Experiment set3S350 for Phocaeicola dorei CL03T12C01

polygalacturonic acid; autoclaved 2.5 mg/ml carbon source

Group: carbon source
Media: Varel_Bryant_medium + polygalacturonic acid; autoclaved (2.5 mg/ml)
Culturing: Bdorei_CL03T12C01_ML9, 96 deep-well microplate; 1.2 mL volume, Anaerobic, at 37 (C), shaken=0 rpm
By: Surya Tripathi on 3/20/24
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 14 genes in this experiment

For carbon source polygalacturonic acid; autoclaved in Phocaeicola dorei CL03T12C01

For carbon source polygalacturonic acid; autoclaved across organisms

SEED Subsystems

Subsystem	#Specific
Fatty Acid Biosynthesis FASII	1
KDO2-Lipid A biosynthesis	1
Menaquinone and Phylloquinone Biosynthesis	1
Restriction-Modification System	1
Universal GTPases	1
mycolic acid synthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Biosynthesis of unsaturated fatty acids

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
gondoate biosynthesis (anaerobic)	4	4	1
octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)	12	9	3
palmitate biosynthesis III	29	21	7
tetradecanoate biosynthesis (mitochondria)	25	17	6
palmitate biosynthesis II (type II fatty acid synthase)	31	29	7
palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate)	9	8	2
oleate biosynthesis IV (anaerobic)	14	13	3
superpathway of fatty acids biosynthesis (E. coli)	53	47	11
fatty acid elongation -- saturated	5	5	1
superpathway of unsaturated fatty acids biosynthesis (E. coli)	20	17	4
8-amino-7-oxononanoate biosynthesis IV	5	4	1
cis-vaccenate biosynthesis	5	4	1
superpathway of fatty acid biosynthesis II (plant)	43	37	8
8-amino-7-oxononanoate biosynthesis I	11	9	2
anteiso-branched-chain fatty acid biosynthesis	34	25	6
odd iso-branched-chain fatty acid biosynthesis	34	25	6
even iso-branched-chain fatty acid biosynthesis	34	25	6
stearate biosynthesis II (bacteria and plants)	6	5	1
(5Z)-dodecenoate biosynthesis I	6	5	1
stearate biosynthesis IV	6	4	1
(5Z)-dodecenoate biosynthesis II	6	4	1
petroselinate biosynthesis	6	2	1
streptorubin B biosynthesis	34	20	5
2-carboxy-1,4-naphthoquinol biosynthesis	7	5	1
biotin biosynthesis I	15	13	2
superpathway of fatty acid biosynthesis I (E. coli)	16	14	2
2-allylmalonyl-CoA biosynthesis	8	2	1
superpathway of demethylmenaquinol-8 biosynthesis I	9	7	1
superpathway of demethylmenaquinol-9 biosynthesis	9	6	1
superpathway of demethylmenaquinol-6 biosynthesis I	9	6	1
superpathway of menaquinol-8 biosynthesis I	10	8	1
superpathway of menaquinol-6 biosynthesis	10	7	1
superpathway of menaquinol-11 biosynthesis	10	7	1
superpathway of menaquinol-10 biosynthesis	10	7	1
superpathway of menaquinol-12 biosynthesis	10	7	1
superpathway of menaquinol-7 biosynthesis	10	7	1
superpathway of menaquinol-13 biosynthesis	10	7	1
superpathway of menaquinol-9 biosynthesis	10	7	1
superpathway of phylloquinol biosynthesis	15	6	1
mycolate biosynthesis	205	23	5
superpathway of mycolate biosynthesis	239	24	5
superpathway of chorismate metabolism	59	38	1