Experiment set2IT042 for Rhodospirillum rubrum S1H

carbon source anaerobic Succinic Acid 31.25 mM

Group: carbon source
Media: MELiSSA_defined_50mMCarbonate_noCarbon + Succinic Acid (31.25 mM)
Culturing: Rubrum_ML4a, flask, Anaerobic, at 28 (C), shaken=215 rpm
Growth: about 5.1 generations
By: Baptiste on 1-Jun-18_c
Media components: 0.051 mM Manganese (II) chloride tetrahydrate, 0.0811 mM Magnesium Sulfate Heptahydrate, 3.801 mM Sodium sulfate, 35.33 mM Ammonium chloride, 0.34 mM Calcium chloride dihydrate, 0.068 mM EDTA, 3.601 mM Potassium phosphate monobasic, 0.072 mM Iron (II) sulfate heptahydrate, 50 mM Sodium bicarbonate, 100.4 mM 3-(N-morpholino)propanesulfonic acid, 2.985 mM Potassium phosphate dibasic, 1.902 uM Nickel (II) sulfate hexahydrate, 0.348 uM Zinc sulfate heptahydrate, 0.02 uM Copper (II) sulfate pentahydrate, 1.623 uM Boric Acid, 0.207 uM Sodium Molybdate Dihydrate, 0.06 uM biotin

Specific Phenotypes

For 45 genes in this experiment

For carbon source Succinic Acid in Rhodospirillum rubrum S1H

For carbon source Succinic Acid across organisms

SEED Subsystems

Subsystem	#Specific
Bacterial Chemotaxis	3
D-ribose utilization	3
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	2
Polyamine Metabolism	2
ABC transporter dipeptide (TC 3.A.1.5.2)	1
Butanol Biosynthesis	1
Carotenoids	1
Coenzyme B12 biosynthesis	1
DNA-replication	1
Deoxyribose and Deoxynucleoside Catabolism	1
Dihydroxyacetone kinases	1
Fermentations: Mixed acid	1
Flagellar motility	1
Flagellum	1
Flagellum in Campylobacter	1
Histidine Degradation	1
Ketoisovalerate oxidoreductase	1
Methionine Biosynthesis	1
Orphan regulatory proteins	1
Phosphate metabolism	1
Polyhydroxybutyrate metabolism	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Queuosine-Archaeosine Biosynthesis	1
Ton and Tol transport systems	1
Transcription factors bacterial	1
Two-component regulatory systems in Campylobacter	1
cAMP signaling in bacteria	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Biosynthesis of plant hormones
• Pentose phosphate pathway
• Lipopolysaccharide biosynthesis
• Pyruvate metabolism
• Naphthalene and anthracene degradation
• Propanoate metabolism
• Butanoate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Nicotinate and nicotinamide metabolism
• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Glutamate metabolism
• Methionine metabolism
• Cysteine metabolism
• Geraniol degradation
• Lysine biosynthesis
• Arginine and proline metabolism
• Histidine metabolism
• Tyrosine metabolism
• 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
• Benzoate degradation via hydroxylation
• Tryptophan metabolism
• Selenoamino acid metabolism
• Glycerolipid metabolism
• 1- and 2-Methylnaphthalene degradation
• Folate biosynthesis
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Sulfur metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
long-chain fatty acid activation	1	1	1
acetate conversion to acetyl-CoA	1	1	1
acetate and ATP formation from acetyl-CoA III	1	1	1
polyphosphate metabolism	2	2	1
reductive monocarboxylic acid cycle	2	2	1
glycerol degradation II	2	1	1
ribose phosphorylation	2	1	1
4-aminobutanoate degradation III	2	1	1
γ-linolenate biosynthesis II (animals)	2	1	1
linoleate biosynthesis II (animals)	2	1	1
superpathway of acetate utilization and formation	3	3	1
ethanol degradation II	3	3	1
pyruvate fermentation to acetate IV	3	3	1
ethanol degradation IV	3	3	1
pyruvate fermentation to ethanol I	3	2	1
2-deoxy-D-ribose degradation I	3	2	1
ethanol degradation III	3	2	1
L-isoleucine biosynthesis V	3	2	1
3-methyl-branched fatty acid α-oxidation	6	3	2
alkane biosynthesis II	3	1	1
oleate biosynthesis I (plants)	3	1	1
phytol degradation	4	3	1
queuosine biosynthesis I (de novo)	4	2	1
wax esters biosynthesis II	4	1	1
long chain fatty acid ester synthesis (engineered)	4	1	1
superpathway of glycerol degradation to 1,3-propanediol	4	1	1
chitin deacetylation	4	1	1
phosphatidylcholine acyl editing	4	1	1
sporopollenin precursors biosynthesis	18	4	4
L-histidine degradation II	5	5	1
2-methylcitrate cycle I	5	5	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
queuosine biosynthesis III (queuosine salvage)	5	2	1
octane oxidation	5	2	1
L-lysine degradation IV	5	2	1
L-threonine degradation I	6	6	1
ppGpp metabolism	6	6	1
stearate biosynthesis II (bacteria and plants)	6	5	1
fatty acid salvage	6	5	1
L-isoleucine biosynthesis IV	6	4	1
hydrogen sulfide biosynthesis II (mammalian)	6	4	1
2-methylcitrate cycle II	6	4	1
stearate biosynthesis IV	6	4	1
L-lysine degradation X	6	4	1
β-alanine biosynthesis II	6	4	1
okenone biosynthesis	6	2	1
6-gingerol analog biosynthesis (engineered)	6	2	1
superpathway of bitter acids biosynthesis	18	3	3
stearate biosynthesis I (animals)	6	1	1
colupulone and cohumulone biosynthesis	6	1	1
L-lysine degradation III	6	1	1
adlupulone and adhumulone biosynthesis	6	1	1
lupulone and humulone biosynthesis	6	1	1
incomplete reductive TCA cycle	7	6	1
L-lysine degradation I	7	3	1
ceramide degradation by α-oxidation	7	2	1
capsaicin biosynthesis	7	1	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
TCA cycle V (2-oxoglutarate synthase)	9	9	1
TCA cycle VII (acetate-producers)	9	8	1
TCA cycle VI (Helicobacter)	9	7	1
reductive glycine pathway of autotrophic CO2 fixation	9	6	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	6	1
cis-geranyl-CoA degradation	9	2	1
superpathway of coenzyme A biosynthesis II (plants)	10	8	1
peptidoglycan recycling II	10	2	1
suberin monomers biosynthesis	20	2	2
superpathway of fatty acid biosynthesis II (plant)	43	38	4
reductive TCA cycle I	11	9	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	11	1
reductive TCA cycle II	12	8	1
cob(II)yrinate a,c-diamide biosynthesis II (late cobalt incorporation)	13	12	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	10	1
peptidoglycan recycling I	14	7	1
palmitate biosynthesis II (type II fatty acid synthase)	31	29	2
glycerol degradation to butanol	16	12	1
mixed acid fermentation	16	11	1
cutin biosynthesis	16	1	1
superpathway of L-threonine metabolism	18	13	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
superpathway of N-acetylneuraminate degradation	22	13	1
superpathway of fatty acids biosynthesis (E. coli)	53	48	2
palmitate biosynthesis III	29	21	1
adenosylcobalamin biosynthesis II (aerobic)	33	29	1
oleate β-oxidation	35	29	1
superpathway of L-lysine degradation	43	12	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1