Experiment set18IT045 for Klebsiella michiganensis M5al

D-Glucose carbon source and no Nitrogen; normal Wolfe's minerals with nitroloacetic acid; 8 days

Group: nitrogen fixation
Media: RCH2_defined_noCarbon_minimalN + D-Glucose (20 mM)
Culturing: Koxy_ML2, serum bottle, Anaerobic, at 30 (C), shaken=0 rpm
Growth: about 1.5 generations
By: Kelly Wetmore; Jordan Baker on 26-Mar-19
Media components: 0.1 g/L Potassium Chloride, 0.49 g/L Sodium phosphate monobasic monohydrate, 0.97 g/L Potassium phosphate dibasic, 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 15 genes in this experiment

For nitrogen fixation D-Glucose in Klebsiella michiganensis M5al

For nitrogen fixation D-Glucose across organisms

SEED Subsystems

Subsystem	#Specific
Nitrogen fixation	8
Ribonucleotide reduction	2
Methionine Degradation	1
Pyruvate:ferredoxin oxidoreductase	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pyruvate metabolism
• Glycolysis / Gluconeogenesis
• Tetrachloroethene degradation
• Butanoate metabolism
• Citrate cycle (TCA cycle)
• Fatty acid metabolism
• Purine metabolism
• Pyrimidine metabolism
• Glycine, serine and threonine metabolism
• Lysine biosynthesis
• Tyrosine metabolism
• 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
• gamma-Hexachlorocyclohexane degradation
• Bisphenol A degradation
• 1- and 2-Methylnaphthalene degradation
• 1,4-Dichlorobenzene degradation
• Trinitrotoluene degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Reductive carboxylate cycle (CO2 fixation)
• Retinol metabolism
• Nitrogen metabolism
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
pyruvate fermentation to ethanol III	3	3	3
ethanol degradation I	2	2	2
pyruvate decarboxylation to acetyl CoA III	1	1	1
nitrogen fixation I (ferredoxin)	1	1	1
acetaldehyde biosynthesis I	1	1	1
pyruvate fermentation to ethanol I	3	3	2
reductive monocarboxylic acid cycle	2	2	1
L-alanine degradation V (oxidative Stickland reaction)	2	2	1
pyruvate fermentation to ethanol II	2	2	1
L-threonine degradation IV	2	2	1
pyruvate fermentation to acetate III	2	1	1
ethanolamine utilization	5	5	2
acetylene degradation (anaerobic)	5	4	2
superpathway of fermentation (Chlamydomonas reinhardtii)	9	9	3
ethanol degradation II	3	3	1
pyruvate fermentation to acetate VII	3	3	1
pyruvate fermentation to acetate I	3	3	1
2-deoxy-D-ribose degradation I	3	3	1
2-hydroxypenta-2,4-dienoate degradation	3	3	1
2-deoxy-α-D-ribose 1-phosphate degradation	3	3	1
pyruvate fermentation to acetate VI	3	2	1
L-methionine degradation III	3	2	1
L-isoleucine degradation II	3	2	1
pyruvate fermentation to acetate and alanine	3	2	1
L-valine degradation II	3	2	1
L-leucine degradation III	3	2	1
FeMo cofactor biosynthesis	6	2	2
2-aminoethylphosphonate degradation I	3	1	1
sulfoacetaldehyde degradation IV	3	1	1
pyrimidine deoxyribonucleotides de novo biosynthesis II	7	7	2
adenosine deoxyribonucleotides de novo biosynthesis II	4	4	1
guanosine deoxyribonucleotides de novo biosynthesis II	4	4	1
pyruvate fermentation to acetate and lactate II	4	4	1
phytol degradation	4	3	1
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
salidroside biosynthesis	4	2	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	7	3
(S)-propane-1,2-diol degradation	5	5	1
catechol degradation I (meta-cleavage pathway)	5	4	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
pyruvate fermentation to acetone	5	3	1
phenylethanol biosynthesis	5	2	1
isopropanol biosynthesis (engineered)	5	2	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	9	3
superpathway of pyrimidine deoxyribonucleosides degradation	6	6	1
triethylamine degradation	6	1	1
noradrenaline and adrenaline degradation	13	4	2
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli)	14	14	2
superpathway of adenosine nucleotides de novo biosynthesis II	7	7	1
superpathway of purine deoxyribonucleosides degradation	7	7	1
3-methylbutanol biosynthesis (engineered)	7	6	1
incomplete reductive TCA cycle	7	5	1
catechol degradation II (meta-cleavage pathway)	7	4	1
toluene degradation V (aerobic) (via toluene-cis-diol)	7	4	1
pyruvate fermentation to butanoate	7	4	1
toluene degradation I (aerobic) (via o-cresol)	7	4	1
serotonin degradation	7	3	1
mixed acid fermentation	16	16	2
superpathway of guanosine nucleotides de novo biosynthesis II	8	8	1
3-phenylpropanoate and 3-(3-hydroxyphenyl)propanoate degradation	8	6	1
lactate fermentation to acetate, CO2 and hydrogen (Desulfovibrionales)	8	5	1
pyruvate fermentation to butanol I	8	4	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
p-cumate degradation	8	3	1
heterolactic fermentation	18	16	2
superpathway of L-alanine fermentation (Stickland reaction)	9	7	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	7	1
reductive glycine pathway of autotrophic CO2 fixation	9	6	1
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	6	1
L-lysine biosynthesis IV	9	2	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	19	2
meta cleavage pathway of aromatic compounds	10	6	1
L-lysine biosynthesis V	10	2	1
FR-900098 and FR-33289 antibiotics biosynthesis	10	1	1
superpathway of N-acetylneuraminate degradation	22	22	2
pyruvate fermentation to hexanol (engineered)	11	8	1
reductive TCA cycle I	11	8	1
p-cymene degradation	11	3	1
L-glutamate degradation VII (to butanoate)	12	7	1
reductive TCA cycle II	12	7	1
naphthalene degradation to acetyl-CoA	12	5	1
L-tryptophan degradation IX	12	4	1
L-tryptophan degradation XII (Geobacillus)	12	4	1
superpathway of purine nucleotides de novo biosynthesis II	26	26	2
toluene degradation IV (aerobic) (via catechol)	13	7	1
L-tryptophan degradation V (side chain pathway)	13	1	1
glycerol degradation to butanol	16	12	1
coenzyme B biosynthesis	16	2	1
superpathway of L-threonine metabolism	18	18	1
mandelate degradation to acetyl-CoA	18	14	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
superpathway of anaerobic sucrose degradation	19	18	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	46	2
purine nucleobases degradation II (anaerobic)	24	17	1
superpathway of aerobic toluene degradation	30	15	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	23	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	17	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	23	1