Experiment set47S222 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 13 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)	5
Queuosine-Archaeosine Biosynthesis	2
Catechol branch of beta-ketoadipate pathway	1
Chloroaromatic degradation pathway	1
Chorismate Synthesis	1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	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:

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

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-aspartate degradation I	1	1	1
L-aspartate biosynthesis	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
malate/L-aspartate shuttle pathway	2	2	1
L-glutamate degradation II	2	2	1
3-dehydroquinate biosynthesis I	2	2	1
3-oxoadipate degradation	2	2	1
L-tyrosine degradation II	2	1	1
atromentin biosynthesis	2	1	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
L-tyrosine biosynthesis I	3	3	1
L-phenylalanine biosynthesis I	3	3	1
L-phenylalanine degradation II (anaerobic)	3	2	1
L-asparagine degradation III (mammalian)	3	2	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
sulfolactate degradation III	3	1	1
(R)-cysteate degradation	3	1	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation III	4	2	1
L-tryptophan degradation VIII (to tryptophol)	4	1	1
superpathway of L-tyrosine biosynthesis	10	10	2
superpathway of L-phenylalanine biosynthesis	10	10	2
L-tyrosine degradation I	5	5	1
trans-4-hydroxy-L-proline degradation I	5	3	1
superpathway of plastoquinol biosynthesis	5	2	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	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 aromatic amino acid biosynthesis	18	18	3
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
chorismate biosynthesis I	7	7	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
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
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-tryptophan biosynthesis	13	13	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
superpathway of chorismate metabolism	59	42	3
aspartate superpathway	25	22	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	4	1
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