Experiment set1IT004 for Sinorhizobium meliloti 1021

L-Arabinose carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + L-Arabinose (20 mM), pH=7
Culturing: Smeli_ML6, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 4.4 generations
By: Mark on 6/2/2015
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: Smeli_carbon_plate1 A4

Specific Phenotypes

For 10 genes in this experiment

For carbon source L-Arabinose in Sinorhizobium meliloti 1021

For carbon source L-Arabinose across organisms

SEED Subsystems

Subsystem	#Specific
L-Arabinose utilization	2
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Methylglyoxal Metabolism	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Ascorbate and aldarate metabolism
• Galactose metabolism
• Glutamate metabolism
• Valine, leucine and isoleucine biosynthesis
• Arginine and proline metabolism
• Pyruvate metabolism
• Pantothenate and CoA biosynthesis
• Nitrogen metabolism
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamine biosynthesis I	1	1	1
L-arabinose degradation III	6	5	4
L-lyxonate degradation	3	2	2
D-galactose degradation II	2	2	1
ammonia assimilation cycle I	2	2	1
L-lactaldehyde degradation (aerobic)	2	1	1
ammonia assimilation cycle II	2	1	1
ammonia assimilation cycle III	3	3	1
methylglyoxal degradation V	3	3	1
D-glucarate degradation II	3	3	1
L-arabinose degradation V	6	4	2
methylglyoxal degradation IV	3	2	1
superpathway of ammonia assimilation (plants)	3	2	1
D-galactarate degradation II	3	2	1
L-aspartate degradation II (aerobic)	3	1	1
L-aspartate degradation III (anaerobic)	3	1	1
L-valine biosynthesis	4	4	1
trans-4-hydroxy-L-proline degradation II	4	3	1
L-arabinose degradation IV	8	5	2
pyruvate fermentation to isobutanol (engineered)	5	4	1
D-glucuronate degradation II	5	4	1
D-galacturonate degradation II	5	3	1
lactate biosynthesis (archaea)	5	3	1
D-xylose degradation III	5	2	1
D-xylose degradation V	5	2	1
L-isoleucine biosynthesis IV	6	4	1
D-arabinose degradation III	6	3	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
L-glutamate and L-glutamine biosynthesis	7	5	1
L-isoleucine biosynthesis III	7	4	1
superpathway of methylglyoxal degradation	8	6	1
L-isoleucine biosynthesis II	8	5	1
L-rhamnose degradation II	8	3	1
superpathway of pentose and pentitol degradation	42	21	5
superpathway of branched chain amino acid biosynthesis	17	17	2
L-arginine biosynthesis II (acetyl cycle)	10	10	1
superpathway of fucose and rhamnose degradation	12	8	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of L-threonine metabolism	18	14	1
superpathway of microbial D-galacturonate and D-glucuronate degradation	31	19	1