Experiment set4IT021 for Rhodanobacter denitrificans FW104-10B01

R2A with lithium chloride 15.625 mM

Group: stress
Media: R2A + Lithium chloride (15.625 mM)
Culturing: rhodanobacter_10B01_ML12, 96 deep-well microplate; 0.8 mL volume, Aerobic, at 30 (C), shaken=700 rpm
By: Hans Carlson and Trenton Owens on 06/22/2021
Media components: 0.5 g/L Bacto Peptone, 0.5 g/L casamino acids, 0.5 g/L Yeast Extract, 0.5 g/L D-Glucose, 0.5 g/L Starch, 0.3 g/L Potassium phosphate dibasic, 0.05 g/L Magnesium Sulfate Heptahydrate, 0.3 g/L Sodium pyruvate
Growth plate: 3 G7

Specific Phenotypes

For 12 genes in this experiment

For stress Lithium chloride in Rhodanobacter denitrificans FW104-10B01

For stress Lithium chloride across organisms

SEED Subsystems

Subsystem	#Specific
Ethanolamine utilization	2
Fermentations: Lactate	2
Fermentations: Mixed acid	2
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	2
Threonine anaerobic catabolism gene cluster	2
DNA Repair Base Excision	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
MLST	1
Propanediol utilization	1
Protein chaperones	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pyruvate metabolism
• Taurine and hypotaurine metabolism
• Propanoate metabolism
• Carbon fixation in photosynthetic organisms
• Pentose phosphate pathway
• Methane metabolism
• Reductive carboxylate cycle (CO2 fixation)

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetate and ATP formation from acetyl-CoA I	2	2	2
pyruvate fermentation to acetate II	3	3	2
superpathway of acetate utilization and formation	3	3	2
pyruvate fermentation to acetate I	3	2	2
pyruvate fermentation to acetate VII	3	2	2
pyruvate fermentation to acetate IV	3	2	2
pyruvate fermentation to acetate and (S)-lactate I	4	3	2
pyruvate fermentation to acetate and lactate II	4	2	2
sulfoacetaldehyde degradation I	2	1	1
glycine degradation (reductive Stickland reaction)	2	1	1
(S)-propane-1,2-diol degradation	5	3	2
acetylene degradation (anaerobic)	5	3	2
ethanolamine utilization	5	3	2
L-threonine degradation I	6	5	2
methanogenesis from acetate	6	2	2
acetyl-CoA fermentation to butanoate	7	5	2
lactate fermentation to acetate, CO2 and hydrogen (Desulfovibrionales)	8	2	2
sulfolactate degradation II	4	1	1
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	5	2
superpathway of fermentation (Chlamydomonas reinhardtii)	9	5	2
superpathway of L-alanine fermentation (Stickland reaction)	9	4	2
Bifidobacterium shunt	15	14	3
L-lysine fermentation to acetate and butanoate	10	3	2
gallate degradation III (anaerobic)	11	3	2
superpathway of sulfolactate degradation	6	2	1
superpathway of taurine degradation	6	1	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	3
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	5	2
superpathway of N-acetylneuraminate degradation	22	16	3
mixed acid fermentation	16	12	2
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	6	2
heterolactic fermentation	18	15	2
superpathway of L-threonine metabolism	18	13	2
reductive glycine pathway of autotrophic CO2 fixation	9	5	1
glycolysis V (Pyrococcus)	10	7	1
superpathway of methanogenesis	21	2	2
glycolysis II (from fructose 6-phosphate)	11	11	1
purine nucleobases degradation II (anaerobic)	24	9	2
glycolysis I (from glucose 6-phosphate)	13	12	1
gluconeogenesis I	13	11	1
purine nucleobases degradation I (anaerobic)	15	3	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	16	1
superpathway of hexitol degradation (bacteria)	18	14	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	8	1
superpathway of anaerobic sucrose degradation	19	16	1
superpathway of L-lysine degradation	43	7	2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	23	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	25	1