Experiment set7IT024 for Herbaspirillum seropedicae SmR1

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D-Glucose carbon source with ammonium chloride; anaerobic; 3 days

Group: nitrogen fixation control
Media: RCH2_defined_noCarbon + D-Glucose (20 mM)
Culturing: HerbieS_ML4a, serum bottle, Anaerobic, at 30 (C), shaken=0 rpm
Growth: about 0.6 generations
By: Kelly Wetmore; Jordan Baker on 26-Mar-19
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 9 genes in this experiment

For nitrogen fixation control D-Glucose in Herbaspirillum seropedicae SmR1

For nitrogen fixation control D-Glucose across organisms

SEED Subsystems

Subsystem #Specific
Bacterial Chemotaxis 1
Hydantoin metabolism 1
Phosphate metabolism 1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 1
Serine-glyoxylate cycle 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
glyoxylate cycle 6 6 1
NAD(P)/NADPH interconversion 6 3 1
superpathway of glyoxylate bypass and TCA 12 10 1
superpathway of glyoxylate cycle and fatty acid degradation 14 10 1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass 26 22 1