Experiment set2S491 for Hydrogenophaga sp. GW460-11-11-14-LB1

Compare to:

Ying_all64 rep C; time point 3

Group: carbon source
Media: SDM_noCarbon + 1X Ying_all64
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_all64 1x includes: 40 uM Sucrose, 40 uM D-Glucose, 40 uM D-Trehalose dihydrate, 40 uM m-Inositol, 40 uM D-Xylose, 40 uM D-Mannitol, 40 uM N-Acetyl-D-Glucosamine, 40 uM Sodium L-Lactate, 40 uM D,L-Malic Acid, 40 uM Citric Acid, 40 uM Succinic Acid, 40 uM Sodium pyruvate, 40 uM a-Ketoglutaric acid disodium salt hydrate, 40 uM L-Citrulline, 40 uM 5-methyluridine, 40 uM Adenine, 40 uM Adenosine, 40 uM Cytidine, 40 uM Cytosine, 40 uM Guanine, 40 uM Guanosine, 40 uM Hypoxanthine, 40 uM Inosine, 40 uM Thymine, 40 uM Uracil, 40 uM Uridine, 40 uM Xanthine, 40 uM Xanthosine, 40 uM L-Alanine, 40 uM L-Arginine, 40 uM L-Asparagine, 40 uM L-Aspartic Acid, 40 uM L-Cysteine, 40 uM L-Glutamic acid, 40 uM L-Glutamine, 40 uM Glycine, 40 uM L-Histidine, 40 uM L-Isoleucine, 40 uM L-Leucine, 40 uM L-Lysine, 40 uM L-Methionine, 40 uM L-Phenylalanine, 40 uM L-Proline, 40 uM L-Serine, 40 uM L-Threonine, 40 uM L-Tryptophan, 40 uM L-tyrosine, 40 uM L-Valine, 40 uM Gamma-Aminobutyric Acid Hydrochloride, 40 uM Ectoine, 40 uM Betaine, 40 uM N-Acetyl-L-glutamic acid, 40 uM Nicotinamide, 40 uM L-Ornithine, 40 uM Shikimic Acid, 40 uM spermidine, 40 uM Taurine, 40 uM Trigonelline HCl, 40 uM L-Carnitine hydrochloride, 40 uM Choline, 40 uM N-alpha-Acetyl-L-glutamate, 40 uM n-Acetyl-lysine, 40 uM n-Acetyl-muramic acid, 40 uM sn-glycero-3-phosphocholine

Specific Phenotypes

For 31 genes in this experiment

For carbon source Ying_all64 in Hydrogenophaga sp. GW460-11-11-14-LB1

For carbon source Ying_all64 across organisms

SEED Subsystems

Subsystem #Specific
Glutathione: Non-redox reactions 3
Entner-Doudoroff Pathway 2
Glycolate, glyoxylate interconversions 2
Photorespiration (oxidative C2 cycle) 2
ABC transporter branched-chain amino acid (TC 3.A.1.4.1) 1
Branched-Chain Amino Acid Biosynthesis 1
Central meta-cleavage pathway of aromatic compound degradation 1
Cyanophycin Metabolism 1
Glycolysis and Gluconeogenesis 1
Glycolysis and Gluconeogenesis, including Archaeal enzymes 1
Methylglyoxal Metabolism 1
Pentose phosphate pathway 1
Potassium homeostasis 1
Propionate-CoA to Succinate Module 1
Pyruvate metabolism I: anaplerotic reactions, PEP 1
RNA processing and degradation, bacterial 1
Ribosome LSU bacterial 1
Serine-glyoxylate cycle 1
Sex pheromones in Enterococcus faecalis and other Firmicutes 1
TCA Cycle 1
Threonine degradation 1
Type IV pilus 1
ZZ gjo need homes 1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
cyanophycin metabolism 6 4 4
L-methionine degradation II 3 2 2
glycolate and glyoxylate degradation II 2 2 1
L-threonine degradation I 6 5 3
L-threonine degradation V 2 1 1
L-isoleucine biosynthesis I (from threonine) 7 7 3
glyoxylate cycle 6 6 2
methylglyoxal degradation VIII 3 3 1
pentose phosphate pathway (oxidative branch) I 3 2 1
methylglyoxal degradation I 3 2 1
glycolate and glyoxylate degradation III 3 1 1
gallate degradation I 4 4 1
partial TCA cycle (obligate autotrophs) 8 7 2
nitrogen remobilization from senescing leaves 8 6 2
3,4-dichlorobenzoate degradation 4 3 1
glycolate and glyoxylate degradation I 4 3 1
4-hydroxy-2-nonenal detoxification 4 1 1
superpathway of L-isoleucine biosynthesis I 13 13 3
Entner-Doudoroff pathway I 9 9 2
TCA cycle IV (2-oxoglutarate decarboxylase) 9 8 2
TCA cycle V (2-oxoglutarate synthase) 9 8 2
TCA cycle II (plants and fungi) 9 7 2
TCA cycle VI (Helicobacter) 9 6 2
TCA cycle VII (acetate-producers) 9 6 2
hypoglycin biosynthesis 14 4 3
TCA cycle I (prokaryotic) 10 8 2
tRNA processing 10 8 2
TCA cycle III (animals) 10 7 2
pentachlorophenol degradation 10 6 2
cytosolic NADPH production (yeast) 5 3 1
mixed acid fermentation 16 11 3
reductive TCA cycle I 11 7 2
superpathway of branched chain amino acid biosynthesis 17 17 3
methylgallate degradation 6 6 1
superpathway of glyoxylate bypass and TCA 12 10 2
superpathway of L-threonine metabolism 18 13 3
syringate degradation 12 8 2
reductive TCA cycle II 12 6 2
3-chlorobenzoate degradation II (via protocatechuate) 6 3 1
formaldehyde oxidation I 6 3 1
anaerobic energy metabolism (invertebrates, cytosol) 7 7 1
L-lysine biosynthesis VI 7 6 1
superpathway of glyoxylate cycle and fatty acid degradation 14 11 2
superpathway of glycol metabolism and degradation 7 5 1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle 22 18 3
protocatechuate degradation I (meta-cleavage pathway) 8 8 1
pentose phosphate pathway 8 7 1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast) 8 4 1
superpathway of methylglyoxal degradation 8 4 1
glutathione-mediated detoxification I 8 3 1
superpathway of glycolysis and the Entner-Doudoroff pathway 17 15 2
superpathway of glucose and xylose degradation 17 13 2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass 26 22 3
L-lysine biosynthesis I 9 9 1
L-lysine biosynthesis II 9 7 1
heterolactic fermentation 18 12 2
Entner-Doudoroff pathway III (semi-phosphorylative) 9 6 1
photorespiration I 9 4 1
Entner-Doudoroff pathway II (non-phosphorylative) 9 4 1
photorespiration III 9 4 1
gliotoxin biosynthesis 9 1 1
glutathione-mediated detoxification II 9 1 1
methylaspartate cycle 19 12 2
Rubisco shunt 10 10 1
superpathway of vanillin and vanillate degradation 10 9 1
glycolysis IV 10 8 1
glycolysis V (Pyrococcus) 10 7 1
photorespiration II 10 4 1
glycolysis II (from fructose 6-phosphate) 11 10 1
glycolysis III (from glucose) 11 10 1
glycolysis VI (from fructose) 11 8 1
homolactic fermentation 12 10 1
indole glucosinolate activation (intact plant cell) 12 3 1
camalexin biosynthesis 12 2 1
ethene biosynthesis V (engineered) 25 19 2
glycolysis I (from glucose 6-phosphate) 13 11 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II 15 13 1
Bifidobacterium shunt 15 12 1
cyclosporin A biosynthesis 15 2 1
glycerol degradation to butanol 16 10 1
superpathway of anaerobic energy metabolism (invertebrates) 17 13 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 17 1
superpathway of hexitol degradation (bacteria) 18 11 1
superpathway of anaerobic sucrose degradation 19 14 1
hexitol fermentation to lactate, formate, ethanol and acetate 19 13 1
superpathway of N-acetylneuraminate degradation 22 13 1
aspartate superpathway 25 24 1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered) 26 19 1
1-butanol autotrophic biosynthesis (engineered) 27 20 1