- 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 - 27 -------qvdrlbcefghsnujx-t- RecG [LK] COG1200 RecG-like helicases - 136 a-mp--yq-drlbcefghsnujx-tw SrmB [LKJ] COG0513 Superfamily II DNA and RNA helicases - 29 --------vdrlbcefghsnujxit- Mfd [LK] COG1197 Transcription-repair coupling factor - superfamily II helicase - 26 a-m----q-dr-bcef-h--uj---w HypB [OK] COG0378 Ni2+-binding GTPase involved in regulation of expression and maturation of urease and hydrogenase - 39 -------qvdrlbcefghsnuj--tw SpoT [TK] COG0317 Guanosine polyphosphate pyrophosphohydrolases/synthetases - 122 ---------drlbcefghsn-j---- CitB [TK] COG2197 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain - 218 -------qvdrlbcefghsnujxi-- OmpR [TK] COG0745 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain - 21 --------v-r-bc-fg----j-it- RsbU [TK] COG2208 Serine phosphatase RsbU, regulator of sigma subunit - 17 --------v---bcefg--------- PspF [TK] COG1221 Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain - 5 --------------e-gh-------- MetJ [EK] COG3060 Transcriptional regulator of met regulon