_3385 ribonucleoside-diphosphate reductase, alpha subunit	K00525 E1.17.4.1A; ribonucleoside-diphosphate reductase alpha chain [EC:1.17.4.1] 
D      Pnap_3755 ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent	K00525 E1.17.4.1A; ribonucleoside-diphosphate reductase alpha chain [EC:1.17.4.1] 
D      Pnap_3386 Ribonucleoside-diphosphate reductase	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