Experiment set7IT004 for Pseudomonas syringae pv. syringae B728a

D-Gluconic acid carbon source

Group: carbon source
Media: M9 minimal media_noCarbon + D-Gluconic acid (20.39151713 mM)
Culturing: SyringaeB728a_ML2, 24 well microplate, Aerobic, at 28 (C), shaken=250 rpm
By: Tyler Helmann on 10/29/18
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 11 genes in this experiment

For carbon source D-Gluconic acid in Pseudomonas syringae pv. syringae B728a

For carbon source D-Gluconic acid across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter oligopeptide (TC 3.A.1.5.1)	1
Arginine and Ornithine Degradation	1
D-gluconate and ketogluconates metabolism	1
DNA-binding regulatory proteins, strays	1
Entner-Doudoroff Pathway	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
NAD and NADP cofactor biosynthesis global	1
NAD regulation	1
Purine conversions	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pyruvate metabolism
• Purine metabolism
• Alanine and aspartate metabolism
• Arginine and proline metabolism
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Fatty acid biosynthesis
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• Ether lipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Butanoate metabolism
• Carbon fixation in photosynthetic organisms
• Nicotinate and nicotinamide metabolism
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
adenosine nucleotides degradation III	1	1	1
L-arginine degradation II (AST pathway)	5	5	1
NAD de novo biosynthesis IV (anaerobic)	6	5	1
NAD de novo biosynthesis I	6	5	1
anaerobic energy metabolism (invertebrates, cytosol)	7	5	1
incomplete reductive TCA cycle	7	4	1
Entner-Doudoroff pathway I	9	8	1
Entner-Doudoroff pathway III (semi-phosphorylative)	9	7	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	6	1
nicotine biosynthesis	9	3	1
Rubisco shunt	10	8	1
glycolysis V (Pyrococcus)	10	7	1
glycolysis IV	10	7	1
glycolysis II (from fructose 6-phosphate)	11	9	1
glycolysis III (from glucose)	11	9	1
glycolysis VI (from fructose)	11	7	1
reductive TCA cycle I	11	7	1
gluconeogenesis III	12	9	1
homolactic fermentation	12	9	1
superpathway of nicotine biosynthesis	12	4	1
glycolysis I (from glucose 6-phosphate)	13	10	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	5	1
Bifidobacterium shunt	15	12	1
mixed acid fermentation	16	11	1
glycerol degradation to butanol	16	11	1
superpathway of glucose and xylose degradation	17	15	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	14	1
superpathway of anaerobic energy metabolism (invertebrates)	17	11	1
superpathway of hexitol degradation (bacteria)	18	12	1
heterolactic fermentation	18	12	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
superpathway of anaerobic sucrose degradation	19	14	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	13	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	1
superpathway of N-acetylneuraminate degradation	22	12	1
aspartate superpathway	25	22	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	23	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1