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Home , Butyrate kinase, Erythritol kinase, Phosphofructokinase, Phosphoglycerate kinase, Quinolinate synthase

Table S3: List of genes used to reconstruct metabolic map of bin O “Ca. Sabulitectum silens”

Glycolysis (complete) No. Gene(s) Gene EC no. contig G1 glkA 2.7.1.2 contig00029 G2 pgi -6- 5.3.1.9 contig00016 G3 pfkA 6- 1 2.7.1.11 contig00003 G4 Pyrophosphate--fructose 6-phosphate 1- 2.7.1.90 contig00009 G5 fba Fructose-bisphosphate aldolase 4.1.2.13 contig00010 G6 tpiA Triosephosphate isomerase 5.3.1.1 contig00009 G7 gap Glyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 contig00009 G8 pgk Phosphoglycerate 2.7.2.3 contig00009 G9 pgk/tpi Bifunctional PGK/TIM 2.7.2.3/5.3.1.1 contig00009 G10 apgM 2,3-bisphosphoglycerate-independent 5.4.2.12 contig00048 G11 eno 4.2.1.11 contig00002 G12 pyk 2.7.1.40 contig00002 G13 ppdK Pyruvate, phosphate dikinase 2.7.9.1 contig00002 G14 pckA Phosphoenolpyruvate carboxykinase [ATP] 4.1.1.49 contig00002

Nonoxidative pentose phosphate pathway (complete) No. Gene(s) Gene product EC no. contig P1 tkt Transketolase 2.2.1.1 contig00046 P2 tal Transaldolase 2.2.1.2 contig00046 P3 rpe Ribulose-phosphate 3-epimerase 5.1.3.1 contig00051 P4 rpiB Ribose-5-phosphate isomerase B 5.3.1.- contig00002 P5 prs Ribose-phosphate pyrophosphokinase 2.7.6.1 contig00002 P6 deoB Phosphopentomutase 5.4.2.7 contig00002 P7 deoC Deoxyribose-phosphate aldolase 4.1.2.4 contig00046

Starch and sucrose (complete) No. Gene(s) Gene product EC no. contig S1 algC Phosphomannomutase/phosphoglucomutase 5.4.2.2 contig00016 S2 glgC Glucose-1-phosphate adenylyltransferase 2.7.7.27 contig00025 S3 rmlA Glucose-1-phosphate thymidylyltransferase 2.7.7.24 contig00003 S4 glgA1 Glycogen synthase 1 2.4.1.21 contig00002 S5 glgB 1,4-alpha-glucan branching GlgB 2.4.1.18 contig00079 S6 malQ 4-alpha-glucanotransferase 2.4.1.25 contig00013

Glycosyl / No. Gene(s) Gene product EC no. contig GH1 Glycosyl family 85 3.2.1.96 contig00013 GH2 Cellulase (glycosyl hydrolase family 5) 3.2.1.-. contig00002 GH3 Glycosyl hydrolase family 94 2.4.1.-. contig00016 GT1 Glycosyltransferase family 9 (heptosyltransferase) 2.4.1.-. contig00084 GT2 Glycosyl transferases group 1 2.4.-.-. contig00003 GT3 Glycosyl family 2 2.4.-.-. contig00081

Fermentation No. Gene(s) Gene product EC no. contig F1 nifJ Pyruvate-flavodoxin 1.2.7.1 contig00048 F2 pta Phosphate acetyltransferase 2.3.1.8 contig00013 F3 ackA 2.7.2.1 contig00009 F4 Aldehyde ferredoxin oxidoreductase, domains 2 %26 3 1.2.7.5 contig00010 F5 aldHT Aldehyde dehydrogenase, thermostable 1.2.1.5 contig00002 F6 adhT dehydrogenase 1.1.1.1 contig00016 F7 buk2 putative 2 2.7.2.7 contig00042 F8 phosphate butyryltransferase 2.3.1.19 contig00002 F9 gdhA NAD(P)-specific glutamate dehydrogenase 1.4.1.3 contig00002 F10 korA 2-oxoglutarate oxidoreductase subunit KorA 1.2.7.3 contig00003 F10 korB 2-oxoglutarate oxidoreductase subunit KorB 1.2.7.3 contig00003 F11 sucD Succinyl-CoA [ADP-forming] subunit alpha 6.2.1.5 contig00013 F12 gltD Glutamate synthase [NADPH] small chain 1.4.7.1 contig00002 F13 NAD-dependent malic enzyme 1.1.1.40 contig00009 F14 fumarate hydratase 4.2.1.2 contig00009 F15 citE Citrate subunit beta 4.1.3.6 contig00002 F16 acsA Acetyl-coenzyme A synthetase 6.2.1.1 contig00112 F17 scpA Methylmalonyl-CoA mutase 5.4.99.2 contig00002 F18 Methylmalonyl-CoA carboxyltransferase 12S subunit 2.1.3.1 contig00002

MEP/DOXP pathway (complete) No. Gene(s) Gene product EC no. contig I1 dxs 1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 contig00010 I2 dxr 1-deoxy-D-xylulose 5-phosphate reductoisomerase 1.1.1.267 contig00046 I3 ispD 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 2.7.7.60 contig00002 I4 ispE 4-diphosphocytidyl-2-C-methyl-D- 2.7.1.148 contig00003 I5 ispF 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase 4.6.1.12 contig00002 I6 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase 1.17.7.1 contig00013 I7 ispH 4-hydroxy-3-methylbut-2-enyl diphosphate 1.17.1.2 contig00010 I8 ispA Farnesyl diphosphate synthase 2.5.1.1 contig00009

Nicotidamide synthesis No. Gene(s) Gene product EC no. contig C1 nadB L-aspartate oxidase 1.4.3.16 contig00016 C2 nadA Quinolinate synthase A 2.5.1.72 contig00048 C3 nadC Nicotinate- pyrophosphorylase [carboxylating] 2.4.2.19 contig00082 C4 nadD Nicotinate-nucleotide adenylyltransferase 2.7.7.18 contig00076 C5 nadE NH(3)-dependent NAD(+) synthetase 6.3.1.5 contig00009

Biotin synthesis No. Gene(s) Gene product EC no. contig C6 bioA Adenosylmethionine-8-amino-7-oxononanoate aminotransferase 2.6.1.62 contig00029 C7 bioB Biotin synthase 2.8.1.6 contig00029 C8 bioC Malonyl-[acyl-carrier protein] O-methyltransferase 2.1.1.197 contig00029 C9 bioD1 ATP-dependent dethiobiotin synthetase BioD 1 6.3.3.3 contig00029 C10 bioF 8-amino-7-oxononanoate synthase 2 2.3.1.47 contig00029

Thiamine synthesis No. Gene(s) Gene product EC no. contig C11 thiC Phosphomethylpyrimidine synthase 4.1.99.17 contig00082 C12 thiE Thiamine-phosphate synthase 2.5.1.3 contig00002 C13 thiH 2-iminoacetate synthase 4.1.99.19 contig00002 C14 thiM Hydroxyethylthiazole kinase 2.7.1.50 contig00002 C15 thiD Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase 2.7.4.7 contig00002 C16 thiL Thiamine-monophosphate kinase 2.7.4.16 contig00002

Riboflavin synthesis No. Gene(s) Gene product EC no. contig C17 ribBA Riboflavin biosynthesis protein RibBA 4.1.99.12/3.5.4.25 contig00002 C18 ribH 6,7-dimethyl-8-ribityllumazine synthase 2.5.1.78 contig00002 C19 ribE 2.5.1.9 contig00002 C20 ribD Riboflavin biosynthesis protein RibD 3.5.4.26/1.1.1.193 contig00002

Nuo-like NADH Oxidoreductase No. Gene(s) Gene product EC no. contig N1 nuoE NADH-quinone oxidoreductase subunit E 1.6.5.11 contig00002 N1 nuoC1 NADH-quinone oxidoreductase subunit C 1 1.6.5.11 contig00002 N1 nuoD NADH-quinone oxidoreductase subunit D 1.6.5.11 contig00002 N1 nuoH NADH-quinone oxidoreductase subunit H 1.6.5.11 contig00002 N1 nuoI NADH-quinone oxidoreductase subunit I 1.6.5.11 contig00002 N1 ndhK NAD(P)H-quinone oxidoreductase subunit K 1.6.5.11 contig00002 N1 nox NADH dehydrogenase 1.6.99.3 contig00002

Hyd-like (Fe) Hydrogenase No. Gene(s) Gene product EC no. contig H1 hydA Periplasmic [Fe] hydrogenase large subunit 1.12.7.2 contig00084 H1 hndC NADP-reducing hydrogenase subunit HndC 1.12.1.3 contig00084 H1 hndD NADP-reducing hydrogenase subunit HndD 1.12.1.3 contig00084 H1 nqo2 NADH-quinone oxidoreductase subunit 2 1.6.5.11 contig00084 H1 Iron hydrogenase 1 1.12.7.2 contig00084

Hnd-like Hydrogenase No. Gene(s) Gene product EC no. contig H2 hndA NADP-reducing hydrogenase subunit HndA 1.-.-.- contig00010 H2 hndC NADP-reducing hydrogenase subunit HndC 1.-.-.- contig00010 H2 hndD NADP-reducing hydrogenase subunit HndD 1.-.-.- contig00010

Hox-like Hydrogenase No. Gene(s) Gene product EC no. contig H3 hoxE bidirectional hydrogenase complex protein HoxE 1.12.1.2 contig00010 H3 hoxF NAD-reducing hydrogenase HoxS subunit alpha 1.12.1.2 contig00048 H3 hoxH NAD-reducing hydrogenase HoxS subunit beta 1.12.1.2 contig00048 H3 hoxU NAD-reducing hydrogenase HoxS subunit gamma 1.12.1.2 contig00048 H3 hoxY NAD-reducing hydrogenase HoxS subunit delta 1.12.1.2 contig00048

Hyp-like Hydrogenase chaperone No. Gene(s) Gene product EC no. contig H4 hypA hydrogenase nickel incorporation protein HypA - contig00003 H4 hypB Hydrogenase/urease nickel incorporation protein HypB - contig00003 H4 hypD Hydrogenase isoenzymes formation protein HypD - contig00048 H4 hypE Hydrogenase expression/formation protein HypE - contig00048 H4 hypF Carbamoyltransferase HypF - contig00048

V-type proton/sodium ATPase No. Gene(s) Gene product EC no. contig V1 ntpA V-type sodium ATPase catalytic subunit A 3.6.3.- contig00013 V1 ntpB V-type sodium ATPase subunit B 3.6.3.- contig00013 V1 ntpK V-type sodium ATPase subunit K 3.6.3.- contig00013 V1 ntpD V-type sodium ATPase subunit D 3.6.3.- contig00013 V1 ntpG V-type sodium ATPase subunit G 3.6.3.- contig00013 V1 atpC V-type ATP synthase subunit C 3.6.3.- contig00013 V1 atpE V-type proton ATPase subunit E 3.6.3.- contig00013 V1 V-type ATP synthase subunit I 3.6.3.- contig00013

Electron transport complex No. Gene(s) Gene product EC no. contig E1 rnfA Electron transport complex protein RnfA 1.18.1.3 contig00055 E1 rnfB Electron transport complex protein RnfB - contig00055 E1 rnfC Electron transport complex protein RnfC - contig00055 E1 rnfD Electron transport complex protein RnfD - contig00055 E1 rnfE Electron transport complex protein RnfE - contig00055 E1 rnfG Electron transport complex protein RnfG - contig00055

Phosphate uptake No. Gene(s) Gene product EC no. contig T1 pstA Phosphate transport system permease protein PstA - contig00003 T1 pstB Phosphate import ATP-binding protein PstB - contig00003 T1 pstB3 Phosphate import ATP-binding protein PstB 3 - contig00003 T1 pstC Phosphate transport system permease protein PstC - contig00003

Na+/Pi-cotransporter contig00003

Potassium uptake No. Gene(s) Gene product EC no. contig T2 trkA Trk system potassium uptake protein TrkA - contig00002 T2 trkG Trk system potassium uptake protein TrkG - contig00002 T2 trkH Trk system potassium uptake protein TrkH - contig00002

T3 ktrA Ktr system potassium uptake protein A - contig00010 T3 ktrB Ktr system potassium uptake protein B - contig00010

Iron uptake No. Gene(s) Gene product EC no. contig T4 FeoA domain protein - contig00010 T4 ferrous iron transport protein A - contig00010 T4 feoB Ferrous iron transport protein B - contig00010 T4 FeoC like transcriptional regulator - contig00010

T5 irtA Iron import ATP-binding/permease protein IrtA - contig00084 T5 irtB Iron import ATP-binding/permease protein IrtB - contig00048

High-affinity zinc uptake system No. Gene(s) Gene product EC no. contig T6 znuA High-affinity zinc uptake system binding-protein ZnuA precursor - contig00025 T6 znuB High-affinity zinc uptake system membrane protein ZnuB - contig00025 T6 znuC High-affinity zinc uptake system ATP-binding protein ZnuC - contig00025

PTS System No. Gene(s) Gene product EC no. contig T7 ptsI Phosphoenolpyruvate-protein phosphotransferase - contig00016 T7 ptsH Phosphocarrier protein HPr - contig00016 T7 hprK HPr kinase/ - contig00016

Cation/Proton Antiporters No. Gene(s) Gene product EC no. contig T8 nhaP2 K(+)/H(+) antiporter NhaP2 - contig00046 T9 nhaP Na(+)/H(+) antiporter NhaP - contig00010 T10 mrpA Na(+)/H(+) antiporter subunit A - contig00002 T10 putative monovalent cation/H+ antiporter subunit B - contig00002 T10 mrpF Na(+)/H(+) antiporter subunit F - contig00002 T10 putative monovalent cation/H+ antiporter subunit E - contig00002 T10 mnhC1 Na(+)/H(+) antiporter subunit C1 - contig00002

Cation efflux No. Gene(s) Gene product EC no. contig T11 cusA Cation efflux system protein CusA - contig00010 T11 cusB Cation efflux system protein CusB precursor - contig00010 T11 czcA Cobalt-zinc-cadmium resistance protein CzcA - contig00010

Lipopolysaccharide export T12 lptB Lipopolysaccharide export system ATP-binding protein LptB - contig00025 T12 Lipopolysaccharide-assembly, LptC-related - contig00025

Copper export No. Gene(s) Gene product EC no. contig T13 copA Copper-exporting P-type ATPase A - contig00042 T13 ctpV putative copper-exporting P-type ATPase V - contig00042

Fluoroquinolone Export (very low transcription) No. Gene(s) Gene product EC no. contig M1 Fluoroquinolones export ATP-binding proteinc/MT2762 - contig00003 M1 Fluoroquinolones export permease proteinc/MT2761 - contig00003 M1 Fluoroquinolones export permease proteinc/MT2760 - contig00003

Multidrug resistance No. Gene(s) Gene product EC no. contig M2 mdtA Multidrug resistance protein MdtA - contig00002 M2 mdtB Multidrug resistance protein MdtB - contig00002 M2 cnrA Nickel and cobalt resistance protein CnrA - contig00002

M2 mdtA Multidrug resistance protein MdtA precursor - contig00098 M2 mdtC Multidrug resistance protein MdtC - contig00098 M2 mdtE Multidrug resistance protein MdtE precursor - contig00098

M2 emrK putative multidrug resistance protein EmrK - contig00042 M2 mdtB Multidrug resistance protein MdtB - contig00042 M2 mdtJ Spermidine export protein MdtJ - contig00042 M2 periplasmic multidrug efflux lipoprotein precursor - contig00042 M2 cnrA Nickel and cobalt resistance protein CnrA - contig00042

M2 mdlB Multidrug resistance-like ATP-binding protein MdlB - contig00002 putative multidrug resistance ABC transporter ATP-binding/permease M2 yheI protein YheI - contig00002 M2 mepA Multidrug export protein MepA - contig00002 M2 Putative multidrug export ATP-binding/permease protein - contig00002

OM Protein Assembly Bam complex No. Gene(s) Gene product EC no. contig O1 bamA Outer membrane protein assembly factor BamA - contig00003 O1 bamB Outer membrane protein assembly factor BamB - contig00003 O1 bamD Outer membrane protein assembly factor BamD - contig00010

O3 surA Chaperone SurA - contig00009 O4 skp Chaperone protein Skp precursor - contig00025 O5 degP1 putative periplasmic serine endoprotease DegP-like precursor - contig00084 O5 degQ Periplasmic pH-dependent serine endoprotease DegQ precursor - contig00013

Ton complex No. Gene(s) Gene product EC no. contig O2 Gram-negative bacterial tonB protein - contig00003 O2 exbB Biopolymer transport protein ExbB - contig00003 O2 exbD Biopolymer transport protein ExbD - contig00003 O2 Biopolymer transport protein ExbD/TolR - contig00003

O6 TonB dependent receptor - contig00029 O6 TonB-dependent Receptor Plug Domain protein - contig00016

O7 tolB Protein TolB - contig00003 O7 tolC Outer membrane protein TolC precursor - contig00002

Protein secretion No. Gene(s) Gene product EC no. contig Y1 secA Protein subunit SecA - contig00010 Y1 secD Protein translocase subunit SecD - contig00013 Y1 secE Protein translocase subunit SecE - contig00003 Y1 secF Protein-export membrane protein SecF - contig00013 Y1 secG preprotein translocase subunit SecG - contig00084 Y1 secY Protein translocase subunit SecY - contig00003

Y2 tatAd Sec-independent protein translocase protein TatAd - contig00016 Y2 tatC Sec-independent protein translocase protein TatC - contig00002 Y2 tatC2 Sec-independent protein translocase protein TatCy - contig00002

Y3 epsE Type II secretion system protein E - contig00025 Y3 xcpT Type II secretion system protein G precursor - contig00025 Y3 epsF Type II secretion system protein F - contig00025

Lipoprotein-releasing system No. Gene(s) Gene product EC no. contig Y4 outer membrane-specific lipoprotein transporter subunit LolE - contig00002 Y4 lolE Lipoprotein-releasing system transmembrane protein LolE - contig00002 Y4 lolD Lipoprotein-releasing system ATP-binding protein LolD - contig00025 Y4 lolC Lipoprotein-releasing system transmembrane protein LolC - contig00025

Oxidative stress protection No. Gene(s) Gene product EC no. contig fprA Nitric oxide reductase 1.7.1.14 contig00002 ftnA Ferritin 1.16.3.1 contig00002 trxA Thioredoxin - contig00002 trxB Thioredoxin reductase 1.8.1.9 contig00029 tpx Thiol peroxidase 1.11.1.- contig00076 hrb High molecular weight rubredoxin - contig00002 Rubrerythrin - contig00003 norV Anaerobic nitric oxide reductase flavorubredoxin - contig00042

Fatty acid synthesis (incomplete) No. Gene(s) Gene product EC no. contig acpP Acyl carrier protein - contig00003 Methylmalonyl-CoA carboxyltransferase 12S subunit 2.1.3.1 contig00002 fabD Malonyl CoA-acyl carrier protein transacylase 2.3.1.39 contig00002 fabF 3-oxoacyl-[acyl-carrier-protein] synthase 2 2.3.1.179 contig00003 fabH 3-oxoacyl-[acyl-carrier-protein] synthase 3 2.3.1.180 contig00003 fabG 3-oxoacyl-[acyl-carrier-protein] reductase FabG 1.1.1.100 contig00003 fabG1 3-oxoacyl-[acyl-carrier-protein] reductase FabG1 1.1.1.100 contig00003 fabZ 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabZ 4.2.1.59 contig00025 fabL Enoyl-[acyl-carrier-protein] reductase [NADPH] FabL

Fatty acid beta oxidation (incomplete) No. Gene(s) Gene product EC no. contig Long-chain-fatty-acid--CoA ligase FadD15 6.2.1.3 contig00003 acdA Acyl-CoA dehydrogenase 1.3.99.- contig00003 Enoyl-CoA hydratase Ketothiolase

Sulfur metabolism No. Gene(s) Gene product EC no. contig sat Sulfate adenylyltransferase 2.7.7.4 contig00003 cysC putative adenylyl-sulfate kinase 2.7.1.25 contig00009

Metalloproteases No. Gene(s) Gene product EC no. contig ftsH ATP-dependent zinc metalloprotease FtsH 3.4.24.- contig00002 shpI Neutral metalloprotease precursor 3.4.24.- contig00112 Putative zinc metalloprotease 3.4.24.- contig00046 rip3 Putative zinc metalloprotease Rip3 3.4.24.- contig00003

Cell wall No. Gene(s) Gene product EC no. contig putative undecaprenyl-phosphate N-acetylglucosaminyl 1-phosphate tagO transferase 2.7.8.33 contig00081 tagD -3-phosphate cytidylyltransferase 2.7.7.39 contig00016 tagH Teichoic acids export ATP-binding protein TagH 3.6.3.40 contig00081 tagB Putative CDP-glycerol:glycerophosphate glycerophosphotransferase - contig00016

tuaD UDP-glucose 6-dehydrogenase TuaD 1.1.1.22 contig00055 tuaC Putative teichuronic acid biosynthesis glycosyltransferase TuaC 2.4.-.- contig00003 UDP-glucose:undecaprenyl-phosphate glucose-1-phosphate wcaJ transferase 2.7.8.31 contig00029

Carotenoid biosynthesis No. Gene(s) Gene product EC no. contig crtN Dehydrosqualene desaturase 1.3.8.2 contig00003 crtI Phytoene desaturase (neurosporene-forming) 1.3.99.28 contig00013 crtP Diapolycopene oxygenase 1.14.99.44 contig00013

Morphology/Motility No. Gene(s) Gene product EC no. contig mrdB Rod shape-determining protein RodA - contig00009 mreB Rod shape-determining protein MreB - contig00009 mreC Cell shape-determining protein MreC precursor - contig00009

pilQ Type IV pilus biogenesis and competence protein PilQ precursor - contig00025 Pilus assembly protein, PilO - contig00025 pilT Twitching mobility protein - contig00025

comC Type 4 prepilin-like proteins leader peptide-processing enzyme 3.4.23.43/2.1.1.- contig00002 PilZ domain protein - contig00079

flagellar basal body rod modification protein - contig00003 mglA Mutual gliding-motility protein MglA - contig00003 swrC Swarming motility protein SwrC - contig00002

Sporulation (incomplete/putative) No. Gene(s) Gene product EC no. contig soj Sporulation initiation inhibitor protein Soj 3.6.-.- contig00013 kinE Sporulation kinase E 2.7.13.3 contig00084 cotSA Spore coat protein SA 2.4.-.- contig00003 cotH Inner spore coat protein H - contig00013 ydhD Putative sporulation-specific glycosylase YdhD 3.2.-.- contig00048 spoVD Stage V sporulation protein D - contig00009 stoA Sporulation thiol-disulfide oxidoreductase A precursor - contig00002 cwlC Sporulation-specific N-acetylmuramoyl-L- amidase 3.5.1.28 contig00002