Authors: Zheng Zhao, Delft University of Technology Marcel A. van den Broek, Delft University of Technology S. Aljoscha Wahl, Delft University of Technology Wilbert H. Heijne, DSM Biotechnology Center Roel A. Bovenberg, DSM Biotechnology Center Joseph J. Heijnen, Delft University of Technology 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. Marco A. van den Berg, DSM Biotechnology Center Peter J.T. Verheijen, Delft University of Technology Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. PchrCyc: Penicillium rubens Wisconsin 54-1255 Cellular Overview Connections between pathways are omitted for legibility. Liang Wu, DSM Biotechnology Center Walter M. van Gulik, Delft University of Technology L-quinate phosphate a sugar a sugar a sugar a sugar multidrug multidrug a dicarboxylate phosphate a proteinogenic 2+ 2+ + met met nicotinate Mg Mg a cation a cation K + L-fucose L-fucose L-quinate L-quinate L-quinate ammonium UDP ammonium ammonium H O pro met amino acid a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar K oxaloacetate L-carnitine L-carnitine L-carnitine 2 phosphate quinic acid brain-specific hypothetical hypothetical hypothetical hypothetical ATP-binding mitochondrial permease high-affinity Na-dependent high-affinity sugar sugar sugar sugar hypothetical hypothetical mitochondrial cation-Cl- potassium L-fucose L-fucose cassette hypothetical MFS quinate quinic acid quinic acid dicarboxylate ammonium ammonium ammonium aquaporin high affinity high affinity hypothetical sugar transport sugar sugar sugar sugar transport sugar transport sugar sugar sugar transport sugar sugar K+/H+ oxaloacetate QA-Y - inorganic inorganic UDP-N-acetylglucosamine- carnitine carnitine carnitine proline methionine uptake nicotinic acid transporter transporter transporter transporter magnesium/ magnesium/ cation cotransporter- transport permease permease multidrug multidrug efflux transport permease permease transport transport transport transport water channel methionine methionine neutral amino protein Stl1 - transporter transporter transporter protein Stl1 - protein Stl1 - transporter transporter protein Stl1 - transporter transporter exchanger Kha1 transporter Oac1 Neurospora phosphate/H+ phosphate -dolichyl-phosphate N- transporter Agp2 transporter Agp2 transporter Agp2 transporter Put4 protein Mup3 - permease Tna1 - encoded by encoded by encoded by encoded by cobalt transport cobalt transport transporter Mmt1 interacting protein Trk2 - fucP - fucP - transport transporter - protein qutD QA-Y - QA-Y - protein protein Mep2 - protein Mep2 - protein Mep3 - protein Aqy2 - permease Mup1 - permease Mup1 - acid permease Saccharomyces Sut2 -Pichia Sut2 -Pichia Sut2 -Pichia Saccharomyces Saccharomyces Sut2 -Pichia Sut2 -Pichia Saccharomyces Sut2 - Sut2 -Pichia -Saccharomyces - Saccharomyces crassa symporter Pho84 cotransporter acetylglucosaminephosphotransferase - Saccharomyces - Saccharomyces - Saccharomyces - Saccharomyces Saccharomyces Saccharomyces DRA0271 - DRA0271 - DRA0271 - DRA0271 - protein sll0671 - protein sll0671 - - Saccharomyces protein CIP1 - Saccharomyces Escherichia Escherichia protein atrB Schizosaccharomyces - Aspergillus Neurospora Neurospora like protein Saccharomyces Saccharomyces Saccharomyces Saccharomyces Saccharomyces Saccharomyces - Neurospora cerevisiae stipitis stipitis stipitis cerevisiae cerevisiae stipitis stipitis cerevisiae Pichia stipitis stipitis cerevisiae cerevisiae [putative - Saccharomyces like protein Alg7 - Saccharomyces cerevisiae cerevisiae cerevisiae cerevisiae cerevisiae cerevisiae cerevisiae Deinococcus Deinococcus Deinococcus Deinococcus Synechocystis sp Synechocystis sp cerevisiae Homo sapiens cerevisiae coli coli - Aspergillus pombe nidulans crassa crassa An02g01730 - cerevisiae cerevisiae cerevisiae cerevisiae cerevisiae cerevisiae crassa hypothetical sequencing cerevisiae An04g02720 - radiodurans radiodurans radiodurans radiodurans nidulans Aspergillus niger neutral amino error] Aspergillus niger a proteinogenic a proteinogenic acid permease amino acid amino acid UDP - Neurospora a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar K + multidrug oxaloacetate L-carnitine L-carnitine L-carnitine nicotinate Mg 2+ Mg 2+ a cation a cation K + L-fucose L-fucose L-quinate L-quinate L-quinate ammonium phosphate ammonium ammonium H O pro met a proteinogenic crassa 2 met met a sugar a sugar a sugar a sugar multidrug a dicarboxylate phosphate amino acid L-quinate phosphate hypothetical 1D-myo-inositol neutral amino a proteinogenic a proteinogenic 1,2,3,4,5,6- acid permease amino acid amino acid hexakisphosphate Other Biosynthesis Amino Acid Degradation - Neurospora phytase phyA Tetrapyrrole Biosynthesis crassa from patent 3-amino-3- D-ribose 5- a [BCAA a [BCAA RNase III mRNA 6-phospho- D-fructose- a branched- (25R)-3α,7α,12α- a (2S)-2- tetrahydrofolate biosynthesis II Cofactor, Carrier, and Vitamin Biosynthesis respiration (anaerobic) Respiration leucine degradation I a DNA containing an succinyl-CoA a 3-oxo acid an acyl-[acyl- sn-glycerol- a nucleoside 3'-ketolactose Peptide N-acetyl- a proteinogenic an acyl-CoA WO2003038111- flavin biosynthesis III (fungi) ubiquinone-8 ubiquinone-10 ubiquinone-9 ubiquinone-7 biosynthesis (eukaryotic) superpathway of NAD biosynthesis in eukaryotes NAD salvage biotin biosynthesis I (R,R)-butanediol 2-ketoglutarate dehydrogenase complex valine degradation I isoleucine degradation I leucine degradation III deoxy-D-fructose phosphate dehydrogenase dehydrogenase processing RNA D-gluconate 6-phosphate chain 2-keto acid trihydroxy-5β- methylacyl-CoA heme biosynthesis II Aromatic Compound Biosynthesis tyrosine degradation I arginine degradation glycine cleavage complex isoleucine degradation II Aldehyde Degradation apurinic/apyrimidinic site carrier protein] 3-phosphate triphosphate adenosine L-citrulline amino acid dicarboxylic A2-Penicillium biosynthesis (eukaryotic) biosynthesis (eukaryotic) biosynthesis (eukaryotic) pathway II biosynthesis 6-phosphate 2-keto-3- E2 protein] N 6 4-methyl-2- E2 protein] N 6 substrate decarboxylating fructose-2,6- dehydrogenase methionine-N- cholestanoyl-CoA hypothetical acyl-CoA all-trans- a [2-oxoglutarate VI (arginase 2 pathway) branched-chain hypothetical L-amino-acid amino acid D-myo-inositolchrysogenum: phyA GDP/GTP 2-phospho-D-glycerate a [glycine-cleavage methyl-valerate -lipoyl-L-lysine oxopentanoate -lipoyl-L-lysine phosphogluconate bisphosphate acetyltransferase protein a oxydaseproteinogenic tylP - a proteinogenic GTP formylTHF biosynthesis II heptaprenyl chorismate biosynthesis I dehydrogenase leu 6 apurinic endonuclease beta- alpha-ketoacid protein oxidase lox - permease Dip5 - (1,2,4,5,6)- chorismate 4-hydroxybenzoate 4-hydroxybenzoate formylTHF biosynthesis I 4-hydroxybenzoate trp NADP + ala gly (R)-acetoin val ile leu complex H protein] N glycine ile methylglyoxal degradation I methylglyoxal Succinyl CoA: dehydrogenase like 2-phosphatase Nat2 - CAD16864.1 Streptomyces exchange GTP pimeloyl-CoA chorismate biosynthesis 4-hydroxybenzoate 6 tyr sn-glycerol- DNA-directed acetylornithine amino acid amino acid GDP GDP para-hydroxybenzoate- para-hydroxybenzoate- diphosphate enolase BAC82549- E2 protein] N oxoglutarate branched-chain- arg -[(R)-lipoyl]-L-lysine decarboxylase Apn1 - Saccharomyces transketolase 3-oxoacid CoA ribonuclease protein An11g06120 galactosidase dehydrogenase CAD16864.1 Neurospora Saccharomyces pentakisphosphate protein Rom1 - acid 5-aminolevulinic acid from 3-dehydroquinate biosynthesis I (animals) 2,3-butanediol branched-chain- branched-chain- degradation V 3-phosphate RNA polymerase Fbp26 - Saccharomyces inosine-uridine - Ralstonia deacetylase fradiae: GTP GTP GTP -polyprenyltransferase -polyprenyltransferase indoleamine 2,3- D-erythrose- Penicillium -lipoyl-L-lysine dehydrogenase amino-acid arginase argA subunit H cerevisiae [putative like protein branched-chain branched-chain transferase III like protein -Aspergillus niger: lacA - kinase BCKDK - Ralstonia crassa: cerevisiae Saccharomyces 3,4-dihydroxy- tetrahydrofolate 7,8-dihydropteroate phosphatase synthase hemA - dehydrogenase branched-chain- branched-chain- aromatic aminotransferase amino-acid amino-acid methylglyoxal acyltransferase III 82 KD Saccharomyces cerevisiae: nucleosid solanacearum: argE - PC22G07740 cyclohydrolase ppt1p - ppt1p - dioxygenase IDO - Mus 8-amino-7- 4-phosphate chrysogenum: precursor of (lipoamide) Kgd1 aminotransferase -Aspergillus precursor of like protein methylglyoxal sequencing error]: An02g06430 alpha-keto acid alpha-keto acid SCOT - Homo An03g00790 PC12G08920 Aspergillus - Rattus solanacearum: PC20G15180 cerevisiae 2-butanone 4-hydroxybenzoate aphA - Aspergillus nidulans: phe-inhibited 3-dehydroquinate 4-hydroxyphenylpyruvate ADH - amino-acid amino-acid I Aro8 - Saccharomyces aminotransferase aminotransferase glyoxalase I Glo1 like protein subunit Rpc82 - cerevisiae: PC20G00190 hydrolase PC21G07860 Myxococcus acyl-CoA I Fol2 - Schizosaccharomyces Schizosaccharomyces musculus: PC22G11860 oxononanoate PC14G01740 dihydrolipoamide - Saccharomyces Bat2 - niger: dihydrolipoamide An08g04390 - PC22G09800 - Aspergillus