Experiment set5S217 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 19 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
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	2
Polyamine Metabolism	2
Protein degradation	2
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more.	1
Folate Biosynthesis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Methionine Biosynthesis	1
Methionine Degradation	1
Orphan regulatory proteins	1
Queuosine-Archaeosine Biosynthesis	1
Terminal cytochrome C oxidases	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
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Phenylalanine metabolism
• Tryptophan metabolism
• Phenylpropanoid biosynthesis
• Insect hormone biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Fructose and mannose metabolism
• C21-Steroid hormone metabolism
• Oxidative phosphorylation
• 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
• Phenylalanine, tyrosine and tryptophan biosynthesis
• 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
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
N-end rule pathway I (prokaryotic)	2	2	2
L-aspartate degradation I	1	1	1
L-aspartate biosynthesis	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-glutamate degradation II	2	2	1
4-aminobenzoate biosynthesis II	2	2	1
4-aminobenzoate biosynthesis I	2	2	1
atromentin biosynthesis	2	1	1
L-tyrosine degradation II	2	1	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
arsenite to oxygen electron transfer	2	1	1
malate/L-aspartate shuttle pathway	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
sulfolactate degradation III	3	2	1
L-asparagine degradation III (mammalian)	3	2	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
(R)-cysteate degradation	3	1	1
arsenite to oxygen electron transfer (via azurin)	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	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
aerobic respiration I (cytochrome c)	4	3	1
aerobic respiration II (cytochrome c) (yeast)	4	3	1
superpathway of polyamine biosynthesis III	8	5	2
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
superpathway of plastoquinol biosynthesis	5	2	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	2
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
Fe(II) oxidation	6	3	1
coenzyme M biosynthesis II	6	1	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	2
anaerobic energy metabolism (invertebrates, cytosol)	7	4	1
superpathway of aromatic amino acid biosynthesis	18	18	2
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	5	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	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 rosmarinic acid biosynthesis	14	2	1
superpathway of anaerobic energy metabolism (invertebrates)	17	8	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
superpathway of chorismate metabolism	59	43	3
aspartate superpathway	25	22	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	4	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	20	1