Experiment set5S218 for Pseudomonas sp. RS175

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: Pseudomonas_RS175_ML2, 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 17 genes in this experiment

For mixed carbon source Trisodium citrate dihydrate in Pseudomonas sp. RS175

For mixed carbon source Trisodium citrate dihydrate across organisms

SEED Subsystems

Subsystem	#Specific
Polyamine Metabolism	3
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	2
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more.	1
Chorismate Synthesis	1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	1
Folate Biosynthesis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Orphan regulatory proteins	1
Protein degradation	1
Queuosine-Archaeosine Biosynthesis	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:

• Tyrosine metabolism
• Alkaloid biosynthesis I
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Phenylalanine metabolism
• Tryptophan metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Phenylpropanoid biosynthesis
• Insect hormone biosynthesis
• Biosynthesis of plant hormones
• Fructose and mannose metabolism
• C21-Steroid hormone metabolism
• Purine metabolism
• Glutamate metabolism
• Alanine and aspartate metabolism
• Glycine, serine and threonine metabolism
• Cysteine metabolism
• Arginine and proline metabolism
• Histidine metabolism
• 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
• Benzoate degradation via hydroxylation
• Bisphenol A degradation
• Novobiocin biosynthesis
• Benzoxazinone biosynthesis
• Nucleotide sugars metabolism
• Polyketide sugar unit biosynthesis
• Aminosugars metabolism
• Linoleic acid metabolism
• Pyruvate metabolism
• Biphenyl degradation
• 1- and 2-Methylnaphthalene degradation
• Tetrachloroethene degradation
• Naphthalene and anthracene degradation
• Fluorene degradation
• Benzoate degradation via CoA ligation
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Carbon fixation in photosynthetic organisms
• Folate biosynthesis
• Retinol metabolism
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide products
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-aspartate degradation I	1	1	1
L-aspartate biosynthesis	1	1	1
4-aminobenzoate biosynthesis I	2	2	1
4-aminobenzoate biosynthesis II	2	2	1
3-dehydroquinate biosynthesis I	2	2	1
L-glutamate degradation II	2	2	1
atromentin biosynthesis	2	1	1
malate/L-aspartate shuttle pathway	2	1	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
L-tyrosine degradation II	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
sulfolactate degradation III	3	2	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
Arg/N-end rule pathway (eukaryotic)	14	8	4
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
spermidine biosynthesis II	4	3	1
superpathway of polyamine biosynthesis III	8	5	2
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-phenylalanine biosynthesis	10	10	2
superpathway of L-tyrosine 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
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	2
superpathway of aromatic amino acid biosynthesis	18	18	3
superpathway of L-threonine biosynthesis	6	6	1
TCA cycle VIII (Chlamydia)	6	4	1
norspermidine biosynthesis	6	4	1
superpathway of sulfolactate degradation	6	3	1
coenzyme M biosynthesis II	6	1	1
chorismate biosynthesis I	7	7	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	2
anaerobic energy metabolism (invertebrates, cytosol)	7	4	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	5	1
superpathway of tetrahydrofolate biosynthesis	10	8	1
rosmarinic acid biosynthesis I	10	2	1
superpathway of candicidin biosynthesis	11	4	1
(S)-reticuline biosynthesis I	11	1	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	1
indole-3-acetate biosynthesis II	12	4	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of L-tryptophan biosynthesis	13	13	1
superpathway of rosmarinic acid biosynthesis	14	2	1
superpathway of chorismate metabolism	59	43	4
superpathway of anaerobic energy metabolism (invertebrates)	17	8	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
aspartate superpathway	25	22	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	4	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	20	1