Experiment set1IT032 for Variovorax sp. OAS795

L-Histidine carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + L-Histidine (20 mM)
Culturing: Variovorax_OAS795_ML2, 96 deep-well microplate; 0.8 mL volume, Aerobic, at 30 (C), shaken=700 rpm
By: Marta on 10-Apr-21
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)

Specific Phenotypes

For 38 genes in this experiment

For carbon source L-Histidine in Variovorax sp. OAS795

For carbon source L-Histidine across organisms

SEED Subsystems

Subsystem	#Specific
Histidine Degradation	4
Transport of Iron	4
Iron acquisition in Vibrio	3
Molybdenum cofactor biosynthesis	3
Transport of Molybdenum	3
Oxidative stress	2
2-phosphoglycolate salvage	1
Alanine biosynthesis	1
Benzoate degradation	1
Branched-Chain Amino Acid Biosynthesis	1
DNA-binding regulatory proteins, strays	1
DNA-replication	1
DNA repair, bacterial	1
DNA repair, bacterial RecFOR pathway	1
Orphan regulatory proteins	1
Photorespiration (oxidative C2 cycle)	1
Protein degradation	1
Pyruvate Alanine Serine Interconversions	1
Queuosine-Archaeosine Biosynthesis	1
Siderophore Pyoverdine	1
TCA Cycle	1
Thioredoxin-disulfide reductase	1
Urea decomposition	1
p-Aminobenzoyl-Glutamate Utilization	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Histidine metabolism
• Glyoxylate and dicarboxylate metabolism
• Citrate cycle (TCA cycle)
• Tryptophan metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine biosynthesis
• Phenylalanine metabolism
• Benzoate degradation via hydroxylation
• Benzoxazinone biosynthesis
• Toluene and xylene degradation
• Methane metabolism
• Diterpenoid biosynthesis
• Biosynthesis of siderophore group nonribosomal peptides
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-histidine degradation II	5	5	4
L-alanine biosynthesis I	2	2	1
superoxide radicals degradation	2	2	1
L-histidine degradation I	4	3	2
methanol oxidation to formaldehyde IV	2	1	1
partial TCA cycle (obligate autotrophs)	8	7	3
TCA cycle II (plants and fungi)	9	9	3
TCA cycle V (2-oxoglutarate synthase)	9	9	3
glyoxylate cycle	6	6	2
ethanol degradation IV	3	3	1
TCA cycle IV (2-oxoglutarate decarboxylase)	9	8	3
TCA cycle VII (acetate-producers)	9	7	3
TCA cycle VI (Helicobacter)	9	7	3
L-histidine degradation III	6	4	2
molybdenum cofactor biosynthesis	3	2	1
D-phenylglycine degradation	3	1	1
microcin B17 biosynthesis	3	1	1
TCA cycle I (prokaryotic)	10	9	3
TCA cycle III (animals)	10	9	3
reductive TCA cycle I	11	8	3
reactive oxygen species degradation	4	4	1
superpathway of L-alanine biosynthesis	4	4	1
superpathway of glyoxylate bypass and TCA	12	11	3
L-histidine degradation VI	8	7	2
nitrogen remobilization from senescing leaves	8	7	2
reductive TCA cycle II	12	7	3
superpathway of glyoxylate cycle and fatty acid degradation	14	11	3
peptidoglycan recycling II	10	6	2
mandelate degradation I	5	3	1
mixed acid fermentation	16	12	3
TCA cycle VIII (Chlamydia)	6	6	1
4-hydroxymandelate degradation	6	4	1
methylaspartate cycle	19	12	3
incomplete reductive TCA cycle	7	5	1
pyruvate fermentation to propanoate I	7	4	1
indole-3-acetate degradation II	7	2	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	20	3
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	24	3
photorespiration I	9	6	1
photorespiration III	9	6	1
photorespiration II	10	6	1
anaerobic energy metabolism (invertebrates, mitochondrial)	10	6	1
L-glutamate degradation VIII (to propanoate)	11	4	1
ethene biosynthesis V (engineered)	25	19	2
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	7	1
peptidoglycan recycling I	14	10	1
superpathway of anaerobic energy metabolism (invertebrates)	17	13	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	25	2
mandelate degradation to acetyl-CoA	18	14	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	22	2
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	24	1