Experiment set2IT004 for Bacteroides thetaiotaomicron VPI-5482

D-Arabinose carbon source

Group: carbon source
Media: Varel_Bryant_medium + D-Arabinose (20 mM)
Culturing: Btheta_ML6, 24-well transparent microplate, Anaerobic, at 37 (C), shaken=0 rpm
By: Hualan on 8-May-17
Media components: 15 uM Hemin, 134 uM L-Methionine, 15 uM Iron (II) sulfate heptahydrate, 8.25 mM L-Cysteine, 23.8 mM Sodium bicarbonate, Mineral 3B solution (6.6 mM Potassium phosphate monobasic, 15.4 mM Sodium Chloride, 98 uM Magnesium chloride hexahydrate, 176.5 uM Calcium chloride dihydrate, 4.2 uM Cobalt chloride hexahydrate, 50.5 uM Manganese (II) chloride tetrahydrate, 9.3 mM Ammonium chloride, 1.75 mM Sodium sulfate)

Specific Phenotypes

For 6 genes in this experiment

For carbon source D-Arabinose in Bacteroides thetaiotaomicron VPI-5482

For carbon source D-Arabinose across organisms

SEED Subsystems

Subsystem	#Specific
L-fucose utilization	4
De Novo Purine Biosynthesis	1
L-fucose utilization temp	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:

• Fructose and mannose metabolism
• Pentose and glucuronate interconversions
• Purine metabolism
• Glutamate metabolism
• Pyruvate metabolism
• Carbon fixation in photosynthetic organisms
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
D-arabinose degradation I	2	2	2
L-fucose degradation I	4	4	3
D-arabinose degradation II	4	3	3
ribitol degradation I	2	1	1
D-arabinose degradation V	3	1	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	2
superpathway of fucose and rhamnose degradation	12	10	3
5-aminoimidazole ribonucleotide biosynthesis II	5	5	1
5-aminoimidazole ribonucleotide biosynthesis I	5	5	1
lactate biosynthesis (archaea)	5	2	1
superpathway of 5-aminoimidazole ribonucleotide biosynthesis	6	6	1
nucleoside and nucleotide degradation (halobacteria)	6	3	1
methylgallate degradation	6	2	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	7	2
protocatechuate degradation I (meta-cleavage pathway)	8	3	1
superpathway of vanillin and vanillate degradation	10	3	1
superpathway of pentose and pentitol degradation	42	12	4
syringate degradation	12	3	1
gluconeogenesis I	13	11	1
superpathway of purine nucleotides de novo biosynthesis I	21	21	1
superpathway of purine nucleotides de novo biosynthesis II	26	23	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	42	1