Cell Atlas

Book catalogue checked against Aquifex

This page checks the book's groups, not the minimal cell. It tests each of the 233 groups in the X-ray of Life catalogue against the genes of Aquifex aeolicus. The 1,051 proteins of the minimal cell, and how they were chosen, are on How the working minimum was reached.

Partly checked. All 233 groups have been checked against the Aquifex aeolicus VF5 inventory (1,553 genes). The genes shown for each group were read by hand, and the correction notes say why. Groups marked “lacks” were judged by gene symbol where a pattern was given, and by protein name otherwise, so a few may still have a gene that the inventory names differently. The B1–B3 section was checked by hand as well.

Counts by label: aquifex evidence 130 · book requires, Aquifex lacks 80 · repeat (counted once) 15 · not first-cell 7. Total 233 groups.

1. The 233 catalogue groups

IDGroup (book)PageLabelGenesAquifex genes (first 6)
g0Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase (CODH/ACS)498Aquifex evidence checked by hand1- aq_1192
Only a name-level CO dehydrogenase (aq_1192). No acsA/cdh gene was found by name, so the CODH/ACS complex is not confirmed. Check the genome by hand.
g1rTCA cycle (excluding standard TCA cycle enzymes)498Aquifex evidence checked by hand7- aq_1166, forA2 aq_1167, forB2 aq_1168, forG2 aq_1169, forA1 aq_1195, forB1 aq_1196 +1 more
Reverse TCA uses the ferredoxin oxidoreductase gene sets (forA/B/G, two copies, as in the memory note on forABG) and the 2-oxoglutarate oxidoreductase (aq_1166). The earlier hit rtcA (RNA cyclase) was wrong and is removed.
g2Wood-Ljungdahl pathway498Book requires, Aquifex lacks checked by hand0none by name
No ACS gene confirmed. The CO dehydrogenase candidate is listed under g0.
g3Carbonic anhydrase498Aquifex evidence checked by hand1- aq_1660
Gamma carbonic anhydrase family, by name.
g4THF derivative-related enzyme group498Aquifex evidence checked by hand3trmFO aq_691, metF aq_1429, folD aq_1898
FolD, MetF and TrmFO. These are folate-dependent one-carbon enzymes, so the group fits.
g5SAM synthesis enzyme group498Aquifex evidence checked by hand2metK aq_1154, mat aq_1226
Two S-adenosylmethionine synthases (metK, mat). The earlier hits map and metG were wrong and are removed.
g6Methionine cycle and SAM/SAH metabolism498Aquifex evidence checked by hand1metE aq_1710
Cobalamin-independent methionine synthase (metE). The earlier hit map (methionine aminopeptidase) was wrong and is removed.
g7Methyl transfer and SAM-related498Book requires, Aquifex lacks checked by hand0none by name
No SAM-dependent methyltransferase group was identified by name. Check by hand: trm and rlm genes are tRNA methylases, not this group.
g8Biotin biosynthesis498Aquifex evidence checked by hand9bioA aq_170, bioD aq_557, bioF aq_626, bioB aq_975, bioW aq_1659, accB aq_1363 +3 more
Biotin synthesis (bioB, bioA, bioD, bioF, bioW, birA). The acc genes (accB, accC1, accC2) are carboxylases of fatty-acid synthesis, so they are kept as biotin-dependent enzymes, not biosynthesis.
g9Thiamine biosynthesis498Aquifex evidence checked by hand4thiL aq_2119, thiE1 aq_558, thiC aq_1204, thiE2 aq_1366
Thiamine phosphate synthesis and kinase (thiL, thiE1, thiC, thiE2).
g10Wood-Ljungdahl pathway498Repeat (counted once) checked by hand0none by name
Printed twice in the book; counted once in g0 and g2.
g11One-carbon metabolism498Book requires, Aquifex lacks checked by hand0none by name
The earlier hits (dabA, cstA) are transporters, not one-carbon metabolism, and are removed. No candidate was found by name.
g12Cobalamin biosynthesis499Aquifex evidence checked by hand2cobA aq_207, cobW aq_147
Uroporphyrinogen C-methyltransferase (cobA) and CobW. Cobalamin is still missing its corrin ring genes, so treat this as partial.
g13Cobalamin recycling499Book requires, Aquifex lacks checked by hand0none by name
No cobalamin recycling gene found by name. The metE hit is listed under g6.
g14Flavin-related biosynthesis499Aquifex evidence checked by hand8ribH aq_132, ribD aq_138, ribBA aq_350, ribD2 aq_436, ribF aq_139, ubiX aq_528 +2 more
Riboflavin pathway (ribD, ribD2, ribBA, ribH, ribE, ribF), UbiX and the FMN transferase. The thyX hit (thymidine synthase) was wrong and is removed.
g15Pantothenate and CoA biosynthesis499Aquifex evidence checked by hand6dfp aq_815, coaD aq_253, coaX aq_1924, panB aq_1973, coaE aq_1985, panC aq_2132
CoA and pantothenate pathway (coaD, coaE, dfp, coaX, panB, panC).
g16Cobalamin reductase499Book requires, Aquifex lacks checked by hand0none by name
No cobalamin reductase found by name.
g17Cytochrome bc1 complex III499Aquifex evidence checked by hand2petB aq_044, petA aq_045
Cytochrome b and the Rieske protein (petB, petA). The complex III core subunits are not all present, so treat it as partial.
g18Cytochrome c oxidase complex499Not first-cell checked by hand6cydA aq_1357, cydB aq_1358, coxB aq_2190, coxA1 aq_2191, coxA2 aq_2192, coxC aq_2188
Cytochrome c oxidase and cytochrome bd oxidase. Both need O2, so they are not first-cell enzymes (Vol. III pp. 424–425, 499).
g19NADH dehydrogenase Complex I-related499Aquifex evidence checked by hand25nuoC1 aq_551, nuoA2 aq_1310, nuoB aq_1312, nuoC2 aq_1314, nuoI aq_1317, nuoK1 aq_1319 +19 more
NADH dehydrogenase (complex I). The nuo subunits and nueM are selected by name pattern.
g20ATP Synthase Complex V499Aquifex evidence checked by hand10atpE aq_177, atpC aq_673, atpA aq_679, atpF aq_1586, atpD aq_2038, atpB aq_179 +4 more
ATP synthase subunits (atpA–atpH, atpG2). The atpF gene is present twice, as the memory note requires. fliI (flagellar ATPase) is removed: it is not ATP synthase.
g21Hydrogen Oxidation499Aquifex evidence checked by hand11mbhS1 aq_660, mbhL1 aq_662, hoxZ aq_665, mbhS3 aq_802, mbhL2 aq_960, mbhS2 aq_965 +5 more
Hydrogenases: mbh subunits, shyS, hupDE, hoxX and hoxZ. This group was empty in the first pass.
g22Sulfur Metabolism basic499Aquifex evidence checked by hand8iscU aq_896, - aq_1807, dhsU aq_232, fccB' aq_235, sor aq_455, nifS2 aq_739 +2 more
Sulfur metabolism: IscU, nifS1/2 (cysteine desulfurases), sor, soxA/B, dhsU and fccB. The earlier hits moeB (molybdopterin), lipA (lipoyl synthase), petA and glpC were removed.
g23Succinate dehydrogenase and hydrogenase499Aquifex evidence checked by hand3frdA aq_594, frdB1 aq_553, frdB2 aq_655
Succinate dehydrogenase and fumarate reductase (frdA, frdB1, frdB2). This group was empty in the first pass.
g24Oxidoreductase for anaerobic metabolism499Aquifex evidence checked by hand2forD2 aq_1171, forD1 aq_1191.1
ForD ferredoxin oxidoreductase subunits. Their function is not named in the inventory, so this is an open check.
g25Ferredoxin-based electron transport499Aquifex evidence checked by hand3fdx4 aq_107, fdx1 aq_919.1, fdx5 aq_659
Ferredoxins (fdx1, fdx4, fdx5). This group was empty in the first pass.
g26Sulfur metabolism pathway enzymes499Aquifex evidence checked by hand3mrp aq_737, cysG aq_1237, - aq_1421
Sulfite-reductase siroheme (cysG), a sulfur carrier and an Fe-S carrier (mrp).
g27NAD+ biosynthesis via Aspartate499Aquifex evidence checked by hand4pyrB aq_409, nadB aq_777, asd aq_1866, aspC aq_1969
NAD+ from aspartate: nadB (L-aspartate oxidase), aspC, asd and pyrB. The rimO, argG, purA, aspS and lysC hits were wrong and are removed.
g28Alternative electron transport499Aquifex evidence checked by hand3pyrD aq_046, - aq_1305, - aq_2098
Dihydroorotate dehydrogenases with their electron-transfer subunits (pyrD, aq_1305, aq_2098).
g29Iron-Sulfur Clusters - electron transport499Book requires, Aquifex lacks checked by hand0none by name
The ferredoxins are listed under g25. No separate electron-transport Fe-S protein was found by name.
g30Iron-Sulfur Clusters - electron transfer499Book requires, Aquifex lacks checked by hand0none by name
No Fe-S electron-transfer protein beyond the ferredoxins in g25 was found by name.
g31Magnesium Ions (Mg2+) - phosphate transfer499Book requires, Aquifex lacks checked by hand0none by name
No Mg2+ phosphate-transfer gene was found by name. The earlier hits were wrong.
g32Magnesium Ions (Mg2+) - second system499Aquifex evidence checked by hand1corA aq_851
Magnesium transport protein CorA.
g33Molybdenum Cofactor - oxidation-reduction499Book requires, Aquifex lacks checked by hand0none by name
Molybdenum oxidoreductases were not found by name. The cofactor genes are listed under g229.
g34Molybdenum Cofactor - sulfur/nitrogen metabolism499Aquifex evidence checked by hand1moeB aq_1329
Molybdopterin sulfur transfer (moeB), the sulfur/nitrogen-linked step.
g35Manganese Ions (Mn2+) - antioxidant defense499Book requires, Aquifex lacks checked by hand3sodB aq_1499, sodC2 aq_238, sodC1 aq_1050
Only Fe-SOD (sodB) and Cu/Zn-SOD (sodC1, sodC2) are present. The book's Mn-SOD is absent by name, so this group is not met.
g36NAD+ transporter499Book requires, Aquifex lacks checked by hand0none by name
No NAD+ transporter was found by name.
g37Beta-alanine biosynthesis499Aquifex evidence checked by hand1panD aq_476
Aspartate 1-decarboxylase (panD) is the beta-alanine source for pantothenate.
g38De novo purine biosynthesis499Aquifex evidence checked by hand2purB aq_597, purA aq_1290
Adenylosuccinate synthetase (purA) and lyase (purB). Other de novo purine genes are not named in the inventory, so this group is partial.
g39Purine biosynthesis - adenine pathway499Book requires, Aquifex lacks checked by hand0none by name
No adenine phosphoribosyltransferase (apt) was found by name.
g40Purine biosynthesis - guanine pathway500Aquifex evidence checked by hand2hpt aq_544, guaB aq_2023
IMP dehydrogenase (guaB) and hypoxanthine-guanine phosphoribosyltransferase (hpt).
g41De novo pyrimidine biosynthesis500Aquifex evidence checked by hand1pyrB aq_409
Aspartate carbamoyltransferase (pyrB), the first pyrimidine step.
g42Uracil biosynthesis500Aquifex evidence checked by hand3pyrF aq_1580, pyrE aq_1907, upp aq_2163
Uracil phosphoribosyltransferase (upp), with pyrE and pyrF if present. The earlier hits ribD, trmFO and dplF were wrong and are removed.
g43Cytosine nucleotide biosynthesis500Aquifex evidence checked by hand1pyrG aq_1334
CTP synthase (pyrG).
g44Thymine biosynthesis500Aquifex evidence checked by hand1thyX aq_640
Flavin-dependent thymidylate synthase (thyX). It belongs here, not to flavin biosynthesis (g14).
g45Nucleotide phosphorylation500Aquifex evidence checked by hand3adk aq_078, ndk aq_1590, cmk aq_2153
Nucleoside diphosphate kinase and related nucleotide kinases, by name.
g46Nucleotide Salvage500Aquifex evidence checked by hand1hpt aq_544
Hypoxanthine-guanine phosphoribosyltransferase (hpt), the salvage step. Shared with g40. The other salvage genes (deoD, add, cdd, tdk) are not in the inventory.
g47RNA processing and degradation500Aquifex evidence checked by hand4rnc aq_946, rph aq_924, pnp aq_221, rnr aq_2046
RNA processing and degradation nucleases, by gene name. rph (RNase PH) is shared with g99.
g48Serine biosynthesis500Aquifex evidence checked by hand2glyA aq_479, serA aq_1905
Serine biosynthesis: D-3-phosphoglycerate dehydrogenase (serA) and serine hydroxymethyltransferase (glyA). The tRNA ligase serS and the protease hits are removed.
g49Glycine cleavage system500Aquifex evidence checked by hand8gcvPB aq_1903, gcvH5 aq_402, gcvH3 aq_944, gcvH1 aq_1052, gcvH4 aq_1108, gcvPA aq_1109 +2 more
Glycine cleavage system (gcvP, gcvH, gcvT).
g50Serine and sulfide to cysteine500Aquifex evidence checked by hand1cysM aq_1556
Cysteine synthase (cysM), the serine and sulfide step. The tRNA ligases cysS are left to g113.
g51Lysine biosynthesis via diaminopimelate500Aquifex evidence checked by hand6dapL aq_273, dapB aq_916, dapA aq_1143, lysA aq_1208, dapF aq_1838, dapE aq_547
Diaminopimelate pathway genes by name.
g52Alanine metabolism500Aquifex evidence checked by hand2ddl aq_521, alr aq_1827
Alanine racemase (alr) and D-alanine ligase (ddl). alaS is a tRNA ligase, so it is left to g113.
g53Valine biosynthesis500Aquifex evidence checked by hand4ilvD aq_837, ilvC aq_1245, ilvH aq_1851, ilvB aq_451
Valine biosynthesis (ilvB, ilvC, ilvD, ilvN). The tRNA ligase valS is left to g113.
g54Leucine biosynthesis500Aquifex evidence checked by hand4leuB aq_244, leuC aq_940, leuA aq_2090, leuD aq_1398
Leucine biosynthesis (leuA, leuB, leuC, leuD). leuS, a tRNA ligase, is left to g113.
g55Isoleucine biosynthesis500Book requires, Aquifex lacks checked by hand0none by name
No threonine deaminase (ilvA) was found by name. ileS, a tRNA ligase, is left to g113.
g56Histidine biosynthesis500Aquifex evidence checked by hand9hisF aq_181, hisH aq_732, hisD aq_782, hisI aq_1968, hisB aq_039, hisZ aq_1155 +3 more
Histidine biosynthesis by name. hisS (tRNA ligase) and the histidine kinases are excluded.
g57Tryptophan biosynthesis500Aquifex evidence checked by hand8trpD aq_196, trpE aq_582, trpB1 aq_706, trpB2 aq_1410, trpA aq_1548, trpC aq_1787 +2 more
Tryptophan synthase and pathway genes. trpS, a tRNA ligase, is left to g113.
g58Tyrosine biosynthesis500Aquifex evidence checked by hand1tyrA aq_1755
Prephenate dehydrogenase (tyrA). tyrS, a tRNA ligase, is left to g113.
g59Phenylalanine biosynthesis500Aquifex evidence checked by hand1pheA aq_951
Chorismate mutase (pheA), the phenylalanine branch point.
g60Aspartate metabolism500Aquifex evidence checked by hand1lysC aq_1152
Aspartokinase (lysC). The earlier hits (rimO, argG, purA, aspS) were wrong and are removed.
g61Asparagine metabolism500Book requires, Aquifex lacks checked by hand0none by name
No asparagine synthetase was found by name.
g62Methionine biosynthesis500Book requires, Aquifex lacks checked by hand0none by name
No cystathionine or homocysteine pathway gene was found by name. map and metG were wrong and are removed; metK and metE are in g5 and g6.
g63Threonine biosynthesis500Aquifex evidence checked by hand3thrC2 aq_425, thrC1 aq_608, thrA aq_1812
Homoserine dehydrogenase (thrA) and threonine synthases (thrC1, thrC2). The protein-phosphatase and kinase hits are removed.
g64Glutamate-related essential group500Aquifex evidence checked by hand8glnA aq_111, hemL aq_816, proA aq_1071, proB aq_1134, gltB aq_1565, gltP aq_1330 +2 more
Glutamate-family enzymes: glutamine synthetase (glnA), glutamate synthase (gltB, gltD), glutamate symporter (gltP), glnE, hemL, and the proline genes proA, proB. The murE and ArgJ hits were wrong and are removed.
g65Expanded glutamate-related500Aquifex evidence checked by hand3hemA aq_1279, murD aq_2075, murI aq_325
Expanded group: glutamate racemase (murI), murD and the glutamyl-tRNA reductase (hemA). Printed as an expansion of g64, so it overlaps.
g66Ornithine and arginine biosynthesis500Aquifex evidence checked by hand5argJ aq_970, argG aq_1140, argC aq_1879, argB aq_2068, argH aq_1372
Arginine biosynthesis: argB, argC, argG, argH, argJ.
g67Ornithine and proline metabolism500Aquifex evidence checked by hand2proC aq_166, speC aq_728
Pyrroline-5-carboxylate reductase (proC) and ornithine decarboxylase (speC).
g68Amino acid synthesis regulation500Aquifex evidence checked by hand2dapF aq_1838, ilvE aq_1893
Diaminopimelate epimerase (dapF) and the branched-chain aminotransferase (ilvE).
g69Additional regulation500Book requires, Aquifex lacks checked by hand0none by name
The book's additional regulation has no named gene in the inventory.
g70Urea cycle500Book requires, Aquifex lacks checked by hand0none by name
No urea-cycle or urease gene was found by name. The book gives no first-cell role for this cycle (see the catalogue note).
g71Fatty acid synthesis initiation500Aquifex evidence checked by hand2fabH aq_1099, fabD aq_892
Fatty-acid initiation: FabH and FabD.
g72Fatty acid synthesis elongation500Aquifex evidence checked by hand3fabG aq_1716, fabZ aq_056, fabF aq_1717
Fatty-acid elongation: FabF, FabG and FabZ. fabB is not in the inventory.
g73Fatty acid synthesis termination500Aquifex evidence checked by hand1fabI aq_1552
Enoyl-ACP reductase FabI (termination step).
g74Fatty Acid Elongation501Aquifex evidence checked by hand1fadD aq_999
Long-chain fatty-acid CoA ligase (fadD), the fatty-acid activation step.
g75Phospholipid biosynthesis501Aquifex evidence checked by hand1plsY aq_676
Glycerol-3-phosphate acyltransferase (plsY). cfa (cyclopropane synthase) was wrong here and is removed.
g76Glycerophospholipid biosynthesis501Book requires, Aquifex lacks checked by hand0none by name
No phosphatidylserine synthase or decarboxylase was found by name.
g77Alternative glycerophospholipid biosynthesis501Book requires, Aquifex lacks checked by hand0none by name
No alternative glycerophospholipid pathway gene was found by name.
g78Phospholipid transport501Book requires, Aquifex lacks checked by hand0none by name
No Mla phospholipid-transport gene was found by name. cfa was wrong here and is removed.
g79Phospholipid degradation501Book requires, Aquifex lacks checked by hand0none by name
No phospholipase (pldA) was found by name. cfa was wrong here and is removed.
g80Lipid reuse and recycling501Aquifex evidence checked by hand7kdtA aq_326, lpxC aq_1772, lpxK aq_1656, lpxD aq_538, lpxA aq_604, lpxB aq_1427 +1 more
Lipid A and lipid II genes (kdtA, lpxK, lpxB, murJ). atpE was wrong here and is removed.
g81CDP-diacylglycerol pathway501Aquifex evidence checked by hand3cdsA aq_1249, pgsA2 aq_958, pgsA aq_2154
CDP-diacylglycerol pathway: cdsA, pgsA and pgsA2.
g82Mevalonate pathway501Book requires, Aquifex lacks checked by hand0none by name
No mevalonate-pathway gene was found by name.
g83Non-mevalonate pathway501Aquifex evidence checked by hand7ispG aq_1540, ispH aq_1739, dxr aq_404, dxs aq_881, ispE aq_915, ispF aq_957 +1 more
Non-mevalonate pathway: ispG, ispH, dxr, dxs, ispE, ispF, ispD.
g84Peptidoglycan biosynthesis501Aquifex evidence checked by hand10mraY aq_053, murE aq_1747, murB aq_520, ddl aq_521, murF aq_821, murG aq_1177 +4 more
Peptidoglycan biosynthesis: mraY, murA, murB, murC, murD, murE, murF, murG, ddl and ftsW. The genes overlap g52, g64 and g65.
g85Peptidoglycan cross-linking501Aquifex evidence checked by hand3mrcA aq_624, pbpA2 aq_556, pbpA1 aq_1189
Penicillin-binding proteins pbpA1, pbpA2 and mrcA. Check pbp names by hand: the memory note says aq_556 and aq_1189 share a name but have different KOs.
g86DNA replication initiation501Aquifex evidence checked by hand3dnaA aq_322, dnaB aq_1472, dnaC aq_910
Replication initiation: DnaA, DnaB and DnaC. dnaG is listed under g87, and the core polymerase genes under g88.
g87DNA replication primase501Aquifex evidence checked by hand1dnaG aq_1493
DNA primase (dnaG).
g88DNA replication core501Aquifex evidence checked by hand7dnaQ aq_932, dnaE aq_1008, holA aq_1104, dpbF aq_1422, dnaX aq_1855, dnaN aq_1882 +1 more
DNA polymerase III core: dnaQ, dnaE, holA, dnaX, dnaN, dpbF and polA.
g89DNA replication termination501Book requires, Aquifex lacks checked by hand0none by name
No replication terminator (Tus/ter) was found by name. dnaA and dnaC are initiation genes, so they are not listed here.
g90DNA Supercoiling Control501Aquifex evidence checked by hand2gyrA aq_980, gyrB aq_1026
DNA gyrase subunits A and B (gyrA, gyrB).
g91Auxiliary DNA replication501Aquifex evidence checked by hand1ssb aq_064
Single-strand DNA-binding protein (ssb).
g92DNA repair501Aquifex evidence checked by hand6uvrA aq_686, uvrB aq_1856, recA aq_2150, mutS aq_308, mutL aq_1578, uvrC aq_2126
DNA repair: uvrA, uvrB, uvrC, recA, mutS and mutL. The mismatch genes overlap g94.
g93Chromosome segregation501Aquifex evidence checked by hand1smc aq_629
Chromosome segregation: smc only. parA, parB, scpA, scpB and mukB are not in the inventory, so this group is partial.
g94DNA mismatch recognition501Aquifex evidence checked by hand1mutS aq_308
Mismatch recognition (mutS). mutL is listed under g92.
g95DNA Topoisomerase501Aquifex evidence checked by hand1topA aq_657
DNA topoisomerase I (topA).
g96DNA topology management501Book requires, Aquifex lacks checked by hand0none by name
No topology gene (hns, hup, dps, him) was found by name.
g97DNA precursor synthesis501Not first-cell checked by hand2nrdA aq_094, nrdB aq_1505
Class I ribonucleotide reductase (nrdA, nrdB). It needs O2 for its radical, so it is not first-cell (see the catalogue C0 note).
g98DNA precursor metabolism501Aquifex evidence checked by hand3dut aq_220, tmk aq_969, dcd aq_1607
dUTPase (dut), dCTP deaminase (dcd) and thymidylate kinase (tmk).
g99RNA recycling501Aquifex evidence checked by hand1rph aq_924
RNase PH (rph), shared with g113.
g100Early life essential proteins501Book requires, Aquifex lacks checked by hand0none by name
The book's list of early essential proteins has no single gene name to match.
g101Transcription factors501Aquifex evidence checked by hand5rho aq_873, nusG aq_1931, nusB aq_133, nusA aq_259, dksA aq_2095
Transcription termination and antitermination: rho, nusG, nusB, nusA, dksA. The same genes are split across g106 and g107.
g102Regulatory proteins501Aquifex evidence checked by hand4glnB aq_109, - aq_601, - aq_862, - aq_1575
Nitrogen regulator P-II (glnB, two copies), a response regulator and a transcriptional regulator. cobB, hisZ and the other hits were not regulators of this kind and are removed.
g103RNA Polymerase501Aquifex evidence checked by hand4rpoA aq_070, rpoB aq_1939, rpoC aq_1945, rpoZ aq_183.1
RNA polymerase core: rpoA, rpoB, rpoC and rpoZ. Sigma factors are in g104.
g104Sigma factors501Aquifex evidence checked by hand4rpoD aq_1490, rpoN aq_599, fliA aq_1218, rpoS aq_1452
Sigma factors rpoD (SigA), rpoS, rpoN and fliA. fliA is the flagellar sigma factor, so it is not a first-cell requirement.
g105Primary sigma factor σ70501Aquifex evidence checked by hand1rpoD aq_1490
Primary sigma factor sigma70 (rpoD, SigA).
g106Transcription regulation501Aquifex evidence checked by hand2nusG aq_1931, dksA aq_2095
Transcription regulation: dksA and nusG.
g107Transcription termination501Aquifex evidence checked by hand3rho aq_873, nusB aq_133, nusA aq_259
Transcription termination: rho, nusA and nusB.
g108Early transcription processing502Book requires, Aquifex lacks checked by hand0none by name
No early transcription-processing gene was found by name beyond the nus genes in g107.
g109Transcription fidelity502Book requires, Aquifex lacks checked by hand0none by name
No transcription-fidelity gene (greA, greB, mfd) was found by name.
g110Aminoacyl-tRNA synthetase502Aquifex evidence checked by hand20serS aq_298, ileS aq_305, leuS aq_351, proS aq_365, pheS aq_953, trpS aq_992 +14 more
The aminoacyl-tRNA synthetases by name. These are shared with g113.
g111tRNA synthesis and modification502Aquifex evidence checked by hand2mnmG aq_761, mnmE aq_871
tRNA modification MnmG and MnmE (mnmG, mnmE).
g112tRNA modification502Aquifex evidence checked by hand14trm1 aq_841, trmB aq_065, miaB aq_284, mtaB aq_474, trmFO aq_691, truB aq_705 +8 more
tRNA modification by name (trm, tru, tsaD, tadA, miaB, mtaB, tilS). mnmG and mnmE are listed under g111.
g113tRNA recycling502Aquifex evidence checked by hand7- aq_2158, gatB aq_461, rph aq_924, gatA aq_247, pth aq_346, - aq_411 +1 more
tRNA processing: CCA and A-adding tRNA nucleotidyltransferases, RNase PH, peptidyl-tRNA hydrolase (pth), D-aminoacyl-tRNA deacylase (dtd), and the amidotransferase subunits gatA and gatB.
g114Translation initiation502Aquifex evidence checked by hand3infA aq_075.1, infC aq_1777, infB aq_2032
Translation initiation factors IF-1 (infA), IF-3 (infC) and IF-2 (infB). The elongation factor selB is not an initiation factor.
g115Ribosomal proteins - small subunit502Aquifex evidence checked by hand28rsgA aq_168, rpsE aq_1645, rsmA aq_1816, rsmH aq_1875, rpsL1; rpsL2 aq_1834, rpsJ aq_008 +22 more
Small-subunit ribosomal proteins (rps), methyltransferases (rsm) and rsgA. aq_1834 holds the two rpsL copies.
g116Ribosomal proteins - large subunit502Aquifex evidence checked by hand32rpmA aq_1773.1, rplC aq_009, rplD aq_011, rplW aq_012, rplB aq_013, rplV aq_016 +26 more
Large-subunit ribosomal proteins (rpl, rpm). rlmN is a methylase and is listed under g157.
g117Translation termination502Aquifex evidence checked by hand2prfA aq_876, prfB aq_1840
Release factors prfA and prfB. prfC is not in the inventory.
g118Protein phosphorylation code502Not first-cell checked by hand6hksP4 aq_231, hksP2 aq_316, hksP3 aq_905, hksP1 aq_1115, - aq_1825, - aq_204
Bacterial histidine kinases (hksP1-4) and a Ser/Thr kinase. The bacterial ones fit a first cell, but the book's protein kinase A and C are eukaryotic (see the catalogue note).
g119Protein dephosphorylation code502Aquifex evidence checked by hand2- aq_575, - aq_933
Ser/Thr protein phosphatases by name.
g120Post-translational modification code502Book requires, Aquifex lacks checked by hand0none by name
No post-translational modification gene set was identified by name.
g121PhoR-PhoB signaling system502Aquifex evidence checked by hand2phoU aq_906, phoB aq_319
PhoB and PhoU are present. PhoR is absent, so the two-component pair is incomplete.
g122Quorum sensing system502Book requires, Aquifex lacks checked by hand0none by name
No quorum-sensing gene was found by name.
g123LuxPQ-LuxU-LuxO system502Book requires, Aquifex lacks checked by hand0none by name
No LuxPQ-LuxU-LuxO gene was found by name.
g124Signaling metabolites502Aquifex evidence checked by hand1- aq_1400
Cyclic di-GMP-binding protein by name. Other signalling metabolites are not named in the inventory.
g125ATP/ADP Energy Balance Code502Book requires, Aquifex lacks checked by hand0none by name
No ATP/ADP balance sensor was identified by name.
g126Redox Code pathway502Aquifex evidence checked by hand1nox aq_835
NADH oxidase (nox), the redox sensor by name. It is oxygen-dependent, so check its status before relying on it.
g127Energy sensing and adaptation502Book requires, Aquifex lacks checked by hand0none by name
No energy-sensing gene was identified by name.
g128Nutrient sensing and adaptation502Aquifex evidence checked by hand1glnB aq_109
Nitrogen regulatory protein P-II (glnB), the nutrient sensor by name.
g129Gene regulators502Book requires, Aquifex lacks checked by hand0none by name
No gene regulator was identified beyond the ones in g102.
g130Calcium gradient sensing502Not first-cell checked by hand0none by name
The book's calcium sensing is through CaMKII, a eukaryotic kinase (Vol. III ch. 2). No bacterial calcium gene was matched.
g131Ion Channels and Transporters502Book requires, Aquifex lacks checked by hand0none by name
No ion-channel gene was found by name.
g132P-Type ATPase502Aquifex evidence checked by hand3ctrA3 aq_1125, ctrA2 aq_1445, ctrA1 aq_724
Cation-transporting P-type ATPases (ctrA1, ctrA2, ctrA3). The earlier ATP-synthase hits were wrong and are removed.
g133Metal ion transporters502Aquifex evidence checked by hand1feoB aq_1255
Ferrous-iron transporter FeoB. Other metal-transport genes are not in the inventory.
g134Aquaporins502Book requires, Aquifex lacks checked by hand0none by name
No aquaporin gene was found by name.
g135Symporter and antiporter503Aquifex evidence checked by hand1gltP aq_1330
Glutamate-sodium symporter (gltP) and Na+/H+ antiporter genes by name.
g136ABC transporters503Book requires, Aquifex lacks checked by hand0none by name
The ABC transporters are not assigned by name: the inventory has many ABC-type entries, each needs its own check.
g137Nutrient uptake503Book requires, Aquifex lacks checked by hand0none by name
No nutrient-uptake gene was identified by name.
g138Sugar transporters503Book requires, Aquifex lacks checked by hand0none by name
No sugar-transporter gene (pts, crr, mgl, xylE) was found by name.
g139Carbon source transporters503Aquifex evidence checked by hand2dabA aq_863, cstA aq_1265
Carbon-starvation protein CstA and inorganic carbon transporter DabA, both by name.
g140Amino acid transporters503Aquifex evidence checked by hand2gltP aq_1330, oppA aq_1441
Glutamate symporter (gltP, shared with g135) and the oligopeptide-binding protein oppA.
g141Co-factor transporters503Book requires, Aquifex lacks checked by hand0none by name
No cofactor-transporter gene was found by name.
g142Folate transporters503Book requires, Aquifex lacks checked by hand0none by name
No folate-transporter gene was found by name.
g143Phosphate transport503Aquifex evidence checked by hand5phoU aq_906, pstB aq_1055, pstS aq_2016, pstC aq_2018, pstA aq_2019
Phosphate transport: pstS, pstA, pstB, pstC and phoU. The 66 earlier hits matched the word phosphate and are removed.
g144Magnesium transport503Aquifex evidence checked by hand1corA aq_851
Magnesium transporter CorA (shared with g32).
g145Additional amino acid transport503Book requires, Aquifex lacks checked by hand0none by name
No additional amino-acid transporter was found by name. The biosynthesis hits (bioA, bioF, argJ, dapF, ilvE) were wrong and are removed.
g146SAM transporters503Book requires, Aquifex lacks checked by hand0none by name
No SAM transporter was found by name.
g147Third amino acid transport503Book requires, Aquifex lacks checked by hand0none by name
No third amino-acid transporter was found by name.
g148Fatty Acid transport503Aquifex evidence checked by hand1fadD aq_999
Fatty-acid activation by fadD, shared with g74.
g149Additional phosphate transport503Book requires, Aquifex lacks checked by hand0none by name
The 66 earlier hits matched the word 'phosphate' and are removed. No additional phosphate-transport gene was found by name.
g150Nucleotide/serine/ethanolamine503Book requires, Aquifex lacks checked by hand0none by name
No nucleotide, serine or ethanolamine transporter was found by name.
g151Additional ABC transport503Book requires, Aquifex lacks checked by hand0none by name
No additional ABC transporter was found by name.
g152TrkA family potassium uptake503Book requires, Aquifex lacks checked by hand0none by name
No TrkA-family potassium-uptake gene was found by name.
g153P4-ATPase family503Not first-cell checked by hand0none by name
P4-ATPase flippases are eukaryotic, and none is named in Aquifex. The ctrA ATPases in g132 are E1-E2 type and are not P4 enzymes.
g154Drug efflux pumps503Aquifex evidence checked by hand1emrB aq_1062
Multidrug efflux: emrB.
g155Sodium/proton pumps503Book requires, Aquifex lacks checked by hand0none by name
No Na+ pump gene (nqr, nha) was found by name.
g156Specialized transporters503Book requires, Aquifex lacks checked by hand0none by name
No specialised-transporter gene was identified by name.
g157rRNA synthesis QC503Aquifex evidence checked by hand6rlmN aq_416, rsmA aq_1816, rsmH aq_1875, rsmE aq_165, rsmI aq_1111, rsmG aq_1582
rRNA methyltransferases (rsmA, rsmE, rsmG, rsmH, rsmI) and rlmN. These are shared with g115 and g116.
g158tRNA quality control503Aquifex evidence checked by hand2pth aq_346, dtd aq_428
tRNA quality control: peptidyl-tRNA hydrolase (pth) and D-aminoacyl-tRNA deacylase (dtd), shared with g113.
g159rRNA modification503Aquifex evidence checked by hand1rlmN aq_416
rRNA methylase rlmN (shared with g157).
g160Ribosomal protein QC503Aquifex evidence checked by hand4rsgA aq_168, lepA aq_1725, rimP aq_260, rimM aq_1057
Ribosome quality and biogenesis: EF-4 (lepA), rsgA, rimP and rimM. The ribosomal proteins are listed under g115 and g116.
g16130S assembly error detection503Book requires, Aquifex lacks checked by hand0none by name
No 30S assembly error-detection gene was identified by name.
g16250S subunit repair503Book requires, Aquifex lacks checked by hand0none by name
No 50S repair gene was identified by name.
g16370S assembly maintenance503Book requires, Aquifex lacks checked by hand0none by name
No 70S maintenance gene was identified by name.
g164Ribosome assembly QC503Book requires, Aquifex lacks checked by hand0none by name
No ribosome-assembly QC gene was identified by name.
g165Ribosome biogenesis control503Book requires, Aquifex lacks checked by hand0none by name
No ribosome biogenesis control gene was identified by name.
g166Translation quality control503Book requires, Aquifex lacks checked by hand0none by name
No translation QC gene was identified by name.
g167Chiral checkpoints503Book requires, Aquifex lacks checked by hand0none by name
No chiral-checkpoint gene was identified by name (dtd is in g158).
g168Post-translation QC503Book requires, Aquifex lacks checked by hand0none by name
No post-translation QC gene was identified by name.
g169Protein folding QC503Book requires, Aquifex lacks checked by hand0none by name
No protein-folding QC gene was identified by name. The chaperones are in the stress group (g204).
g170Ribosomal rescue503Aquifex evidence checked by hand1smpB aq_287
SmpB is present. ssrA (tmRNA) is not in the inventory, so the tmRNA system is partial.
g171Protein modification QC503Book requires, Aquifex lacks checked by hand0none by name
No protein-modification QC gene was identified by name. mnmG and mnmE are tRNA genes (g111) and are removed.
g172Ribosome recycling503Aquifex evidence checked by hand4mutS2 aq_1242, ychF aq_609, frr aq_712, hpf aq_1603
Ribosome recycling: RRF (frr), hibernation factor (hpf), YchF (ychF) and MutS2, which carries a ribosome-associated QC role.
g173Error checking pathways503Book requires, Aquifex lacks checked by hand0none by name
No error-checking pathway gene was identified by name.
g174Membrane maintenance504Book requires, Aquifex lacks checked by hand0none by name
No membrane-maintenance gene was identified by name.
g175General secretion504Aquifex evidence checked by hand4gspG aq_418, - aq_585, gspD aq_1288, gspE aq_1474
Type II secretion: gspG, gspD, gspE and the secretin-like protein (aq_585). The FliH hit is a flagellar gene and is removed.
g176Acidocalcisome components504Book requires, Aquifex lacks checked by hand0none by name
No acidocalcisome gene was identified by name.
g177HGT mechanisms504Book requires, Aquifex lacks checked by hand0none by name
No competence gene (com) was found by name.
g178Protein secretion systems504Aquifex evidence checked by hand7secE aq_1930, secY aq_079, secG aq_098, secA aq_1870, secD aq_973, tatC aq_1267 +1 more
Sec translocon (secA, secD, secE, secF, secG, secY) and TatC.
g179Protein export machinery504Aquifex evidence checked by hand3ftsY aq_920, ffh aq_1720, yidC aq_175
YidC, Ffh and FtsY, the membrane insertion machinery.
g180Cell division proteins504Aquifex evidence checked by hand5ftsZ aq_525, ftsA aq_523, minD2 aq_877, ftsW aq_1139, sufI aq_1130
Division genes: FtsZ, FtsA, MinD2, FtsW and SufI, by name. FtsW is shared with g84.
g181Min system proteins504Aquifex evidence checked by hand3minD2 aq_877, minC aq_878, minD1 aq_1217
MinD2 is listed under g180. No MinC or MinE was found by name.
g182DNA management proteins504Aquifex evidence checked by hand1ssb aq_064
DNA management: ssb (single-strand binding). dps, hup and hns are not in the inventory.
g183Regulation and timing504Book requires, Aquifex lacks checked by hand0none by name
No regulation-and-timing gene was identified by name.
g184Protein phosphorylation504Repeat (counted once) checked by hand0none by name
Repeat of Cell Category 10 (see the catalogue). Counted once there.
g185Protein dephosphorylation504Repeat (counted once) checked by hand0none by name
Repeat of Cell Category 10 (see the catalogue). Counted once there.
g186DNA repair group504Aquifex evidence checked by hand3radA aq_552, rad50 aq_1006, recN aq_561
DNA repair: RadA, Rad50 and RecN, by name. mutS and mutL are listed under g92. nnr is a NAD(P)H-hydrate repair enzyme and is removed.
g187ATP/ADP balance504Repeat (counted once) checked by hand0none by name
Repeat of Cell Category 10 (see the catalogue). Counted once there.
g188Redox pathway504Repeat (counted once) checked by hand0none by name
Repeat of Cell Category 10 (see the catalogue). Counted once there.
g189Osmoregulation504Book requires, Aquifex lacks checked by hand0none by name
No osmoregulation gene (kdp, opu, proP, betA) was found by name.
g190Cytoskeleton pathway504Aquifex evidence checked by hand1mreB aq_845
Cytoskeleton: mreB. mreC, mreD, mbl and crvA are not in the inventory.
g191PhoR-PhoB system504Repeat (counted once) checked by hand0none by name
Repeat of Cell Category 10 (see the catalogue). Counted once there.
g192Signaling metabolites504Repeat (counted once) checked by hand0none by name
Repeat of Cell Category 10 (see the catalogue). Counted once there.
g193Quorum sensing504Repeat (counted once) checked by hand0none by name
Repeat of Cell Category 10 (see the catalogue). Counted once there.
g194LuxPQ-LuxU-LuxO504Repeat (counted once) checked by hand0none by name
Repeat of Cell Category 10 (see the catalogue). Counted once there.
g195Gene regulators504Repeat (counted once) checked by hand0none by name
Repeat of Cell Category 10 (see the catalogue). Counted once there.
g196Post-translational modification504Repeat (counted once) checked by hand0none by name
Repeat of Cell Category 10 (see the catalogue). Counted once there.
g197Calcium gradient504Repeat (counted once) checked by hand0none by name
Repeat of Cell Category 10 (see the catalogue). Counted once there.
g198Osmosis regulation504Book requires, Aquifex lacks checked by hand0none by name
Osmosis regulation overlaps g189; no separate gene was found by name.
g199Energy metabolism504Repeat (counted once) checked by hand0none by name
Repeat of Cell Category 10 (see the catalogue). Counted once there.
g200pH regulation504Book requires, Aquifex lacks checked by hand0none by name
No pH-regulation gene (gadB, gadC, kefB, cadA) was found by name.
g201Nutrient homeostasis504Repeat (counted once) checked by hand0none by name
Repeat of Cell Category 10 (see the catalogue). Counted once there.
g202Ion concentration504Not first-cell checked by hand0none by name
The book's ion-management set (Vol. III 3.5) is taken from human proteins (see the catalogue note).
g203Temperature regulation504Aquifex evidence checked by hand5dnaK aq_996, clpB aq_1672, groEL aq_2200, grpE aq_433, groES aq_2199
Temperature-stress genes (chaperones and cold-shock proteins) by name. These are shared with g204.
g204Stress response system505Aquifex evidence checked by hand5dnaK aq_996, clpB aq_1672, groEL aq_2200, grpE aq_433, groES aq_2199
Stress-response chaperones and regulators by name. These overlap g203.
g205Cellular defense505Book requires, Aquifex lacks checked by hand0none by name
Defence against viruses (restriction-modification, toxin-antitoxin, CRISPR) is listed in B1 on the B6 page, not in this group. No defence gene is matched here.
g206Bacterial-Host Interactions505Book requires, Aquifex lacks checked by hand0none by name
No bacterial-host interaction gene was identified by name.
g207ROS management505Aquifex evidence checked by hand3sodB aq_1499, sodC2 aq_238, sodC1 aq_1050
Reactive-oxygen management by name: Fe-SOD (sodB) and Cu/Zn-SOD (sodC1, sodC2). The Cu/Zn enzymes are oxygen-dependent, so check their status.
g208Proteolysis pathway505Book requires, Aquifex lacks checked by hand0none by name
A broad proteolysis group. Its genes are listed under g209 and g210.
g209Proteolytic systems505Aquifex evidence checked by hand1clpP aq_1339
ATP-dependent Clp protease proteolytic subunit (clpP).
g210Lon protease505Aquifex evidence checked by hand8lon aq_242, clpP aq_1339, hslV aq_1671, hslU aq_192, clpX aq_1337, htrA aq_1450 +2 more
Lon, ClpP, ClpX, ClpC, HslU, HslV, HtrA and HtpX, by name. The subtilisin-like and neutral proteases are removed.
g211Metalloprotease pathway505Aquifex evidence checked by hand2ftsH aq_936, - aq_1964
Zinc metalloprotease FtsH and a putative zinc metalloprotease (aq_1964).
g212Serine protease pathway505Aquifex evidence checked by hand1- aq_814
Periplasmic serine protease (aq_814). htrA is listed under g210.
g213Peptidase pathway505Aquifex evidence checked by hand4map aq_076, lspA aq_1837, lepB aq_955, pilD aq_1601
Peptidase pathway: methionine aminopeptidase (map), lspA, lepB and pilD, by name.
g214Iron-sulfur cluster biosynthesis505Aquifex evidence checked by hand3iscU aq_896, nifS2 aq_739, nifS1 aq_1053
Fe-S cluster biosynthesis: IscU and the cysteine desulfurases NifS1 and NifS2, by name.
g215[NiFe-4S] cluster synthesis505Aquifex evidence checked by hand5hypF aq_672, hypA aq_1021, hypB aq_671, hypE aq_1019, hypD aq_1157
Hydrogenase maturation (hypA, hypB, hypD, hypE, hypF) by name, for the [NiFe]-cluster.
g216[5Fe-4S] cluster synthesis505Book requires, Aquifex lacks checked by hand0none by name
No 5Fe-4S cluster protein was identified by name. The IscU and Fe-S carrier hits belong to g214 and g217.
g217[4Fe-4S] cluster synthesis505Aquifex evidence checked by hand2iscU aq_896, mrp aq_737
IscU and the Fe-S carrier Mrp, by name. The four-iron cluster step is not confirmed.
g218[Fe-Mo-Co] synthesis505Book requires, Aquifex lacks checked by hand0none by name
No nitrogenase cofactor gene was found by name.
g219[Fe-only] cluster synthesis505Book requires, Aquifex lacks checked by hand0none by name
No Fe-only hydrogenase gene (hydA, hydE, hydG) was found by name.
g220[2Fe-2S]-[4Fe-4S] hybrid clusters505Repeat (counted once) checked by hand0none by name
Printed twice in the book (see the catalogue). Counted once in g214.
g221CODH/ACS complex metal clusters505Book requires, Aquifex lacks checked by hand0none by name
No CODH/ACS metal-cluster gene was found by name (see g0).
g222Siderophore biosynthesis505Book requires, Aquifex lacks checked by hand0none by name
No siderophore biosynthesis gene (ent, dhb) was found by name.
g223Siderophore export505Book requires, Aquifex lacks checked by hand0none by name
No siderophore export gene (entS, entJ, mdtA) was found by name.
g224Ferrisiderophore transport505Book requires, Aquifex lacks checked by hand0none by name
No ferrisiderophore-transport gene (fhu, fec, btuB) was found by name.
g225Sulfur mobilization505Book requires, Aquifex lacks checked by hand0none by name
No sulfur-mobilisation gene beyond IscU and NifS (g214) was found by name.
g226Sulfur transfer505Aquifex evidence checked by hand2moeB aq_1329, - aq_1421
Sulfur transfer: MoeB (moeB) and the sulfur carrier aq_1421.
g227Scaffold Proteins505Aquifex evidence checked by hand1iscU aq_896
IscU scaffold, shared with g214.
g228Manganese utilization505Book requires, Aquifex lacks checked by hand0none by name
No manganese-utilisation gene was found by name.
g229Mo/W cofactor biosynthesis505Aquifex evidence checked by hand8moaC aq_527, moeB aq_1329, mobA aq_1419, moaE aq_2181, moaA aq_2183, moeA1 aq_030 +2 more
Molybdenum cofactor biosynthesis by name: moaA, moaC, moaE, moeA1, mog, mobA, mobB and moeB.
g230Nickel center biosynthesis505Half repeated (2 of 4 counted) checked by hand0none by name
Half repeated: HypA and HypB are printed here and under g215, so they are counted once. The other 2 of the 4 enzymes are counted here; they are not yet matched by name.
g231Zinc utilization505Book requires, Aquifex lacks checked by hand0none by name
No zinc-uptake gene (znuA, znuB, znuC) was found by name.
g232Copper center utilization505Not first-cell checked by hand2sodC2 aq_238, sodC1 aq_1050
Cu/Zn superoxide dismutases (sodC1, sodC2). These use copper and are not first-cell requirements (see the catalogue note).

2. Required by the books but absent from Chapter 14 (B1–B3)

Checked by hand against the inventory. The status says whether the gene is present, partial or absent. Proteins only: an RNA gene such as tmRNA cannot appear in a protein inventory.

ItemRequired elementWhere the books say itStatusAquifex genes (locus gene)
B1Type I restriction-modification (HsdR, HsdM, HsdS)
No hsd gene by name. aq_037 and aq_1194 are restriction-endonuclease-domain proteins of unknown type, listed under type II.
Vol. III pp. 233–235Absentnone by name
B1Type II restriction-modification (endonuclease and methylase)
Two restriction-endonuclease-domain proteins, type unknown. No methyltransferase by name, so the system is incomplete.
Vol. III pp. 236–237Partialaq_037, aq_1194
B1Type III restriction-modification (Mod, Res)
No Mod or Res gene by name. The type III hits in the inventory are CRISPR and secretion genes.
Vol. III pp. 239–240Absentnone by name
B1Type II toxin-antitoxin (VapBC)
Two VapC ribonucleases. No VapB antitoxin by name, so the pair is incomplete.
Vol. III pp. 242–243Partialaq_aa03 vapC1, aq_1901 VapC-like
B1CRISPR-Cas (type I or III, see C1)
Type III-B (Cmr) plus type I-like Cas genes, so the system is present. No cas9 (type II), which matches C1.
Vol. III p. 770; CUM p. 247Presentaq_369 cas1, aq_371 cas3, aq_370 cas4, aq_373 cas5, aq_173 cas6, aq_386 cmr3, aq_384 cmr5, aq_380–382, aq_385 (type III-associated)
B1Integrase and defence methyltransferase
Integrases present. No defence methyltransferase by name.
Vol. II pp. 441, 462, 487Partialaq_1137 integrase, aq_aa09 integrase/recombinase
B2Sigma factors σS and σ54 (with σ70)
σS and σ54 are present. σ32 (rpoH) is absent by name.
Vol. II pp. 504–510Partialaq_1452 rpoS, aq_599 rpoN, aq_1490 rpoD (σ70)
B2LexA, FNR and Fur regulators
FNR and Fur are present. No LexA by name.
Vol. II pp. 504–510, 590–591Partialaq_490 fnr, aq_1418 furR2
B2RelA / SpoT / DksA stringent response
SpoT and DksA are present. No RelA by name.
CUM p. 282, 286Partialaq_844 spoT, aq_2095 dksA
B3Inorganic pyrophosphatase
The dUTP and dITP pyrophosphatases (aq_1718, aq_202) are different enzymes.
CUM p. 243Presentaq_1547 ppa
B3tmRNA / SmpB
SmpB is present. tmRNA (ssrA) is an RNA gene, so it cannot be in a protein inventory: check the genome directly.
Vol. III pp. 274, 303; CUM p. 198Partialaq_287 smpB
B3Glycyl-tRNA synthetase (GlyRS)
Both subunits are present.
Vol. II aaRS countPresentaq_945 glyQ (alpha), aq_2141 glyS (beta)
B3Photolyase
No phr or photolyase gene by name.
Vol. II p. 529Absentnone by name
B3Reverse gyrase (hyperthermophile)
Both reverse-gyrase genes are present, which fits a thermophilic cell.
Vol. II gap listPresentaq_886 rgy1, aq_1159 rgy2
B3pH-sensing two-component system
Histidine kinases and response regulators are present, but no specific pH sensor is identified by name. PhoR is absent (see g121).
CUM p. 238PartialhksP1–4 (histidine kinases)