- 22 --m-k---vd-lb-efgh---j---- RsmC [J] COG2813 16S RNA G1207 methylase RsmC - 64 -------qvdrlbcefghsnujxit- RsuA [J] COG1187 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases - 21 a-mpkz-qvd--b-ef-----j---- LigT [J] COG1514 2'-5' RNA ligase - 59 aompkz-qvdr-bcefghsnujxit- MiaB [J] COG0621 2-methylthioadenine synthetase - 99 -o-pk-y-vdrlb-efgh-nujx--w RimL [J] COG1670 Acetyltransferases, including N-acetylases of ribosomal proteins - 43 aompkzyqvdrlbcefghsnujxitw AlaS [J] COG0013 Alanyl-tRNA synthetase - 5 ---------drl---f-----j---- Aph [J] COG3231 Aminoglycoside phosphotransferase - 9 aompkz-------------------- GatE [J] COG2511 Archaeal Glu-tRNAGln amidotransferase subunit E (contains GAD domain) - 45 aompkzyqvdrlbcefghsnujxitw ArgS [J] COG0018 Arginyl-tRNA synthetase - 66 aom--zyqvdrlbc-f---nujxitw GatA [J] COG0154 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases - 33 aom--zyqvdrlbc-f---nujxitw GatB [J] COG0064 Asp-tRNAAsn/Glu-tRNAGln amidotransferase B subunit (PET112 homolog) - 30 aom--z-qvdrlbc-f---nujxitw GatC [J] COG0721 Asp-tRNAAsn/Glu-tRNAGln amidotransferase C subunit - 34 ------yqvdrlbcefghsnujxitw AspS [J] COG0173 Aspartyl-tRNA synthetase - 40 aompkzy--d-lbce-ghs-----tw AsnS [J] COG0017 Aspartyl/asparaginyl-tRNA synthetases - 43 ao-pkzyqvdrlbcefghsnujxitw CysS [J] COG0215 Cysteinyl-tRNA synthetase - 17 ------yqvdrlb-efgh-n------ Dtd [J] COG1490 D-Tyr-tRNAtyr deacylase - 12 aompkzy--------------j---- DYS1 [J] COG1899 Deoxyhypusine synthase - 49 aompkzyqvdrlbcefghsnujxitw KsgA [J] COG0030 Dimethyladenosine transferase (rRNA methylation) - 10 aompkzy------------------- DPH5 [J] COG1798 Diphthamide biosynthesis methyltransferase DPH5 - 11 aompkzy------------------- DPH2 [J] COG1736 Diphthamide synthase subunit DPH2 - 10 aompkzy------------------- TIF6 [J] COG1976 Eukaryotic translation initiation factor 6 (EIF6) - 10 aompkzy------------------- NOP1 [J] COG1889 Fibrillarin-like rRNA methylase - 78 aompkzyqvdrlbcefghsnujxitw TufB [JE] COG0050 GTPases - translation elongation factors - 71 aompkzyqvdrlbcefghsnujxitw GlnS [J] COG0008 Glutamyl- and glutaminyl-tRNA synthetases - 25 -------qv--lbcefghsnujxi-- GlyQ [J] COG0752 Glycyl-tRNA synthetase, alpha subunit - 25 -------qv--lbcefghsnujxi-- GlyS [J] COG0751 Glycyl-tRNA synthetase, beta subunit - 19 aompkzy--dr-------------tw GRS1 [J] COG0423 Glycyl-tRNA synthetase, class II - 49 aompkzyqvdrlbcefghsnujxitw HisS [J] COG0124 Histidyl-tRNA synthetase - 3 a-m----q------------------ - [J] COG1431 Homologs of the eukaryotic argonaute protein, possible role in translation - 44 aompkzyqvdrlbcefghsnujxitw IleS [J] COG0060 Isoleucyl-tRNA synthetase - 45 aompkzyqvdrlbcefghsnujxitw LeuS [J] COG0495 Leucyl-tRNA synthetase - 14 aompkz---------------jx-t- LysS [J] COG1384 Lysyl-tRNA synthetase class I - 35 ------yqvdrlbcefghsnu--i-w LysU [J] COG1190 Lysyl-tRNA synthetase class II - 51 aompkzyqvdrlbcefghsnujxitw Map [J] COG0024 Methionine aminopeptidase - 39 ------yqvdrlbcefghsnujxitw Fmt [J] COG0223 Methionyl-tRNA formyltransferase - 45 aompkzyqvdrlbcefghsnujxitw MetG [J] COG0143 Methionyl-tRNA synthetase - 25 aomp--y-------efghsn-jx-t- FtsJ [J] COG0293 Methyltransferase involved in cell division - 37 -------qvdrlbcefghsnujxitw Def [J] COG0242 N-formylmethionyl-tRNA deformylase - 11 aompkzyq------------------ TRM1 [J] COG1867 N2,N2-dimethylguanosine tRNA methyltransferase - 11 aompkzy------------------- NMD3 [J] COG1499 NMD protein affecting ribosome stability and mRNA decay - 14 aompkzy------------------- - [J] COG2016 PUA domain (predicted RNA-binding domain) - 11 aompkzyq------------------ eRF1 [J] COG1503 Peptide chain release factor eRF1 - 34 ------yqvdrlbcefghsnujxitw Pth [J] COG0193 Peptidyl-tRNA hydrolase - 44 aompkzyqvdrlbcefghsnujxitw PheS [J] COG0016 Phenylalanyl-tRNA synthetase alpha subunit - 3 a-m----------------------- - [J] COG2024 Phenylalanyl-tRNA synthetase alpha subunit, archaeal type - 44 aompkzyqvdrlbcefghsnujxitw PheT [J] COG0072 Phenylalanyl-tRNA synthetase beta subunit - 30 -------qvdrlbcefghsnujxit- Pnp [J] COG1185 Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) - 9 aompkz-------------------- - [J] COG2263 Predicted RNA methylase - 9 aompkz-------------------- - [J] COG1491 Predicted RNA-binding protein - 7 a-mpkz-------------------- - [J] COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) - 20 aom-kz-----lb-efghsn------ - [J] COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein - 14 aompkzyqv-r--------------- GCD14 [J] COG2519 Predicted SAM-dependent methyltransferase involved in tRNA-Met maturation - 10 aompkzy------------------- - [J] COG2260 Predicted Zn-ribbon RNA-binding protein - 9 aompkz-------------------- - [J] COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation - 19 aompkzy--d---c-fg----j---- YSH1 [J] COG1236 Predicted exonuclease of the beta-lactamase fold involved in RNA processing - 7 aom-kz-------------------- - [J] COG1325 Predicted exosome subunit - 10 aompkzy------------------- - [J] COG1500 Predicted exosome subunit - 9 aompkz-------------------- - [J] COG1258 Predicted pseudouridylate synthase - 26 ---------drlbcefghsnuj-i-w CspR [J] COG0219 Predicted rRNA methylase (SpoU class) - 18 a------qv-rlbc------ujx-tw - [J] COG1189 Predicted rRNA methylases - 56 aompk-yqvdrlbcefghsnujxitw HemK [J] COG2890 Predicted rRNA or tRNA methylase - 10 --------v--lb-----------tw - [J] COG2868 Predicted ribosomal protein - 5 -om-k--------------------- - [J] COG2117 Predicted subunit of tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain - 38 ------yqvdrlbcefghsnujxitw TrmU [J] COG0482 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain - 44 aompkzyqvdrlbcefghsnujxitw ProS [J] COG0442 Prolyl-tRNA synthetase - 34 ------yqvdrlbcefghsnujxitw PrfA [J] COG0216 Protein chain release factor A - 39 ------yqvdrlbcefghsnujxit- PrfB [J] COG1186 Protein chain release factor B - 8 a-m-kzy------------------- IMP4 [J] COG2136 Protein containing the IMP4 domain present in small nuclear ribonucleoproteins; implicated in RNA processing - 12 aompkzy------------------- SIK1 [J] COG1498 Protein implicated in ribosomal biogenesis, Nop56p homolog - 6 a-m-kzy------------------- NIP7 [J] COG1374 Protein involved in ribosomal biogenesis, contains PUA domain - 42 aompkzyqvdrlbcefghsnujxitw TruB [J] COG0130 Pseudouridine synthase - 44 aompk-yqvdrlbcefghsnujxitw TruA [J] COG0101 Pseudouridylate synthase (tRNA psi55) - 97 ------yqvdrlbcefghsnujxitw RluA [J] COG0564 Pseudouridylate synthases, 23S RNA-specific - 53 aompkzyqvdrlbcefghsn-jxitw SUA5 [J] COG0009 Putative translation factor (SUA5) - 74 -o--kzyqvdrlbcefghsnuj---- TdcF [J] COG0251 Putative translation initiation inhibitor - 8 aompk--------------------- - [J] COG1549 Queuine tRNA-ribosyltransferases, contain PUA domain - 38 aompkz-qvd-lbcefghsnujxit- Tgt [J] COG0343 Queuine/archaeosine tRNA-ribosyltransferase - 9 a-mpkzy------------------- RRP4 [J] COG1097 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) - 10 aompkzy------------------- GAR1 [J] COG3277 RNA-binding protein involved in rRNA processing - 12 a--pkzy--d----ef---------- KptA [J] COG1859 RNA:NAD 2'-phosphotransferase - 10 aompkzy------------------- POP4 [J] COG1588 RNAse P protein subunit P29 - 10 aompkzy------------------- RPR2 [J] COG2023 RNAse P protein subunit RPR2 - 32 --------vdrlbcefghsnujxitw RnpA [J] COG0594 RNase P protein component - 8 aom-kzy------------------- POP5 [J] COG1369 RNase P subunit P14 and its archaeal orthologs - 28 a-mpkzyq-dr-b-efghsn-jx--- Rph [J] COG0689 RNase PH - 9 a-mpkzy------------------- - [J] COG2123 RNase PH-related exoribonuclease - 17 ------y---r--cefghs--jx--- Rnd [J] COG0349 Ribonuclease D - 6 --------------e--h---j---- Rna [J] COG3719 Ribonuclease I - 8 aom-kzy------------------- - [J] COG1603 Ribonuclease P subunit Rpp30 - 36 -o--kz-qv-r-bcefghsnujxi-- CafA [J] COG1530 Ribonucleases G and E - 21 aompkzy-v--lb------------- RPL8A [J] COG1358 Ribosomal protein HS6-type (S12/L30/L7a) - 45 aompkzyqvdrlbcefghsnujxitw RplA [J] COG0081 Ribosomal protein L1 - 45 aompkzyqvdrlbcefghsnujxitw RplJ [J] COG0244 Ribosomal protein L10 - 46 aompkzyqvdrlbcefghsnujxitw RplK [J] COG0080 Ribosomal protein L11 - 22 -------qvd-lbcefghsnuj---- PrmA [J] COG2264 Ribosomal protein L11 methylase - 13 aompkzy------------------- RPP1A [J] COG2058 Ribosomal protein L12E/L44/L45/RPP1/RPP2 - 45 aompkzyqvdrlbcefghsnujxitw RplM [J] COG0102 Ribosomal protein L13 - 45 aompkzyqvdrlbcefghsnujxitw RplN [J] COG0093 Ribosomal protein L14 - 7 --m-kzy------------------- RPL14A [J] COG2163 Ribosomal protein L14E - 44 aompkzyqvdrlbcefghsnujxitw RplO [J] COG0200 Ribosomal protein L15 - 11 aompkzy------------------- RPL15A [J] COG1632 Ribosomal protein L15E - 44 aompkzyqvdrlbcefghsnujxitw RplP [J] COG0197 Ribosomal protein L16/L10E - 34 ------yqvdrlbcefghsnujxitw RplQ [J] COG0203 Ribosomal protein L17 - 43 aompkzyqvdrlbcefghsnujxitw RplR [J] COG0256 Ribosomal protein L18 - 11 aompkzy------------------- RPL18A [J] COG1727 Ribosomal protein L18E - 34 ------yqvdrlbcefghsnujxitw RplS [J] COG0335 Ribosomal protein L19 - 11 aompkzy------------------- RPL19A [J] COG2147 Ribosomal protein L19E - 45 aompkzyqvdrlbcefghsnujxitw RplB [J] COG0090 Ribosomal protein L2 - 33 -------qvdrlbcefghsnujxitw RplT [J] COG0292 Ribosomal protein L20 - 8 a-m-kzy------------------- RPL20A [J] COG2157 Ribosomal protein L20A (L18A) - 33 -------qvdrlbcefghsnujxitw RplU [J] COG0261 Ribosomal protein L21 - 11 aompkzy------------------- RPL21A [J] COG2139 Ribosomal protein L21E - 45 aompkzyqvdrlbcefghsnujxitw RplV [J] COG0091 Ribosomal protein L22 - 43 aompkzyqvdrlbcefghsnujxitw RplW [J] COG0089 Ribosomal protein L23 - 44 aompkzyqvdrlbcefghsnujxitw RplX [J] COG0198 Ribosomal protein L24 - 12 aompkzy------------------- RPL24A [J] COG2075 Ribosomal protein L24E - 28 -------qvdr-bcefghsnujxit- RplY [J] COG1825 Ribosomal protein L25 (general stress protein Ctc) - 34 ------yqvdrlbcefghsnujxitw RpmA [J] COG0211 Ribosomal protein L27 - 34 ------yqvdrlbcefghsnujxitw RpmB [J] COG0227 Ribosomal protein L28 - 44 aompkzyqvdrlbcefghsnujxitw RpmC [J] COG0255 Ribosomal protein L29 - 44 aompkzyqvdrlbcefghsnujxitw RplC [J] COG0087 Ribosomal protein L3 - 37 aompkzyqvdrlb-efghsn-jx-t- RpmD [J] COG1841 Ribosomal protein L30/L7E - 7 a-m-kzy------------------- RPL30 [J] COG1911 Ribosomal protein L30E - 43 -------qvdrlbcefghsnujxitw RpmE [J] COG0254 Ribosomal protein L31 - 11 aompkzy------------------- RPL31A [J] COG2097 Ribosomal protein L31E - 32 ------yqvd-lbcefghsnujxitw RpmF [J] COG0333 Ribosomal protein L32 - 10 aompkzy------------------- RPL32 [J] COG1717 Ribosomal protein L32E - 40 ------yqvdrlbcefghsnujxitw RpmG [J] COG0267 Ribosomal protein L33 - 34 ------yqvdrlbcefghsnujxitw RpmH [J] COG0230 Ribosomal protein L34 - 7 --m-kzy------------------- RPL34A [J] COG2174 Ribosomal protein L34E - 34 ------yqvdrlbcefghsnujxitw RpmI [J] COG0291 Ribosomal protein L35 - 5 ----kzy------------------- - [J] COG2451 Ribosomal protein L35AE/L33A - 38 ------yqvdrlbcefghsnujxitw RpmJ [J] COG0257 Ribosomal protein L36 - 11 aompkzy------------------- RPL43A [J] COG1997 Ribosomal protein L37AE/L43A - 11 aompkzy------------------- RPL37A [J] COG2126 Ribosomal protein L37E - 10 aompkzy------------------- RPL39 [J] COG2167 Ribosomal protein L39E - 45 aompkzyqvdrlbcefghsnujxitw RplD [J] COG0088 Ribosomal protein L4 - 11 aompkzy------------------- RPL40A [J] COG1552 Ribosomal protein L40E - 11 aompkzy------------------- RPL42A [J] COG1631 Ribosomal protein L44E - 45 aompkzyqvdrlbcefghsnujxitw RplE [J] COG0094 Ribosomal protein L5 - 45 aompkzyqvdrlbcefghsnujxitw RplF [J] COG0097 Ribosomal protein L6 - 35 ------yqvdrlbcefghsnujxitw RplL [J] COG0222 Ribosomal protein L7/L12 - 33 -------qvdrlbcefghsnujxitw RplI [J] COG0359 Ribosomal protein L9 - 33 ------yqvdrlbcefghsnujxit- RpsA [J] COG0539 Ribosomal protein S1 - 9 ------y-vd-lb------------- VacB [J] COG1098 Ribosomal protein S1 domains - 45 aompkzyqvdrlbcefghsnujxitw RpsJ [J] COG0051 Ribosomal protein S10 - 45 aompkzyqvdrlbcefghsnujxitw RpsK [J] COG0100 Ribosomal protein S11 - 46 aompkzyqvdrlbcefghsnujxitw RpsL [J] COG0048 Ribosomal protein S12 - 45 aompkzyqvdrlbcefghsnujxitw RpsM [J] COG0099 Ribosomal protein S13 - 49 aompkzyqvdrlbcefghsnujxitw RpsN [J] COG0199 Ribosomal protein S14 - 45 aompkzyqvdrlbcefghsnujxitw RpsO [J] COG0184 Ribosomal protein S15P/S13E - 34 ------yqvdrlbcefghsnujxitw RpsP [J] COG0228 Ribosomal protein S16 - 45 aompkzyqvdrlbcefghsnujxitw RpsQ [J] COG0186 Ribosomal protein S17 - 11 aompkzy------------------- RPS17A [J] COG1383 Ribosomal protein S17E - 35 ------yqvdrlbcefghsnujxitw RpsR [J] COG0238 Ribosomal protein S18 - 44 aompkzyqvdrlbcefghsnujxitw RpsS [J] COG0185 Ribosomal protein S19 - 11 aompkzy------------------- RPS19A [J] COG2238 Ribosomal protein S19E (S16A) - 45 aompkzyqvdrlbcefghsnujxitw RpsB [J] COG0052 Ribosomal protein S2 - 33 -------qvdrlbcefghsnujxitw RpsT [J] COG0268 Ribosomal protein S20 - 29 -------q---lbcefghsnujxitw RpsU [J] COG0828 Ribosomal protein S21 - 11 aompkzy------------------- RPS24A [J] COG2004 Ribosomal protein S24E - 10 aompkzy------------------- RPS31 [J] COG1998 Ribosomal protein S27AE - 11 aompkzy------------------- RPS27A [J] COG2051 Ribosomal protein S27E - 11 aompkzy------------------- RPS28A [J] COG2053 Ribosomal protein S28E/S33 - 43 aompkzyqvdrlbcefghsnujxitw RpsC [J] COG0092 Ribosomal protein S3 - 11 aompkzy------------------- RPS1A [J] COG1890 Ribosomal protein S3AE - 46 aompkzyqvdrlbcefghsnujxitw RpsD [J] COG0522 Ribosomal protein S4 and related proteins - 11 aompkzy------------------- RPS4A [J] COG1471 Ribosomal protein S4E - 44 aompkzyqvdrlbcefghsnujxitw RpsE [J] COG0098 Ribosomal protein S5 - 34 ------yqvdrlbcefghsnujxitw RpsF [J] COG0360 Ribosomal protein S6 - 11 aompkzy------------------- RPS6A [J] COG2125 Ribosomal protein S6E (S10) - 45 aompkzyqvdrlbcefghsnujxitw RpsG [J] COG0049 Ribosomal protein S7 - 45 aompkzyqvdrlbcefghsnujxitw RpsH [J] COG0096 Ribosomal protein S8 - 12 aompkzy------------------- RPS8A [J] COG2007 Ribosomal protein S8E - 45 aompkzyqvdrlbcefghsnujxitw RpsI [J] COG0103 Ribosomal protein S9 - 4 --------------efg--------- Rmf [J] COG3130 Ribosome modulation factor - 34 ------yqvdrlbcefghsnujxitw Frr [J] COG0233 Ribosome recycling factor - 19 --------v--lb-efgh-nuj---- - [J] COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) - 25 -------qvdrlbcefghs--jxit- - [J] COG1544 Ribosome-associated protein Y (PSrp-1) - 33 -------qvdrlbcefghsnujxitw RbfA [J] COG0858 Ribosome-binding factor A - 28 -------qvdrlbcefghsnujx-t- RimM [J] COG0806 RimM protein, required for 16S rRNA processing - 26 -------qvd-lbcefghsnujx-t- QueA [J] COG0809 S-adenosylmethionine:tRNA-ribosyltransferase-isomerase (queuine synthetase) - 42 ----k-yqv-rlbcefghsnuj-i-- TrmA [J] COG2265 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase - 7 -------q------ef-h--u----- SelB [J] COG3276 Selenocysteine-specific translation elongation factor - 44 aompkzyqvdrlbcefghsnujxitw SerS [J] COG0172 Seryl-tRNA synthetase - 16 --------------efghsn-jx--- SmpA [J] COG2913 Small protein A (tmRNA-binding) - 48 aompkzyqvdrlbcefghsnujxitw ThrS [J] COG0441 Threonyl-tRNA synthetase - 74 aompkzyqvdrlbcefghsnujxitw FusA [J] COG0480 Translation elongation and release factors (GTPases) - 10 aompkzy------------------- EFB1 [J] COG2092 Translation elongation factor EF-1beta - 51 aompkzyqvdrlbcefghsnujxitw Efp [J] COG0231 Translation elongation factor P/translation initiation factor eIF-5A - 33 -------qvdrlbcefghsnujxitw Tsf [J] COG0264 Translation elongation factor Ts - 19 aompkzy------cefgh-------- SUI1 [J] COG0023 Translation initiation factor (SUI1) - 47 aompkzyqvdrlbcefghsnujxitw InfB [J] COG0532 Translation initiation factor 2 (GTPase) - 45 aompkzyqvdrlbcefghsnujxitw InfA [J] COG0361 Translation initiation factor IF-1 - 33 -------qvdrlbcefghsnujxitw InfC [J] COG0290 Translation initiation factor IF3 - 11 aompkzy------------------- GCD7 [J] COG1601 Translation initiation factor eIF-2, beta subunit/eIF-5 N-terminal domain - 16 a-mpkzyqv---bc-f--s--j---- GCN3 [J] COG0182 Translation initiation factor eIF-2B alpha subunit - 15 aompkzy-v----------------- GCD2 [J] COG1184 Translation initiation factor eIF-2B delta subunit - 10 aompkzy------------------- SUI2 [J] COG1093 Translation initiation factor eIF2alpha - 11 -------q------e-ghs--j--t- - [J] COG2269 Truncated, possibly inactive Class II lysyl-tRNA synthetase - 47 aompkzyqvdrlbcefghsnujxitw TrpS [J] COG0180 Tryptophanyl-tRNA synthetase - 48 aompkzyqvdrlbcefghsnujxitw TyrS [J] COG0162 Tyrosyl-tRNA synthetase - 5 -----------lb------------w - [J] COG3557 Uncharacterized domain/protein associated with RNAses G and E - 43 aompkzyqvdrlbcefghsnujxitw ValS [J] COG0525 Valyl-tRNA synthetase - 22 aomp-z---d---cefghsn-j---- LasT [J] COG0565 rRNA methylase - 65 a-----yqvdrlbcefghsnujxitw SpoU [J] COG0566 rRNA methylases - 51 aom-kzy-vdrlbcefghsnuj-i-- Sun [J] COG0144 tRNA and rRNA cytosine-C5-methylases - 31 ------yqvdrlbcefghsnujxit- MiaA [J] COG0324 tRNA delta(2)-isopentenylpyrophosphate transferase - 9 aompkz-------------------- CCA1 [J] COG1746 tRNA nucleotidyltransferase (CCA-adding enzyme) - 48 ------yqvdrlbcefghsnujxit- PcnB [J] COG0617 tRNA nucleotidyltransferase/poly(A) polymerase - 12 aompkzy------------------- SEN2 [J] COG1676 tRNA splicing endonuclease - 33 -------qvdrlbcefghsnujxitw TrmD [J] COG0336 tRNA-(guanine-N1)-methyltransferase - 8 ----------r---efg--------- MalT [K] COG2909 ATP-dependent transcriptional regulator - 246 --------v-rlbcefghsnuj---- AraC [K] COG2207 AraC-type DNA-binding domain-containing proteins - 10 a-mpkz-------------------- Ssh10b [K] COG1581 Archaeal DNA-binding protein - 4 ------------b-e----n------ - [K] COG2732 Barstar, RNAse (barnase) inhibitor - 14 ao--k----d-lb-efghs------- BirA [KH] COG1654 Biotin operon repressor - 67 -o-----qvdrlb-efghsn-jx--- CspC [K] COG1278 Cold shock proteins - 58 ---------drlbcefg----j---- CsgD [K] COG2771 DNA-binding HTH domains - 14 ----------r-b-e-g----j---- CadC [K] COG3710 DNA-binding winged-HTH domains - 44 aompkzyqvdrlbcefghsnujxitw RpoA [K] COG0202 DNA-directed RNA polymerase alpha subunit/40 kD subunit - 49 aompkzyqvdrlbcefghsnujxitw RpoB [K] COG0085 DNA-directed RNA polymerase beta subunit/140 kD subunit (split gene in Mjan, Mthe, Aful) - 60 aompkzyqvdrlbcefghsnujxitw RpoC [K] COG0086 DNA-directed RNA polymerase beta' subunit/160 kD subunit (split gene in archaea and Syn) - 7 -----------lb------------w RpoE [K] COG3343 DNA-directed RNA polymerase delta subunit - 66 -------qvdrlbcefghsnujxitw RpoD [K] COG0568 DNA-directed RNA polymerase sigma subunits (sigma70/sigma32) - 23 -------qv-r-bcefg---u--it- FliA [K] COG1191 DNA-directed RNA polymerase specialized sigma subunit - 109 --------vdrlbcefghsn-j--t- RpoE [K] COG1595 DNA-directed RNA polymerase specialized sigma subunits, sigma24 homologs - 20 -------q----b-efg-snuj-it- RpoN [K] COG1508 DNA-directed RNA polymerase specialized sigma subunits, sigma54 homologs - 11 aompkzy------------------- RPB7 [K] COG1095 DNA-directed RNA polymerase subunit E' - 9 aompkz-------------------- - [K] COG2093 DNA-directed RNA polymerase subunit E'' - 37 aompkzyqvdrlbcefghsnujx-t- RpoZ [K] COG1758 DNA-directed RNA polymerase subunit K/omega - 15 aompkzy------------------- RPB9 [K] COG1594 DNA-directed RNA polymerase subunit M/Transcription elongation factor TFIIS - 10 aompkzy------------------- RPC10 [K] COG1996 DNA-directed RNA polymerase subunit RPC10 (contains C4-type Zn-finger) - 10 aompkzy------------------- RPB5 [K] COG2012 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 - 11 aompkzy------------------- RPB11 [K] COG1761 DNA-directed RNA polymerase, subunit L - 10 aompkzy------------------- RPB10 [K] COG1644 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) - 10 aompk-y-v----------------- ELP3 [K] COG1243 ELP3 component of the RNA polymerase II complex, consists of an N-terminal BioB/LipA-like domain and a C-terminal histone acetyltransferase domain (only BioB/LipA-like domain in Thermotoga) - 45 -o----yqvd-lbcefghsnuj-itw VacB [K] COG0557 Exoribonucleases - 10 --------------efghsn------ Fis [KL] COG2901 Factor for inversion stimulation Fis, transcriptional activator - 7 --------v---b-e----------- GlpP [K] COG1954 Glycerol-3-phosphate responsive antiterminator (mRNA-binding) - 309 aompkzyqvdrlbcefghsnuj-i-w WecD [KR] COG0454 Histone acetyltransferase HPA2 and related acetyltransferases - 35 aompkz--vdrlb-e---s--j-it- TroR [K] COG1321 Mn-dependent transcriptional regulator - 8 -------qv---b-efg--------- FlgM [KN] COG2747 Negative regulator of flagellin synthesis (anti-sigma-28 factor) - 5 -----------l--e--h-n------ - [K] COG3561 Phage anti-repressor protein - 3 ----------r-b-e----------- PaaX [K] COG3327 Phenylacetic acid-responsive transcriptional repressor - 21 aompkzy-vd-lbc------u---t- - [K] COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP - 13 ---------drlb-------uj---w - [K] COG2740 Predicted nucleic-acid-binding protein implicated in transcription termination - 11 aompkzy------------------- - [K] COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 - 42 -------qvdrlbcefghsnujx--- - [K] COG1959 Predicted transcriptional regulator - 12 ---p-----dr-bc--g--------- - [K] COG2345 Predicted transcriptional regulator - 20 ---------dr-b-efg-snuj---- - [K] COG2378 Predicted transcriptional regulator - 6 a-m-kz-------------------- - [K] COG2462 Predicted transcriptional regulator - 24 -----------l--ef-hsn-j---- - [K] COG2932 Predicted transcriptional regulator - 9 --------------e-g-sn------ - [K] COG2944 Predicted transcriptional regulator - 11 --------------e-g-s------- AlpA [K] COG3311 Predicted transcriptional regulator - 9 aom----------------------- - [K] COG3355 Predicted transcriptional regulator - 5 --------------e--h-n------ Nlp [K] COG3423 Predicted transcriptional regulator - 11 a-mp-z-------------------- - [K] COG3432 Predicted transcriptional regulator - 6 -----------------hs--j---- - [K] COG3636 Predicted transcriptional regulator - 7 ------------b--f-----j---- - [K] COG3655 Predicted transcriptional regulator - 10 ----k-----rl-c-------j---- - [K] COG3682 Predicted transcriptional regulator - 5 ----k----d----------u----w - [K] COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen - 3 ao--k--------------------- - [K] COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon - 29 a--pk---vdrlbc-f--sn-j--tw - [K] COG1386 Predicted transcriptional regulator containing the HTH domain - 5 aom--z-------------------- - [K] COG2524 Predicted transcriptional regulator with C-terminal CBS domains - 6 ao-pk--------------------- - [K] COG3620 Predicted transcriptional regulator with C-terminal CBS domains - 22 --------vdrlbcefghsn-j-i-- - [K] COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains - 152 aompkz-qvdrlbcefghsnuj---- ArsR [K] COG0640 Predicted transcriptional regulators - 89 a------q-drlbcefghsnuj---- SoxR [K] COG0789 Predicted transcriptional regulators - 8 a-m-kz-qv----------------- - [K] COG1318 Predicted transcriptional regulators - 23 aompkz---d--b------------- - [K] COG1378 Predicted transcriptional regulators - 9 aompkz-------------------- - [K] COG1395 Predicted transcriptional regulators - 168 --m----qvdrlb-efghsn-jx-t- HipB [K] COG1396 Predicted transcriptional regulators - 58 aom-kz-q-drlb-efg-snujxit- Spo0J [K] COG1475 Predicted transcriptional regulators - 19 aom-k----d-lb--f-----j---- - [K] COG1476 Predicted transcriptional regulators - 6 aomp---------------------- - [K] COG1497 Predicted transcriptional regulators - 7 --m-k-------b------------- - [K] COG1510 Predicted transcriptional regulators - 65 aompkz--vdrlb-e-g----j---- - [K] COG1695 Predicted transcriptional regulators - 9 aompkz---------f---------- - [K] COG1709 Predicted transcriptional regulators - 12 ---p----v-rlbc------------ - [K] COG1725 Predicted transcriptional regulators - 62 aomp-z---drlbcefghs-uj---- - [K] COG1733 Predicted transcriptional regulators - 9 aompk--------------------- - [K] COG1777 Predicted transcriptional regulators - 22 aompkz----r-b-e---s--j---- - [K] COG3609 Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain - 19 aom-kz---d--b-e-----uj---- NikR [K] COG0864 Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain and a metal-binding domain - 14 -----------l--ef-hs------- - [K] COG3617 Prophage antirepressor - 11 ----k---v--lb-e-g--------- PspC [KT] COG1983 Putative stress-responsive transcriptional regulator - 19 ---pkzy----lb----h--u----- TenA [K] COG0819 Putative transcription activator - 17 ---------dr---efghsn-jxi-- - [K] COG1678 Putative transcriptional regulator - 18 -------qvdr-bc-f--snuj--t- - [K] COG1521 Putative transcriptional regulators, homologs of Bvg accessory factor - 12 aom-kzyq------ef---------- RCL1 [K] COG0430 RNA phosphate cyclase - 48 ------y------c--g---u---t- - [K] COG0724 RNA-binding proteins (RRM domain) - 4 --------------efg--------- Rsd [K] COG3160 Regulator of sigma D - 22 ao--kz----r-b--------j---- AbrB [K] COG2002 Regulators of stationary/sporulation gene expression - 10 --------v----c-fg-s------- - [KT] COG3437 Response regulator containing a CheY-like receiver domain and an HD-GYP domain - 20 -----------lb-efg-s--j---- LytT [KT] COG3279 Response regulator of the LytR/AlgR family - 24 --------vdrlbcefghs--j---- LexA [KT] COG1974 SOS-response transcriptional repressors (RecA-mediated autopeptidases) - 28 aompkzy------------------- LSM1 [K] COG1958 Small nuclear ribonucleoprotein (snRNP) homolog - 7 ------------b-efgh-------- - [KT] COG3835 Sugar diacid utilization regulator - 56 ao-pkzy-vdrlbcefghs----i-w HepA [KL] COG0553 Superfamily II DNA/RNA helicases, SNF2 family - 47 aompkzyqvdrlbcefghsnujxitw NusG [K] COG0250 Transcription antiterminator - 47 aompkz-qvdrlbcefghsnujxitw NusA [K] COG0195 Transcription elongation factor - 50 --------vdrlb-efghsnujxitw GreA [K] COG0782 Transcription elongation factor - 10 aompkzy------------------- EGD2 [K] COG1308 Transcription factor homologous to NACalpha-BTF3 - 26 aompkzy------------------- SUA7 [K] COG1405 Transcription initiation factor IIB - 8 aom-kzy------------------- TFA1 [K] COG1675 Transcription initiation factor IIE, large subunit - 20 aompkzy------------------- SPT15 [K] COG2101 Transcription initiation factor TFIID (TATA-binding protein) - 33 -------qvdrlbcefghsnujxitw NusB [K] COG0781 Transcription termination factor - 27 -------qvdr-b-efghsnujxit- Rho [K] COG1158 Transcription termination factor - 24 -----------lb-e----------- BglG [K] COG3711 Transcriptional antiterminator - 443 a-m----q-drlbcefghsnuj---- LysR [K] COG0583 Transcriptional regulator - 309 aom-k--qvdrlbcefghsnuj---w AcrR [K] COG1309 Transcriptional regulator - 26 --------vdrlbc----------t- LytR [K] COG1316 Transcriptional regulator - 47 -o-----qvdr-b-efgh--uj---- IclR [K] COG1414 Transcriptional regulator - 9 ------y--d--b--f--s--j---- PaiB [K] COG2808 Transcriptional regulator - 6 --------------e-gh-------- MtlR [K] COG3722 Transcriptional regulator - 14 -------q------efg----j--t- FhlA [KT] COG3604 Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains - 12 -------q----b-ef---------- RocR [KT] COG3829 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains - 9 aompkz-------------------- - [K] COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon - 7 --------------efgh-------- TyrR [K] COG3283 Transcriptional regulator of aromatic amino acids metabolism - 19 --------v-rlbc----s-uj-i-w HrcA [K] COG1420 Transcriptional regulator of heat shock gene - 19 ---------d-lb-e-gh---j---- DeoR [K] COG2390 Transcriptional regulator, contains sigma factor-related N-terminal domain - 153 aompkz---dr-b-efgh-n-j---- Lrp [K] COG1522 Transcriptional regulators - 134 --------vdrlb-efghs--j---- PurR [K] COG1609 Transcriptional regulators - 44 --------v--lb-efgh-n-j---- RpiR [K] COG1737 Transcriptional regulators - 61 ---p----vdrlb-efg--n-j---- GntR [K] COG1802 Transcriptional regulators - 149 aompkz--vdrlb-efg-sn-j---- MarR [K] COG1846 Transcriptional regulators - 74 ao-p-z-qvdrlbce-gh---j--t- NagC [K] COG1940 Transcriptional regulators - 54 ---------dr-b-efgh-n-j---- FadR [K] COG2186 Transcriptional regulators - 55 ---------drlb-efg----j---w PhnF [K] COG2188 Transcriptional regulators - 57 ---pkzy-vdrlb-efgh---j---- ARO8 [KE] COG1167 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs - 72 -------qvd-lb-efgh-n-j---- GlpR [KG] COG1349 Transcriptional regulators of sugar metabolism - 12 -------q-dr-b--------jx-t- - [K] COG1329 Transcriptional regulators, similar to M. xanthus CarD - 7 --------------e-ghs----i-- TrpR [K] COG2973 Trp operon repressor - 36 ------yqvdrlbcefghsnujxitw Rnc [K] COG0571 dsRNA-specific ribonuclease - 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]