- 10 --------------efghsn------ Fis [KL] COG2901 Factor for inversion stimulation Fis, transcriptional activator - 56 ao-pkzy-vdrlbcefghs----i-w HepA [KL] COG0553 Superfamily II DNA/RNA helicases, SNF2 family - 23 aom-kzy--dr-bcefg-s--j---- AlkA [L] COG0122 3-Methyladenine DNA glycosylase - 17 ----------rlb-efgh-n-j---- Tag [L] COG2818 3-Methyladenine DNA glycosylase - 10 -----z---dr-b--f-----jxit- Mpg [L] COG2094 3-methyladenine DNA glycosylase - 56 aompkzyqvdrlbcefghsnujxitw Exo [L] COG0258 5'-3' exonuclease (including N-terminal domain of PolI) - 28 -om--z---drlb-efghsnuj-it- MutY [L] COG1194 A/G-specific DNA glycosylase - 38 aompkzyq--r-b--fgh-nuj---- CDC9 [L] COG1793 ATP-dependent DNA ligase - 7 a-m-kz-q------------------ - [L] COG1423 ATP-dependent DNA ligase, homolog of eukaryotic ligase III - 25 ----------rlb-efghsnujxit- RecB [L] COG1074 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) - 28 --m---y--drlb-efghsnuj-it- RecD [L] COG0507 ATP-dependent exoDNAse (exonuclease V), alpha subunit - helicase superfamily I member - 21 aompkz-qvd-lbcefg-------t- SbcC [L] COG0419 ATPase involved in DNA repair - 65 aompkzyqvdrlbcefghsnu-xitw HolB [L] COG0470 ATPase involved in DNA replication - 47 -------qvdrlbcefghsnujxitw DnaA [L] COG0593 ATPase involved in DNA replication initiation - 25 -------q-drlbcefghsnujx-t- RecN [L] COG0497 ATPases involved in DNA repair - 19 a--p-------------hsnuj---w - [L] COG2189 Adenine specific DNA methylase Mod - 21 --m-k-----rlb----h--uj---w - [L] COG0827 Adenine-specific DNA methylase - 4 ------------b-------u----- - [L] COG3392 Adenine-specific DNA methylase - 9 ----------r---efg-s--j---- AlkB [L] COG3145 Alkylated DNA repair protein - 7 aom-k--------------------- - [L] COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain - 72 ---p---qvdrlbcefghsnujxitw HimA [L] COG0776 Bacterial nucleoid DNA-binding protein - 31 aompkzy------------------- CDC6 [LO] COG1474 Cdc6-related protein, AAA superfamily ATPase - 4 --------------e----n-j---- Vsr [L] COG3727 DNA G:T-mismatch repair endonuclease - 62 ao-p--yqvdrlbcefghsnujxitw GyrA [L] COG0188 DNA gyrase (topoisomerase II) A subunit - 61 ao-p--yqvdrlbcefghsnujxitw GyrB [L] COG0187 DNA gyrase (topoisomerase II) B subunit - 9 ------------b-e------j---- - [L] COG3449 DNA gyrase inhibitor - 6 a---kzy------------------- TIP49 [L] COG1224 DNA helicase TIP49, TBP-interacting protein - 31 -o----yqvd-lbcefghsn-jxit- MutL [L] COG0323 DNA mismatch repair enzyme (predicted ATPase) - 5 --------------e-gh-------- MutH [L] COG3066 DNA mismatch repair protein - 41 -ompk---vd-lb-e-ghsnuj---- - [L] COG0863 DNA modification methylase - 29 ao-pkzy--drl--e-g-------t- SSL2 [L] COG1061 DNA or RNA helicases of superfamily II - 30 ------yqvdrlbcefghsnujxit- PolA [L] COG0749 DNA polymerase I - 3'-5' exonuclease and polymerase domains - 9 aompk-y------------------- HYS2 [L] COG1311 DNA polymerase II small subunit (predicted phosphatase) - 39 -------qvdrlbcefghsnujxitw DnaE [L] COG0587 DNA polymerase III alpha subunit - 8 --------v--lb------------w PolC [L] COG2176 DNA polymerase III alpha subunit, the Gram-positive type - 12 --------------efghsn-jx--- HolC [L] COG2927 DNA polymerase III chi subunit - 32 -------qvdrlbcefghsnujxitw HolA [L] COG1466 DNA polymerase III delta subunit - 58 a--p--yqvdrlbcefghsnujxit- DnaQ [L] COG0847 DNA polymerase III epsilon subunit and related 3'-5' exonucleases - 37 -------qvdrlbcefghsnujxitw DnaX [L] COG2812 DNA polymerase III, gamma/tau subunits - 4 --------------e-gh-------- HolD [L] COG3050 DNA polymerase III, psi subunit - 8 --mp--yq-d--b------------- POL4 [L] COG1796 DNA polymerase IV (family X) - 28 aompkzy-------efg--------- PolB [L] COG0417 DNA polymerase elongation subunit (family B) - 46 aompkzyqvdrlbcefghsnujxitw DnaN [L] COG0592 DNA polymerase sliding clamp subunit (PCNA homolog) - 46 aompkz-qvdrlbcefghsnujxitw DnaG [L] COG0358 DNA primase (bacterial type) - 9 --------------efghsn------ RdgC [L] COG2974 DNA recombination-dependent growth factor C - 26 aompkzyqvdrlbcefg-------t- SbcD [L] COG0420 DNA repair exonuclease - 20 a-mpkz--v-r-bc-f-----j---- SplB [L] COG1533 DNA repair photolyase - 25 -------qv--lbcefghsn-j---- RadC [L] COG2003 DNA repair proteins - 30 -------q--rlb-e------j---w DnaC [L] COG1484 DNA replication protein - 8 aom-kzy------------------- - [L] COG1697 DNA topoisomerase VI, subunit A - 7 aom-kz-------------------- - [L] COG1389 DNA topoisomerase VI, subunit B - 24 --------vdrlbcefghsnu----- ComEA [L] COG1555 DNA uptake protein and related DNA-binding proteins - 7 -----------l--e-ghs------- RelB [L] COG3077 DNA-damage-inducible protein J - 14 ao-pkz-qvd--b-e---s------- Nfi [L] COG1515 Deoxyinosine 3'endonuclease (endonuclease V) - 17 -om---y----l-cefg--n-j---- PhrB [L] COG0415 Deoxyribodipyrimidine photolyase - 9 aompk-y------------------- MPH1 [L] COG1111 ERCC4-like helicases - 10 aom-kzy------------------- MUS81 [L] COG1948 ERCC4-type nucleases - 7 ---------d--b-efg--------- EndA [L] COG2356 Endonuclease I - 9 --mp---qv-----------u----- - [L] COG2231 Endonuclease III related proteins - 26 -ompkzyqv-r-b-e-g------i-w Nfo [L] COG0648 Endonuclease IV - 10 aompkzy------------------- PRI2 [L] COG2219 Eukaryotic-type DNA primase, large subunit - 11 aompkzy------------------- PRI1 [L] COG1467 Eukaryotic-type DNA primase, small subunit - 36 -om----qvdrlbcefghsnujxitw UvrA [L] COG0178 Excinuclease ATPase subunit - 8 --------------efghs------- SbcB [L] COG2925 Exonuclease I - 37 a-mp--y--drlbcefghsnujx-t- XthA [L] COG0708 Exonuclease III - 14 ----------r---efghsn---it- RecC [L] COG1330 Exonuclease V gamma subunit - 23 --------vdrlb-efghsnujx--- XseB [L] COG1722 Exonuclease VII small subunit - 26 --------vdrlb-efghsnujxi-- XseA [L] COG1570 Exonuclease VII, large subunit - 28 ---------drlbcefghsn-j---w Nei [L] COG0266 Formamidopyrimidine-DNA glycosylase - 8 ---------d----e--h-nuj---- Mug [L] COG3663 G:T/U mismatch-specific DNA glycosylase - 11 --m-k--q-d--bce-----u----- McrB [L] COG1401 GTPase subunit of restriction endonuclease - 35 -om----qvdrlbcefghsnujxitw UvrB [L] COG0556 Helicase subunit of the DNA excision repair complex - 21 aom-k-y------------------- HHT1 [L] COG2036 Histones H3 and H4 - 7 aom-kz-------------------- - [L] COG1591 Holliday junction resolvase - archaeal type - 31 --------vdrlbcefghsnujxitw RuvA [L] COG0632 Holliday junction resolvasome DNA-binding subunit - 23 --------vdr--cefghsnujxit- RuvC [L] COG0817 Holliday junction resolvasome endonuclease subunit - 32 --------vdrlbcefghsnujxitw RuvB [L] COG2255 Holliday junction resolvasome helicase subunit - 28 ------y--d----efghsn-j--t- HrpA [L] COG1643 HrpA-like helicases - 45 -o-p----------e-g--n------ - [L] COG3039 IS5 transposase - 17 -------q-----ce--h-------- InsB [L] COG1662 Insertion element IS1 protein InsB, putative transposase - 219 aompkz-qvdrlbcefghsnujxitw XerC [L] COG0582 Integrase - 64 --mpkzyq-dr-bc------------ - [L] COG1372 Inteins - 5 --m-kz-------------------- - [L] COG3780 Intron_maturase, DNA endonuclease (intein-related) - 46 aompkzyqv-rlb-efghsnuj-it- Ada [L] COG0350 Methylated DNA-protein cysteine methyltransferase - 56 --m-kzyqvdrlbcefghsnujxitw TatD [L] COG0084 Mg-dependent DNase - 22 -om-k-yq----b--f-h-nuj---w - [L] COG1525 Micrococcal nuclease (thermonuclease) homologs - 17 -om-k--qvd-lbc------u---t- - [L] COG1193 MutS-like ATPases involved in mismatch repair, family 1 - 35 -o-p--yqvd-lbcefghsn-jxit- MutS [L] COG0249 MutS-like ATPases involved in mismatch repair, family 2 - 29 --------vdrlbcefghsnujxit- - [L] COG0742 N6-adenine-specific methylase - 10 aompk--------------------- - [L] COG1933 NA polymerase II large subunit - 35 -------qvdrlbcefghsnujxitw Lig [L] COG0272 NAD-dependent DNA ligase (contains BRCT domain type II) - 11 ------y--dr---efgh---j---- NPY1 [L] COG2816 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding - 198 aomp-zyqvdrlbcefghsnujxit- MutT [LR] COG0494 NTP pyrophosphohydrolases including oxidative damage repair enzymes - 5 --------------e-gh-------- SeqA [L] COG3057 Negative regulator of replication initiationR - 40 -om----qvdrlbcefghsnujxitw UvrC [L] COG0322 Nuclease subunit of the excinuclease complex - 35 -o----y---rlbcefgh-n-j---w DinP [L] COG0389 Nucleotidyltransferase/DNA polymerase involved in DNA repair - 8 -----------lb-e------j---- XtmA [L] COG3728 Phage terminase, small subunit - 6 -------------------nu----- - [L] COG3298 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB - 11 --m----------cefgh--uj---- - [L] COG3593 Predicted ATP-dependent endonuclease of the OLD family - 23 aompkzy------------------- MCM2 [L] COG1241 Predicted ATPase involved in replication control, Cdc46/Mcm family - 5 a---kz--v----------------- - [L] COG1743 Predicted DNA methylase containing a Zn-ribbon module - 12 aompkzy------------------- - [L] COG1041 Predicted DNA modification methylase - 5 ------y--d-----f-----j---- - [L] COG3569 Predicted DNA topoisomerase IB - 46 aompkzyqvdrlbcefghsnujxit- Nth [L] COG0177 Predicted EndoIII-related endonuclease - 5 a-m-kz-------------------- - [L] COG2254 Predicted HD superfamily hydrolase, possibly a nuclease - 21 a-m-kz---d-lbcefghsn------ - [L] COG0116 Predicted N6-adenine-specific DNA methylases - 25 -------qvdrlbcefghsnuj--t- Smf [LN] COG0758 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake - 20 -o---------lb-efg--n-j---- - [L] COG2827 Predicted endonuclease containing a URI domain - 21 -------qvdr--cefghsnuj--t- - [L] COG0792 Predicted endonuclease distantly related to archaeal Holliday junction resolvase - 6 --------vd--bc------u----- - [L] COG1787 Predicted endonuclease distantly related to archaeal Holliday junction resolvase and Mrr-like restriction enzymes - 31 -------qvdrlbcefghsnujxi-w - [L] COG0816 Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B. subtilis) - 9 ----------r-b--f-----j---- - [L] COG3285 Predicted eukaryotic-type DNA primase - 4 -om---------b------------- - [L] COG3359 Predicted exonuclease - 7 ---------drl--efg--------- - [L] COG3695 Predicted methylated DNA-protein cysteine methyltransferase - 9 -om-kz----r--------------- - [L] COG1637 Predicted nuclease of the RecB family - 4 ---------d-----fg----j---- - [L] COG3183 Predicted restriction endonuclease - 5 ---p-----d----e----n------ - [L] COG3440 Predicted restriction endonuclease - 11 --mpk-----r--------------- - [L] COG2452 Predicted site-specific integrase-resolvase - 23 a--p-----dr---efgh-n-j---- - [L] COG1425 Predicted transposase - 56 -o-p----vd--b-efgh-nuj---- - [L] COG1943 Predicted transposase - 64 ---------dr--c-------j---- - [L] COG3293 Predicted transposase - 33 ---p------rlb-e------j---w - [L] COG3328 Predicted transposase - 60 a--p-----d--bce----n-j---- - [L] COG3335 Predicted transposase - 61 -o-p-----d--bce----------- - [L] COG3385 Predicted transposase - 88 -ompk--qvdr--ce---s-u---t- - [L] COG0675 Predicted transposases - 5 ----kz---d--------------t- - [L] COG2810 Predicted type IV restriction endonuclease - 30 -------qvdrlbcefghsnujxit- PriA [L] COG1198 Primosomal protein N' (replication factor Y) - superfamily II helicase - 7 --------------e-gh-n------ PriB [L] COG2965 Primosomal replication protein N - 10 ------------b---g-sn------ - [L] COG2946 Putative phage replication protein RstA - 135 ---p-----drlbcefgh-n-j---w Tra5 [L] COG2801 Putative transposase - 15 aom----q----------s--j---- - [L] COG3316 Putative transposase - 12 ao-p-----d--b------------- - [L] COG3415 Putative transposase - 34 -ompkzyq--rlb-efghsn-j---- DinG [L] COG1199 Rad3-related DNA helicases - 4 -------q---l------s--j---- RepA [L] COG3598 RecA-family ATPase - 57 aompkzyqvdrlbcefghsnujxitw RecA [L] COG0468 RecA/RadA recombinase - 14 a-m-kz-qv--lb------------- - [L] COG1468 RecB family exonuclease - 12 --m--z----r---------ujx-t- - [L] COG2887 RecB family exonuclease - 27 -------qvdrlbcefghsnujx-t- RecG [LK] COG1200 RecG-like helicases - 20 ---------drlbcefghs--jxit- RecF [L] COG1195 Recombinational DNA repair ATPase (RecF pathway) - 6 -----------lb-e----------- RecT [L] COG3723 Recombinational DNA repair protein (RecE pathway) - 28 -------q-drlbcefghsnujxitw RecR [L] COG0353 Recombinational DNA repair protein (RecF pathway) - 24 ---------drlbcefghsn-jxitw RecO [L] COG1381 Recombinational DNA repair protein (RecF pathway) - 18 aompkzy------------------- - [L] COG1599 Replication factor A large subunit and related ssDNA-binding proteins - 7 -----------lb------------w DnaB [L] COG3611 Replication initiation/membrane attachment protein - 38 -------qvdrlbcefghsnujxitw DnaB [L] COG0305 Replicative DNA helicase - 20 ---------drlbce---s--j---- McrA [L] COG1403 Restriction endonuclease - 6 -om------dr---e----------- Mrr [L] COG1715 Restriction endonuclease - 6 -----------------h-nu----- - [L] COG3587 Restriction endonuclease - 50 aompk-----rl--efghs-uj---w HsdS [L] COG0732 Restriction endonuclease S subunits - 32 aom-k------l--efghsnuj---w HsdR [L] COG0610 Restriction enzymes type I helicase subunits and related helicases - 11 ----------r-bcefg--------- - [L] COG3344 Retron-type reverse transcriptase - 11 a-m-kz-qv----------------- - [L] COG1110 Reverse gyrase - 26 -o----y--dr-bcefghsnujx-t- RnhA [L] COG0328 Ribonuclease HI - 38 aompkzyqvdrlbcefghsnujxit- RnhB [L] COG0164 Ribonuclease HII - 9 -------q---lb----------i-w - [L] COG1039 Ribonuclease HII Family 2 - 49 ------yqvdrlbcefghsnujxitw Ssb [L] COG0629 Single-stranded DNA-binding protein - 48 aompk--qvd-lbcefghsnujxit- RecJ [L] COG0608 Single-stranded DNA-specific exonuclease - 37 --m-kz-----lbce-ghsnuj---w Dcm [L] COG0270 Site-specific DNA methylase - 18 --mpk-------bce-ghsnu---t- Dam [L] COG0338 Site-specific DNA methylase - 34 ---pk----drlb-efg-s--j---- PinR [L] COG1961 Site-specific recombinases, DNA invertase Pin homologs - 17 a-mpk--q---lb-----------tw - [L] COG1658 Small primase-like proteins (Toprim domain) - 23 -o-------d-lbcefghs-ujx-t- Dps [L] COG0783 Starvation-inducible DNA-binding protein - 76 -omp--yqvdrlbcefghsnujxitw UvrD [L] COG0210 Superfamily I DNA and RNA helicases - 37 aompk-yqv-r--cef--s-u----w - [L] COG1112 Superfamily I DNA and RNA helicases and helicase subunits - 136 a-mp--yq-drlbcefghsnujx-tw SrmB [LKJ] COG0513 Superfamily II DNA and RNA helicases - 22 -----zy--d-lbcefghsn-j--t- RecQ [L] COG0514 Superfamily II DNA helicase - 6 a-mp---qv----------------- - [L] COG1059 Thermostable 8-oxoguanine DNA glycosylase - 58 aompkzyqvdrlbcefghsnujxitw TopA [L] COG0550 Topoisomerase IA - 29 --------vdrlbcefghsnujxit- Mfd [LK] COG1197 Transcription-repair coupling factor - superfamily II helicase - 5 a-m-kz-------------------- - [L] COG2178 Translin (RNA-binding protein, recombination hotspot binding in eukaryotes) - 118 ---p-----drlb-efgh---j---- - [L] COG2963 Transposase - 47 -o-p-----d-l--e------j---- - [L] COG3436 Transposase - 52 ---p------r-b--------j---- - [L] COG3464 Transposase - 73 ----------rlb--f---n-j---- - [L] COG3547 Transposase - 25 -----------lb--f-----j---- - [L] COG3666 Transposase - 30 -o---------------h-n------ - [L] COG3676 Transposase - 15 -o--k--------ce----------- - [L] COG3677 Transposase - 47 ----------rlb-e----n-j---- Tra8 [L] COG2826 Transposase, IS30 family - 40 aom-k-----rl--efghsnuj---w HsdM [L] COG0286 Type I restriction-modification system methyltransferase subunit - 29 -omp-----d--b-e----nuj--t- - [L] COG1002 Type II restriction enzyme, methylase subunits - 24 ------y-vdrlb-efghsnuj---w - [L] COG2256 Uncharacterized ATPase related to the helicase subunit of the Holliday junction resolvase - 27 ------y--drlb-efghsnu--itw Ung [L] COG0692 Uracil DNA glycosylase - 34 ao-pkz-qvdrl-c--gh-nujx-t- - [L] COG1573 Uracil-DNA glycosylase - 40 aompk---v--lb-efghsnu--itw TopA [L] COG0551 Zn-finger domain associated with topoisomerase type I