Authors: Pallavi Subhraveti Peter D Karp Ingrid Keseler An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Anamika Kothari Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_000442315Cyc: Rubellimicrobium thermophilum DSM 16684 Cellular Overview Connections between pathways are omitted for legibility. Ron Caspi lipid II (meso phosphate diaminopimelate sn-glycerol containing) phosphate dCTP 3-phosphate predicted ABC RS07495 RS12165 RS03605 transporter RS13105 of phosphate lipid II (meso dCTP sn-glycerol diaminopimelate phosphate 3-phosphate containing) phosphate Secondary Metabolite Degradation Storage Compound Biosynthesis Tetrapyrrole Biosynthesis Hormone Biosynthesis Aromatic Compound Aldehyde Degradation UDP-N-acetyl- Biosynthesis undecaprenyl- a mature (4R)-4-hydroxy- an L-glutamyl- a [protein]-L- queuosine at Macromolecule Modification myo-inositol degradation I α-D-glucosamine adenosylcobinamide a purine L-canavanine 5'-deoxyadenosine sec Metabolic Regulator Biosynthesis Amine and Polyamine Biosynthesis polyhydroxybutanoate biosynthesis siroheme biosynthesis methylglyoxal degradation I diphospho-N- peptidoglycan 2-oxoglutarate Gln β-isoaspartate glu position 34 ser a tRNA indole-3-acetate 4-deoxy-L-threo-hex-4- D-fructuronate degradation L-idonate ribonucleoside (n) [tRNA ] ATP roseoflavin chorismate biosynthesis I acetylmuramoyl- (meso-DAP protein-L- of a tRNA Asp enopyranuronate degradation degradation Asp-tRNA(Asn) 5'-phosphate Aminoacyl-tRNA Charging glutaminyl-tRNA gln biosynthesis via transamidation biosynthesis tRNA-uridine 2-thiolation and selenation (bacteria) L-alanyl-γ-D- 5'-triphosphate containing) isoaspartate O- ppGpp metabolism spermidine biosynthesis III acetyl-CoA uroporphyrinogen-III myo-inositol S-methyl-5'- /Glu-tRNA(Gln) trehalose biosynthesis I putrescine spermidine biosynthesis I IV (bacteria) D-erythrose 4-deoxy-L-threo-hex- D-fructuronate methylglyoxal glutamyl-L-lysyl- Arginase/agmatinase/ bifunctional methyltransferase: trehalose siroheme synthase: (indole-3-yl) 4-enopyranuronate L-idonate lactoylglutathione lyase: bifunctional formimionoglutamate thioadenosine 4-hydroxy-2- amidotransferase tRNA glutamyl- serine- biosynthesis I acetyl-CoA C- 4-phosphate inositol 2- D-alanyl-D-alanine RUTHE_RS00520 bifunctional glu biosynthesis V RUTHE_RS00605 acetonitrile cys D-mannonate L-idonate 5- RUTHE_RS06270 UDP-N- adenosylcobinamide lytic hydrolase phosphorylase: oxoglutarate subunit GatB: gatB Q(34) synthetase -tRNA pppGpp D-glucopyranose arg SAM acyltransferase: dehydrogenase: protein-L- riboflavin kinase/ UDP-α-D-glucose SAM uroporphyrinogen-III oxidoreductase: dehydrogenase: acetylglucosamine- kinase/ transglycosylase arginase family: mtnP aldolase/2- Asp-tRNA(Asn) GluQRS: ligase: a glycogen 6-phosphate RUTHE_RS13365 3-deoxy- iolG lactoylglutathione lyase: isoaspartate(D- FAD synthetase: bifunctional (p)ppGpp arg C-methyltransferase: RUTHE_RS11770 RUTHE_RS11800 -N-acetylmuramyl- adenosylcobinamide- domain-containing RUTHE_RS02820 dehydro-3-deoxy- /Glu-tRNA(Gln) RUTHE_RS04050 serS isoamylase: (indol-3-yl) D-arabino- 5-dehydro-4-deoxy- 5-dehydro- RUTHE_RS06595 aspartate) O- RUTHE_RS03210 synthetase/guanosine- [+ 2 isozymes] cobA scyllo-inosose (R)-S-lactoylglutathione (pentapeptide) phosphate protein: phosphogluconate amidotransferase guanosine 3'- glgX trehalose-6- acetamide heptulosonate D-glucuronate D-mannonate D-gluconate arginase: rocF α methyltransferase: 3',5'-bis(diphosphate) 3'- precorrin-1 pyrophosphoryl- guanylyltransferase: RUTHE_RS01915 5-deoxy- -ribose aldolase: eda subunit GatC: gatC glutamyl- diphosphate 5'- a maltodextrin phosphate acetoacetyl-CoA 7-phosphate adenine RUTHE_RS00315 roseoflavin an L-seryl- an L-glutamyl- pyrophosphohydrolase: agmatine amidase: an [L-cysteine desulfurase]- myo-inosose-2 5-dehydro- mannonate hydroxyacylglutathione undecaprenol N- cobU [+ 5 isozymes] 1-phosphate an L-glutaminyl- a protein L-β- queuosine at triphosphate 3'- synthase: 3-dehydroquinate Gln [tRNA sec ] Gln agmatine dAdoMet uroporphyrinogen-III RUTHE_RS08370 S-sulfanyl-L-cysteine dehydratase: iolE 4-deoxy-D- acetylglucosamine [tRNA ] adenine [tRNA ] RUTHE_RS04610 diphosphatase: malto- RUTHE_RS07565 putrescine dAdoMet synthase: dehydratase: D-galactonate degradation hydrolase: gloB urea isoaspartate position 34 Arginase/agmatinase/ C-methyltransferase: glucuronate adenosyl- L-canaline Asp dinucleotide oligosyltrehalose 3D-(3,5/4)- uxuA transferase: a mature GlcNAc-1,6- glyoxylate pyruvate α-methyl ester of a tRNA Asp-tRNA(Asn) RUTHE_RS04610 formimionoglutamate cobA (indol-3-yl)acetate RUTHE_RS04375 isomerase: D-gluconate cobinamide synthase: treY α,α-trehalose polyamine trihydroxycyclohexane- (R)-lactate ditrans,octacisRUTHE_RS03610- UDP a purine peptidoglycan anhMurNAc- /Glu-tRNA(Gln) hydrolase polyamine (3R)-3- kduI 2-dehydro-3- D-galactonate phosphate (n) gln aminopropyltransferase: 3-dehydroquinate 1,2-dione gluconokinase: undecaprenyldiphospho- (meso-DAP L-Ala-γ-D-Glu- amidotransferase a maltooligosyl- 6-phosphate arginase family: aminopropyltransferase: hydroxybutanoyl- poly-[(R)-3- precorrin-2 a [TusA sulfur-carrier protein]- deoxy-D-gluconate ribonucleoside speE 3D-(3,5/4)- 3-deoxy-D-glycero- D-galactonate RUTHE_RS10490 N-acetyl-(N-acetyl-β-D- containing) DAP-D-Ala subunit GatB: gatB GTP ppGpp trehalose trehalose- RUTHE_RS02820 speE CoA hydroxybutanoate] type II 3- S-sulfanyl-L-cysteine 5'-diphosphate Asp-tRNA(Asn) siroheme synthase: trihydroxycyclohexane- 2,5-hexodiulosonate dehydratase: D-gluconate glucosaminyl)muramoyl- Asp-tRNA(Asn) malto- phosphatase: 1 dehydroquinate /Glu-tRNA(Gln) N -(3- [+ 2 isozymes] class I poly(R)- RUTHE_RS00605 1,2-dione acylhydrolase 2-dehydro- RUTHE_RS02350 6-phosphate L-alanyl-γ-D-glutamyl-L- /Glu-tRNA(Gln) oligosyltrehalose otsB aminopropyl) dehydratase: aroQ pyruvate a reduced amidotransferase nucleoside- bifunctional (p)ppGpp putrescine spermidine hydroxyalkanoic (decyclizing): iolD 3-deoxy-D- 2-dehydro-3-deoxy- lysyl-D-alanyl-D-alanine amidotransferase trehalohydrolase: α α agmatine KDGP H O c-type subunit GatB: gatB diphosphate kinase: synthetase/guanosine- , -trehalose acid synthase: sirohydrochlorin 3-dehydroshikimate a [TusD sulfur-carrier protein]- gluconate 5- D-galactonate 2 cytochrome- subunit GatC: gatC treZ 5-deoxy-D-glucuronate cytochrome [+ 3 isozymes] RUTHE_RS14460 3',5'-bis(diphosphate) 3'- phaC S-sulfanyl-L-cysteine dehydrogenase 2-dehydro-3- c oxidase, an oxidized a 5-phosphooxy- UDP-N-acetyl- undecaprenyldiphospho- a DNA containing UDP-N-acetyl- phosphoenol pyrophosphohydrolase: α,α-trehalose siroheme synthase: shikimate 5- KduD: kduD a nucleoside an L-aspartyl- oleoyl-CoA H O 34 O cbb3-type c-type L-glutamyl- bifunctional deoxygalactonokinase: D-sorbitol degradation I α-D-glucosamine N-acetylmuramoyl-L- an apurinic/ α D-glt H O 3'-AMP ala 2 a cytidine lys 2 ammonium a ribonucleic acid -D-muramoyl- 2 Asn pyruvate UDP-N-acetyl- Gln RUTHE_RS04610 poly-[(R)-3- RUTHE_RS00605 dehydrogenase: triphosphate GTP [tRNA ] dGDP Ile2 acytochrome reduced [tRNA ] 2-dehydro-3- 4-hydroxy-2- RUTHE_RS08865 alanyl-γ-D-glutamyl-meso apyrimidinic site L-alanine α-D-muramate in tRNA spermidine hydroxybutanoate] RUTHE_RS12865 2-dehydro-3-deoxy- Asp-tRNA(Asn) 5'/3'-nucleotidase H O c-type siroheme a [TusE sulfur carrier 5-dehydro-2- deoxy-D-gluconate oxoglutarate D-sorbitol -2,6-diaminopimeloyl- SurE: surE 2 cytochrome Asp-tRNA(Asn) a uridine 34 in tRNA D-galactonate /Glu-tRNA(Gln) tol-pal system- ancytochrome oxidized shikimate protein]-S-sulfanylcysteine deoxy-D-gluconate aldolase/2- L-iditol 2- D-alanyl-D-alanine endonuclease DNA- tRNA c oxidase /Glu-tRNA(Gln) GDP 6-phosphate UDP-N- GTPase amidotransferase bifunctional 2',3'- UDP-N- associated O c-type dehydro-3-deoxy- directed RNA 2 5-dehydro-2- dehydrogenase: III: nth acetylmuramoyl- HflX: hflX subunit GatB: gatB pyruvate cyclic-nucleotide 2'- acetylmuramate-- acyl-CoA lysidine(34) a reduced amidotransferase shikimate kinase: phosphogluconate UDP-N- polymerase: cytochrome tRNA 2-thiouridine(34) deoxygluconokinase: 2-dehydro-3-deoxy-6- RUTHE_RS10505 bifunctional DNA- L-alanine--D- [+ 2 isozymes] Asp-tRNA(Asn) kinase: pyk phosphodiesterase/ L-alanine ligase: thioesterase: synthetase H O c-type subunit GatB: gatB RUTHE_RS04380 aldolase: eda keto-D-fructose acetylglucosamine- rpoB rpoC 2 synthase MnmA: mnmA iolC KDGP phosphogalactonate formamidopyrimidine glutamate ligase: /Glu-tRNA(Gln) 3'-nucleotidase: RUTHE_RS03615 ybgC TilS: tilS cytochrome Asp-tRNA(Asn) -N-acetylmuramyl- RS12765 an oxidized shikimate 3- 5-dehydro-2-deoxy-D- aldolase: glycosylase/ DNA-directed RUTHE_RS06155 amidotransferase RUTHE_RS11010 /Glu-tRNA(Gln) D-glyceraldehyde (pentapeptide) phosphate H + O c-type phosphate a 2-thiouridine 34 in tRNA gluconate 6-phosphate pyruvate RUTHE_RS08860 DNA-(apurinic RNA polymerase GDP subunit GatC: gatC pyruvate UDP-N-acetyl- a lysidine 34 2 amidotransferase bifunctional 3-phosphate pyrophosphoryl- an L-asparaginyl- dGTP adenosine H + RS00710 cytochromeH + 3-phosphoshikimate 1- or apyrimidinic subunit alpha: UDP-N-acetyl- α-D-muramoyl- oleate in tRNA Ile2 subunit GatC: gatC 4-hydroxy-2- undecaprenol N- Asn tRNA uridine-5- D-glyceraldehyde β-D-fructofuranose