| COG0084 | Mg-dependent DNase |
| COG0116 | Predicted N6-adenine-specific DNA methylase |
| COG0122 | 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase |
| COG0164 | Ribonuclease HII |
| COG0177 | Predicted EndoIII-related endonuclease |
| COG0178 | Excinuclease ATPase subunit |
| COG0187 | Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), B subunit |
| COG0188 | Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit |
| COG0210 | Superfamily I DNA and RNA helicases |
| COG0249 | Mismatch repair ATPase (MutS family) |
| COG0258 | 5'-3' exonuclease (including N-terminal domain of PolI) |
| COG0266 | Formamidopyrimidine-DNA glycosylase |
| COG0270 | Site-specific DNA methylase |
| COG0272 | NAD-dependent DNA ligase (contains BRCT domain type II) |
| COG0305 | Replicative DNA helicase |
| COG0322 | Nuclease subunit of the excinuclease complex |
| COG0323 | DNA mismatch repair enzyme (predicted ATPase) |
| COG0328 | Ribonuclease HI |
| COG0338 | Site-specific DNA methylase |
| COG0350 | Methylated DNA-protein cysteine methyltransferase |
| COG0353 | Recombinational DNA repair protein (RecF pathway) |
| COG0358 | DNA primase (bacterial type) |
| COG0389 | Nucleotidyltransferase/DNA polymerase involved in DNA repair |
| COG0415 | Deoxyribodipyrimidine photolyase |
| COG0417 | DNA polymerase elongation subunit (family B) |
| COG0419 | ATPase involved in DNA repair |
| COG0420 | DNA repair exonuclease |
| COG0468 | RecA/RadA recombinase |
| COG0470 | ATPase involved in DNA replication |
| COG0494 | NTP pyrophosphohydrolases including oxidative damage repair enzymes |
| COG0497 | ATPase involved in DNA repair |
| COG0507 | ATP-dependent exoDNAse (exonuclease V), alpha subunit - helicase superfamily I member |
| COG0513 | Superfamily II DNA and RNA helicases |
| COG0514 | Superfamily II DNA helicase |
| COG0515 | Serine/threonine protein kinase |
| COG0550 | Topoisomerase IA |
| COG0551 | Zn-finger domain associated with topoisomerase type I |
| COG0553 | Superfamily II DNA/RNA helicases, SNF2 family |
| COG0556 | Helicase subunit of the DNA excision repair complex |
| COG0582 | Integrase |
| COG0587 | DNA polymerase III, alpha subunit |
| COG0592 | DNA polymerase sliding clamp subunit (PCNA homolog) |
| COG0593 | ATPase involved in DNA replication initiation |
| COG0608 | Single-stranded DNA-specific exonuclease |
| COG0629 | Single-stranded DNA-binding protein |
| COG0632 | Holliday junction resolvasome, DNA-binding subunit |
| COG0648 | Endonuclease IV |
| COG0675 | Transposase and inactivated derivatives |
| COG0692 | Uracil DNA glycosylase |
| COG0708 | Exonuclease III |
| COG0742 | N6-adenine-specific methylase |
| COG0749 | DNA polymerase I - 3'-5' exonuclease and polymerase domains |
| COG0758 | Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake |
| COG0776 | Bacterial nucleoid DNA-binding protein |
| COG0792 | Predicted endonuclease distantly related to archaeal Holliday junction resolvase |
| COG0816 | Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B. subtilis) |
| COG0817 | Holliday junction resolvasome, endonuclease subunit |
| COG0827 | Adenine-specific DNA methylase |
| COG0847 | DNA polymerase III, epsilon subunit and related 3'-5' exonucleases |
| COG0863 | DNA modification methylase |
| COG1039 | Ribonuclease HIII |
| COG1041 | Predicted DNA modification methylase |
| COG1059 | Thermostable 8-oxoguanine DNA glycosylase |
| COG1061 | DNA or RNA helicases of superfamily II |
| COG1074 | ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) |
| COG1107 | Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain |
| COG1110 | Reverse gyrase |
| COG1111 | ERCC4-like helicases |
| COG1112 | Superfamily I DNA and RNA helicases and helicase subunits |
| COG1193 | Mismatch repair ATPase (MutS family) |
| COG1194 | A/G-specific DNA glycosylase |
| COG1195 | Recombinational DNA repair ATPase (RecF pathway) |
| COG1197 | Transcription-repair coupling factor (superfamily II helicase) |
| COG1198 | Primosomal protein N' (replication factor Y) - superfamily II helicase |
| COG1199 | Rad3-related DNA helicases |
| COG1200 | RecG-like helicase |
| COG1241 | Predicted ATPase involved in replication control, Cdc46/Mcm family |
| COG1311 | Archaeal DNA polymerase II, small subunit/DNA polymerase delta, subunit B |
| COG1315 | Predicted polymerase, most proteins contain PALM domain, HD hydrolase domain and Zn-ribbon domain |
| COG1330 | Exonuclease V gamma subunit |
| COG1332 | Uncharacterized protein predicted to be involved in DNA repair (RAMP superfamily) |
| COG1336 | Uncharacterized protein predicted to be involved in DNA repair (RAMP superfamily) |
| COG1337 | Uncharacterized protein predicted to be involved in DNA repair (RAMP superfamily) |
| COG1343 | Uncharacterized protein predicted to be involved in DNA repair |
| COG1367 | Uncharacterized protein predicted to be involved in DNA repair (RAMP superfamily) |
| COG1372 | Intein/homing endonuclease |
| COG1381 | Recombinational DNA repair protein (RecF pathway) |
| COG1389 | DNA topoisomerase VI, subunit B |
| COG1421 | Uncharacterized protein predicted to be involved in DNA repair |
| COG1423 | ATP-dependent DNA ligase, homolog of eukaryotic ligase III |
| COG1466 | DNA polymerase III, delta subunit |
| COG1467 | Eukaryotic-type DNA primase, catalytic (small) subunit |
| COG1468 | RecB family exonuclease |
| COG1474 | Cdc6-related protein, AAA superfamily ATPase |
| COG1484 | DNA replication protein |
| COG1515 | Deoxyinosine 3'endonuclease (endonuclease V) |
| COG1517 | Uncharacterized protein predicted to be involved in DNA repair |
| COG1518 | Uncharacterized protein predicted to be involved in DNA repair |
| COG1525 | Micrococcal nuclease (thermonuclease) homologs |
| COG1533 | DNA repair photolyase |
| COG1555 | DNA uptake protein and related DNA-binding proteins |
| COG1567 | Uncharacterized protein predicted to be involved in DNA repair (RAMP superfamily) |
| COG1570 | Exonuclease VII, large subunit |
| COG1573 | Uracil-DNA glycosylase |
| COG1583 | Uncharacterized protein predicted to be involved in DNA repair (RAMP superfamily) |
| COG1591 | Holliday junction resolvase - archaeal type |
| COG1599 | Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins |
| COG1604 | Uncharacterized protein predicted to be involved in DNA repair (RAMP superfamily) |
| COG1637 | Predicted nuclease of the RecB family |
| COG1643 | HrpA-like helicases |
| COG1658 | Small primase-like proteins (Toprim domain) |
| COG1662 | Transposase and inactivated derivatives, IS1 family |
| COG1688 | Uncharacterized protein predicted to be involved in DNA repair (RAMP superfamily) |
| COG1697 | DNA topoisomerase VI, subunit A |
| COG1722 | Exonuclease VII small subunit |
| COG1743 | Adenine-specific DNA methylase containing a Zn-ribbon |
| COG1769 | Uncharacterized protein predicted to be involved in DNA repair (RAMP superfamily) |
| COG1793 | ATP-dependent DNA ligase |
| COG1796 | DNA polymerase IV (family X) |
| COG1857 | Uncharacterized protein predicted to be involved in DNA repair |
| COG1933 | Archaeal DNA polymerase II, large subunit |
| COG1943 | Transposase and inactivated derivatives |
| COG1948 | ERCC4-type nuclease |
| COG1961 | Site-specific recombinases, DNA invertase Pin homologs |
| COG2003 | DNA repair proteins |
| COG2094 | 3-methyladenine DNA glycosylase |
| COG2176 | DNA polymerase III, alpha subunit (gram-positive type) |
| COG2189 | Adenine specific DNA methylase Mod |
| COG2219 | Eukaryotic-type DNA primase, large subunit |
| COG2231 | Uncharacterized protein related to Endonuclease III |
| COG2254 | Predicted HD superfamily hydrolase, possibly a nuclease |
| COG2255 | Holliday junction resolvasome, helicase subunit |
| COG2256 | ATPase related to the helicase subunit of the Holliday junction resolvase |
| COG2356 | Endonuclease I |
| COG2452 | Predicted site-specific integrase-resolvase |
| COG2801 | Transposase and inactivated derivatives |
| COG2812 | DNA polymerase III, gamma/tau subunits |
| COG2816 | NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding |
| COG2818 | 3-methyladenine DNA glycosylase |
| COG2826 | Transposase and inactivated derivatives, IS30 family |
| COG2827 | Predicted endonuclease containing a URI domain |
| COG2887 | RecB family exonuclease |
| COG2901 | Factor for inversion stimulation Fis, transcriptional activator |
| COG2925 | Exonuclease I |
| COG2927 | DNA polymerase III, chi subunit |
| COG2946 | Putative phage replication protein RstA |
| COG2963 | Transposase and inactivated derivatives |
| COG2965 | Primosomal replication protein N |
| COG2974 | DNA recombination-dependent growth factor C |
| COG3039 | Transposase and inactivated derivatives, IS5 family |
| COG3050 | DNA polymerase III, psi subunit |
| COG3057 | Negative regulator of replication initiationR |
| COG3066 | DNA mismatch repair protein |
| COG3077 | DNA-damage-inducible protein J |
| COG3145 | Alkylated DNA repair protein |
| COG3285 | Predicted eukaryotic-type DNA primase |
| COG3293 | Transposase and inactivated derivatives |
| COG3298 | Predicted 3'-5' exonuclease related to the exonuclease domain of PolB |
| COG3316 | Transposase and inactivated derivatives |
| COG3328 | Transposase and inactivated derivatives |
| COG3335 | Transposase and inactivated derivatives |
| COG3337 | Uncharacterized protein predicted to be involved in DNA repair |
| COG3344 | Retron-type reverse transcriptase |
| COG3359 | Predicted exonuclease |
| COG3385 | FOG: Transposase and inactivated derivatives |
| COG3392 | Adenine-specific DNA methylase |
| COG3415 | Transposase and inactivated derivatives |
| COG3436 | Transposase and inactivated derivatives |
| COG3449 | DNA gyrase inhibitor |
| COG3464 | Transposase and inactivated derivatives |
| COG3547 | Transposase and inactivated derivatives |
| COG3569 | Topoisomerase IB |
| COG3593 | Predicted ATP-dependent endonuclease of the OLD family |
| COG3598 | RecA-family ATPase |
| COG3611 | Replication initiation/membrane attachment protein |
| COG3649 | Uncharacterized protein predicted to be involved in DNA repair |
| COG3663 | G:T/U mismatch-specific DNA glycosylase |
| COG3666 | Transposase and inactivated derivatives |
| COG3676 | Transposase and inactivated derivatives |
| COG3677 | Transposase and inactivated derivatives |
| COG3695 | Predicted methylated DNA-protein cysteine methyltransferase |
| COG3723 | Recombinational DNA repair protein (RecE pathway) |
| COG3727 | DNA G:T-mismatch repair endonuclease |
| COG3728 | Phage terminase, small subunit |
| COG3747 | Phage terminase, small subunit |
| COG3780 | DNA endonuclease related to intein-encoded endonucleases |
| COG3857 | ATP-dependent nuclease, subunit B |
| COG3886 | Predicted HKD family nuclease |
| COG3893 | Inactivated superfamily I helicase |
| COG3923 | Primosomal replication protein N'' |
| COG3935 | Putative primosome component and related proteins |
| COG4080 | RecB-family nuclease |
| COG4098 | Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) |
| COG4119 | Predicted NTP pyrophosphohydrolase |
| COG4220 | Phage DNA packaging protein, Nu1 subunit of terminase |
| COG4227 | Antirestriction protein |
| COG4294 | UV damage repair endonuclease |
| COG4335 | DNA alkylation repair enzyme |
| COG4389 | Site-specific recombinase |
| COG4570 | Holliday junction resolvase |
| COG4581 | Superfamily II RNA helicase |
| COG4584 | Transposase and inactivated derivatives |
| COG4644 | Transposase and inactivated derivatives, TnpA family |
| COG4646 | DNA methylase |
| COG4912 | Predicted DNA alkylation repair enzyme |
| COG4973 | Site-specific recombinase XerC |
| COG4974 | Site-specific recombinase XerD |
| COG4998 | Predicted endonuclease (RecB family) |
| COG5032 | Phosphatidylinositol kinase and protein kinases of the PI-3 kinase family |
| COG5049 | 5'-3' exonuclease |
| COG5055 | Recombination DNA repair protein (RAD52 pathway) |
| COG5067 | Protein kinase essential for the initiation of DNA replication |
| COG5142 | Oxidation resistance protein |
| COG5144 | RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB2 |
| COG5145 | DNA excision repair protein |
| COG5151 | RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 |
| COG5165 | Nucleosome-binding factor SPN, POB3 subunit |
| COG5214 | DNA polymerase alpha-primase complex, polymerase-associated subunit B |
| COG5220 | Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 |
| COG5235 | Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit |
| COG5241 | Nucleotide excision repair endonuclease NEF1, RAD10 subunit |
| COG5242 | RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 |
| COG5260 | DNA polymerase sigma |
| COG5333 | Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit |
| COG5377 | Phage-related protein, predicted endonuclease |
| COG5406 | Nucleosome binding factor SPN, SPT16 subunit |
| COG5421 | Transposase |
| COG5433 | Transposase |
| COG5519 | Superfamily II helicase and inactivated derivatives |
| COG5527 | Protein involved in initiation of plasmid replication |
| COG5534 | Plasmid replication initiator protein |
| COG5535 | DNA repair protein RAD4 |
| COG5558 | Transposase |
| COG5575 | Origin recognition complex, subunit 2 |
| COG5600 | Transcription-associated recombination protein |
| COG5627 | DNA repair protein MMS21 |
| COG5655 | Plasmid rolling circle replication initiator protein and truncated derivatives |
| COG5659 | FOG: Transposase |
