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. Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. ShigellaCyc: Shigella flexneri 2a str. 2457T Cellular Overview Connections between pathways are omitted for legibility. Author: Jonathan Wagg, SRI International a proteinogenic a proteinogenic amino acid a dipeptide GTP D-sorbitol a long-chain + a proteinogenic a proteinogenic a proteinogenic a proteinogenic a proteinogenic a proteinogenic a proteinogenic a proteinogenic a proteinogenic a proteinogenic (R)- formate sn-glycerol sn-glycerol sn-glycerol sn-glycerol H a proteinogenic amino acid a proteinogenic cob(I)alamin cob(I)alamin cob(I)alamin 2-oxoglutarate (S)-lactate D-xylose sulfate sulfate sulfate phosphate phosphate taurine taurine taurine L-carnitine amino acid amino acid amino acid a dipeptide a dipeptide a dipeptide amino acid amino acid amino acid amino acid amino acid amino acid amino acid fatty acid pantothenate L-fucose uracil D-xylose N-acetylneuraminate 3-phosphate maltose maltose maltose 3-phosphate 3-phosphate 3-phosphate D-gluconate D-gluconate D-gluconate D-galactopyranose D-galactopyranose melibiose amino acid amino acid predicted putative predicted transporter putative amino ATP-driven BtuC BtuD BtuE Ffh PanF KgtP FucP LldP FocA UraA XylE XylG NanT UgpB MalK MalG MalF UgpA UgpE GlpT GntP GntT GntU MglA GalP CysW CysA CysZ PitA PstB TauC TauA TauB complex of MelB CaiT AtpH LivG AroP YeaN BrnQ amino acid acid/amine DppA transporter DppB DppC LivM LivH YbaT YjdE YifK YeeF YcjJ LivJ FadL SORBITOL antiporter transport complex of protein a dipeptide + a long-chain (R)- formate uracil H cob(I)alamin cob(I)alamin cob(I)alamin GTP 2-oxoglutarate L-fucose (S)-lactate D-xylose D-xylose N-acetylneuraminate sn-glycerol maltose maltose maltose sn-glycerol sn-glycerol sn-glycerol D-gluconate D-gluconate D-gluconate D-galactopyranose D-galactopyranose sulfate sulfate sulfate taurine taurine taurine melibiose L-carnitine a proteinogenic a proteinogenic a proteinogenic a proteinogenic a dipeptide a dipeptide a dipeptide a proteinogenic a proteinogenic a proteinogenic a proteinogenic a proteinogenic a proteinogenic a proteinogenic a proteinogenic fatty acid pantothenate phosphate phosphate 3-phosphate 3-phosphate 3-phosphate 3-phosphate D-sorbitol amino acid amino acid amino acid amino acid a proteinogenic amino acid amino acid amino acid amino acid amino acid amino acid amino acid amino acid 6-phosphate amino acid a proteinogenic a dipeptide amino acid an osmoregulated a phosphatidylglycerol periplasmic glucan Chemoautotrophic Carbohydrate Degradation Metabolic Regulator Polyprenyl Biosynthesis Energy Metabolism UDP-N-acetyl- undecaprenyl- [1-(2-amino-7-methyl- 4-(β-D- a linear malto- (S)-3- a (7Z,10Z,13Z a [protein]- a mismatched Biosynthesis α an alkylated DNA oxaloacetate a lipid II a [DsrC]-trisulfide RNA N-acetyl- acetyl-CoA nitrite superpathway of ubiquinol-8 Cofactor, Carrier, and Vitamin Biosynthesis Fermentation homolactic fermentation superpathway of glucose and xylose degradation -D-glucosamine diphospho-N- 4-oxo-7,8-dihydro- 4-(β-D-ribofuranosyl) ribofuranosyl) (7,8-dihydropterin- oligosaccharide a type IV prepilin hydroxybutanoyl- ,16Z,19Z)-3- L-histidine DNA base pair phosphoglycerol superpathway of menaquinol-8 biosynthesis I superpathway of tetrahydrofolate biosynthesis and salvage flavin biosynthesis I superpathway of superpathway of coenzyme A biosynthesis I (bacteria) superpathway of adenosylcobalamin salvage from cobinamide I NAD salvage pathway I (PNC VI cycle) hydrogen fucose degradation D-galactose degradation I (Leloir pathway) D-arabinose degradation I L-arabinose ITP L-citrulline biosynthesis (early decarboxylation) thiamine geranyl diphosphate acetylmuramoyl- 3H-pteridin-6-yl) aminobenzene- aminobenzene- 6-yl)methyl CoA oxodocosa- acetyl CoA methyl- nitrate transferase I: mdoB (bacteria and plants) demethylmenaquinol-8 biosynthesis I ppGpp metabolism degradation I 4-enzyme protein diphosphate biosynthesis oxidation D-glucopyranose L-alanyl-γ-D- ]ethyl diphosphate 5'-phosphate 5'-phosphate diphosphate 7,10,13,16,19- carboxylase, directed reductase 3-methyl-2- a 5,10- D-glucopyranose I (aerobic) β glycogen D-alanyl-D-alanine protein, 3- 3-oxoacyl- histidine IPP chorismate salvage I cob(II)inamide NAD + 6-phosphate -L-fucopyranose β-D-galactopyranose D-arabinopyranose glutamyl-L-lysyl- 3-methyl- sulfite tRNA pentaenoyl-[acp] biotin mismatch 1, delta GTP chorismate oxobutanoate methylenetetrahydrofolate L-arabinopyranose phosphorylase: carboxypeptidase, prepilin hydroxyacyl-CoA acetylornithine [acyl-carrier- kinase/ an osmoregulated GTP pppGpp H D-alanyl-D-alanine adenine DNA reductase, nucleotidyl carboxylase repair subunit: thiamine IPP glucokinase: 2 glucose-6- L-fucose phosphoenolpyruvate fraction A; peptidase deacetylase: protein] phosphatase a 1,2-diacyl-sn-glycerol isochorismate cob(I)alamin putative aldose-1- L-arabinose UDP-N- dihydropteroate dihydropteroate glgP glycosylase dehydrogenase; alpha transferase: periplasmic glucan with isopentenyl isochorismate thiamin 3-methyl-2-oxobutanoate geranyltranstransferase glk hydrogenase- phosphate isomerase: carboxykinase: pckA penicillin-binding dependent argE reductase: subunit: accC sensor protein: narJ hydroxymutase GTP adenolsyltransferase: epimerase: yihR isomerase: araA acetylglucosamine:N- synthase: S2703 synthase: S2703 maltodextrin II: alkA 3-hydroxybutyryl- subunit: cysI cca a (3R,7Z,10Z phosphoglycerol substituent diphosphate GTP hydroxymutase kinase: (p)ppGpp synthetase (farnesyldiphosphate 2 component: dehydrogenase: phosphoenolpyruvate for OmpR, mutH 2: menF cyclohydrolase hydroxymethyltransferase: btuR D-glucopyranose galactose-1- fucI L-ribulose acetylmuramyl- phosphorylase: protein 5: dacA protein CoA epimerase; ,13Z,16Z,19ZfabG)-3- acetyl CoA probable isomerase: cyclohydrolase 2: menF ycfN synthase): ispA hybD α 3-methyl- putative RNase panB II and guanosine-3,5- geranyl 6-phosphate zwf -L-fucopyranose (pentapeptide) carboxylase: ppc B: ppdB hydroxydocosa- carboxylase, modulates methyl- nitrate S3074 I: folE thiamine [corrinoid adenosyltranferase]- NMN epimerase D-ribulose malP adenine DNA delta(3)-cis- PH: rph isochorismate II: ribA bis pyrophosphate 3- [+ 6 isozymes] 6-phospho L-ribulokinase: pyrophosphoryl- [1-(2-amino-7-methyl- 7,8-dihydropterin- sulfite acetate L-citrulline car: accD expression directed reductase 7,8- 2,5-diamino-6- isochorismate phosphate asp cob(II)inamide diphosphate glucosephosphate L-fucose (mutarotase): galM a N- prepilin delta(2)-trans- 7,10,13,16,19- Ins(1,2,3,4,5,6)P pyrophosphohydrolase: A(H2) D-glucono- araB 4-oxo-7,8-dihydro- 6-ylmethyl-4-(β- glycosylase reductase: accA accB of ompF and 3: napA 6 DMAPP dihydroneopterin (5-phospho-D- isomerase: undecaprenol N- α D-ala acetylglucosamine- peptidase enoyl-CoA pentaenoyl-[acp] mismatch 2-oxoglutarate thiamin- 2-dehydropantoate spoT guanosine isomerase: pgi 1,5-lactone α -D- a linear malto- I: tag phosphoenolpyruvate yccK periplasmic 3'-triphosphate 2-oxoglutarate aspartate 1- -D-galactopyranose acetylglucosamine 3H-pteridin-6-yl)]ethyl- D-ribofuranosyl) -N-acetylmuramyl- dependent isomerase; a nucleoside malonyl-CoA ompC: envZ repair nitrate decarboxylase; ribosylamino) monophosphate pentaphosphatase, fucI L-ribulose 5-phosphate β glucopyranose oligosaccharide IDP RNA a [protein]- glucose-1- geranyltranstransferase decarboxylase; decarboxylase: (p)ppGpp F6P 6-phosphogluconolactonase: transferase: murG 4-( -D-ribofuranosyl) aminobenzene (tetrapeptide) protein enoyl-CoA diphosphate protein: SHCHC pyrimidin- kinase: thiL ketopantoate exopolyphosphatase: D-ribulose ditrans,octacis- UDP 1-phosphate a DNA containing N-phospho- phosphatase: (farnesyldiphosphate SHCHC panD synthetase I (GTP ybhE L-fuculose putative putative aminobenzene 5'-phosphate an alkylated pyrophosphoryl- C: ppdC hydratase: fadB a [DsrC mutS 4(3H)-one reductase: apbA [corrinoid adenosyltranferase]- nicotinamide gppA 1-phosphate undecaprenyldiphospho- sulfite L-histidine a properly agp synthase: menD synthase: menD thiamine pyrophosphokinase): relA 6-phosphofructokinase galactokinase: wcaK 5'-phosphate nucleobase an apurinic/ protein]-dithiol D-myo-inositol synthase): ispA 7,8- bifunctional cob(I)inamide D-gluconate epimerase/ N-acetyl-(N-acetyl-β-D- undecaprenol matched 2-succinyl-5- diphosphate β-alanine II: pfkB Other galactokinase: galK apyrimidinic site acetoacetyl-CoA (1,2,4,5,6)- geranyl dihydroneopterin pyrimidine 2-succinyl-5- (R)-pantoate cob(I)alamin glutathionylspermidine 6-phosphate aldolase: sgaE glucosaminyl)muramoyl- enolpyruvoyl- an N-terminal DNA base pair pentakisphosphate diphosphate 3'-phosphate deaminase/ enolpyruvoyl- adenolsyltransferase: synthetase/amidase: gsp 6-phosphofructokinase gluconate-6- L-ribulose-5- L-alanyl-γ-D-glutamyl-L- 6-hydroxy-3- GTP ppGpp α α L-phenylalanyl- a peptide 6-hydroxy-3- btuR I: pfkA malate/L-aspartate L-fuculose -D-galactose 1-phosphate UDP- -D-glucose phosphate 4- geranyltranstransferase cyclohexene- reductase: acyl carrier protein metabolism pantothenate [+ 5 isozymes] phosphate lysyl-D-alanyl-D-alanine [type IV prepilin] cyclohexene- β-D-fructose 1,6- shuttle pathway 1-phosphate