Experiment set3S237 for Rhodanobacter sp000427505 FW510-R12

defined media with 20AA_mix

Group: nutrient
Media: NLDM_defined_nocarbon + D-Glucose (20 mM) + 1x 20AA_mix
Culturing: rhodanobacter_R12_ML3, tube, Aerobic, at 23 (C), shaken=200 rpm
By: Hira on 03/23/2025
Media components: 1 mM Ammonium chloride, 3.3 mM Potassium Chloride, 0.812 mM Magnesium Sulfate Heptahydrate, 0.68 mM Calcium chloride dihydrate, 4.05 mM Disodium phosphate, 0.95 mM Sodium phosphate monobasic, ATCC Wolfe's mineral mix (5 mg/L EDTA, 3 mg/L Magnesium Sulfate Heptahydrate, 5 mg/L Manganese (II) sulfate monohydrate, 10 mg/L Sodium Chloride, 1 mg/L Iron (II) sulfate heptahydrate, 1 mg/L Cobalt(II) nitrate hexahydrate, 1 mg/L Calcium chloride dihydrate, 1 mg/L Zinc sulfate heptahydrate, 0.1 mg/L Copper (II) sulfate pentahydrate, 0.1 mg/L Aluminum potassium sulfate dodecahydrate, 0.1 mg/L Boric Acid, 0.1 mg/L Sodium Molybdate Dihydrate, 0.01 mg/L Sodium selenite pentahydrate, 0.1 mg/L Sodium tungstate dihydrate, 0.2 mg/L Nickel (II) chloride hexahydrate), ATCC Wolfe's vitamin mix (20 ug/L Folic Acid, 100 ug/L Pyridoxine HCl, 50 ug/L Riboflavin, 20 ug/L biotin, 50 ug/L Thiamine HCl, 50 ug/L Nicotinic Acid, 50 ug/L calcium pantothenate, 1 ug/L Cyanocobalamin, 50 ug/L 4-Aminobenzoic acid, 50 ug/L Lipoic acid)

20AA_mix 1x includes: 0.5 mM L-Arginine, 0.5 mM L-Histidine, 0.5 mM L-Lysine, 0.5 mM L-Aspartic Acid, 0.5 mM L-Glutamic acid monopotassium salt monohydrate, 0.5 mM L-Serine, 0.5 mM L-Threonine, 0.5 mM L-Asparagine, 0.5 mM L-Glutamine, 0.5 mM L-Cysteine hydrochloride monohydrate, 0.5 mM Glycine, 0.5 mM L-Proline, 0.5 mM L-Alanine, 0.5 mM L-Valine, 0.5 mM L-Isoleucine, 0.5 mM L-Leucine, 0.5 mM L-Methionine, 0.5 mM L-Phenylalanine, 0.5 mM L-tyrosine disodium salt, 0.5 mM L-Tryptophan

Specific Phenotypes

For 19 genes in this experiment

For nutrient D-Glucose in Rhodanobacter sp000427505 FW510-R12

For nutrient D-Glucose across organisms

SEED Subsystems

Subsystem	#Specific
Biogenesis of cytochrome c oxidases	3
Calvin-Benson cycle	1
Campylobacter Iron Metabolism	1
Glycine Biosynthesis	1
Heat shock dnaK gene cluster extended	1
Iron acquisition in Vibrio	1
Mannose Metabolism	1
Methionine Biosynthesis	1
Methionine Degradation	1
Oxidative stress	1
Oxygen and light sensor PpaA-PpsR	1
Pentose phosphate pathway	1
Protein chaperones	1
Threonine degradation	1
Transport of Iron	1
Type IV pilus	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pentose phosphate pathway
• Ubiquinone and menaquinone biosynthesis
• Glycine, serine and threonine metabolism
• Methionine metabolism
• Tryptophan metabolism
• Carbon fixation in photosynthetic organisms
• Riboflavin metabolism
• Porphyrin and chlorophyll metabolism
• Terpenoid biosynthesis
• Carotenoid biosynthesis - General
• Biosynthesis of ansamycins
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
pentose phosphate pathway (partial)	3	3	2
L-threonine degradation III (to methylglyoxal)	3	2	2
L-threonine degradation II	2	2	1
aminopropanol phosphate biosynthesis II	4	2	2
pentose phosphate pathway (non-oxidative branch) I	5	5	2
pentose phosphate pathway (non-oxidative branch) II	6	5	2
pentose phosphate pathway	8	8	2
heme a biosynthesis	4	2	1
formaldehyde assimilation II (assimilatory RuMP Cycle)	9	7	2
Rubisco shunt	10	8	2
formaldehyde assimilation III (dihydroxyacetone cycle)	12	10	2
Calvin-Benson-Bassham cycle	13	10	2
superpathway of glucose and xylose degradation	17	14	2
oxygenic photosynthesis	17	11	2
superpathway of L-threonine metabolism	18	14	2
ethene biosynthesis V (engineered)	25	18	2
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	18	2
1-butanol autotrophic biosynthesis (engineered)	27	19	2
Bifidobacterium shunt	15	14	1