Experiment set47S220 for Pseudomonas putida KT2440

mixed carbon sources Trisodium citrate dihydrate 10 mM and 4-azido-L-phenylalanine 10 mM

Group: mixed carbon source
Media: MME_noCarbon + Trisodium citrate dihydrate (10 mM) + 4-azido-L-phenylalanine (10 mM)
Culturing: Putida_ML5_PNNL, 96 deep well, Aerobic, at 30 (C), shaken=1200 rpm
By: Andrew Frank on 11/17/23
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium Chloride, 10 mM Ammonium 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 14 genes in this experiment

For mixed carbon source Trisodium citrate dihydrate in Pseudomonas putida KT2440

For mixed carbon source Trisodium citrate dihydrate across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	3
Queuosine-Archaeosine Biosynthesis	2
Catechol branch of beta-ketoadipate pathway	1
Chloroaromatic degradation pathway	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Protocatechuate branch of beta-ketoadipate pathway	1
Threonine and Homoserine Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glutamate metabolism
• Alanine and aspartate metabolism
• Cysteine metabolism
• Geraniol degradation
• Arginine and proline metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Benzoate degradation via hydroxylation
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• 1- and 2-Methylnaphthalene degradation
• Carbon fixation in photosynthetic organisms
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-aspartate degradation I	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-aspartate biosynthesis	1	1	1
malate/L-aspartate shuttle pathway	2	2	1
3-oxoadipate degradation	2	2	1
L-glutamate degradation II	2	2	1
atromentin biosynthesis	2	1	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
L-tyrosine degradation II	2	1	1
L-phenylalanine biosynthesis I	3	3	1
L-tyrosine biosynthesis I	3	3	1
L-phenylalanine degradation II (anaerobic)	3	2	1
L-asparagine degradation III (mammalian)	3	2	1
sulfolactate degradation III	3	1	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
(R)-cysteate degradation	3	1	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
L-tryptophan degradation VIII (to tryptophol)	4	1	1
L-tyrosine degradation I	5	5	1
trans-4-hydroxy-L-proline degradation I	5	3	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	2	1
superpathway of plastoquinol biosynthesis	5	2	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	7	2
superpathway of L-threonine biosynthesis	6	6	1
catechol degradation III (ortho-cleavage pathway)	6	6	1
TCA cycle VIII (Chlamydia)	6	5	1
superpathway of sulfolactate degradation	6	2	1
coenzyme M biosynthesis II	6	1	1
superpathway of salicylate degradation	7	7	1
anaerobic energy metabolism (invertebrates, cytosol)	7	5	1
4-methylcatechol degradation (ortho cleavage)	7	5	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	8	2
superpathway of aromatic amino acid biosynthesis	18	18	2
aromatic compounds degradation via β-ketoadipate	9	9	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	6	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
rosmarinic acid biosynthesis I	10	2	1
toluene degradation III (aerobic) (via p-cresol)	11	7	1
(S)-reticuline biosynthesis I	11	3	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	1
indole-3-acetate biosynthesis II	12	5	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of rosmarinic acid biosynthesis	14	2	1
superpathway of anaerobic energy metabolism (invertebrates)	17	10	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
mandelate degradation to acetyl-CoA	18	11	1
aspartate superpathway	25	22	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	4	1
superpathway of chorismate metabolism	59	42	2
superpathway of aerobic toluene degradation	30	13	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	19	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1