Experiment set7IT022 for Pseudomonas syringae pv. syringae B728a

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L-Malic acid carbon source

Group: carbon source
Media: M9 minimal media_noCarbon + L-Malic acid (29.83071072 mM)
Culturing: SyringaeB728a_ML2, 24 well microplate, Aerobic, at 28 (C), shaken=250 rpm
By: Tyler Helmann on 1/6/19
Media components: 2 mM Magnesium sulfate, 0.1 mM Calcium chloride, 12.8 g/L Sodium phosphate dibasic heptahydrate, 3 g/L Potassium phosphate monobasic, 0.5 g/L Sodium Chloride, 1 g/L Ammonium chloride

Specific Phenotypes

For 42 genes in this experiment

For carbon source L-Malic acid in Pseudomonas syringae pv. syringae B728a

For carbon source L-Malic acid across organisms

SEED Subsystems

Subsystem #Specific
Oxidative stress 3
Polyamine Metabolism 3
Arginine and Ornithine Degradation 2
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 2
Ammonia assimilation 1
Bacterial Cell Division 1
Conserved gene cluster associated with Met-tRNA formyltransferase 1
Lipid A modifications 1
NAD and NADP cofactor biosynthesis global 1
NAD regulation 1
Peptidoglycan Biosynthesis 1
Potassium homeostasis 1
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization 1
Ribosomal protein S12p Asp methylthiotransferase 1
Thiamin biosynthesis 1
Threonine and Homoserine Biosynthesis 1
Ton and Tol transport systems 1
Twin-arginine translocation system 1
tRNA processing 1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
L-glutamate biosynthesis I 2 2 2
L-alanine biosynthesis II 1 1 1
L-glutamine degradation II 1 1 1
L-glutamine degradation I 1 1 1
L-aspartate biosynthesis 1 1 1
L-aspartate degradation I 1 1 1
L-alanine degradation III 1 1 1
3-(4-hydroxyphenyl)pyruvate biosynthesis 1 1 1
glyphosate degradation II 1 1 1
ammonia assimilation cycle III 3 3 2
GDP-mannose biosynthesis 4 4 2
superpathway of L-alanine biosynthesis 4 4 2
L-glutamate degradation II 2 2 1
malate/L-aspartate shuttle pathway 2 2 1
L-alanine biosynthesis I 2 2 1
spermidine biosynthesis I 2 2 1
atromentin biosynthesis 2 1 1
D-mannose degradation II 2 1 1
spermine biosynthesis 2 1 1
L-tryptophan degradation IV (via indole-3-lactate) 2 1 1
L-alanine degradation V (oxidative Stickland reaction) 2 1 1
L-tyrosine degradation II 2 1 1
D-mannose degradation I 2 1 1
C4 photosynthetic carbon assimilation cycle, NAD-ME type 11 8 4
aminopropylcadaverine biosynthesis 3 3 1
L-phenylalanine biosynthesis I 3 3 1
L-tyrosine biosynthesis I 3 3 1
L-alanine degradation II (to D-lactate) 3 2 1
L-asparagine degradation III (mammalian) 3 2 1
β-1,4-D-mannosyl-N-acetyl-D-glucosamine degradation 3 2 1
L-phenylalanine degradation II (anaerobic) 3 2 1
mannitol biosynthesis 3 1 1
(R)-cysteate degradation 3 1 1
sulfolactate degradation III 3 1 1
pyruvate fermentation to acetate and alanine 3 1 1
L-tyrosine degradation IV (to 4-methylphenol) 3 1 1
indole-3-acetate biosynthesis VI (bacteria) 3 1 1
anaerobic energy metabolism (invertebrates, cytosol) 7 5 2
L-glutamate and L-glutamine biosynthesis 7 5 2
C4 photosynthetic carbon assimilation cycle, PEPCK type 14 9 4
L-asparagine biosynthesis III (tRNA-dependent) 4 4 1
superpathway of L-aspartate and L-asparagine biosynthesis 4 3 1
glutaminyl-tRNAgln biosynthesis via transamidation 4 3 1
L-phenylalanine degradation III 4 2 1
spermidine biosynthesis III 4 2 1
mannitol degradation II 4 2 1
L-tyrosine degradation III 4 2 1
4-chlorobenzoate degradation 4 2 1
putrescine degradation II 4 1 1
L-tryptophan degradation VIII (to tryptophol) 4 1 1
L-arginine degradation II (AST pathway) 5 5 1
4-hydroxybenzoate biosynthesis III (plants) 5 4 1
L-tyrosine degradation I 5 4 1
trans-4-hydroxy-L-proline degradation I 5 3 1
superpathway of plastoquinol biosynthesis 5 2 1
1,5-anhydrofructose degradation 5 2 1
4-hydroxybenzoate biosynthesis I (eukaryotes) 5 1 1
L-tryptophan degradation XIII (reductive Stickland reaction) 5 1 1
L-phenylalanine degradation VI (reductive Stickland reaction) 5 1 1
L-tyrosine degradation V (reductive Stickland reaction) 5 1 1
colanic acid building blocks biosynthesis 11 9 2
superpathway of L-threonine biosynthesis 6 6 1
TCA cycle VIII (Chlamydia) 6 6 1
NAD de novo biosynthesis I 6 5 1
NAD de novo biosynthesis IV (anaerobic) 6 5 1
superpathway of sulfolactate degradation 6 3 1
coenzyme M biosynthesis II 6 2 1
L-alanine degradation VI (reductive Stickland reaction) 6 1 1
thiazole component of thiamine diphosphate biosynthesis II 7 6 1
superpathway of GDP-mannose-derived O-antigen building blocks biosynthesis 14 7 2
β-(1,4)-mannan degradation 7 2 1
superpathway of polyamine biosynthesis II 8 7 1
L-citrulline biosynthesis 8 7 1
superpathway of polyamine biosynthesis I 8 7 1
superpathway of ornithine degradation 8 4 1
butanol and isobutanol biosynthesis (engineered) 8 3 1
superpathway of anaerobic energy metabolism (invertebrates) 17 11 2
superpathway of aromatic amino acid biosynthesis 18 18 2
superpathway of L-methionine biosynthesis (transsulfuration) 9 7 1
L-phenylalanine degradation IV (mammalian, via side chain) 9 4 1
nicotine biosynthesis 9 3 1
superpathway of L-alanine fermentation (Stickland reaction) 9 3 1
superpathway of L-tyrosine biosynthesis 10 10 1
superpathway of L-phenylalanine biosynthesis 10 10 1
rosmarinic acid biosynthesis I 10 3 1
L-methionine salvage cycle III 11 10 1
superpathway of thiamine diphosphate biosynthesis II 11 10 1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation 11 5 1
(S)-reticuline biosynthesis I 11 1 1
superpathway of L-methionine biosynthesis (by sulfhydrylation) 12 12 1
superpathway of L-citrulline metabolism 12 9 1
L-methionine salvage cycle I (bacteria and plants) 12 9 1
superpathway of nicotine biosynthesis 12 4 1
indole-3-acetate biosynthesis II 12 4 1
aspartate superpathway 25 22 2
superpathway of L-isoleucine biosynthesis I 13 13 1
superpathway of L-arginine and L-ornithine degradation 13 7 1
superpathway of rosmarinic acid biosynthesis 14 4 1
superpathway of arginine and polyamine biosynthesis 17 16 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 16 1
anaerobic aromatic compound degradation (Thauera aromatica) 27 2 1
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 21 2
superpathway of chorismate metabolism 59 42 2