Experiment set7IT011 for Pseudomonas syringae pv. syringae B728a

D-Mannose carbon source

Group: carbon source
Media: M9 minimal media_noCarbon + D-Mannose (22.20248668 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 21 genes in this experiment

For carbon source D-Mannose in Pseudomonas syringae pv. syringae B728a

For carbon source D-Mannose across organisms

SEED Subsystems

Subsystem	#Specific
Mannitol Utilization	2
DNA-binding regulatory proteins, strays	1
Fructose and Mannose Inducible PTS	1
Fructose utilization	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Polyamine Metabolism	1
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	1
Serine-glyoxylate cycle	1
Sialic Acid Metabolism	1
tRNA processing	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Nucleotide sugars metabolism
• Arginine and proline metabolism
• Aminosugars metabolism
• Glycolysis / Gluconeogenesis
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• alpha-Linolenic acid metabolism
• Pyruvate metabolism
• Benzoate degradation via CoA ligation
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Citrate cycle (TCA cycle)
• Galactose metabolism
• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• C21-Steroid hormone metabolism
• Urea cycle and metabolism of amino groups
• Puromycin biosynthesis
• Pyrimidine metabolism
• Glutamate metabolism
• Alanine and aspartate metabolism
• Glycine, serine and threonine metabolism
• Methionine metabolism
• Bisphenol A degradation
• Starch and sucrose metabolism
• Polyketide sugar unit biosynthesis
• Linoleic acid metabolism
• Tetrachloroethene degradation
• Trinitrotoluene degradation
• Butanoate metabolism
• Retinol metabolism
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Biosynthesis of type II polyketide products
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamine biosynthesis I	1	1	1
spermidine biosynthesis I	2	2	1
ammonia assimilation cycle I	2	2	1
spermine biosynthesis	2	1	1
pseudouridine degradation	2	1	1
ammonia assimilation cycle II	2	1	1
ammonia assimilation cycle III	3	3	1
aminopropylcadaverine biosynthesis	3	3	1
L-aspartate degradation II (aerobic)	3	2	1
superpathway of ammonia assimilation (plants)	3	2	1
L-aspartate degradation III (anaerobic)	3	2	1
N-acetylneuraminate and N-acetylmannosamine degradation II	3	1	1
spermidine biosynthesis III	4	2	1
sulfoquinovose degradation III	4	1	1
putrescine degradation II	4	1	1
mannitol cycle	5	3	1
sulfoquinovose degradation I	5	1	1
sulfoquinovose degradation VI	5	1	1
L-glutamate and L-glutamine biosynthesis	7	5	1
incomplete reductive TCA cycle	7	4	1
sulfoquinovose degradation V	7	1	1
superpathway of polyamine biosynthesis I	8	7	1
superpathway of polyamine biosynthesis II	8	7	1
superpathway of ornithine degradation	8	4	1
L-arginine biosynthesis II (acetyl cycle)	10	10	1
L-methionine salvage cycle III	11	10	1
reductive TCA cycle I	11	7	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	5	1
gluconeogenesis III	12	9	1
L-methionine salvage cycle I (bacteria and plants)	12	9	1
superpathway of L-arginine and L-ornithine degradation	13	7	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	5	1
superpathway of arginine and polyamine biosynthesis	17	16	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1