Experiment set6S757 for Mycobacterium tuberculosis H37Rv

pH 4.5

Group: pH
Media: 7H9, pH=4.5
Culturing: MycoTube_ML10, tube, Aerobic, at 37 (C)
By: Kayla Dinshaw on 3/9/25
Media components: 0.5 g/L Ammonium Sulfate, 0.5 g/L L-Glutamic acid, 0.1 g/L Trisodium citrate dihydrate, 0.001 g/L Pyridoxine HCl, 0.0005 g/L biotin, 2.5 g/L Disodium phosphate, 1 g/L Potassium phosphate monobasic, 0.04 g/L Ferric ammonium citrate, 0.05 g/L Magnesium sulfate, 0.0005 g/L Calcium chloride, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L copper (II) chloride dihydrate, 5 g/L bovine serum albumin, 2 g/L D-Glucose, 4.25 g/L Sodium Chloride, 0.5 vol% Tween 80

Specific Phenotypes

For 21 genes in this experiment

SEED Subsystems

Subsystem	#Specific
High affinity phosphate transporter and control of PHO regulon	3
Phosphate metabolism	3
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	2
Acid resistance mechanisms	1
Arginine and Ornithine Degradation	1
Ethanolamine utilization	1
Fermentations: Lactate	1
Fermentations: Mixed acid	1
MLST	1
Polyamine Metabolism	1
Propanediol utilization	1
Redox-dependent regulation of nucleus processes	1
Serine-glyoxylate cycle	1
Succinate dehydrogenase	1
TCA Cycle	1
Threonine anaerobic catabolism gene cluster	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Butanoate metabolism
• Tyrosine metabolism
• Nucleotide sugars metabolism
• Lipopolysaccharide biosynthesis
• alpha-Linolenic acid metabolism
• Ethylbenzene degradation
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Caprolactam degradation
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Citrate cycle (TCA cycle)
• Fatty acid biosynthesis
• Fatty acid metabolism
• Oxidative phosphorylation
• Urea cycle and metabolism of amino groups
• Puromycin biosynthesis
• Glutamate metabolism
• Alanine and aspartate metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine biosynthesis
• Lysine degradation
• Arginine and proline metabolism
• Histidine metabolism
• Phenylalanine metabolism
• beta-Alanine metabolism
• Taurine and hypotaurine metabolism
• Glutathione metabolism
• Glycerophospholipid metabolism
• Ether lipid metabolism
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• 1,4-Dichlorobenzene degradation
• Trinitrotoluene degradation
• Reductive carboxylate cycle (CO2 fixation)
• Nicotinate and nicotinamide metabolism
• Porphyrin and chlorophyll metabolism
• Diterpenoid biosynthesis
• Anthocyanin biosynthesis
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
cadaverine biosynthesis	1	1	1
arginine dependent acid resistance	1	1	1
long-chain fatty acid activation	1	1	1
4-aminobutanoate degradation II	2	2	1
acetate and ATP formation from acetyl-CoA I	2	2	1
4-aminobutanoate degradation I	2	2	1
4-aminobutanoate degradation III	2	2	1
γ-linolenate biosynthesis II (animals)	2	2	1
putrescine biosynthesis I	2	1	1
linoleate biosynthesis II (animals)	2	1	1
L-arginine degradation III (arginine decarboxylase/agmatinase pathway)	2	1	1
sulfoacetaldehyde degradation I	2	1	1
superpathway of acetate utilization and formation	3	3	1
superpathway of 4-aminobutanoate degradation	3	3	1
pyruvate fermentation to acetate VII	3	2	1
pyruvate fermentation to acetate II	3	2	1
oleate biosynthesis I (plants)	3	2	1
pyruvate fermentation to acetate IV	3	2	1
pyruvate fermentation to acetate I	3	2	1
3-methyl-branched fatty acid α-oxidation	6	3	2
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	1	1
aminopropylcadaverine biosynthesis	3	1	1
putrescine biosynthesis II	3	1	1
alkane biosynthesis II	3	1	1
GABA shunt I	4	3	1
GABA shunt II	4	3	1
phytol degradation	4	3	1
pyruvate fermentation to acetate and (S)-lactate I	4	2	1
pyruvate fermentation to acetate and lactate II	4	2	1
long chain fatty acid ester synthesis (engineered)	4	2	1
superpathway of polyamine biosynthesis I	8	3	2
sulfolactate degradation II	4	1	1
superpathway of putrescine biosynthesis	4	1	1
wax esters biosynthesis II	4	1	1
spermidine biosynthesis III	4	1	1
phosphatidylcholine acyl editing	4	1	1
sporopollenin precursors biosynthesis	18	4	4
octane oxidation	5	4	1
(S)-propane-1,2-diol degradation	5	4	1
acetylene degradation (anaerobic)	5	4	1
ethanolamine utilization	5	4	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
desferrioxamine B biosynthesis	5	1	1
lupanine biosynthesis	5	1	1
desferrioxamine E biosynthesis	5	1	1
bisucaberin biosynthesis	5	1	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	5	2
stearate biosynthesis II (bacteria and plants)	6	5	1
fatty acid salvage	6	5	1
L-threonine degradation I	6	5	1
stearate biosynthesis IV	6	4	1
superpathway of taurine degradation	6	3	1
6-gingerol analog biosynthesis (engineered)	6	2	1
superpathway of sulfolactate degradation	6	2	1
methanogenesis from acetate	6	2	1
stearate biosynthesis I (animals)	6	1	1
L-lysine degradation X	6	1	1
superpathway of L-arginine and L-ornithine degradation	13	6	2
acetyl-CoA fermentation to butanoate	7	4	1
4-aminobutanoate degradation V	7	3	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	2	1
ceramide degradation by α-oxidation	7	2	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	2	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
capsaicin biosynthesis	7	1	1
L-lysine degradation I	7	1	1
L-valine degradation I	8	7	1
lactate fermentation to acetate, CO2 and hydrogen (Desulfovibrionales)	8	4	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
superpathway of polyamine biosynthesis II	8	2	1
superpathway of arginine and polyamine biosynthesis	17	11	2
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	6	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	5	1
superpathway of L-alanine fermentation (Stickland reaction)	9	3	1
L-lysine fermentation to acetate and butanoate	10	4	1
suberin monomers biosynthesis	20	2	2
superpathway of fatty acid biosynthesis II (plant)	43	34	4
gallate degradation III (anaerobic)	11	4	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	8	1
palmitate biosynthesis II (type II fatty acid synthase)	31	24	2
mixed acid fermentation	16	13	1
cutin biosynthesis	16	1	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	8	1
nicotine degradation I (pyridine pathway)	17	5	1
mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	18	18	1
heterolactic fermentation	18	13	1
superpathway of L-threonine metabolism	18	12	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	16	1
mycolate biosynthesis	205	165	10
superpathway of methanogenesis	21	2	1
superpathway of L-lysine degradation	43	10	2
superpathway of N-acetylneuraminate degradation	22	16	1
superpathway of mycolate biosynthesis	239	166	10
purine nucleobases degradation II (anaerobic)	24	12	1
superpathway of fatty acids biosynthesis (E. coli)	53	39	2
palmitate biosynthesis III	29	16	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	33	1
oleate β-oxidation	35	27	1