Experiment set6IT069 for Escherichia coli BW25113

outer cut, LB soft agar motility assay

Group: motility
Media: LB + Agar (3 g/L)
Culturing: Keio_ML9, Agar plate, Aerobic, at 30 (C), shaken=0 rpm, (Solid)
By: Mark on 2/2/2015
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride

Specific Phenotypes

For 44 genes in this experiment

For motility Agar in Escherichia coli BW25113

For motility Agar across organisms

SEED Subsystems

Subsystem	#Specific
Flagellum	15
Flagellar motility	6
Bacterial Chemotaxis	3
Maltose and Maltodextrin Utilization	2
Serine-glyoxylate cycle	2
Succinate dehydrogenase	2
TCA Cycle	2
Capsular heptose biosynthesis	1
Coenzyme B12 biosynthesis	1
DNA repair, bacterial	1
Folate Biosynthesis	1
Glycine Biosynthesis	1
Glycine and Serine Utilization	1
Hexose Phosphate Uptake System	1
LOS core oligosaccharide biosynthesis	1
Listeria phi-A118-like prophages	1
Molybdenum cofactor biosynthesis	1
Selenocysteine metabolism	1
Trehalose Uptake and Utilization	1
Two-component regulatory systems in Campylobacter	1
Universal stress protein family	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Oxidative phosphorylation
• Citrate cycle (TCA cycle)
• Pentose and glucuronate interconversions
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Photosynthesis
• Pyrimidine metabolism
• Glycine, serine and threonine metabolism
• Selenoamino acid metabolism
• Nucleotide sugars metabolism
• Glycosaminoglycan degradation
• Inositol phosphate metabolism
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Aminoacyl-tRNA biosynthesis
• Drug metabolism - other enzymes
• Biosynthesis of ansamycins
• Biosynthesis of phenylpropanoids

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
succinate to cytochrome bd oxidase electron transfer	2	2	1
L-threonine degradation II	2	2	1
glycerol-3-phosphate to fumarate electron transfer	2	2	1
NADH to fumarate electron transfer	2	2	1
succinate to cytochrome aa3 oxidase electron transfer	2	1	1
hydrogen to fumarate electron transfer	2	1	1
succinate to cytochrome bo oxidase electron transfer	2	1	1
pyrimidine deoxyribonucleosides salvage	5	4	2
L-selenocysteine biosynthesis I (bacteria)	3	3	1
L-aspartate degradation III (anaerobic)	3	3	1
L-aspartate degradation II (aerobic)	3	3	1
aerobic respiration III (alternative oxidase pathway)	3	2	1
aerobic respiration II (cytochrome c) (yeast)	4	2	1
aerobic respiration I (cytochrome c)	4	2	1
GDP-D-glycero-α-D-manno-heptose biosynthesis	4	1	1
superpathway of pyrimidine deoxyribonucleoside salvage	9	8	2
ADP-L-glycero-β-D-manno-heptose biosynthesis	5	5	1
molybdopterin biosynthesis	6	6	1
pyruvate fermentation to propanoate I	7	5	1
incomplete reductive TCA cycle	7	5	1
TCA cycle VI (Helicobacter)	9	7	1
TCA cycle III (animals)	10	8	1
reductive TCA cycle I	11	8	1
L-glutamate degradation VIII (to propanoate)	11	5	1
reductive TCA cycle II	12	8	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	10	1
mixed acid fermentation	16	16	1
superpathway of L-threonine metabolism	18	16	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	22	1