Experiment set1IT046 for Pseudomonas sp. S08-1

Sodium octanoate carbon source

Group: carbon source
Media: MME_noNitrogen_noCarbon + Sodium octanoate (7.5 mM) + Ammonium chloride (10 mM)
Culturing: Pseudomonas_S08_1_ML2, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=1200 rpm
By: Joshua Elmore on 8-June-22
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium Chloride, 0.41 mM Magnesium Sulfate Heptahydrate, 0.07 mM Calcium chloride dihydrate, MME Trace Minerals (0.5 mg/L EDTA tetrasodium tetrahydrate salt, 2 mg/L Ferric chloride, 0.05 mg/L Boric Acid, 0.05 mg/L Zinc chloride, 0.03 mg/L copper (II) chloride dihydrate, 0.05 mg/L Manganese (II) chloride tetrahydrate, 0.05 mg/L Diammonium molybdate, 0.05 mg/L Cobalt chloride hexahydrate, 0.05 mg/L Nickel (II) chloride hexahydrate)

Specific Phenotypes

For 57 genes in this experiment

For carbon source Sodium octanoate in Pseudomonas sp. S08-1

For carbon source Sodium octanoate across organisms

SEED Subsystems

Subsystem	#Specific
Flagellum	9
Flagellar motility	3
Multidrug Resistance Efflux Pumps	3
Rhamnose containing glycans	3
dTDP-rhamnose synthesis	3
linker unit-arabinogalactan synthesis	3
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon)	2
ABC transporter alkylphosphonate (TC 3.A.1.9.1)	1
ATP-dependent RNA helicases, bacterial	1
Alginate metabolism	1
Bacterial Chemotaxis	1
Bacterial Cytoskeleton	1
Capsular heptose biosynthesis	1
Fatty Acid Biosynthesis FASII	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Lacto-N-Biose I and Galacto-N-Biose Metabolic Pathway	1
Lactose and Galactose Uptake and Utilization	1
Mannose Metabolism	1
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	1
N-linked Glycosylation in Bacteria	1
Ton and Tol transport systems	1
Transcription initiation, bacterial sigma factors	1
Two-component regulatory systems in Campylobacter	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:

• Nucleotide sugars metabolism
• Galactose metabolism
• Starch and sucrose metabolism
• Streptomycin biosynthesis
• Polyketide sugar unit biosynthesis
• Pentose and glucuronate interconversions
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Tryptophan metabolism
• Glutathione metabolism
• Glycosaminoglycan degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of siderophore group nonribosomal peptides
• Biosynthesis of vancomycin group antibiotics

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
UDP-α-D-galactose biosynthesis	1	1	1
S-methyl-5'-thioadenosine degradation II	1	1	1
UDP-N-acetyl-D-galactosamine biosynthesis I	1	1	1
adenine and adenosine salvage III	4	4	3
adenine and adenosine salvage V	3	2	2
dTDP-4-O-demethyl-β-L-noviose biosynthesis	5	4	3
UDP-α-D-glucose biosynthesis	2	2	1
adenine and adenosine salvage I	2	2	1
purine ribonucleosides degradation	6	5	3
UDP-α-D-galactofuranose biosynthesis	2	1	1
dTDP-β-L-rhamnose biosynthesis	5	5	2
adenosine nucleotides degradation II	5	3	2
CDP-4-dehydro-3,6-dideoxy-D-glucose biosynthesis	3	3	1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	4	2
dTDP-sibirosamine biosynthesis	6	3	2
dTDP-L-daunosamine biosynthesis	6	3	2
D-galactose detoxification	3	1	1
L-rhamnose degradation III	7	3	2
stachyose degradation	7	2	2
octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)	12	12	3
gondoate biosynthesis (anaerobic)	4	4	1
dTDP-N-acetylthomosamine biosynthesis	4	2	1
dTDP-β-D-fucofuranose biosynthesis	4	2	1
dTDP-6-deoxy-α-D-allose biosynthesis	4	2	1
dTDP-N-acetylviosamine biosynthesis	4	2	1
L-rhamnose degradation II	8	3	2
palmitate biosynthesis III	29	28	7
tetradecanoate biosynthesis (mitochondria)	25	23	6
palmitate biosynthesis II (type II fatty acid synthase)	31	29	7
palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate)	9	9	2
oleate biosynthesis IV (anaerobic)	14	13	3
superpathway of fatty acids biosynthesis (E. coli)	53	51	11
superpathway of unsaturated fatty acids biosynthesis (E. coli)	20	20	4
fatty acid elongation -- saturated	5	5	1
cis-vaccenate biosynthesis	5	5	1
peptidoglycan recycling II	10	8	2
8-amino-7-oxononanoate biosynthesis IV	5	4	1
sucrose degradation II (sucrose synthase)	5	4	1
CDP-6-deoxy-D-gulose biosynthesis	5	3	1
dTDP-α-D-mycaminose biosynthesis	5	2	1
dTDP-3-acetamido-3,6-dideoxy-α-D-glucose biosynthesis	5	2	1
dTDP-3-acetamido-α-D-fucose biosynthesis	5	2	1
D-galactose degradation I (Leloir pathway)	5	2	1
superpathway of fatty acid biosynthesis II (plant)	43	38	8
O-antigen building blocks biosynthesis (E. coli)	11	10	2
colanic acid building blocks biosynthesis	11	9	2
8-amino-7-oxononanoate biosynthesis I	11	9	2
purine nucleotides degradation II (aerobic)	11	8	2
anteiso-branched-chain fatty acid biosynthesis	34	30	6
odd iso-branched-chain fatty acid biosynthesis	34	30	6
even iso-branched-chain fatty acid biosynthesis	34	30	6
(5Z)-dodecenoate biosynthesis I	6	6	1
stearate biosynthesis II (bacteria and plants)	6	5	1
(5Z)-dodecenoate biosynthesis II	6	5	1
stearate biosynthesis IV	6	4	1
dTDP-α-D-ravidosamine and dTDP-4-acetyl-α-D-ravidosamine biosynthesis	6	2	1
petroselinate biosynthesis	6	2	1
dTDP-D-desosamine biosynthesis	6	2	1
superpathway of novobiocin biosynthesis	19	5	3
streptorubin B biosynthesis	34	20	5
peptidoglycan recycling I	14	10	2
UDP-N-acetyl-D-galactosamine biosynthesis II	7	4	1
dTDP-β-L-olivose biosynthesis	7	3	1
dTDP-β-L-digitoxose biosynthesis	7	3	1
dTDP-β-L-mycarose biosynthesis	7	2	1
biotin biosynthesis I	15	13	2
superpathway of fatty acid biosynthesis I (E. coli)	16	15	2
sucrose biosynthesis II	8	6	1
dTDP-β-L-megosamine biosynthesis	8	3	1
superpathway of CDP-glucose-derived O-antigen building blocks biosynthesis	8	3	1
dTDP-β-L-4-epi-vancosamine biosynthesis	8	3	1
2-allylmalonyl-CoA biosynthesis	8	2	1
sucrose biosynthesis I (from photosynthesis)	9	7	1
UDP-sugars interconversion	9	3	1
dTDP-α-D-forosamine biosynthesis	9	3	1
dTDP-α-D-olivose, dTDP-α-D-oliose and dTDP-α-D-mycarose biosynthesis	9	3	1
teichuronic acid biosynthesis (B. subtilis 168)	9	2	1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis	19	5	2
superpathway of enterobacterial common antigen biosynthesis	10	4	1
nucleoside and nucleotide degradation (archaea)	10	2	1
L-methionine salvage cycle III	11	10	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	12	3
superpathway of purine nucleotide salvage	14	13	1
type I lipoteichoic acid biosynthesis (S. aureus)	17	5	1
streptomycin biosynthesis	18	2	1
mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	18	1	1
superpathway of anaerobic sucrose degradation	19	14	1
superpathway of erythromycin biosynthesis	19	2	1
superpathway of megalomicin A biosynthesis	22	3	1
superpathway of dTDP-glucose-derived antibiotic building blocks biosynthesis	23	3	1
mycolate biosynthesis	205	20	5
superpathway of mycolate biosynthesis	239	21	5