2.0 2012-05-31 10:22:23 -0600 2015-09-13 12:56:06 -0600 ECMDB00161 M2MDB000063 L-Alanine Alanine is an amino acid made from the conversion of the carbohydrate pyruvate or the breakdown of DNA and the dipeptides carnosine and anserine. Alanine is an important participant as well as regulator in glucose metabolism. Normal alanine metabolism, like that of other amino acids, is highly dependent upon enzymes that contain vitamin B6. (http://www.dcnutrition.com/AminoAcids/) (2S)-2-Aminopropanoate (2S)-2-Aminopropanoic acid (S)-(+)-Alanine (S)-2-amino-Propanoate (S)-2-amino-Propanoic acid (S)-2-Aminopropanoate (S)-2-Aminopropanoic acid (S)-Alanine 2-Aminopropanoate 2-Aminopropanoic acid 2-Aminopropionate 2-Aminopropionic acid 2-Ammoniopropanoate 2-Ammoniopropanoic acid A A-Alanine a-Aminopropanoate a-Aminopropanoic acid A-Aminopropionate A-Aminopropionic acid Ala Alanine Alpha-Alanine Alpha-Aminopropanoate Alpha-Aminopropanoic acid Alpha-Aminopropionate Alpha-Aminopropionic acid L-&alpha;-alanine L-(+)-Alanine L-2-Aminopropanoate L-2-Aminopropanoic acid L-2-Aminopropionate L-2-Aminopropionic acid L-a-Alanine L-a-Aminopropionate L-a-Aminopropionic acid L-alpha-Alanine L-alpha-Aminopropionate L-alpha-Aminopropionic acid L-α-Alanine L-α-Aminopropionate L-α-Aminopropionic acid α-Alanine α-Aminopropanoate α-Aminopropanoic acid α-Aminopropionate α-Aminopropionic acid C3H7NO2 89.0932 89.047678473 (2S)-2-aminopropanoic acid L-alanine 56-41-7 C[C@H](N)C(O)=O InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1 QNAYBMKLOCPYGJ-REOHCLBHSA-N Solid Cytosol Extra-organism Periplasm logp -3.05 ALOGPS logs 0.70 ALOGPS solubility 4.47e+02 g/l ALOGPS melting_point 300 oC logp -2.8 ChemAxon pka_strongest_acidic 2.47 ChemAxon pka_strongest_basic 9.48 ChemAxon iupac (2S)-2-aminopropanoic acid ChemAxon average_mass 89.0932 ChemAxon mono_mass 89.047678473 ChemAxon smiles C[C@H](N)C(O)=O ChemAxon formula C3H7NO2 ChemAxon inchi InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1 ChemAxon inchikey QNAYBMKLOCPYGJ-REOHCLBHSA-N ChemAxon polar_surface_area 63.32 ChemAxon refractivity 20.5 ChemAxon polarizability 8.49 ChemAxon rotatable_bond_count 1 ChemAxon acceptor_count 3 ChemAxon donor_count 2 ChemAxon physiological_charge 0 ChemAxon formal_charge 0 ChemAxon Alanine, aspartate and glutamate metabolism ec00250 Cysteine and methionine metabolism ec00270 Valine, leucine and isoleucine biosynthesis ec00290 Selenoamino acid metabolism ec00450 Aminoacyl-tRNA biosynthesis ec00970 Peptidoglycan biosynthesis ec00550 Biotin metabolism Biotin (vitamin H or vitamin B7) is the essential cofactor of biotin-dependent carboxylases, such as pyruvate carboxylase and acetyl-CoA carboxylase.In E. coli and many organisms, pimelate thioester is derived from malonyl-ACP. The pathway starts with a malonyl-[acp] interacting with S-adenosylmethionine through a biotin synthesis protein BioC resulting in a S-adenosylhomocysteine and a malonyl-[acp] methyl ester. The latter compound is then involved in the synthesis of a 3-ketoglutaryl-[acp] methyl ester through a 3-oxoacyl-[acyl-carrier-protein] synthase. The compound 3-ketoglutaryl-[acp] methyl ester is reduced by a NADPH mediated 3-oxoacyl-[acyl-carrier-protein] reductase resulting in a 3R-hydroxyglutaryl-[acp] methyl ester. This compound is then dehydrated through ad (3R)-hydroxymyristoyl-[acp] dehydratase producing a enoylglutaryl-[acp] methyl ester. This compound is then reduced through a NADPH mediated enoyl-acp-reductase [NADH] resulting in a glutaryl-[acp] methyl ester. This compound interacts with a malonyl-[acp] through a 3-oxoacyl-[acp] synthase 2 resulting in a 3-ketopimeloyl [acp] methyl ester. This compound is then reduced through a NADPH 3-oxoacyl [acp] reductase producing a 3-hydroxypimeloyl-[acp] methyl ester and then dehydrated by (3R)-hydroxymyristoyl-[acp] dehydratase to produce a enoylpimeloyl-[acp] methyl ester. This compound is then reduced by a NADPH dependent enoyl-[acp]reductase resulting in a pimeloyl-[acp] methyl ester. This compound then reacts with water through a carboxylesterase resulting in a pimeloyl-[acp] and a methanol. The pimeloyl-acp reacts with L-alanine through a 8-amino-7-oxononanoate synthase resulting in 8-amino-7-oxononanoate which in turn reacts with S-adenosylmethionine through a 7,8 diaminonanoate transaminase resulting in a S-adenosyl-4-methylthio-2-oxobutanoate and 7,8 diaminononanoate. The latter compound is then dephosphorylated through a dethiobiotin synthetase resulting in a dethiobiotin. This compound interacts with a sulfurated[sulfur carrier), a hydrogen ion and a S-adenosylmethionine through a biotin synthase to produce Biotin and releasing l-methionine and a 5-deoxyadenosine. Biotin is then metabolized by a bifunctional protein resulting in pyrophosphate and Biotinyl-5-AMP which in turn reacts with the same protein (bifunctional protein birA resulting ina biotin caroxyl carrying protein.This product then enters the fatty acid biosynthesis. PW000762 ec00780 Metabolic D-Alanine metabolism L-alanine is an essential component of protein and peptidoglycan. The latter also contains about three molecules of D-alanine for every L-alanine. Only about 10 percent of the total alanine synthesized flows into peptidoglycan. Refer to L-alanine metabolism (pathway PW000788 ). Through this single pathway D-alanine can be degraded to pyruvate through a D-amino acid dehydrogenase, which enters central metabolism and thereby can serve as a total source of carbon and energy. This pathway is unique among those through which L-amino acids are degraded, in that the L form must first be converted to the D form. This first step of the pathway, which can be catalyzed by either of two racemases( biosynthetic or catabolic), also serves an essential role in biosynthesis because its product, D-alanine, is an essential component of cell wall peptidoglycan (murein). D-alanine is metabolized by an ATP driven D-alanine ligase A and B resulting in D-alanyl-D-alanine. This product is incorporated into the peptidoglycan biosynthesis. PW000768 ec00473 Metabolic Taurine and hypotaurine metabolism ec00430 D-Glutamine and D-glutamate metabolism L-glutamine is transported into the cytoplasm through a glutamine ABC transporter. Once inside, L-glutamine is metabolized with glutaminase to produce an L-glutamic acid. This process can be reversed through a glutamine synthetase resulting in L-glutamine. L-glutamic acid can also be transported into the cytoplasm through various methods: a glutamate/aspartate:H+ symporter GltP, a glutamate: sodium symporter or a glutamate/aspartate ABC transporter. L-glutamic acid can proceed to L-glutamate metabolism or it can undergo a reversible reaction through a glutamate racemase resulting in D-glutamic acid. This compound can also be obtained from D-glutamine interacting with a glutaminase. D-glutamic acid reacts with UDP-N-acetylmuramoyl-L-alanine through an ATP driven UDP-N-acetylmuramoylalanine-D-glutamate ligase resulting in a UDP-N-acetylmuramoyl-L-alanyl-D-glutamate which is then integrated into the peptidoglycan biosynthesis UDP-N-acetylmuramoyl-L-alanine comes from the amino sugar and nucleotide sugar metabolism product, UDP-N-acetylmuraminate which reacts with L-alanine through an ATP-driven UDP-N-acetylmuramate-L-alanine ligase. PW000769 ec00471 Metabolic Microbial metabolism in diverse environments ec01120 ABC transporters ec02010 Sulfur relay system ec04122 Metabolic pathways eco01100 L-alanine metabolism L-alanine is an essential component of proteins and peptidoglycan. The latter also contains about three molecules of D-alanine for every L-alanine. Only about 10 percent of the total alanine synthesized flows into peptidoglycan. There are at least 3 ways to begin the biosynthesis of alanine. The first method for alanine biosynthesis begins with L-cysteine produced from L-cysteine biosynthesis pathway. L-cysteine reacts with an [L-cysteine desulfurase] L-cysteine persulfide through a cysteine desulfurase resulting in a release of [L-cysteine desulfurase] l-cysteine persulfide and L-alanine. The second method starts with pyruvic acid reacting with L-glutamic acid through a glutamate-pyruvate aminotransferase resulting in a oxoglutaric acid and L-alanine. The third method starts with L-glutamic acid interacting with Alpha-ketoisovaleric acid through a valine transaminase resulting in an oxoglutaric acid and L-valine. L-valine reacts with pyruvic acid through a valine-pyruvate aminotransferase resulting Alpha-ketoisovaleric acid and L-alanine. This first step of the pathway, which can be catalyzed by either of two racemases( biosynthetic or catabolic), also serves an essential role in biosynthesis because its product, D-alanine, is an essential component of cell wall peptidoglycan (murein). D-alanine is metabolized by an ATP driven D-alanine ligase A and B resulting in D-alanyl-D-alanine. This product is incorporated into the peptidoglycan biosynthesis. L-alanine is metabolized with alanine racemase, either catabolic or metabolic resulting in a D-alanine. This compound reacts with water and a quinone through a D-amino acid dehydrogenase resulting in Pyruvic acid, hydroquinone and ammonium, thus entering the central metabolism and thereby can serve as a total source of carbon and energy. This pathway is unique among those through which L-amino acids are degraded, in that the L form must first be converted to the D form. D-alanine, is an essential component of cell wall peptidoglycan (murein). The role of the alr racemase is predominately biosynthetic: it is produced constitutively in small amounts. The role of the dadX racemase is degradative: it is induced to high levels by alanine and is subject to catabolite repression. PW000788 Metabolic inner membrane transport list of inner membrane transport complexes, transporting compounds from the periplasmic space to the cytosol This pathway should be updated regularly with the new inner membrae transports added PW000786 Metabolic peptidoglycan biosynthesis I Peptidoglycan is a net-like polymer which surrounds the cytoplasmic membrane of most bacteria and functions to maintain cell shape and prevent rupture due to the internal turgor.In E. coli K-12, the peptidoglycan consists of glycan strands of alternating subunits of N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc) which are cross-linked by short peptides. The pathway for constructing this net involves two cell compartments: cytoplasm and periplasmic space. The pathway starts with a beta-D-fructofuranose going through a mannose PTS permease, phosphorylating the compund and producing a beta-D-fructofuranose 6 phosphate. This compound can be obtained from the glycolysis and pyruvate dehydrogenase or from an isomerization reaction of Beta-D-glucose 6-phosphate through a glucose-6-phosphate isomerase.The compound Beta-D-fructofuranose 6 phosphate and L-Glutamine react with a glucosamine fructose-6-phosphate aminotransferase, thus producing a glucosamine 6-phosphate and a l-glutamic acid. The glucosamine 6-phosphate interacts with phosphoglucosamine mutase in a reversible reaction producing glucosamine-1P. Glucosamine-1p and acetyl coa undergo acetylation throuhg a bifunctional protein glmU releasing Coa and a hydrogen ion and producing a N-acetyl-glucosamine 1-phosphate. Glmu, being a bifunctional protein, follows catalyze the interaction of N-acetyl-glucosamine 1-phosphate, hydrogen ion and UTP into UDP-N-acetylglucosamine and pyrophosphate. UDP-N-acetylglucosamine then interacts with phosphoenolpyruvic acid and a UDP-N acetylglucosamine 1- carboxyvinyltransferase realeasing a phosphate and the compound UDP-N-acetyl-alpha-D-glucosamine-enolpyruvate. This compound undergoes a NADPH dependent reduction producing a UDP-N-acetyl-alpha-D-muramate through a UDP-N-acetylenolpyruvoylglucosamine reductase. UDP-N-acetyl-alpha-D-muramate and L-alanine react in an ATP-mediated ligation through a UDP-N-acetylmuramate-alanine ligase releasing an ADP, hydrogen ion, a phosphate and a UDP-N-acetylmuramoyl-L-alanine. This compound interacts with D-glutamic acid and ATP through UDP-N-acetylmuramoylalanine-D-glutamate ligase releasing ADP, A phosphate and UDP-N-acetylmuramoyl-L-alanyl-D-glutamate. The latter compound then interacts with meso-diaminopimelate in an ATP mediated ligation through a UDP-N-acetylmuramoylalanine-D-glutamate-2,6-diaminopimelate ligase resulting in ADP, phosphate, hydrogen ion and UDP-N-Acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelate. This compound in turn with D-alanyl-D-alanine react in an ATP-mediated ligation through UDP-N-Acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase to produce UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gama-D-glutamyl-meso-2,6-diaminopimeloyl-Dalanyl-D-alanine and hydrogen ion, ADP, phosphate. UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gama-D-glutamyl-meso-2,6-diaminopimeloyl-Dalanyl-D-alanine interacts with di-trans,octa-cis-undecaprenyl phosphate through a phospho-N-acetylmuramoyl-pentapeptide-transferase, resulting in UMP and Undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine which in turn reacts with a UDP-N-acetylglucosamine through a N-acetylglucosaminyl transferase to produce a hydrogen, UDP and ditrans,octacis-undecaprenyldiphospho-N-acetyl-(N-acetylglucosaminyl)muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine. This compound ends the cytoplasmic part of the pathway. ditrans,octacis-undecaprenyldiphospho-N-acetyl-(N-acetylglucosaminyl)muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine is transported through a lipi II flippase. Once in the periplasmic space, the compound reacts with a penicillin binding protein 1A prodducing a peptidoglycan dimer, a hydrogen ion, and UDP. The peptidoglycan dimer then reacts with a penicillin binding protein 1B producing a peptidoglycan with D,D, cross-links and a D-alanine. PW000906 Metabolic tRNA Charging 2 This pathway groups together all E. coli tRNA charging reactions. PW000803 Metabolic tRNA charging This pathway groups together all E. coli tRNA charging reactions. PW000799 Metabolic peptidoglycan biosynthesis I 2 Peptidoglycan is a net-like polymer which surrounds the cytoplasmic membrane of most bacteria and functions to maintain cell shape and prevent rupture due to the internal turgor.In E. coli K-12, the peptidoglycan consists of glycan strands of alternating subunits of N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc) which are cross-linked by short peptides. The pathway for constructing this net involves two cell compartments: cytoplasm and periplasmic space. The pathway starts with a beta-D-fructofuranose going through a mannose PTS permease, phosphorylating the compund and producing a beta-D-fructofuranose 6 phosphate. This compound can be obtained from the glycolysis and pyruvate dehydrogenase or from an isomerization reaction of Beta-D-glucose 6-phosphate through a glucose-6-phosphate isomerase.The compound Beta-D-fructofuranose 6 phosphate and L-Glutamine react with a glucosamine fructose-6-phosphate aminotransferase, thus producing a glucosamine 6-phosphate and a l-glutamic acid. The glucosamine 6-phosphate interacts with phosphoglucosamine mutase in a reversible reaction producing glucosamine-1P. Glucosamine-1p and acetyl coa undergo acetylation throuhg a bifunctional protein glmU releasing Coa and a hydrogen ion and producing a N-acetyl-glucosamine 1-phosphate. Glmu, being a bifunctional protein, follows catalyze the interaction of N-acetyl-glucosamine 1-phosphate, hydrogen ion and UTP into UDP-N-acetylglucosamine and pyrophosphate. UDP-N-acetylglucosamine then interacts with phosphoenolpyruvic acid and a UDP-N acetylglucosamine 1- carboxyvinyltransferase realeasing a phosphate and the compound UDP-N-acetyl-alpha-D-glucosamine-enolpyruvate. This compound undergoes a NADPH dependent reduction producing a UDP-N-acetyl-alpha-D-muramate through a UDP-N-acetylenolpyruvoylglucosamine reductase. UDP-N-acetyl-alpha-D-muramate and L-alanine react in an ATP-mediated ligation through a UDP-N-acetylmuramate-alanine ligase releasing an ADP, hydrogen ion, a phosphate and a UDP-N-acetylmuramoyl-L-alanine. This compound interacts with D-glutamic acid and ATP through UDP-N-acetylmuramoylalanine-D-glutamate ligase releasing ADP, A phosphate and UDP-N-acetylmuramoyl-L-alanyl-D-glutamate. The latter compound then interacts with meso-diaminopimelate in an ATP mediated ligation through a UDP-N-acetylmuramoylalanine-D-glutamate-2,6-diaminopimelate ligase resulting in ADP, phosphate, hydrogen ion and UDP-N-Acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelate. This compound in turn with D-alanyl-D-alanine react in an ATP-mediated ligation through UDP-N-Acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase to produce UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gama-D-glutamyl-meso-2,6-diaminopimeloyl-Dalanyl-D-alanine and hydrogen ion, ADP, phosphate. UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gama-D-glutamyl-meso-2,6-diaminopimeloyl-Dalanyl-D-alanine interacts with di-trans,octa-cis-undecaprenyl phosphate through a phospho-N-acetylmuramoyl-pentapeptide-transferase, resulting in UMP and N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine-diphosphoundecaprenol which in turn reacts with a UDP-N-acetylglucosamine through a N-acetylglucosaminyl transferase to produce a hydrogen, UDP and Undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-glutaminyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine. This compound ends the cytoplasmic part of the pathway. Undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-glutaminyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine is transported through a lipi II flippase. Once in the periplasmic space, the compound reacts with a penicillin binding protein 1A prodducing a peptidoglycan dimer, a hydrogen ion, and UDP. The peptidoglycan dimer then reacts with a penicillin binding protein 1B producing a peptidoglycan with D,D, cross-links and a D-alanine. PW002062 Metabolic thiazole biosynthesis I (E. coli) PWY-6892 molybdenum cofactor biosynthesis PWY-6823 tRNA charging TRNA-CHARGING-PWY alanine biosynthesis II ALANINE-SYN2-PWY alanine biosynthesis I ALANINE-VALINESYN-PWY UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis III (<i>meso</i>-DAP-containing) PWY-6387 7-keto-8-aminopelargonate biosynthesis I PWY-6519 alanine biosynthesis III PWY0-1021 alanine degradation I ALADEG-PWY Specdb::CMs 392 Specdb::CMs 393 Specdb::CMs 394 Specdb::CMs 914 Specdb::CMs 2826 Specdb::CMs 28767 Specdb::CMs 30040 Specdb::CMs 30043 Specdb::CMs 30364 Specdb::CMs 30475 Specdb::CMs 30723 Specdb::CMs 30788 Specdb::CMs 31034 Specdb::CMs 37330 Specdb::CMs 156837 Specdb::CMs 1051759 Specdb::CMs 1051760 Specdb::CMs 1051762 Specdb::NmrOneD 1120 Specdb::NmrOneD 1178 Specdb::NmrOneD 142610 Specdb::NmrOneD 142611 Specdb::NmrOneD 142612 Specdb::NmrOneD 142613 Specdb::NmrOneD 142614 Specdb::NmrOneD 142615 Specdb::NmrOneD 142616 Specdb::NmrOneD 142617 Specdb::NmrOneD 142618 Specdb::NmrOneD 142619 Specdb::NmrOneD 142620 Specdb::NmrOneD 142621 Specdb::NmrOneD 142622 Specdb::NmrOneD 142623 Specdb::NmrOneD 142624 Specdb::NmrOneD 142625 Specdb::NmrOneD 142626 Specdb::NmrOneD 142627 Specdb::NmrOneD 142628 Specdb::NmrOneD 142629 Specdb::MsMs 3221 Specdb::MsMs 3222 Specdb::MsMs 3223 Specdb::MsMs 437096 Specdb::MsMs 437097 Specdb::MsMs 437098 Specdb::MsMs 2226289 Specdb::MsMs 2228648 Specdb::MsMs 2230820 Specdb::MsMs 2230916 Specdb::MsMs 2233269 Specdb::MsMs 2233350 Specdb::MsMs 2235593 Specdb::MsMs 251 Specdb::MsMs 252 Specdb::MsMs 253 Specdb::MsMs 3220 Specdb::MsMs 3224 Specdb::MsMs 3225 Specdb::MsMs 3226 Specdb::MsMs 3227 Specdb::MsMs 3228 Specdb::MsMs 3232 Specdb::MsMs 445526 Specdb::MsMs 445527 Specdb::NmrTwoD 976 Specdb::NmrTwoD 1178 HMDB00161 5950 5735 C00041 16977 L-ALPHA-ALANINE ALA_LFZW Alanine Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. 21097882 Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. 22080510 Vijayendran, C., Barsch, A., Friehs, K., Niehaus, K., Becker, A., Flaschel, E. (2008). "Perceiving molecular evolution processes in Escherichia coli by comprehensive metabolite and gene expression profiling." Genome Biol 9:R72. 18402659 van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. 17765195 Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. 18331064 Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. 19561621 Ishii, N., Nakahigashi, K., Baba, T., Robert, M., Soga, T., Kanai, A., Hirasawa, T., Naba, M., Hirai, K., Hoque, A., Ho, P. Y., Kakazu, Y., Sugawara, K., Igarashi, S., Harada, S., Masuda, T., Sugiyama, N., Togashi, T., Hasegawa, M., Takai, Y., Yugi, K., Arakawa, K., Iwata, N., Toya, Y., Nakayama, Y., Nishioka, T., Shimizu, K., Mori, H., Tomita, M. (2007). "Multiple high-throughput analyses monitor the response of E. coli to perturbations." Science 316:593-597. 17379776 Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. 19212411 Silwood CJ, Lynch E, Claxson AW, Grootveld MC: 1H and (13)C NMR spectroscopic analysis of human saliva. J Dent Res. 2002 Jun;81(6):422-7. 12097436 Nicholson JK, O'Flynn MP, Sadler PJ, Macleod AF, Juul SM, Sonksen PH: Proton-nuclear-magnetic-resonance studies of serum, plasma and urine from fasting normal and diabetic subjects. Biochem J. 1984 Jan 15;217(2):365-75. 6696735 Bairaktari E, Katopodis K, Siamopoulos KC, Tsolas O: Paraquat-induced renal injury studied by 1H nuclear magnetic resonance spectroscopy of urine. Clin Chem. 1998 Jun;44(6 Pt 1):1256-61. 9625050 Wevers RA, Engelke U, Wendel U, de Jong JG, Gabreels FJ, Heerschap A: Standardized method for high-resolution 1H-NMR of cerebrospinal fluid. Clin Chem. 1995 May;41(5):744-51. 7729054 Hagenfeldt L, Bjerkenstedt L, Edman G, Sedvall G, Wiesel FA: Amino acids in plasma and CSF and monoamine metabolites in CSF: interrelationship in healthy subjects. J Neurochem. 1984 Mar;42(3):833-7. 6198473 Peng CT, Wu KH, Lan SJ, Tsai JJ, Tsai FJ, Tsai CH: Amino acid concentrations in cerebrospinal fluid in children with acute lymphoblastic leukemia undergoing chemotherapy. Eur J Cancer. 2005 May;41(8):1158-63. Epub 2005 Apr 14. 15911239 Cynober LA: Plasma amino acid levels with a note on membrane transport: characteristics, regulation, and metabolic significance. Nutrition. 2002 Sep;18(9):761-6. 12297216 Rainesalo S, Keranen T, Palmio J, Peltola J, Oja SS, Saransaari P: Plasma and cerebrospinal fluid amino acids in epileptic patients. Neurochem Res. 2004 Jan;29(1):319-24. 14992292 Klassen P, Furst P, Schulz C, Mazariegos M, Solomons NW: Plasma free amino acid concentrations in healthy Guatemalan adults and in patients with classic dengue. Am J Clin Nutr. 2001 Mar;73(3):647-52. 11237944 Iioka H, Hisanaga H, Moriyama IS, Akada S, Shimamoto T, Yamada Y, Ichijo M: Characterization of human placental activity for transport of L-alanine, using brush border (microvillous) membrane vesicles. Placenta. 1992 Mar-Apr;13(2):179-90. 1631030 Saklatvala J: Hydrolysis of the elastase substrate succinyltrialanine nitroanilide by a metal-dependent enzyme in rheumatoid synovial fluid. J Clin Invest. 1977 May;59(5):794-801. 16038 Stahl A, Frick A, Imler M, Schlienger JL: Semiautomated enzymic microassay for plasma L-alanine. Enzyme. 1979;24(5):294-301. 41707 Chibata I; Kakimoto T; Kato J Enzymatic production of L-alanine by Pseudomonas dacunhae. Applied microbiology (1965), 13(5), 638-45. http://hmdb.ca/system/metabolites/msds/000/000/112/original/HMDB00161.pdf?1358894657 Alanyl-tRNA synthetase P00957 SYA_ECOLI alaS http://ecmdb.ca/proteins/P00957.xml Valine--pyruvate aminotransferase P09053 AVTA_ECOLI avtA http://ecmdb.ca/proteins/P09053.xml Alanine racemase, biosynthetic P0A6B4 ALR1_ECOLI alr http://ecmdb.ca/proteins/P0A6B4.xml Cysteine desulfurase P0A6B7 ISCS_ECOLI iscS http://ecmdb.ca/proteins/P0A6B7.xml Serine hydroxymethyltransferase P0A825 GLYA_ECOLI glyA http://ecmdb.ca/proteins/P0A825.xml 8-amino-7-oxononanoate synthase P12998 BIOF_ECOLI bioF http://ecmdb.ca/proteins/P12998.xml Aminoacyl-histidine dipeptidase P15288 PEPD_ECOLI pepD http://ecmdb.ca/proteins/P15288.xml UDP-N-acetylmuramate--L-alanine ligase P17952 MURC_ECOLI murC http://ecmdb.ca/proteins/P17952.xml N-acetylmuramoyl-L-alanine amidase AmiB P26365 AMIB_ECOLI amiB http://ecmdb.ca/proteins/P26365.xml Alanine racemase, catabolic P29012 ALR2_ECOLI dadX http://ecmdb.ca/proteins/P29012.xml Probable N-acetylmuramoyl-L-alanine amidase AmiA P36548 AMIA_ECOLI amiA http://ecmdb.ca/proteins/P36548.xml N-acetylmuramoyl-L-alanine amidase AmiC P63883 AMIC_ECOLI amiC http://ecmdb.ca/proteins/P63883.xml Low specificity L-threonine aldolase P75823 LTAE_ECOLI ltaE http://ecmdb.ca/proteins/P75823.xml Murein tetrapeptide carboxypeptidase P76008 LDCA_ECOLI ldcA http://ecmdb.ca/proteins/P76008.xml Cysteine desulfurase_ P77444 SUFS_ECOLI sufS http://ecmdb.ca/proteins/P77444.xml Cysteine sulfinate desulfinase Q46925 CSDA_ECOLI csdA http://ecmdb.ca/proteins/Q46925.xml High-affinity branched-chain amino acid transport system permease protein livH P0AEX7 LIVH_ECOLI livH http://ecmdb.ca/proteins/P0AEX7.xml High-affinity branched-chain amino acid transport system permease protein livM P22729 LIVM_ECOLI livM http://ecmdb.ca/proteins/P22729.xml Uncharacterized aminotransferase yfbQ P0A959 YFBQ_ECOLI yfbQ http://ecmdb.ca/proteins/P0A959.xml Cysteine desulfuration protein sufE P76194 SUFE_ECOLI sufE http://ecmdb.ca/proteins/P76194.xml High-affinity branched-chain amino acid transport ATP-binding protein livG P0A9S7 LIVG_ECOLI livG http://ecmdb.ca/proteins/P0A9S7.xml Leu/Ile/Val-binding protein P0AD96 LIVJ_ECOLI livJ http://ecmdb.ca/proteins/P0AD96.xml High-affinity branched-chain amino acid transport ATP-binding protein livF P22731 LIVF_ECOLI livF http://ecmdb.ca/proteins/P22731.xml Uncharacterized aminotransferase yfdZ P77434 YFDZ_ECOLI yfdZ http://ecmdb.ca/proteins/P77434.xml Uncharacterized transporter yaaJ P30143 YAAJ_ECOLI yaaJ http://ecmdb.ca/proteins/P30143.xml Uncharacterized amino-acid ABC transporter ATP-binding protein yecC P37774 YECC_ECOLI yecC http://ecmdb.ca/proteins/P37774.xml Inner membrane amino-acid ABC transporter permease protein yecS P0AFT2 YECS_ECOLI yecS http://ecmdb.ca/proteins/P0AFT2.xml D-serine/D-alanine/glycine transporter P0AAE0 CYCA_ECOLI cycA http://ecmdb.ca/proteins/P0AAE0.xml High-affinity branched-chain amino acid transport system permease protein livH P0AEX7 LIVH_ECOLI livH http://ecmdb.ca/proteins/P0AEX7.xml High-affinity branched-chain amino acid transport system permease protein livM P22729 LIVM_ECOLI livM http://ecmdb.ca/proteins/P22729.xml Outer membrane protein N P77747 OMPN_ECOLI ompN http://ecmdb.ca/proteins/P77747.xml Outer membrane pore protein E P02932 PHOE_ECOLI phoE http://ecmdb.ca/proteins/P02932.xml High-affinity branched-chain amino acid transport ATP-binding protein livG P0A9S7 LIVG_ECOLI livG http://ecmdb.ca/proteins/P0A9S7.xml Leu/Ile/Val-binding protein P0AD96 LIVJ_ECOLI livJ http://ecmdb.ca/proteins/P0AD96.xml High-affinity branched-chain amino acid transport ATP-binding protein livF P22731 LIVF_ECOLI livF http://ecmdb.ca/proteins/P22731.xml Outer membrane protein F P02931 OMPF_ECOLI ompF http://ecmdb.ca/proteins/P02931.xml Outer membrane protein C P06996 OMPC_ECOLI ompC http://ecmdb.ca/proteins/P06996.xml L-Alanine + Pyridoxal 5'-phosphate > Pyridoxamine 5'-phosphate + Pyruvic acid L-Alanine <> D-Alanine R00401 ALARACECAT-RXN L-Cysteine + SufSE sulfur acceptor complex > L-Alanine + SufSE with bound sulfur alpha-Ketoglutarate + L-Alanine <> L-Glutamate + Pyruvic acid R00258 Adenosine triphosphate + Water + L-Alanine > ADP + L-Alanine + Hydrogen ion + Phosphate Adenosine triphosphate + Water + L-Alanine > ADP + L-Alanine + Hydrogen ion + Phosphate L-Alanine + Adenosine triphosphate + UDP-N-Acetylmuraminate <> ADP + Hydrogen ion + Phosphate + UDP-N-Acetylmuramoyl-L-alanine R03193 UDP-NACMUR-ALA-LIG-RXN L-Alanine-L-glutamate + Water > L-Alanine + L-Glutamate L-Alanine + Pimeloyl-[acyl-carrier protein] > 8-Amino-7-oxononanoate + acyl carrier protein + Carbon dioxide L-Cysteine + IscS sulfur acceptor protein > L-Alanine + IscS with bound sulfur L-Alanine + Adenosine triphosphate + tRNA(Ala) > L-Alanyl-tRNA(Ala) + Adenosine monophosphate + Pyrophosphate 3-Sulfinoalanine + 2 Hydrogen ion > L-Alanine + Sulfur dioxide alpha-Ketoisovaleric acid + L-Alanine <> Pyruvic acid + L-Valine + a-Ketoisovaleric acid R01215 VALINE-PYRUVATE-AMINOTRANSFER-RXN L-Valine + Pyruvic acid <> alpha-Ketoisovaleric acid + L-Alanine R01215 Adenosine triphosphate + L-Alanine + tRNA(Ala) + tRNA(Ala) <> Adenosine monophosphate + Pyrophosphate + L-Alanyl-tRNA + L-Alanyl-tRNA R03038 Adenosine triphosphate + UDP-N-Acetylmuraminate + L-Alanine <> ADP + Phosphate + UDP-N-Acetylmuramoyl-L-alanine R03193 6-Carboxyhexanoyl-CoA + L-Alanine + Pimeloyl-[acyl-carrier protein] <> 8-Amino-7-oxononanoate + Coenzyme A + Carbon dioxide + Acyl-carrier protein R03210 Selenocysteine + Reduced acceptor <> Hydrogen selenide + L-Alanine + Acceptor R03599 N-Acetylmuramoyl-Ala + Water <> N-Acetyl-D-muramoate + L-Alanine R04112 [Enzyme]-cysteine + L-Cysteine <> [Enzyme]-S-sulfanylcysteine + L-Alanine R07460 UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate-D-alanine + Water > L-Alanine + UDP-N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate RXN0-2061 Hydrogen ion + L-Alanine + pimeloyl-CoA > Carbon dioxide + Coenzyme A + 8-Amino-7-oxononanoate 7KAPSYN-RXN Oxoglutaric acid + L-Alanine <> L-Glutamate + Pyruvic acid ALANINE-AMINOTRANSFERASE-RXN L-Alanine + Hydrogen ion + Pimeloyl-ACPs > 8-Amino-7-oxononanoate + Carbon dioxide + ACP RXN-11484 L-Cysteine + a sulfur acceptor + Hydrogen ion L-Alanine + <i>S</i>-sulfanyl-[acceptor] RXN-12588 3-Sulfinoalanine + Water Hydrogen ion + L-Alanine + Sulfite RXN0-279 L-Cysteine + L-Cysteine-Desulfurases > L-Alanine + Persulfurated-L-cysteine-desulfurases RXN0-308 ala-asp + Water > L-Alanine + L-Aspartic acid RXN0-6975 ala-gln + Water > L-Alanine + L-Glutamine RXN0-6976 ala-gly + Water > L-Alanine + Glycine RXN0-6977 ala-his + Water > L-Alanine + L-Histidine RXN0-6978 ala-leu + Water > L-Alanine + L-Leucine RXN0-6979 ala-thr + Water > L-Alanine + L-Threonine RXN0-6980 L-Alanyl-L-Glutamate + Water > L-Alanine + L-Glutamate RXN0-6981 methionine-alanine dipeptide + Water > L-Methionine + L-Alanine RXN0-6985 a reduced electron acceptor + Selenocysteine <> L-Alanine + Selenium + an oxidized electron acceptor + Hydrogen ion SELENOCYSTEINE-LYASE-RXN L-Alanine + Oxoglutaric acid > Pyruvic acid + L-Glutamate L-Alanine > D-Alanine L-Valine + Pyruvic acid > a-Ketoisovaleric acid + L-Alanine 6-carboxyhexanoyl-CoA + L-Alanine > 8-Amino-7-oxononanoate + CoA + Carbon dioxide L-Cysteine + acceptor > L-Alanine + S-sulfanyl-acceptor Adenosine triphosphate + UDP-N-Acetylmuraminate + L-Alanine > ADP + Inorganic phosphate + UDP-N-Acetylmuramoyl-L-alanine Selenocysteine + reduced acceptor > Hydrogen selenide + L-Alanine + acceptor a pimeloyl-[acp] + L-Alanine + L-Alanine > Carbon dioxide + a holo-[acyl-carrier protein] + 8-Amino-7-oxononanoate PW_R002495 a sulfurated [sulfur carrier] + L-Alanine + L-Alanine > 8-Amino-7-oxononanoate + Coenzyme A + Carbon dioxide PW_R002496 L-Alanine + L-Alanine <> D-Alanine PW_R002512 L-Alanine + L-Alanine > D-Alanine PW_R003732 UDP-N-acetylmuraminate + Adenosine triphosphate + L-Alanine + UDP-N-Acetylmuraminate + L-Alanine > UDP-N-Acetylmuramoyl-L-alanine + Adenosine diphosphate + Phosphate + ADP PW_R002517 Adenosine triphosphate + L-Alanine + tRNA(Ala) + L-Alanine > Adenosine monophosphate + Pyrophosphate + L-alanyl-tRNA(Ala) PW_R002585 L-Alanine + Oxoglutaric acid + L-Alanine <> L-Glutamic acid + Pyruvic acid + L-Glutamate PW_R002586 L-Alanine + Glyoxylic acid + L-Alanine <> Glycine + Pyruvic acid PW_R002587 Pyruvic acid + L-Glutamic acid + L-Glutamate > Oxoglutaric acid + L-Alanine + L-Alanine PW_R002660 L-Cysteine + an [L-cysteine desulfurase] L-cysteine persulfide > an [L-cysteine desulfurase] L-cysteine persulfide + L-Alanine + L-Alanine PW_R002661 L-Valine + Pyruvic acid + L-Valine > L-Alanine + a-Ketoisovaleric acid + L-Alanine PW_R002662 L-Alanine + Adenosine triphosphate + Hydrogen ion + tRNA(Ala) + L-Alanine > Pyrophosphate + Adenosine monophosphate + L-alanyl-tRNA(Ala) PW_R002826 UDP-N-acetyl-α-D-muramate + L-Alanine + Adenosine triphosphate + L-Alanine > Adenosine diphosphate + Phosphate + Hydrogen ion + UDP-N-Acetylmuramoyl-L-alanine + ADP PW_R003449 UDP-N-acetyl-α-D-muramate + Adenosine triphosphate + L-Alanine > UDP-N-Acetylmuramyl-L-Ala + ADP + Phosphate + Hydrogen ion PW_R006034 6 6-carboxyhexanoyl-CoA + L-Alanine + Pimeloyl-[acyl-carrier protein] <>8 8-Amino-7-oxononanoate + Coenzyme A + Carbon dioxide + Acyl-carrier protein Adenosine triphosphate + L-Alanine + tRNA(Ala) <> Adenosine monophosphate + Pyrophosphate + L-Alanyl-tRNA alpha-Ketoglutarate + L-Alanine <> L-Glutamate + Pyruvic acid N-Acetylmuramoyl-Ala + Water <> N-Acetyl-D-muramoate + L-Alanine [Enzyme]-cysteine + L-Cysteine <> [Enzyme]-S-sulfanylcysteine + L-Alanine L-Alanine + Adenosine triphosphate + UDP-N-Acetylmuraminate <> ADP + Hydrogen ion + Phosphate + UDP-N-Acetylmuramoyl-L-alanine L-Alanine <> D-Alanine Adenosine triphosphate + L-Alanine + tRNA(Ala) <> Adenosine monophosphate + Pyrophosphate + L-Alanyl-tRNA alpha-Ketoglutarate + L-Alanine <> L-Glutamate + Pyruvic acid N-Acetylmuramoyl-Ala + Water <> N-Acetyl-D-muramoate + L-Alanine [Enzyme]-cysteine + L-Cysteine <> [Enzyme]-S-sulfanylcysteine + L-Alanine L-Alanine + Adenosine triphosphate + UDP-N-Acetylmuraminate <> ADP + Hydrogen ion + Phosphate + UDP-N-Acetylmuramoyl-L-alanine alpha-Ketoglutarate + L-Alanine <> L-Glutamate + Pyruvic acid L-Alanine <> D-Alanine Gutnick minimal complete medium (4.7 g/L KH2PO4; 13.5 g/L K2HPO4; 1 g/L K2SO4; 0.1 g/L MgSO4-7H2O; 10 mM NH4Cl) with 4 g/L glucose Shake flask and filter culture 2550.0 uM 0.0 37 oC K12 NCM3722 Mid-Log Phase 10200000 0 Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. 19561621 Gutnick minimal complete medium (4.7 g/L KH2PO4; 13.5 g/L K2HPO4; 1 g/L K2SO4; 0.1 g/L MgSO4-7H2O; 10 mM NH4Cl) with 4 g/L glycerol Shake flask and filter culture 1770.0 uM 0.0 37 oC K12 NCM3722 Mid-Log Phase 7080000 0 Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. 19561621 Gutnick minimal complete medium (4.7 g/L KH2PO4; 13.5 g/L K2HPO4; 1 g/L K2SO4; 0.1 g/L MgSO4-7H2O; 10 mM NH4Cl) with 4 g/L acetate Shake flask and filter culture 879.0 uM 0.0 37 oC K12 NCM3722 Mid-Log Phase 3516000 0 Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. 19561621 48 mM Na2HPO4, 22 mM KH2PO4, 10 mM NaCl, 45 mM (NH4)2SO4, supplemented with 1 mM MgSO4, 1 mg/l thiamine·HCl, 5.6 mg/l CaCl2, 8 mg/l FeCl3, 1 mg/l MnCl2·4H2O, 1.7 mg/l ZnCl2, 0.43 mg/l CuCl2·2H2O, 0.6 mg/l CoCl2·2H2O and 0.6 mg/l Na2MoO4·2H2O. 4 g/L Gluco Bioreactor, pH controlled, O2 and CO2 controlled, dilution rate: 0.2/h 358.0 uM 0.0 37 oC BW25113 Stationary Phase, glucose limited 1432000 0 Ishii, N., Nakahigashi, K., Baba, T., Robert, M., Soga, T., Kanai, A., Hirasawa, T., Naba, M., Hirai, K., Hoque, A., Ho, P. Y., Kakazu, Y., Sugawara, K., Igarashi, S., Harada, S., Masuda, T., Sugiyama, N., Togashi, T., Hasegawa, M., Takai, Y., Yugi, K., Arakawa, K., Iwata, N., Toya, Y., Nakayama, Y., Nishioka, T., Shimizu, K., Mori, H., Tomita, M. (2007). "Multiple high-throughput analyses monitor the response of E. coli to perturbations." Science 316:593-597. 17379776 Luria-Bertani (LB) media Shake flask 832.0 uM true 67.0 37 oC BL21 DE3 Stationary phase cultures (overnight culture) 3328000 268000 Lin, Z., Johnson, L. C., Weissbach, H., Brot, N., Lively, M. O., Lowther, W. T. (2007). "Free methionine-(R)-sulfoxide reductase from Escherichia coli reveals a new GAF domain function." Proc Natl Acad Sci U S A 104:9597-9602. 17535911 Luria-Bertani (LB) media Shake flask 915.0 uM true 43.58 37 oC BL21 DE3 Stationary phase cultures (overnight culture) 3660000 174310 Lin, Z., Johnson, L. C., Weissbach, H., Brot, N., Lively, M. O., Lowther, W. T. (2007). "Free methionine-(R)-sulfoxide reductase from Escherichia coli reveals a new GAF domain function." Proc Natl Acad Sci U S A 104:9597-9602. 17535911