Experiment set6IT091 for Herbaspirillum seropedicae SmR1

Carbon source Deoxyribonucleic acid from herring sperm 5 mg/mL

Group: carbon source
Media: RCH2_defined_noCarbon + Deoxyribonucleic acid from herring sperm (5 mg/mL), pH=7
Culturing: HerbieS_ML4a, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Adam on 5/2/18
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)
Growth plate: HerbieS_plate C4

Specific Phenotypes

For 3 genes in this experiment

For carbon source Deoxyribonucleic acid from herring sperm in Herbaspirillum seropedicae SmR1

For carbon source Deoxyribonucleic acid from herring sperm across organisms

SEED Subsystems

Subsystem	#Specific
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	2
Ammonia assimilation	1
Entner-Doudoroff Pathway	1
Fermentations: Mixed acid	1
Methylglyoxal Metabolism	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycolysis / Gluconeogenesis
• Fatty acid metabolism
• 3-Chloroacrylic acid degradation
• Ascorbate and aldarate metabolism
• Urea cycle and metabolism of amino groups
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Arginine and proline metabolism
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Glycerolipid metabolism
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• Butanoate metabolism
• Retinol metabolism
• Limonene and pinene degradation
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetaldehyde biosynthesis I	1	1	1
ethanol degradation II	3	3	2
phytol degradation	4	3	2
putrescine degradation V	2	1	1
pyruvate fermentation to ethanol II	2	1	1
ethanol degradation I	2	1	1
putrescine degradation I	2	1	1
ethylene glycol degradation	2	1	1
ethanol degradation IV	3	3	1
L-valine degradation II	3	2	1
ethanol degradation III	3	2	1
L-leucine degradation III	3	2	1
L-isoleucine degradation II	3	2	1
hypotaurine degradation	3	2	1
putrescine degradation IV	3	2	1
pyruvate fermentation to ethanol III	3	1	1
L-methionine degradation III	3	1	1
histamine degradation	3	1	1
pyruvate fermentation to ethanol I	3	1	1
noradrenaline and adrenaline degradation	13	4	4
serotonin degradation	7	3	2
salidroside biosynthesis	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation III	4	2	1
D-arabinose degradation II	4	1	1
cytidine-5'-diphosphate-glycerol biosynthesis	4	1	1
putrescine degradation III	4	1	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	1	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
ethanolamine utilization	5	4	1
acetylene degradation (anaerobic)	5	3	1
octane oxidation	5	3	1
mitochondrial NADPH production (yeast)	5	3	1
(S)-propane-1,2-diol degradation	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
phenylethanol biosynthesis	5	2	1
dopamine degradation	5	1	1
3-methyl-branched fatty acid α-oxidation	6	3	1
alkane oxidation	6	1	1
3-methylbutanol biosynthesis (engineered)	7	6	1
superpathway of glycol metabolism and degradation	7	5	1
ceramide degradation by α-oxidation	7	2	1
limonene degradation IV (anaerobic)	7	1	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	6	1
aromatic biogenic amine degradation (bacteria)	8	3	1
superpathway of ornithine degradation	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
butanol and isobutanol biosynthesis (engineered)	8	2	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	6	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	4	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	4	1
superpathway of L-arginine and L-ornithine degradation	13	6	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	5	1
L-tryptophan degradation V (side chain pathway)	13	1	1
mixed acid fermentation	16	12	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	8	1
heterolactic fermentation	18	14	1
superpathway of anaerobic sucrose degradation	19	15	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	13	1
superpathway of N-acetylneuraminate degradation	22	15	1
superpathway of pentose and pentitol degradation	42	19	1