Experiment set2IT060 for Herbaspirillum seropedicae SmR1

D-Mannose carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + D-Mannose (20 mM), pH=7
Culturing: HerbieS_ML4, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 2.4 generations
By: Mark on 3/10/2016
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: CARBON4 C4

Specific Phenotypes

For 6 genes in this experiment

For carbon source D-Mannose in Herbaspirillum seropedicae SmR1

For carbon source D-Mannose across organisms

SEED Subsystems

Subsystem	#Specific
D-ribose utilization	2
Coenzyme A Biosynthesis	1
Mannose Metabolism	1
Terminal cytochrome C oxidases	1
Xylose utilization	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pantothenate and CoA biosynthesis
• Pentose and glucuronate interconversions
• Fructose and mannose metabolism
• Oxidative phosphorylation
• Valine, leucine and isoleucine biosynthesis
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
arsenite to oxygen electron transfer	2	1	1
phosphopantothenate biosynthesis II	3	1	1
arsenite to oxygen electron transfer (via azurin)	3	1	1
phosphopantothenate biosynthesis I	4	4	1
L-valine biosynthesis	4	4	1
aerobic respiration I (cytochrome c)	4	3	1
aerobic respiration II (cytochrome c) (yeast)	4	2	1
D-xylose degradation to ethylene glycol (engineered)	4	1	1
superpathway of coenzyme A biosynthesis III (mammals)	5	5	1
D-xylose degradation V	5	4	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
D-xylose degradation VI	5	3	1
D-xylose degradation III	5	3	1
L-isoleucine biosynthesis IV	6	4	1
Fe(II) oxidation	6	3	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
L-isoleucine biosynthesis III	7	4	1
D-xylose degradation IV	7	3	1
L-isoleucine biosynthesis II	8	6	1
superpathway of branched chain amino acid biosynthesis	17	17	2
superpathway of coenzyme A biosynthesis I (bacteria)	9	9	1
superpathway of coenzyme A biosynthesis II (plants)	10	8	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of L-threonine metabolism	18	13	1
superpathway of pentose and pentitol degradation	42	19	1