Experiment set2S495 for Hydrogenophaga sp. GW460-11-11-14-LB1

Ying_Others16 rep A; time point 3

Group: carbon source
Media: SDM_noCarbon + 1X Ying_Others16
Culturing: Phaga5_ML11, tube, Aerobic, at 28 (C), shaken=180 rpm
By: Ying and Valentine on 9/1/23
Media components: 1.5 g/L Ammonium chloride, 0.6 g/L Potassium phosphate monobasic, 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)

Ying_Others16 1x includes: 160 uM Gamma-Aminobutyric Acid Hydrochloride, 160 uM Ectoine, 160 uM Betaine, 160 uM N-Acetyl-L-Glutamic Acid, 160 uM Nicotinamide, 160 uM L-Ornithine, 160 uM Shikimic Acid, 160 uM spermidine, 160 uM Taurine, 160 uM Trigonelline HCl, 160 uM L-Carnitine hydrochloride, 160 uM Choline, 160 uM N-alpha-Acetyl-L-glutamate, 160 uM n-Acetyl-lysine, 160 uM n-Acetyl-muramic acid, 160 uM sn-glycero-3-phosphocholine

Specific Phenotypes

For 24 genes in this experiment

For carbon source Ying_Others16 in Hydrogenophaga sp. GW460-11-11-14-LB1

For carbon source Ying_Others16 across organisms

SEED Subsystems

Subsystem	#Specific
CO Dehydrogenase	3
Sulfur oxidation	3
Acetyl-CoA fermentation to Butyrate	1
Alkylphosphonate utilization	1
Bacterial RNA-metabolizing Zn-dependent hydrolases	1
Benzoate transport and degradation cluster	1
Butanol Biosynthesis	1
Carbon monoxide dehydrogenase maturation factors	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
DNA topoisomerases, Type I, ATP-independent	1
Denitrification	1
Isoleucine degradation	1
Phosphate metabolism	1
Polyhydroxybutyrate metabolism	1
Ribosome activity modulation	1
Ribosome biogenesis bacterial	1
Valine degradation	1
n-Phenylalkanoic acid degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Lysine degradation
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Limonene and pinene degradation
• Biosynthesis of unsaturated fatty acids
• Fatty acid biosynthesis
• Fatty acid elongation in mitochondria
• Fatty acid metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• Ether lipid metabolism
• alpha-Linolenic acid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• 1- and 2-Methylnaphthalene degradation
• Trinitrotoluene degradation
• Propanoate metabolism
• Ethylbenzene degradation
• Methane metabolism
• Nicotinate and nicotinamide metabolism
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Caprolactam degradation
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of type II polyketide backbone
• Biosynthesis of terpenoids and steroids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
sulfide oxidation II (flavocytochrome c)	1	1	1
benzoyl-CoA biosynthesis	3	3	1
2-methyl-branched fatty acid β-oxidation	14	11	3
adipate degradation	5	5	1
adipate biosynthesis	5	4	1
glutaryl-CoA degradation	5	3	1
fatty acid β-oxidation IV (unsaturated, even number)	5	3	1
fatty acid β-oxidation II (plant peroxisome)	5	3	1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative)	5	1	1
pyruvate fermentation to hexanol (engineered)	11	7	2
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	6	2
oleate β-oxidation	35	29	6
fatty acid salvage	6	5	1
pyruvate fermentation to butanol II (engineered)	6	4	1
L-isoleucine degradation I	6	4	1
methyl ketone biosynthesis (engineered)	6	3	1
NAD(P)/NADPH interconversion	6	3	1
propanoate fermentation to 2-methylbutanoate	6	3	1
benzoyl-CoA degradation I (aerobic)	7	6	1
fatty acid β-oxidation I (generic)	7	5	1
pyruvate fermentation to butanoate	7	4	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	3	1
L-valine degradation I	8	4	1
pyruvate fermentation to butanol I	8	3	1
phenylacetate degradation I (aerobic)	9	8	1
valproate β-oxidation	9	7	1
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	6	1
benzoyl-CoA degradation III (anaerobic)	9	5	1
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	4	1
3-phenylpropanoate degradation	10	5	1
L-glutamate degradation V (via hydroxyglutarate)	10	5	1
superpathway of phenylethylamine degradation	11	9	1
gallate degradation III (anaerobic)	11	3	1
Spodoptera littoralis pheromone biosynthesis	22	4	2
L-glutamate degradation VII (to butanoate)	12	5	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	4	1
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	2	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
docosahexaenoate biosynthesis III (6-desaturase, mammals)	14	2	1
L-tryptophan degradation III (eukaryotic)	15	7	1
glycerol degradation to butanol	16	10	1
crotonate fermentation (to acetate and cyclohexane carboxylate)	16	5	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	7	1
benzoate fermentation (to acetate and cyclohexane carboxylate)	17	6	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	11	1
toluene degradation VI (anaerobic)	18	4	1
platensimycin biosynthesis	26	6	1
1-butanol autotrophic biosynthesis (engineered)	27	20	1