+F Repair protein KO
#
DNA Repair and Recombination Proteins - Paenibacillus sp. JDR-2
%
!
AEukaryotic type
B SSBR (single strand breaks repair)
C Direct repair
C BER (base exicision repair)
D DNA glycosylases
E Pjdr2_3849 uracil-DNA glycosylase K03648 UNG; uracil-DNA glycosylase [EC:3.2.2.27]
E Pjdr2_5140 A/G-specific adenine glycosylase K03575 mutY; A/G-specific adenine glycosylase [EC:3.2.2.31]
E Pjdr2_2478 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
E Pjdr2_3778 type III restriction protein res subunit K10843 ERCC3; DNA excision repair protein ERCC-3 [EC:5.6.2.4]
E Pjdr2_3184 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 Pjdr2_0294 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Pjdr2_6147 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Pjdr2_5291 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Pjdr2_5356 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Pjdr2_6145 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Pjdr2_6146 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Pjdr2_4910 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Pjdr2_3938 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Pjdr2_4660 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Pjdr2_5514 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Pjdr2_0633 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Pjdr2_1480 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Pjdr2_3398 deoxyuridine 5'-triphosphate nucleotidohydrolase Dut K01520 dut; dUTP diphosphatase [EC:3.6.1.23]
#
AProkaryotic type
B SSBR (single strand breaks repair)
C Direct repair
D Pjdr2_5363 transcriptional regulator, AraC family K13530 adaA; AraC family transcriptional regulator, regulatory protein of adaptative response / methylphosphotriester-DNA alkyltransferase methyltransferase [EC:2.1.1.-]
D Pjdr2_5364 methylated-DNA/protein-cysteine methyltransferase K13531 adaB; methylated-DNA-[protein]-cysteine S-methyltransferase [EC:2.1.1.63]
D Pjdr2_2946 methylated-DNA/protein-cysteine methyltransferase K13531 adaB; methylated-DNA-[protein]-cysteine S-methyltransferase [EC:2.1.1.63]
C BER (base exicision repair)
D DNA glycosylases
E Pjdr2_3849 uracil-DNA glycosylase K03648 UNG; uracil-DNA glycosylase [EC:3.2.2.27]
E Pjdr2_5362 DNA-3-methyladenine glycosylase II K01247 alkA; DNA-3-methyladenine glycosylase II [EC:3.2.2.21]
E Pjdr2_5140 A/G-specific adenine glycosylase K03575 mutY; A/G-specific adenine glycosylase [EC:3.2.2.31]
E Pjdr2_1524 formamidopyrimidine-DNA glycosylase K10563 mutM; formamidopyrimidine-DNA glycosylase [EC:3.2.2.23 4.2.99.18]
E Pjdr2_2633 DNA-(apurinic or apyrimidinic site) lyase K10563 mutM; formamidopyrimidine-DNA glycosylase [EC:3.2.2.23 4.2.99.18]
E Pjdr2_2478 endonuclease III K10773 NTHL1; endonuclease III [EC:3.2.2.- 4.2.99.18]
D AP endonucleases
E Pjdr2_0753 exodeoxyribonuclease III Xth K01142 E3.1.11.2; exodeoxyribonuclease III [EC:3.1.11.2]
E Pjdr2_1252 apurinic endonuclease Apn1 K01151 nfo; deoxyribonuclease IV [EC:3.1.21.2]
E Pjdr2_2634 apurinic endonuclease Apn1 K01151 nfo; deoxyribonuclease IV [EC:3.1.21.2]
D RecJ
E Pjdr2_4386 single-stranded-DNA-specific exonuclease RecJ K07462 recJ; single-stranded-DNA-specific exonuclease [EC:3.1.-.-]
D DNA ligase
E Pjdr2_5719 DNA ligase, NAD-dependent K01972 E6.5.1.2; DNA ligase (NAD+) [EC:6.5.1.2]
D DNA polymerase I
E Pjdr2_1523 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 Pjdr2_5728 excinuclease ABC, A subunit K03701 uvrA; excinuclease ABC subunit A
E Pjdr2_5729 excinuclease ABC, B subunit K03702 uvrB; excinuclease ABC subunit B
E Pjdr2_4818 excinuclease ABC, C subunit K03703 uvrC; excinuclease ABC subunit C
E Pjdr2_5720 ATP-dependent DNA helicase PcrA K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4]
E Pjdr2_4306 conserved hypothetical protein K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4]
E Pjdr2_1267 UvrD/REP helicase K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4]
E Pjdr2_2255 conserved hypothetical protein K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4]
E Pjdr2_2957 UvrD/Rep family helicase K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4]
E Pjdr2_1523 DNA polymerase I K02335 polA; DNA polymerase I [EC:2.7.7.7]
E Pjdr2_5719 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 Pjdr2_5691 DNA-directed RNA polymerase, beta subunit K03043 rpoB; DNA-directed RNA polymerase subunit beta [EC:2.7.7.6]
F Pjdr2_5690 DNA-directed RNA polymerase, beta' subunit K03046 rpoC; DNA-directed RNA polymerase subunit beta' [EC:2.7.7.6]
F Pjdr2_5652 DNA-directed RNA polymerase, alpha subunit K03040 rpoA; DNA-directed RNA polymerase subunit alpha [EC:2.7.7.6]
F Pjdr2_0136 DNA-directed RNA polymerase delta subunit K03048 rpoE; DNA-directed RNA polymerase subunit delta
F Pjdr2_3764 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 Pjdr2_0039 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 Pjdr2_2606 DNA mismatch repair protein MutS K03555 mutS; DNA mismatch repair protein MutS
E Pjdr2_1389 MutS2 family protein K07456 mutS2; DNA mismatch repair protein MutS2
E Pjdr2_2645 DNA mismatch repair protein MutS domain protein K07456 mutS2; DNA mismatch repair protein MutS2
D Molecular matchmaker
E Pjdr2_2607 DNA mismatch repair protein MutL K03572 mutL; DNA mismatch repair protein MutL
D Strand discrimination factor
D DNA exonucleases
E Pjdr2_2309 exodeoxyribonuclease VII, large subunit K03601 xseA; exodeoxyribonuclease VII large subunit [EC:3.1.11.6]
E Pjdr2_2310 exodeoxyribonuclease VII, small subunit K03602 xseB; exodeoxyribonuclease VII small subunit [EC:3.1.11.6]
D DNA polymerase III holoenzyme
E Pjdr2_4482 DNA polymerase III, alpha subunit K02337 dnaE; DNA polymerase III subunit alpha [EC:2.7.7.7]
E Pjdr2_3412 DNA polymerase III, alpha subunit K03763 polC; DNA polymerase III subunit alpha, Gram-positive type [EC:2.7.7.7]
E Pjdr2_0002 DNA polymerase III, beta subunit K02338 dnaN; DNA polymerase III subunit beta [EC:2.7.7.7]
E Pjdr2_2197 DNA polymerase III, delta subunit K02340 holA; DNA polymerase III subunit delta [EC:2.7.7.7]
E Pjdr2_0016 DNA polymerase III, delta prime subunit K02341 holB; DNA polymerase III subunit delta' [EC:2.7.7.7]
E Pjdr2_2143 DNA polymerase III, epsilon subunit K02342 dnaQ; DNA polymerase III subunit epsilon [EC:2.7.7.7]
E Pjdr2_0144 DNA polymerase III, subunits gamma and tau K02343 dnaX; DNA polymerase III subunit gamma/tau [EC:2.7.7.7]
D DNA ligase
E Pjdr2_5719 DNA ligase, NAD-dependent K01972 E6.5.1.2; DNA ligase (NAD+) [EC:6.5.1.2]
D Other MMR factors
E Pjdr2_5720 ATP-dependent DNA helicase PcrA K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4]
E Pjdr2_4306 conserved hypothetical protein K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4]
E Pjdr2_1267 UvrD/REP helicase K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4]
E Pjdr2_2255 conserved hypothetical protein K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4]
E Pjdr2_2957 UvrD/Rep family helicase K03657 uvrD; ATP-dependent DNA helicase UvrD/PcrA [EC:5.6.2.4]
E Pjdr2_6272 single-strand binding protein K03111 ssb; single-strand DNA-binding protein
E Pjdr2_4666 DNA mismatch endonuclease Vsr K07458 vsr; DNA mismatch endonuclease, patch repair protein [EC:3.1.-.-]
B DSBR (double strand breaks repair)
C HR (homologous recombination)
D RecBC pathway proteins
E Pjdr2_3379 recA protein K03553 recA; recombination protein RecA
E Pjdr2_4401 Holliday junction DNA helicase RuvA K03550 ruvA; holliday junction DNA helicase RuvA
E Pjdr2_4400 Holliday junction DNA helicase RuvB K03551 ruvB; holliday junction DNA helicase RuvB [EC:5.6.2.4]
E Pjdr2_4402 crossover junction endodeoxyribonuclease RuvC K01159 ruvC; crossover junction endodeoxyribonuclease RuvC [EC:3.1.21.10]
E Pjdr2_3756 primosomal protein N' K04066 priA; primosomal protein N' (replication factor Y) (superfamily II helicase) [EC:5.6.2.4]
E Pjdr2_4629 exonuclease, putative K03546 sbcC; DNA repair protein SbcC/Rad50
E Pjdr2_4630 nuclease SbcCD, D subunit K03547 sbcD; DNA repair protein SbcD/Mre11
D RecFOR pathway proteins
E Pjdr2_3379 recA protein K03553 recA; recombination protein RecA
E Pjdr2_5713 DNA repair protein RadA K04485 radA; DNA repair protein RadA/Sms
E Pjdr2_0004 DNA replication and repair protein RecF K03629 recF; DNA replication and repair protein RecF
E Pjdr2_3741 ATP-dependent DNA helicase RecG K03655 recG; ATP-dependent DNA helicase RecG [EC:5.6.2.4]
E Pjdr2_4386 single-stranded-DNA-specific exonuclease RecJ K07462 recJ; single-stranded-DNA-specific exonuclease [EC:3.1.-.-]
E Pjdr2_2238 DNA repair protein RecO K03584 recO; DNA repair protein RecO (recombination protein O)
E Pjdr2_0146 recombination protein RecR K06187 recR; recombination protein RecR
E Pjdr2_2316 DNA repair protein RecN K03631 recN; DNA repair protein RecN (Recombination protein N)
E Pjdr2_4401 Holliday junction DNA helicase RuvA K03550 ruvA; holliday junction DNA helicase RuvA
E Pjdr2_4400 Holliday junction DNA helicase RuvB K03551 ruvB; holliday junction DNA helicase RuvB [EC:5.6.2.4]
E Pjdr2_4402 crossover junction endodeoxyribonuclease RuvC K01159 ruvC; crossover junction endodeoxyribonuclease RuvC [EC:3.1.21.10]
D AddAB pathway proteins
E Pjdr2_2220 recombination helicase AddA K16898 addA; ATP-dependent helicase/nuclease subunit A [EC:5.6.2.4 3.1.-.-]
E Pjdr2_2219 ATP-dependent nuclease 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 Pjdr2_4629 exonuclease, putative K03546 sbcC; DNA repair protein SbcC/Rad50
E Pjdr2_4630 nuclease SbcCD, D subunit K03547 sbcD; DNA repair protein SbcD/Mre11
C NHEJ (non-homologous end-joining)
D Two-component NHEJ DNA repair complex
E Pjdr2_4983 Ku protein K10979 ku; DNA end-binding protein Ku
E Pjdr2_4984 ATP dependent DNA ligase K01971 ligD; bifunctional non-homologous end joining protein LigD [EC:6.5.1.1]
E Pjdr2_4985 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 Pjdr2_0008 DNA gyrase, A subunit K02469 gyrA; DNA gyrase subunit A [EC:5.6.2.2]
F Pjdr2_0006 DNA gyrase, B subunit K02470 gyrB; DNA gyrase subunit B [EC:5.6.2.2]
F Pjdr2_3465 DNA topoisomerase I K03168 topA; DNA topoisomerase I [EC:5.6.2.1]
E Supressor
F Pjdr2_0049 histone family protein DNA-binding protein K03530 hupB; DNA-binding protein HU-beta
F Pjdr2_2403 histone family protein DNA-binding protein K03530 hupB; DNA-binding protein HU-beta
D SHDIR (short-homology-dependent illegitimate recombination)
E RecET pathway
F Pjdr2_1587 RecT protein K07455 recT; recombination protein RecT
F Pjdr2_4386 single-stranded-DNA-specific exonuclease RecJ K07462 recJ; single-stranded-DNA-specific exonuclease [EC:3.1.-.-]
F Pjdr2_2238 DNA repair protein RecO K03584 recO; DNA repair protein RecO (recombination protein O)
F Pjdr2_0146 recombination protein RecR K06187 recR; recombination protein RecR
F Pjdr2_5719 DNA ligase, NAD-dependent K01972 E6.5.1.2; DNA ligase (NAD+) [EC:6.5.1.2]
E Facilitator
E Supressor
F Pjdr2_4743 ATP-dependent DNA helicase, RecQ family K03654 recQ; ATP-dependent DNA helicase RecQ [EC:5.6.2.4]
F Pjdr2_4470 ATP-dependent DNA helicase RecQ K03654 recQ; ATP-dependent DNA helicase RecQ [EC:5.6.2.4]
F Pjdr2_5728 excinuclease ABC, A subunit K03701 uvrA; excinuclease ABC subunit A
F Pjdr2_5729 excinuclease ABC, B subunit K03702 uvrB; excinuclease ABC subunit B
B TLS (translesion DNA synthesis) factors
C Y-family DNA polymerases
D Pjdr2_2148 DNA-directed DNA polymerase K02346 dinB; DNA polymerase IV [EC:2.7.7.7]
D Pjdr2_3737 DNA-directed DNA polymerase K02346 dinB; DNA polymerase IV [EC:2.7.7.7]
C Other SOS response factors
D Pjdr2_3379 recA protein K03553 recA; recombination protein RecA
D Pjdr2_2621 SOS-response transcriptional repressor, LexA K01356 lexA; repressor LexA [EC:3.4.21.88]
D Pjdr2_1579 transcriptional regulator, XRE family K01356 lexA; repressor LexA [EC:3.4.21.88]
D Pjdr2_1595 transcriptional repressor, LexA family K01356 lexA; repressor LexA [EC:3.4.21.88]
D Pjdr2_2316 DNA repair protein RecN K03631 recN; DNA repair protein RecN (Recombination protein N)
D Pjdr2_6272 single-strand binding protein K03111 ssb; single-strand DNA-binding protein
D Pjdr2_3378 regulatory protein RecX K03565 recX; regulatory protein
B Other factors with a suspected DNA repair function
C DNA polymerase
C DNA helicases
D Pjdr2_2449 DnaQ family exonuclease/DinG family helicase K03722 dinG; ATP-dependent DNA helicase DinG [EC:5.6.2.3]
D Pjdr2_2692 helicase c2 K03722 dinG; ATP-dependent DNA helicase DinG [EC:5.6.2.3]
D Pjdr2_2718 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 Pjdr2_0294 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Pjdr2_6147 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Pjdr2_5291 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Pjdr2_5356 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Pjdr2_6145 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Pjdr2_6146 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Pjdr2_4910 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Pjdr2_3938 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Pjdr2_4660 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Pjdr2_5514 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Pjdr2_0633 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Pjdr2_1480 NUDIX hydrolase K03574 mutT; 8-oxo-dGTP diphosphatase [EC:3.6.1.55]
D Pjdr2_3398 deoxyuridine 5'-triphosphate nucleotidohydrolase Dut K01520 dut; dUTP diphosphatase [EC:3.6.1.23]
D Pjdr2_3990 ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent K00525 E1.17.4.1A; ribonucleoside-diphosphate reductase alpha chain [EC:1.17.4.1]
D Pjdr2_4011 ribonucleoside-diphosphate reductase, alpha subunit K00525 E1.17.4.1A; ribonucleoside-diphosphate reductase alpha chain [EC:1.17.4.1]
D Pjdr2_4010 Ribonucleoside-diphosphate reductase K00526 E1.17.4.1B; ribonucleoside-diphosphate reductase beta chain [EC:1.17.4.1]
C Others
D Pjdr2_3405 phosphoesterase RecJ domain protein K06881 nrnA; bifunctional oligoribonuclease and PAP phosphatase NrnA [EC:3.1.3.7 3.1.13.3]
!
#
#[ BRITE | KEGG2 | KEGG ]
#Last updated: March 29, 2024