Experiment set12IT018 for Shewanella oneidensis MR-1

Survival in PBS at 22C, experiment2, 13 day

Group: survival
Media: LB
Culturing: MR1_ML3b, Bioserve FPA, Anaerobic, at 30 (C)
By: Michael Dougherty on 6-Dec-17
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride

Specific Phenotypes

For 15 genes in this experiment

SEED Subsystems

Subsystem	#Specific
Succinate dehydrogenase	2
Bacterial hemoglobins	1
Cobalamin synthesis	1
Coenzyme B12 biosynthesis	1
Hydrogenases	1
Membrane-bound Ni, Fe-hydrogenase	1
Menaquinone and Phylloquinone Biosynthesis	1
NiFe hydrogenase maturation	1
Serine-glyoxylate cycle	1
TCA Cycle	1
Type IV pilus	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Citrate cycle (TCA cycle)
• Ubiquinone and menaquinone biosynthesis
• Oxidative phosphorylation
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Riboflavin metabolism
• Porphyrin and chlorophyll metabolism
• Biosynthesis of phenylpropanoids

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
hydrogen to dimethyl sulfoxide electron transfer	2	2	1
hydrogen to fumarate electron transfer	2	2	1
succinate to cytochrome bd oxidase electron transfer	2	2	1
hydrogen to trimethylamine N-oxide electron transfer	2	1	1
succinate to cytochrome bo oxidase electron transfer	2	1	1
2-methyladeninyl adenosylcobamide biosynthesis from adenosylcobinamide-GDP	3	3	1
5-methoxy-6-methylbenzimidazolyl adenosylcobamide biosynthesis from adenosylcobinamide-GDP	3	3	1
5-hydroxybenzimidazolyl adenosylcobamide biosynthesis from adenosylcobinamide-GDP	3	3	1
benzimidazolyl adenosylcobamide biosynthesis from adenosylcobinamide-GDP	3	3	1
5-methylbenzimidazolyl adenosylcobamide biosynthesis from adenosylcobinamide-GDP	3	3	1
adeninyl adenosylcobamide biosynthesis from adenosylcobinamide-GDP	3	3	1
adenosylcobalamin biosynthesis from adenosylcobinamide-GDP I	3	3	1
5-methoxybenzimidazolyl adenosylcobamide biosynthesis from adenosylcobinamide-GDP	3	3	1
aerobic respiration III (alternative oxidase pathway)	3	2	1
aerobic respiration I (cytochrome c)	4	3	1
aerobic respiration II (cytochrome c) (yeast)	4	3	1
NiFe(CO)(CN)2 cofactor biosynthesis	10	6	2
2-carboxy-1,4-naphthoquinol biosynthesis	7	7	1
superpathway of adenosylcobalamin salvage from cobinamide I	8	8	1
superpathway of demethylmenaquinol-8 biosynthesis I	9	9	1
superpathway of demethylmenaquinol-9 biosynthesis	9	8	1
superpathway of adenosylcobalamin salvage from cobinamide II	9	8	1
superpathway of demethylmenaquinol-6 biosynthesis I	9	8	1
superpathway of menaquinol-8 biosynthesis I	10	10	1
TCA cycle III (animals)	10	9	1
superpathway of menaquinol-13 biosynthesis	10	9	1
superpathway of menaquinol-10 biosynthesis	10	9	1
superpathway of menaquinol-11 biosynthesis	10	9	1
superpathway of menaquinol-12 biosynthesis	10	9	1
superpathway of menaquinol-6 biosynthesis	10	9	1
superpathway of menaquinol-7 biosynthesis	10	9	1
superpathway of menaquinol-9 biosynthesis	10	9	1
superpathway of phylloquinol biosynthesis	15	8	1
adenosylcobalamin biosynthesis II (aerobic)	33	19	1
adenosylcobalamin biosynthesis I (anaerobic)	36	18	1
superpathway of chorismate metabolism	59	50	1