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| Repair pathways | Molecular functions | T. thermophilus | E. coli | S. cerevisiae | A. thaliana | M. musculus | H. sapiens | Related disease |
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| Direct reversal | | | | | | | | |
| Photoreactivation | Photoreactivation | Phr (TTHB102) | PhrA | PHR1 | PhrB | | | |
|
| Alkyltransfer | Alkyltransfer or recognition | ATL (TTHA1564) | Ada, AGT, ATL | MGT1 | | MGMT | MGMT | |
| alkyltransfer | | AlkB | | | AlkBH1 | ALKBH2, ALKBH3 | |
|
|
| Base excision repair | | | | | | | | |
| Base excision | Remove ring-saturated or fragmented pyrimidines | EndoIII (TTHA0112) | Nth (EndoIII) | Ntg1p, Ntg2p | AT1G05900 | Nthl1 | NTHL1 | |
| remove 3-meA, ethenoA, hypoxanthine | AlkA (TTHA0329) | AlkA, TagA | Mag1p | AT3G12040 (MAG) | Mpg | MPG, (MAG, AAG) | |
| Remove U | UDGA (TTHA0718) | Ung | Ung1p | AT3G18630 uracil DNA glycosylase family protein | Ung | Ung | Hyper IgM syndromes, autosomal recessive type |
| | UDGB (TTHA1149) | | | | | | |
| Remove U, hydroxymethyl U | | | | | Smug1 | SMUG1 | |
| Remove U or T opposite G at CpG sequences | | | | | Mbd4 | MBD4 (MED1) | |
| Remove U, T, or ethenoC opposite G | | Mug | | | Tdg | TDG | |
| Remove 8-oxoG opposite C | MutM (TTHA1806) | Fpg (MutM) | Ogg1p | OGG1 | Ogg1 | OGG1 | Lung cancer |
| Remove A opposite 8-oxoG | MutY (TTHA1898) | MutY | | AT4G12740 (MYH-related) | MUTYH | MUTYH | |
| Remove thymine glycol | | Nei (EndoVIII) | | | Neil1 | NEIL1 | |
| Remove oxidative products of C, U | | | | | | NEIL2 | |
| Not known | | | | | | NEIL3 | |
| Alternative strand incision | Incision of hypoxanthine and uracil | EndoV (TTHA1347) | Nfi (EndoV) | | EndoV | EndoV | EndoV | |
|
| AP site processing and resynthesis | AP endonuclease | EndoIV (Nfo) (TTHA0834) | Nfo (EndoIV) | Apn1p | | | | |
| AP endonuclease | | XthA (ExoIII) | Apn2p (Eyh1) | ARP | Apex1 | APEX1 (APE1, APEX, HAP1, REF1), | |
| AP endonuclease | | | | AT4G36050 | Apex2 | APEX2 | |
| gap-filling DNA polymerase | PolX (TTHA1150) | | | | Pol | Pol | |
| DNA polymerase, flap endonuclease | PolI (TTHA1054) | PolI | | | | | |
| replication and BER in mitochondrial DNA | | | Mip1p | | Pol | Pol | |
| NAD-dependent DNA ligase | LigA (TTHA1097) | LigA | | | | | |
| ATP-dependent DNA ligase | | | | AT1G66730 (ATP-dependent) | Lig3 (ATP-dependent) | LIG3 (ATP-dependent) | |
| accessory factor for LIG3 and BER | | | | AT1G80420 (putative XRCC1) | Xrcc1 | XRCC1 | |
| poly (ADP-ribose) polymerase | | | | PARP2 | Parp1 | PARP1 (ADPRT) | |
| ADPRT-like enzyme | | | | APP (Arabidopsis poly(ADP-ribose) polymerase) | Parp2 | PARP2 (ADPRTL2) |
|
|
| Nucleotide excision repair | | | | | | | | |
| DNA binding | Bind damaged DNA in complex with UvrB | UvrA (TTHA1440) | UvrA | | | | | |
| Catalyze unwinding in preincision complex | UvrB (TTHA1892) | UvrB | | | | | |
| Bind disordered DNA as complex | | | RAD4 | RAD4 | Xpc | XPC | Xeroderma pigmentosum (XP) |
| Bind disordered DNA as complex | | | RAD23 | RAD23 | Rad23b (Hr23b) | RAD23B (HR23B) | |
| RAD23B paralog | | | | | Rad23a (Hr23a) | RAD23A (HHR23A) | |
| Bind DNA and proteins in preincision complex | | | RAD14 | | Xpa | XPA | XP, |
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| TFIIH subunits | - DNA helicase TFIIH subunit | | | SSL2 (RAD25) | XPB2 | Xpb (Ercc3) | XPB (ERCC3) | XP, Cockayne syndrome (CS), Trichothiodystrophy (TTD) |
| - DNA helicase TFIIH subunit | | | RAD3 | UVH6 | Xpd (Ercc2) | ERCC2 | XP, CS, TTD |
| TFIIH subunit p62 | | | TFB1 | AT1G55750 | Gtf2h1 | GTF2H1 | |
| TFIIH subunit p44 | | | SSL1 | GTF2H2 | Gtf2h2 | GTF2H2 | |
| TFIIH subunit p34 | | | TFB4 | AT1G18340 | Gtf2h3 | GTF2H3 | |
| TFIIH subunit p52 | | | TFB2 | AT4G17020 | Gtf2h4 | GTF2H4 | |
| TFIIH subunit p8 | | | TFB5 | AT1G12400 | Gtf2h5 | GTF2H5 (TTDA) | TTD |
| Kinase subunits of TFIIH | | | KIN28 | CDKD1;3 | Cdk7 | CDK7 | |
| Kinase subunits of TFIIH | | | CCL1 | CYCH;1 | Ccnh | CCNH | |
| THIIH subunit | | | TFB3 | AT4G30820 | Mnat1 (Mat1) | MNAT1 (MAT1) | |
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| Strand incision and excision | and incision nuclease | UvrC (TTHA1548) | UvrC | | | | | |
| incision nuclease | | Cho | | | | | |
| incision nuclease | | | RAD2 | UVH3 | Xpg (Ercc5) | ERCC5 | XP, CS |
| incision nuclease subunits | | | RAD10 | ERCC1 | Ercc1 | ERCC1 | XP |
| incision nuclease subunits | | | RAD1 | UVH1 | Xpf (Ercc4) | ERCC4 | XP |
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| Separating two annealed strands | DNA helicase | UvrD (TTHA1427) | UvrD | | | | | |
| Other factors | Transcription- repair coupling factor | Mfd (TTHA0889) | Mfd | | | | | |
| Cockayne syndrome, needed for TC-NER | | | | ERCC6 | Csb (Ercc6) | CSB (ERCC6) | CS, UV-sensitive syndrome (UVS) |
| Cockayne syndrome, needed for TC-NER | | | | AT1G19750 | Csa (Ckn1, Ercc8) | CSA (ERCC8) | CS |
| P127 subunit of DDB | | | | DDB1 | Ddb1 | DDB1 (XPE) | |
| P48 subunit of DDB, defective in XP-E | | | | DDB2 | Ddb2 (Xpe) | DDB2 (XPE) | XP |
| transcription and NER | | | | AT5G48120 | Mms19 | MMS19 |
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| Mismatch repair | | | | | | | | |
| Mismatch recognition | DNA-binding ATPase | MutS (TTHA1324) | MutS | MutS
(MSH2/MSH6)
MutS
(MSH2/MSH3) | MutS
(MSH2/MSH6)
MutS
(MSH2/MSH3) | MutS
(MSH2/MSH6)
MutS
(MSH2/MSH3) | MutS
(MSH2/MSH6)
MutS
(MSH2/MSH3) | Colorectal cancer, Ovarian cancer |
|
| Strand incision | Activation of MutL homologue | DNA polymerase III, subunit (TTHA0001) | — | PCNA | PCNA | PCNA | PCNA | |
| Activation of MutL homologue | DNA polymerase III, , , , subunits (TTHA0788, 1860, 1952) | | RFC (RFC1-5) | RFC (RFC1-5) | RFC (RFC1-5) | RFC (RFC1-5) | |
| Endonuclease ATPase | MutL (TTHA1323) | — | MutL (MLH1/PMS1) MutL (MLH1/MLH2) MutL (MLH1/MLH3) | MutL (MLH1/PMS1) MutL (MLH1/MLH3) | MutL (MLH1/PMS2) MutL (MLH1/PMS1) MutL (MLH1/MLH3) | MutL (MLH1/PMS2) MutL (MLH1/PMS1) MutL (MLH1/MLH3) | Colorectal cancer, Endometrial cancer, Ovarian cancer |
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| Match making | ATPase | — | MutL | — | — | — | — | |
| Strand excision | - exonuclease | RecJ (TTHA1167) | RecJ | | | | | |
| - exonuclease | ExoI (TTHB178) | ExoI | | | | | |
| - exonuclease | | ExoVII | | | | | |
| - exonuclease | | ExoX | | | | | |
| - exonuclease | | | EXO1 | AT1G29630 | Exo1 | EXO1 | |
| Single-stranded DNA binding protein | SSB (TTHA0244) | SSB | | | | | |
| Single-stranded DNA binding protein complex | | | RFA (RFA1-3) | RPA (RPA1-3) | Rpa (Rpa1-3) | RPA (RPA1-3) | |
| DNA helicase | UvrD (TTHA1427) | UvrD | | | | | |
| Recombination repair | | | | | | | | |
|
| End resection and recombinase loading | - exonuclease | RecJ (TTHA1167) | RecJ | | | | | |
| - exonuclease | | | EXO1 | AT1G29630 | Exo1 | EXO1 | |
| -flap endonuclease | | | DNA2 | AT1G08840 | Dna2 | DNA2 | |
| RECQ family DNA helicase | | RecQ | SGS1 | AT1G10930 (RECQ4A) | Blm | BLM | Bloom syndrome |
| Endonuclease, interact with MRN complex | | | SAE2 | AT3G52115 (ATGR1) | CtIP (Rbbp8) | CTIP (RBBP8) | |
| SMC-like ATPase, complex with SbcD (Mre11) | SbcC (TTHA1288) | SbcC | RAD50 | AT2G31970 (RAD50) | Rad50 | RAD50 | Nijmegen breakage syndrome-like disorder |
| - exonuclease, endonuclease, complex with SbcC (Rad50) | SbcD (TTHA1289) | SbcD | MRE11 | AT5G54260 (MRE11) | Mre11a | MRE11A | Ataxia telangiectasia -like disorder |
| Accessory protein for MR complex | | | XRS2 | AT3G02680 (NBS1) | Nbn (Nbs1) | NBN (NBS1) | Nijmegen breakage syndrome |
| SMC-like ATPase | RecN (TTHA1525) | RecN | | | | | |
| Helicase/nuclease complex | | RecB | | | | | |
| Helicase/nuclease complex | | RecC | | | | | |
| Helicase/nuclease complex | | RecD | | | | | |
| - exonuclease | | RecE | | | | | |
| ssDNA annealing | | RecT | | | | | |
| Single-stranded DNA binding protein | SSB (TTHA0244) | Ssb | | | | | |
| Single-stranded DNA binding protein complex | | | RFA (RFA1-3) | RPA (RPA1-3) | Rpa (Rpa1-3) | RPA (RPA1-3) | |
| ATPase, complex with RecR | RecF (TTHA0264) | RecF | | | | | |
| Recombinase mediator, ssDNA annealing | RecO (TTHA0623) | RecO | | | | | |
| DNA binding, complex with RecF and RecO | RecR (TTHA1600) | RecR | | | | | |
| Recombinase mediator, ssDNA annealing | Rad52-like (TTHA0081) | | RAD52 | | Rad52 | RAD52 | |
| Recombinase mediator | | | | AT5G01630 (BRCA2B) | Brca2 | BRCA2 | Pancreatic cancer, Ovarian cancer, Breast cancer, Fanconi anemia |
| RAD54 family DNA translocase, recombinase mediator | | | RAD54 | AT3G19210 (ATRad54) | Rad54l | RAD54L | Adenocarcinoma, Non-Hodgkin lymphoma |
| RAD54 family DNA translocase, recombinase mediator | | | RDH54 | | Rad54b | RAD54B | Colon cancer, Non-Hodgkin lymphoma |
| RAD51-like, recombinase mediator | | | | AT5G64520 (XRCC2) | Xrcc2 | XRCC2 | Breast cancer |
| RAD51-like, recombinase mediator | | | | AT5G57450 (XRCC3) | Xrcc3 | XRCC3 | Breast cancer, Melanoma |
| RAD51-like, recombinase mediator | | | RAD57 | AT2G28560 (RAD51B) | Rad51l1 | RAD51L1 | Uterine leiomyoma |
| RAD51-like, recombinase mediator | | | | AT2G45280 (RAD51C) | Rad51c | RAD51C | Fanconi anemia-like disorder, Breast-Ovarian cancer |
| RAD51-like, recombinase mediator | | | RAD55 | AT1G07745 (RAD51D) | Rad51l3 | RAD51L3 | |
|
| Strand exchange | Recombinase | RecA (TTHA1818) | RecA | | AT2G19490 (recA) | | | |
| Recombinase | | | RAD51 | AT5G20850 (ATRAD51) | Rad51 | RAD51 | |
|
| Branch migration | Branch migration complex | RuvA (TTHA0291) | RuvA | | | | | |
| Branch migration complex | RuvB (TTHA0406) | RuvB | | | | | |
| DNA helicase | RecG (TTHA1266) | RecG | | AT2G01440 (RecG) | | | |
| RecA-like ATPase | RadA/Sms (TTHA0541) | RadA/Sms | | AT5G50340 | | | |
| RAD54 family DNA translocase, recombinase mediator | | | RAD54 | AT3G19210 (ATRad54) | Rad54l | RAD54L | Adenocarcinoma, Non-Hodgkin lymphoma |
| RAD54 family DNA translocase, recombinase mediator | | | RDH54 | | Rad54b | RAD54B | Colon cancer, Non-Hodgkin lymphoma |
| RECQ family DNA helicase | | RecQ | SGS1 | AT1G10930 (RECQ4A) | Blm | BLM | Bloom syndrome |
| RECQ family DNA helicase | | | | | Wrn | WRN | Werner syndrome |
| RECQ family DNA helicase | | | | AT1G31360 (RECQL2) | Recql | RECQL | |
| RECQ family DNA helicase | | | MPH1 | AT1G35530 | Fancm | FANCM | Fanconi anemia |
|
| Holliday junction resolution | HJ resolvase | RuvC (TTHA1090) | RuvC | | | | | |
| HJ resolvase | | RusA | | | | | |
| HJ resolvase | | | YEN1 | AT1G01880 | Gen1 | GEN1 | |
| Structure-specific endonuclease | | | MUS81 | AT4G30870 (MUS81) | Mus81 | MUS81 | |
| complex with MUS81 | | | MMS4 | AT2G22140 (ATEME1B) | Eme1 | EME1 | |
| Structure-specific endonuclease | | | RAD1 | AT5G41150 (UVH1) | Ercc4 | ERCC4 | Xeroderma pigmentosum |
| complex with ERCC4 (RAD1) | | | RAD10 | AT3G05210 (ERCC1) | Ercc1 | ERCC1 | Cerebro-oculo-facio-skeletal syndrome |
| HJ resolvase | | | SLX1 | AT2G30350 | Slx1 (Giyd2) | SLX1 (GIYD2) | |
| Accessory protein for structure-specific nucleases | | | SLX4 | | Slx4 (Btbd12) | SLX4 (BTBD12) | |
|
| Anti-recombination | Recombinase inhibitor | RecX (TTHA0848) | RecX | | AT3G13226 (RecX) | | | |
| DNA helicase | UvrD (TTHA1427) | UvrD | SRS2 | AT4G25120 | | | |
| Structure-specific endonuclease | MutS2 (TTHA1645) | | | AT1G65070 (MutS2) | | | |
|
