Authors: Pallavi Subhraveti Ron Caspi Peter Midford Peter D Karp 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. Ingrid Keseler Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_000299235Cyc: Leptospirillum ferriphilum ML-04 Cellular Overview Connections between pathways are omitted for legibility. Anamika Kothari phosphate phosphate phosphate phosphate ammonium ammonium ammonium predicted ABC transporter RS12230 RS11960 RS10935 RS01775 RS01785 RS04585 of phosphate phosphate phosphate phosphate ammonium ammonium ammonium phosphate Macromolecule Modification Inorganic Nutrient Metabolism tRNA-uridine 2-thiolation UDP-N-acetyl- undecaprenyl- a carboxy- a nascent a peptidoglycan an [amino-group β 34 a nucleoside cob(II)yrinate a,c- Cofactor, Carrier, and Vitamin Biosynthesis selenate reduction α-D-glucosamine diphospho-N- adenylated- peptidoglycan a uracil in DNA D-glycero- -D- a cytidine lys dimer (meso- met carrier protein]- [2Fe-2S] iron-sulfur thioredoxin flavin biosynthesis I (bacteria and plants) lipoate biosynthesis lipoate salvage I benzimidazolyl adenosylcobamide lipoate biosynthesis pyridoxal 5'-phosphate biosynthesis I folate transformations III (E. coli) Fatty Acid and Lipid Biosynthesis and selenation (bacteria) cys ATP triphosphate RNA diamide biosynthesis I acetylmuramoyl- [ThiS sulfur- (meso-DAP manno-heptose in tRNA Ile2 diaminopimelate C-terminal-γ- cluster biosynthesis pathway and incorporation I biosynthesis from and incorporation II amino-acid N- (early cobalt insertion) L-alanyl-γ-D- carrier protein] containing) 1-phosphate containing) (L-glutamate 5- adenosylcobinamide-GDP D-erythrose a tetrahydrofolate palmitate biosynthesis cys selenate uracil-DNA acetyltransferase: uroporphyrinogen-III an oxidized (R)-lipoate 4-phosphate gondoate biosynthesis sulfate glutamyl-L-lysyl- tRNA(Ile)-lysidine DNA- LFML04_RS10300 semialdehyde-2-N-acetyl- L-cysteine desulfurase GTP an octanoyl-[acp] lipoate-- benzimidazole octanoate (type II fatty acid synthase) glycosylase: uroporphyrinogen-III thioredoxin octanoyl-[acyl-carrier (anaerobic) adenylyltransferase: sat D-alanyl-D-alanine D-glycero-beta-D- synthetase: penicillin- directed RNA yl)-L-glutamategamma- protein ligase: nicotinate-nucleotide-- lipoate-- cysteine desulfurase: UDP-N- IscS subfamily lytic transglycosylase LFML04_RS00725 bifunctional C-methyltransferase: cysteine desulfurase: protein] biosynthesis adenosine 5'- manno-heptose LFML04_RS02125 binding polymerase glutamyl- bifunctional LFML04_RS01050 dimethylbenzimidazole protein ligase: an acetoacetyl-[acp] LFML04_RS03125 acetylglucosamine- cysteine desulfurase: domain-containing uracil-DNA glutamate N- cobA LFML04_RS03125 a [lipoyl-carrier [(R)- (mitochondria, yeast) a malonyl-[acp] an oleoyl-[acp] phosphoselenate 1-phosphate protein subunit phosphate 3,4-dihydroxy- phosphoribosyltransferase: a [lipoyl-carrier LFML04_RS01050protein] 4-phospho- IscS subfamily -N-acetylmuramyl- LFML04_RS02340 protein: glycosylase: tRNA acetyltransferase/ an [amino-group precorrin-1 thioredoxin- protein] N 6 - lipoyl]adenylate adenylyltransferase: 2: mrdA omega: rpoZ reductase: IscS subfamily 6 3-oxoacyl-[acyl- cysteine desulfurase: (pentapeptide) cysteine desulfurase: LFML04_RS04415 lysidine(34) amino-acid carrier protein]- 2-butanone- octanoyl-L-lysine cobT N -octanoyl-L-lysine D-erythronate an acetoacetyl-[acp] LFML04_RS05165 rfaE2 argC uroporphyrinogen-III cysteine desulfurase: disulfide lipoate-- benzimidazole carrier-protein] 3-oxoacyl-[acyl- LFML04_RS02340 sulfite oxidation II pyrophosphoryl- LFML04_RS03125 endolytic synthetase [+ 2 isozymes] acetyltransferase C-terminal-γ- 4-phosphate lipoyl lipoyl beta-ketoacyl- C-methyltransferase: LFML04_RS02340 reductase: protein ligase: ribotide phosphate reductase: fabG carrier-protein] an [L-cysteine undecaprenol N- transglycosylase TilS: tilS a peptidoglycan ArgJ: argJ (5-phospho- synthase/GTP synthase: ACP synthase β trxB LFML04_RS01050 synthase: lipA desulfurase]-S- selenite acetylglucosamine MltG: mltG an apyrimidinic uracil ADP-D-glycero- - with D,D cross- D-ala N-acetyl-L- L-glutamyl)- cobA an S-sulfanyl-[L- cyclohydrolase II: lipA cobalamin 5 serine a (3R)-3- reductase: fabG II: fabF sulfite a thiocarboxylated- a [lipoyl-carrier superpathway of thiamine diphosphate biosynthesis II a [lipoyl-carrier (3R)-3-hydroxy-2-oxo- a (3R)-3- sulfanyl-L-cysteine transferase: site in DNA D-manno-heptose links (meso- RNA methionine L-glutamate cysteine desulfurase] LFML04_RS06305 a [lipoyl-carrier phosphate 6 a 7,8-dihydrofolate hydroxymethyltransferase:a 5-methyltetrahydrofolate hydroxybutanoyl-[acp] adenylyl-sulfate ala [ThiS sulfur- 34 precorrin-2 protein]-N 6 -[(R protein]-N -[(R)- 4 phosphooxybutanoate hydroxybutanoyl-[acp] LFML04_RS12585 AMP a lysidine 2,5-diamino-6- 6 glycine cleavage system reductase Ile2 diaminopimelate sulfite RS09035 sulfite scaffold protein]-N -[(R) synthase CobS: dihydrolipoyl]-L-lysine LFML04_RS11350 3-hydroxyacyl- ditrans,octacis- UDP carrier protein] a mature a nascent in tRNA a reduced (5-phospho-D- )-lipoyl]-L-lysine D-glyceraldehyde aminomethyltransferase 3-hydroxyacyl- an (11Z)-3-oxo- subunit alpha: containing) bifunctional precorrin- protein for -dihydrolipoyl]- cys LFML04_RS05805 pyruvate ACP dehydratase undecaprenyldiphospho- peptidoglycan peptidoglycan thioredoxin ribosylamino) Coα-[α-(benzimidazolyl) 3-phosphate GcvT: gcvT ACP dehydratase icos-11-enoyl-[acp] LFML04_RS02365 β 2 dehydrogenase/ iron-sulfur L-lysine a [ThiS sulfur- FabZ: fabZ a [TusA sulfur- selenodiglutathione N-acetyl-(N-acetyl- -D- with (L-alanyl- (meso-DAP pyrimidin- ]-Coβ-adenosylcobamide a (6S)-5-formyltetrahydrofolate FabZ: fabZ 3-oxoacyl-[acyl- APS sirohydrochlorin cluster cysteine desulfurase: carrier protein] 4-phosphooxy- glycine cleavage system bifunctional carrier protein]-S- glucosaminyl)muramoyl- γ-D-glutamyl- containing) with sulfate RS11860 sulfate 4(3H)-one 5'-phosphate 1-deoxy-D- γ ferrochelatase: LFML04_RS03125 protein GcvH: gcvH a (2E)-but-2-enoyl-[acp] carrier-protein] sulfanyl-L-cysteine L-alanyl- -D-glutamyl-L- meso-2,6- GlcNAc terminus assembly: iscU bifunctional L-threonine xylulose-5- methylenetetrahydrofolate5-formyltetrahydrofolate a (2E)-but-2-enoyl-[acp] LFML04_RS12350 an S-sulfanyl-[cysteine reductase: fabG lysyl-D-alanyl-D-alanine diaminopimeloyl- diaminohydroxyphosphoribosylaminopyrimidine IscS subfamily 4-hydroxythreonine- phosphate dehydrogenase/ cyclo-ligase: desulfurase]-[disordered- cysteine desulfurase: methenyltetrahydrofolateLFML04_RS07080 enoyl-ACP enoyl-ACP a (3R,11Z)-3-hydroxy- D-alanine) a reduced sirohydrochlorin deaminase/5-amino-6-(5-phosphoribosylamino) 4-phosphate synthase: glutathioselenol form scaffold LFML04_RS02340 a carboxy- Coα-[α-(benzimidazolyl) cyclohydrolase FolD: folD reductase: reductase: icos-11-enoyl-[acp] a [TusD sulfur- tetrapeptide H O c-type uracil reductase RibD: ribD dehydrogenase dxs sulfate 2 an [L-cysteine adenylated- β a 5,10-methylenetetrahydrofolate a 5,10-methenyltetrahydrofolate LFML04_RS05190 protein] complex 5-amino-6-(5- ]-Co -adenosylcobamide PdxA: pdxA LFML04_RS05190 3-hydroxyacyl- carrier protein]-S- RS08985 cytochrome [cysteine desulfurase]-S- desulfurase]-S- [ThiS sulfur- sulfanyl-L-cysteine an oxidized phospho-D- 3-amino-1- 1-deoxy-D- bifunctional ACP dehydratase a mature peptidoglycan a [bis(guanylyl L-alanyl-γ-D- a peptidoglycan (E)-4-hydroxy-3- O c-type sulfanylcysteine:[acceptor sulfanyl-L-cysteine carrier protein] a butanoyl-[acp] a butanoyl-[acp] [EntB aryl- 2 ribosylamino)uracil hydroxyacetone coenzyme A H O sec D-ribulose D-glyceraldehyde xylulose 5- methylenetetrahydrofolate FabZ: fabZ (meso-diaminopimelate molybdopterin) cys glutamyl-meso-2,6- 2 ile dimer (E. faeciums) methylbut-2-en- ser a tRNA cytochromea reduced cobalt- protein]-cysteine bifunctional hypoxanthine carrier protein] GTP 5-phosphate 3-phosphate 1-phosphate phosphate dehydrogenase/ beta-ketoacyl- hydrogen selenide containing) PRPP cofactor diaminopimeloyl- 1-yl diphosphate H O c-type sirohydrochlorin sulfurtransferase: diaminohydroxyphosphoribosylaminopyrimidine superpathway of coenzyme A biosynthesis I (bacteria) cysteine desulfurase: beta-ketoacyl- a (2E,11Z)-icosa- branched chain flavodoxin- 2 bifunctional methenyltetrahydrofolate ACP synthase a [TusE sulfur chaperone]- D-alanine RS09540 cytochrome LFML04_RS02340 deaminase/5-amino-6-(5-phosphoribosylamino) LFML04_RS03125 1-deoxy-D- pyridoxine 5'- bis(guanylyl molybdopterin) ACP synthase 2,11-dienoyl-[acp] amino acid penicillin- dependent an oxidized a [cysteine desulfurase]- gly 34 carrier protein]-S L-cysteine holo-[acyl- 3,4-dihydroxy- 3-methyl-2- a 5,10- IscS subfamily xylulose-5- cofactor sulfurylation cyclohydrolase FolD: folD II: fabF II: fabF a uridine in tRNA lytic transglycosylase GTPase aminotransferase: binding (E)-4-hydroxy- serine- O c-type S-sulfanyl-[disordered- uracil reductase RibD: ribD phosphate synthase: enoyl-ACP -sulfanylcysteine carrier- 2 2-butanone- 5-amino-6-(5- oxobutanoate methylenetetrahydrofolate cysteine desulfurase: phosphate superpathway of tetrahydrofolate biosynthesis domain-containing hypoxanthine HflX: hflX LFML04_RS02085 protein 3-methylbut- -tRNA cytochromea reduced form