Experiment set7IT032 for Herbaspirillum seropedicae SmR1

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L-Malic acid carbon source with ammonium chloride; anaerobic; 8 days

Group: nitrogen fixation control
Media: RCH2_defined_noCarbon + L-Malic acid (20 mM)
Culturing: HerbieS_ML4a, serum bottle, Anaerobic, at 30 (C), shaken=0 rpm
Growth: about 4.5 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 40 genes in this experiment

For nitrogen fixation control L-Malic acid in Herbaspirillum seropedicae SmR1

For nitrogen fixation control L-Malic acid across organisms

SEED Subsystems

Subsystem #Specific
Bacterial Chemotaxis 2
Bacterial hemoglobins 2
ABC transporter branched-chain amino acid (TC 3.A.1.4.1) 1
Cysteine Biosynthesis 1
Deoxyribose and Deoxynucleoside Catabolism 1
Ethanolamine utilization 1
Fermentations: Lactate 1
Fermentations: Mixed acid 1
Flagellar motility 1
Flagellum 1
Heat shock dnaK gene cluster extended 1
Hydantoin metabolism 1
MLST 1
Oxidative stress 1
Oxygen and light sensor PpaA-PpsR 1
Peptidoglycan Biosynthesis 1
Propanediol utilization 1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 1
Ribosome biogenesis bacterial 1
TCA Cycle 1
Threonine anaerobic catabolism gene cluster 1
Transcription factors bacterial 1
YcfH 1
cAMP signaling in bacteria 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
acetate and ATP formation from acetyl-CoA I 2 2 1
sulfoacetaldehyde degradation I 2 1 1
pyruvate fermentation to acetate II 3 3 1
superpathway of acetate utilization and formation 3 3 1
molybdenum cofactor biosynthesis 3 3 1
pyruvate fermentation to acetate IV 3 2 1
pyruvate fermentation to acetate I 3 2 1
pyruvate fermentation to acetate VII 3 2 1
pyruvate fermentation to acetate and (S)-lactate I 4 3 1
pyruvate fermentation to acetate and lactate II 4 2 1
sulfolactate degradation II 4 1 1
superpathway of Clostridium acetobutylicum acidogenic fermentation 9 6 2
ethanolamine utilization 5 4 1
(S)-propane-1,2-diol degradation 5 3 1
acetylene degradation (anaerobic) 5 3 1
L-threonine degradation I 6 5 1
methanogenesis from acetate 6 2 1
superpathway of sulfolactate degradation 6 2 1
superpathway of taurine degradation 6 2 1
pyruvate fermentation to butanoate 7 4 1
acetyl-CoA fermentation to butanoate 7 4 1
partial TCA cycle (obligate autotrophs) 8 7 1
lactate fermentation to acetate, CO2 and hydrogen (Desulfovibrionales) 8 4 1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation 17 8 2
TCA cycle VI (Helicobacter) 9 7 1
TCA cycle VII (acetate-producers) 9 7 1
superpathway of fermentation (Chlamydomonas reinhardtii) 9 4 1
superpathway of L-alanine fermentation (Stickland reaction) 9 4 1
TCA cycle I (prokaryotic) 10 8 1
L-lysine fermentation to acetate and butanoate 10 3 1
gallate degradation III (anaerobic) 11 3 1
superpathway of glyoxylate bypass and TCA 12 10 1
L-glutamate degradation VII (to butanoate) 12 4 1
(S)-lactate fermentation to propanoate, acetate and hydrogen 13 4 1
mixed acid fermentation 16 12 1
heterolactic fermentation 18 14 1
superpathway of L-threonine metabolism 18 13 1
hexitol fermentation to lactate, formate, ethanol and acetate 19 13 1
superpathway of methanogenesis 21 2 1
superpathway of N-acetylneuraminate degradation 22 15 1
purine nucleobases degradation II (anaerobic) 24 15 1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass 26 22 1
superpathway of L-lysine degradation 43 8 1