Experiment set4S53 for Pseudomonas sp. RS175

L-Hydroxyproline carbon source 10 mM

Group: carbon source
Media: MME_noCarbon + Hydroxy-L-Proline (10 mM)
Culturing: Pseudomonas_RS175_ML2, 96 deep well, Aerobic, at 30 (C), shaken=1200 rpm
By: Andrew Frank on 1/31/23
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 22 genes in this experiment

For carbon source Hydroxy-L-Proline in Pseudomonas sp. RS175

For carbon source Hydroxy-L-Proline across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	5
Proline, 4-hydroxyproline uptake and utilization	5
Threonine and Homoserine Biosynthesis	2
Arginine and Ornithine Degradation	1
Lysine Biosynthesis DAP Pathway	1
Methionine Biosynthesis	1
Respiratory dehydrogenases 1	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Arginine and proline metabolism
• Glycine, serine and threonine metabolism
• Lysine biosynthesis
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones
• Urea cycle and metabolism of amino groups
• Glutamate metabolism
• Methionine metabolism
• Lysine degradation
• Penicillin and cephalosporin biosynthesis
• Phenylalanine metabolism
• Tryptophan metabolism
• Aminophosphonate metabolism
• Cyanoamino acid metabolism
• D-Arginine and D-ornithine metabolism
• Nucleotide sugars metabolism
• Benzoate degradation via CoA ligation
• Styrene degradation
• Caprolactam degradation

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-alanine degradation III	1	1	1
L-alanine biosynthesis II	1	1	1
trans-4-hydroxy-L-proline degradation II	4	4	3
L-proline degradation I	3	3	2
indole-3-acetate biosynthesis III (bacteria)	2	2	1
L-threonine biosynthesis	2	2	1
acrylonitrile degradation I	2	1	1
indole-3-acetate biosynthesis IV (bacteria)	2	1	1
L-alanine degradation V (oxidative Stickland reaction)	2	1	1
superpathway of L-threonine biosynthesis	6	6	2
L-alanine degradation II (to D-lactate)	3	3	1
L-serine biosynthesis I	3	3	1
L-homoserine biosynthesis	3	3	1
L-arginine degradation X (arginine monooxygenase pathway)	3	2	1
L-arginine degradation I (arginase pathway)	3	2	1
pyruvate fermentation to acetate and alanine	3	1	1
superpathway of acrylonitrile degradation	3	1	1
superpathway of L-alanine biosynthesis	4	4	1
superpathway of L-serine and glycine biosynthesis I	4	4	1
dipicolinate biosynthesis	4	3	1
spermidine biosynthesis II	4	3	1
L-methionine biosynthesis IV	4	2	1
ethene biosynthesis II (microbes)	4	1	1
ectoine biosynthesis	5	3	1
L-methionine biosynthesis II	6	5	1
norspermidine biosynthesis	6	4	1
L-alanine degradation VI (reductive Stickland reaction)	6	2	1
(5R)-carbapenem carboxylate biosynthesis	6	1	1
superpathway of L-isoleucine biosynthesis I	13	13	2
L-lysine biosynthesis III	7	6	1
L-lysine biosynthesis VI	7	6	1
L-Nδ-acetylornithine biosynthesis	7	5	1
anaerobic energy metabolism (invertebrates, cytosol)	7	4	1
thiazole component of thiamine diphosphate biosynthesis II	7	4	1
3-dehydroquinate biosynthesis II (archaea)	7	3	1
cremeomycin biosynthesis	7	2	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
L-citrulline biosynthesis	8	7	1
superpathway of L-homoserine and L-methionine biosynthesis	8	6	1
superpathway of polyamine biosynthesis III	8	5	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
grixazone biosynthesis	8	2	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	1
L-lysine biosynthesis I	9	9	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	2
superpathway of S-adenosyl-L-methionine biosynthesis	9	7	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	1
L-lysine biosynthesis II	9	6	1
L-lysine degradation V	9	6	1
superpathway of L-alanine fermentation (Stickland reaction)	9	4	1
superpathway of thiamine diphosphate biosynthesis II	11	8	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	1
superpathway of L-citrulline metabolism	12	9	1
chorismate biosynthesis II (archaea)	12	8	1
indole-3-acetate biosynthesis II	12	4	1
aspartate superpathway	25	22	2
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	1
superpathway of anaerobic energy metabolism (invertebrates)	17	8	1
platensimycin biosynthesis	26	6	1
superpathway of L-lysine degradation	43	18	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	20	1