Experiment set17IT014 for Pseudomonas fluorescens SBW25-INTG

p-Coumaric acid (C) 5 mM

Group: carbon source
Media: MME_noNitrogen_noCarbon + p-Coumaric acid (5 mM) + Ammonium chloride (10 mM)
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=1200 rpm
By: Joshua Elmore on October 1, 2021
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium Chloride, 0.41 mM Magnesium Sulfate Heptahydrate, 0.07 mM Calcium chloride dihydrate, MME Trace Minerals (0.5 mg/L EDTA tetrasodium tetrahydrate salt, 2 mg/L Ferric chloride, 0.05 mg/L Boric Acid, 0.05 mg/L Zinc chloride, 0.03 mg/L copper (II) chloride dihydrate, 0.05 mg/L Manganese (II) chloride tetrahydrate, 0.05 mg/L Diammonium molybdate, 0.05 mg/L Cobalt chloride hexahydrate, 0.05 mg/L Nickel (II) chloride hexahydrate)

Specific Phenotypes

For 58 genes in this experiment

For carbon source p-Coumaric acid in Pseudomonas fluorescens SBW25-INTG

For carbon source p-Coumaric acid across organisms

SEED Subsystems

Subsystem	#Specific
Transport of Zinc	5
Lipid A modifications	4
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	2
Orphan regulatory proteins	2
Polyamine Metabolism	2
Trehalose Uptake and Utilization	2
ABC transporter dipeptide (TC 3.A.1.5.2)	1
ABC transporter oligopeptide (TC 3.A.1.5.1)	1
Acid resistance mechanisms	1
Alanine biosynthesis	1
Alkanesulfonate assimilation	1
Arginine and Ornithine Degradation	1
Bacterial Cytoskeleton	1
Cinnamic Acid Degradation	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
Copper homeostasis	1
DNA repair, bacterial	1
Experimental tye	1
Flagellum	1
Folate Biosynthesis	1
Fructose and Mannose Inducible PTS	1
Fructose utilization	1
Gentisare degradation	1
Mannitol Utilization	1
Multidrug Resistance Efflux Pumps	1
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon)	1
Peptidoglycan Biosynthesis	1
Phenylpropanoid compound degradation	1
Queuosine-Archaeosine Biosynthesis	1
Salicylate and gentisate catabolism	1
Taurine Utilization	1
Thiamin biosynthesis	1
p-Hydroxybenzoate degradation	1
tRNA processing	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Urea cycle and metabolism of amino groups
• Arginine and proline metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Nucleotide sugars metabolism
• Thiamine metabolism
• Glycolysis / Gluconeogenesis
• Fructose and mannose metabolism
• Galactose metabolism
• Fatty acid biosynthesis
• Glycine, serine and threonine metabolism
• Histidine metabolism
• Tyrosine metabolism
• Taurine and hypotaurine metabolism
• Glutathione metabolism
• Starch and sucrose metabolism
• Aminosugars metabolism
• Glycosaminoglycan degradation
• Lipopolysaccharide biosynthesis
• Naphthalene and anthracene degradation
• Folate biosynthesis
• Porphyrin and chlorophyll metabolism
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• T cell receptor signaling pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-cysteine degradation IV	1	1	1
glyphosate degradation II	1	1	1
cadaverine biosynthesis	1	1	1
arginine dependent acid resistance	1	1	1
L-alanine biosynthesis III	1	1	1
taurine degradation IV	1	1	1
superpathway of putrescine biosynthesis	4	4	2
L-arginine degradation III (arginine decarboxylase/agmatinase pathway)	2	2	1
putrescine biosynthesis I	2	2	1
putrescine biosynthesis III	2	2	1
cytidylyl molybdenum cofactor sulfurylation	2	1	1
thiazole component of thiamine diphosphate biosynthesis II	7	5	3
superpathway of polyamine biosynthesis I	8	6	3
fatty acid biosynthesis initiation (type II)	3	3	1
putrescine biosynthesis II	3	3	1
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	3	1
sucrose degradation I (sucrose phosphotransferase)	3	2	1
6-hydroxymethyl-dihydropterin diphosphate biosynthesis IV (Plasmodium)	3	2	1
bis(guanylyl molybdopterin) cofactor sulfurylation	3	1	1
aminopropylcadaverine biosynthesis	3	1	1
superpathway of thiamine diphosphate biosynthesis II	11	9	3
superpathway of L-alanine biosynthesis	4	4	1
superpathway of polyamine biosynthesis II	8	6	2
preQ0 biosynthesis	4	2	1
threo-tetrahydrobiopterin biosynthesis	4	2	1
erythro-tetrahydrobiopterin biosynthesis I	4	2	1
tetrahydromonapterin biosynthesis	4	2	1
tRNA-uridine 2-thiolation (yeast mitochondria)	4	1	1
spermidine biosynthesis III	4	1	1
tRNA-uridine 2-thiolation (mammalian mitochondria)	4	1	1
tRNA processing	10	10	2
superpathway of fatty acid biosynthesis initiation	5	4	1
6-hydroxymethyl-dihydropterin diphosphate biosynthesis I	5	3	1
[2Fe-2S] iron-sulfur cluster biosynthesis	10	4	2
desferrioxamine E biosynthesis	5	1	1
lupanine biosynthesis	5	1	1
desferrioxamine B biosynthesis	5	1	1
bisucaberin biosynthesis	5	1	1
tRNA-uridine 2-thiolation (thermophilic bacteria)	5	1	1
superpathway of arginine and polyamine biosynthesis	17	15	3
fatty acid salvage	6	6	1
L-lysine degradation X	6	5	1
thiazole component of thiamine diphosphate biosynthesis I	6	4	1
molybdopterin biosynthesis	6	4	1
superpathway of taurine degradation	6	2	1
superpathway of L-arginine and L-ornithine degradation	13	9	2
drosopterin and aurodrosopterin biosynthesis	7	5	1
L-lysine degradation I	7	4	1
superpathway of ornithine degradation	8	4	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
tRNA-uridine 2-thiolation (cytoplasmic)	8	1	1
superpathway of thiamine diphosphate biosynthesis I	10	8	1
superpathway of tetrahydrofolate biosynthesis	10	8	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	7	1
tRNA-uridine 2-thiolation and selenation (bacteria)	11	4	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	1
superpathway of fatty acid biosynthesis I (E. coli)	16	14	1
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	4	1
streptorubin B biosynthesis	34	20	1
superpathway of fatty acid biosynthesis II (plant)	43	38	1
superpathway of L-lysine degradation	43	17	1
superpathway of fatty acids biosynthesis (E. coli)	53	49	1
superpathway of chorismate metabolism	59	42	1