Experiment set8IT029 for Xanthomonas campestris pv. campestris strain 8004

Compare to:

Citric Acid 16.67 mM carbon source

Group: carbon source
Media: CaMM_noCarbon + Citric Acid (17 mM)
Culturing: Xantho_ML2, tube, Aerobic, at 28 (C)
By: Alice on 5/19/22
Media components: 10.5 g/L Potassium phosphate dibasic, 4.5 g/L Potassium phosphate monobasic, 1 g/L Ammonium Sulfate, 0.1 mM Calcium chloride, 1 mM Magnesium sulfate, 0.00625 g/L Iron (II) sulfate heptahydrate, 0.0625 g/L EDTA disodium dihydrate, 0.0225 g/L Zinc sulfate heptahydrate, 0.0143 g/L Boric Acid, 0.0063 g/L Manganese (II) chloride tetrahydrate, 0.002 g/L Cobalt chloride hexahydrate, 0.0019 g/L Copper (II) sulfate pentahydrate, 0.0014 g/L Ammonium heptamolybdate tetrahydrate

Specific Phenotypes

For 95 genes in this experiment

For carbon source Citric Acid in Xanthomonas campestris pv. campestris strain 8004

For carbon source Citric Acid across organisms

SEED Subsystems

Subsystem #Specific
Trehalose Biosynthesis 4
Cysteine Biosynthesis 3
Isoleucine degradation 3
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 3
Valine degradation 3
Acetyl-CoA fermentation to Butyrate 2
Anaerobic respiratory reductases 2
Butanol Biosynthesis 2
Glycogen metabolism 2
Maltose and Maltodextrin Utilization 2
Methionine Biosynthesis 2
Queuosine-Archaeosine Biosynthesis 2
Ribosome biogenesis bacterial 2
Terminal cytochrome d ubiquinol oxidases 2
Terminal cytochrome oxidases 2
n-Phenylalkanoic acid degradation 2
ATP-dependent RNA helicases, bacterial 1
Arginine Biosynthesis extended 1
Aromatic amino acid degradation 1
Bacterial RNA-metabolizing Zn-dependent hydrolases 1
Biogenesis of cytochrome c oxidases 1
Biotin biosynthesis 1
Conserved gene cluster associated with Met-tRNA formyltransferase 1
D-ribose utilization 1
Fructose and Mannose Inducible PTS 1
Fructose utilization 1
Glutathione: Biosynthesis and gamma-glutamyl cycle 1
Glutathione: Non-redox reactions 1
Glycerol and Glycerol-3-phosphate Uptake and Utilization 1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria 1
Glycine and Serine Utilization 1
Heat shock dnaK gene cluster extended 1
Heme and Siroheme Biosynthesis 1
Histidine Degradation 1
Isobutyryl-CoA to Propionyl-CoA Module 1
Ketoisovalerate oxidoreductase 1
Leucine Degradation and HMG-CoA Metabolism 1
MLST 1
Mannitol Utilization 1
Methionine Degradation 1
NAD and NADP cofactor biosynthesis global 1
Nudix proteins (nucleoside triphosphate hydrolases) 1
One-carbon metabolism by tetrahydropterines 1
Oxidative stress 1
Peptidyl-prolyl cis-trans isomerase 1
Polyhydroxybutyrate metabolism 1
Potassium homeostasis 1
Protein chaperones 1
Protein degradation 1
RNA processing and degradation, bacterial 1
Ribosomal protein S12p Asp methylthiotransferase 1
Serine-glyoxylate cycle 1
Thioredoxin-disulfide reductase 1
Transport of Zinc 1
Twin-arginine translocation system 1
Type IV pilus 1
Utilization of glutathione as a sulphur source 1
Xanthan Exopolysaccharide Biosynthesis and Export 1
YcfH 1
mycolic acid synthesis 1
tRNA processing 1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
trans, trans-farnesyl diphosphate biosynthesis 2 2 2
γ-linolenate biosynthesis II (animals) 2 2 2
long-chain fatty acid activation 1 1 1
acetate and ATP formation from acetyl-CoA III 1 1 1
acetate conversion to acetyl-CoA 1 1 1
geranyl diphosphate biosynthesis 1 1 1
trehalose biosynthesis IV 1 1 1
fatty acid β-oxidation III (unsaturated, odd number) 1 1 1
benzoyl-CoA biosynthesis 3 3 2
oleate β-oxidation 35 31 20
fatty acid β-oxidation I (generic) 7 6 4
succinate to cytochrome bd oxidase electron transfer 2 2 1
trehalose degradation VI (periplasmic) 2 2 1
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis I 2 2 1
pyruvate to cytochrome bd oxidase electron transfer 2 2 1
trehalose degradation II (cytosolic) 2 2 1
NADH to cytochrome bd oxidase electron transfer I 2 2 1
L-cysteine biosynthesis III (from L-homocysteine) 2 2 1
fatty acid salvage 6 5 3
pyruvate fermentation to butanol II (engineered) 6 4 3
hydrogen sulfide biosynthesis II (mammalian) 6 4 3
all-trans-farnesol biosynthesis 4 2 2
glutathione degradation (DUG pathway) 2 1 1
(3R)-linalool biosynthesis 2 1 1
linoleate biosynthesis II (animals) 2 1 1
NADH to cytochrome bd oxidase electron transfer II 2 1 1
pseudouridine degradation 2 1 1
indole-3-acetate biosynthesis IV (bacteria) 2 1 1
acrylonitrile degradation I 2 1 1
linalool biosynthesis I 2 1 1
(3S)-linalool biosynthesis 2 1 1
10,13-epoxy-11-methyl-octadecadienoate biosynthesis 2 1 1
indole-3-acetate biosynthesis III (bacteria) 2 1 1
oleate β-oxidation (thioesterase-dependent, yeast) 2 1 1
pyruvate fermentation to hexanol (engineered) 11 7 5
2-methylcitrate cycle I 5 5 2
L-ornithine biosynthesis I 5 5 2
adipate degradation 5 5 2
polyisoprenoid biosynthesis (E. coli) 5 5 2
adipate biosynthesis 5 4 2
glutaryl-CoA degradation 5 3 2
fatty acid β-oxidation IV (unsaturated, even number) 5 3 2
fatty acid β-oxidation II (plant peroxisome) 5 3 2
fatty acid β-oxidation V (unsaturated, odd number, di-isomerase-dependent) 5 2 2
(8E,10E)-dodeca-8,10-dienol biosynthesis 11 5 4
2-methyl-branched fatty acid β-oxidation 14 9 5
glyoxylate cycle 6 6 2
2-oxoisovalerate decarboxylation to isobutanoyl-CoA 3 3 1
ethanol degradation IV 3 3 1
L-proline biosynthesis III (from L-ornithine) 3 3 1
pyruvate decarboxylation to acetyl CoA I 3 3 1
ethanol degradation II 3 3 1
L-arginine degradation I (arginase pathway) 3 3 1
L-ornithine biosynthesis II 3 3 1
glycerol degradation I 3 3 1
2-methylcitrate cycle II 6 5 2
L-isoleucine degradation I 6 4 2
ethanol degradation III 3 2 1
superpathway of acetate utilization and formation 3 2 1
trehalose biosynthesis V 3 2 1
L-isoleucine biosynthesis V 3 2 1
L-phenylalanine degradation II (anaerobic) 3 2 1
L-tryptophan degradation I (via anthranilate) 3 2 1
valproate β-oxidation 9 5 3
3-methyl-branched fatty acid α-oxidation 6 3 2
propanoate fermentation to 2-methylbutanoate 6 3 2
methyl ketone biosynthesis (engineered) 6 3 2
bisabolene biosynthesis (engineered) 6 2 2
6-gingerol analog biosynthesis (engineered) 6 2 2
L-arginine degradation X (arginine monooxygenase pathway) 3 1 1
oleate β-oxidation (reductase-dependent, yeast) 3 1 1
superpathway of linalool biosynthesis 3 1 1
superpathway of acrylonitrile degradation 3 1 1
alkane biosynthesis II 3 1 1
molybdenum cofactor biosynthesis 3 1 1
oleate biosynthesis I (plants) 3 1 1
taurine biosynthesis III 3 1 1
superpathway of glyoxylate cycle and fatty acid degradation 14 11 4
Arg/N-end rule pathway (eukaryotic) 14 8 4
fatty acid β-oxidation VI (mammalian peroxisome) 7 3 2
pyruvate fermentation to butanoate 7 3 2
benzoyl-CoA degradation I (aerobic) 7 3 2
arachidonate biosynthesis III (6-desaturase, mammals) 7 2 2
icosapentaenoate biosynthesis II (6-desaturase, mammals) 7 2 2
L-arginine degradation VI (arginase 2 pathway) 4 4 1
glycerol and glycerophosphodiester degradation 4 4 1
partial TCA cycle (obligate autotrophs) 8 7 2
nitrogen remobilization from senescing leaves 8 6 2
L-phenylalanine degradation III 4 3 1
queuosine biosynthesis I (de novo) 4 3 1
homocysteine and cysteine interconversion 4 3 1
phosphatidylcholine acyl editing 4 3 1
phytol degradation 4 3 1
L-valine degradation I 8 5 2
starch degradation V 4 2 1
chitin deacetylation 4 2 1
pyruvate fermentation to butanol I 8 3 2
stellatic acid biosynthesis 8 2 2
ipsdienol biosynthesis 4 1 1
wax esters biosynthesis II 4 1 1
dimethylsulfoniopropanoate biosynthesis III (algae and phytoplankton) 4 1 1
oleate β-oxidation (isomerase-dependent, yeast) 4 1 1
long chain fatty acid ester synthesis (engineered) 4 1 1
methyl phomopsenoate biosynthesis 4 1 1
TCA cycle II (plants and fungi) 9 9 2
L-arginine biosynthesis III (via N-acetyl-L-citrulline) 9 9 2
L-arginine biosynthesis I (via L-ornithine) 9 8 2
TCA cycle V (2-oxoglutarate synthase) 9 8 2
TCA cycle VII (acetate-producers) 9 7 2
TCA cycle IV (2-oxoglutarate decarboxylase) 9 7 2
TCA cycle VI (Helicobacter) 9 6 2
superpathway of Clostridium acetobutylicum acidogenic fermentation 9 4 2
phenylacetate degradation I (aerobic) 9 4 2
benzoate biosynthesis I (CoA-dependent, β-oxidative) 9 3 2
sporopollenin precursors biosynthesis 18 4 4
tRNA processing 10 10 2
TCA cycle III (animals) 10 10 2
NAD salvage pathway II (PNC IV cycle) 5 5 1
TCA cycle I (prokaryotic) 10 9 2
L-arginine biosynthesis II (acetyl cycle) 10 8 2
L-tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde 5 4 1
4-hydroxybenzoate biosynthesis III (plants) 5 4 1
superpathway of L-cysteine biosynthesis (mammalian) 5 4 1
L-glutamate degradation V (via hydroxyglutarate) 10 6 2
L-arginine degradation XIII (reductive Stickland reaction) 5 3 1
octane oxidation 5 3 1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered) 5 3 1
3-hydroxy-4-methyl-anthranilate biosynthesis II 5 3 1
L-tryptophan degradation III (eukaryotic) 15 7 3
sphingosine and sphingosine-1-phosphate metabolism 10 4 2
3-phenylpropanoate degradation 10 4 2
9-cis, 11-trans-octadecadienoyl-CoA degradation (isomerase-dependent, yeast) 10 4 2
queuosine biosynthesis III (queuosine salvage) 5 2 1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative) 5 2 1
superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate) 10 3 2
mono-trans, poly-cis decaprenyl phosphate biosynthesis 5 1 1
L-arginine degradation II (AST pathway) 5 1 1
reductive TCA cycle I 11 6 2
superpathway of phenylethylamine degradation 11 5 2
peptido-conjugates in tissue regeneration biosynthesis 17 6 3
superpathway of glyoxylate bypass and TCA 12 11 2
superpathway of ubiquinol-8 biosynthesis (early decarboxylation) 12 10 2
superpathway of L-cysteine biosynthesis (fungi) 6 5 1
superpathway of geranylgeranyl diphosphate biosynthesis II (via MEP) 12 9 2
stearate biosynthesis II (bacteria and plants) 6 4 1
L-isoleucine biosynthesis IV 6 4 1
stearate biosynthesis IV 6 4 1
β-alanine biosynthesis II 6 3 1
γ-glutamyl cycle 6 3 1
reductive TCA cycle II 12 5 2
L-glutamate degradation VII (to butanoate) 12 4 2
leukotriene biosynthesis 6 2 1
3-hydroxy-4-methyl-anthranilate biosynthesis I 6 2 1
superpathway of bitter acids biosynthesis 18 3 3
adlupulone and adhumulone biosynthesis 6 1 1
stearate biosynthesis I (animals) 6 1 1
colupulone and cohumulone biosynthesis 6 1 1
lupulone and humulone biosynthesis 6 1 1
taxadiene biosynthesis (engineered) 13 9 2
folate transformations I 13 9 2
superpathway of Clostridium acetobutylicum solventogenic fermentation 13 4 2
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase) 13 3 2
ethene biosynthesis III (microbes) 7 6 1
L-Nδ-acetylornithine biosynthesis 7 5 1
superpathway of thiamine diphosphate biosynthesis III (eukaryotes) 7 3 1
capsaicin biosynthesis 7 3 1
L-homomethionine biosynthesis 7 2 1
ceramide degradation by α-oxidation 7 2 1
docosahexaenoate biosynthesis III (6-desaturase, mammals) 14 3 2
icosapentaenoate biosynthesis III (8-desaturase, mammals) 7 1 1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle 22 20 3
Spodoptera littoralis pheromone biosynthesis 22 3 3
L-citrulline biosynthesis 8 6 1
mixed acid fermentation 16 11 2
sucrose biosynthesis II 8 5 1
glycerol degradation to butanol 16 9 2
glycogen degradation I 8 4 1
glycogen biosynthesis III (from α-maltose 1-phosphate) 8 4 1
2-deoxy-D-ribose degradation II 8 3 1
ceramide and sphingolipid recycling and degradation (yeast) 16 4 2
2-methylpropene degradation 8 2 1
crotonate fermentation (to acetate and cyclohexane carboxylate) 16 3 2
superpathway of arginine and polyamine biosynthesis 17 12 2
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation 17 5 2
benzoate fermentation (to acetate and cyclohexane carboxylate) 17 3 2
folate transformations III (E. coli) 9 9 1
L-lysine biosynthesis I 9 9 1
NAD de novo biosynthesis II (from tryptophan) 9 8 1
1-butanol autotrophic biosynthesis (engineered) 27 18 3
chitin biosynthesis 9 6 1
reductive glycine pathway of autotrophic CO2 fixation 9 5 1
3-hydroxypropanoate/4-hydroxybutanate cycle 18 8 2
cis-geranyl-CoA degradation 9 2 1
toluene degradation VI (anaerobic) 18 3 2
starch degradation II 9 1 1
viridicatumtoxin biosynthesis 9 1 1
methylaspartate cycle 19 10 2
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae) 10 9 1
xanthan biosynthesis 10 8 1
superpathway of coenzyme A biosynthesis II (plants) 10 7 1
superpathway of thiamine diphosphate biosynthesis I 10 7 1
reductive acetyl coenzyme A pathway I (homoacetogenic bacteria) 10 3 1
methyl tert-butyl ether degradation 10 2 1
suberin monomers biosynthesis 20 2 2
superpathway of fatty acid biosynthesis II (plant) 43 30 4
folate transformations II (plants) 11 10 1
superpathway of thiamine diphosphate biosynthesis II 11 9 1
gallate degradation III (anaerobic) 11 2 1
superpathway of L-citrulline metabolism 12 8 1
L-tryptophan degradation IX 12 5 1
L-tryptophan degradation XII (Geobacillus) 12 4 1
indole-3-acetate biosynthesis II 12 3 1
10-cis-heptadecenoyl-CoA degradation (yeast) 12 2 1
10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast) 12 2 1
ethene biosynthesis V (engineered) 25 17 2
androstenedione degradation I (aerobic) 25 6 2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass 26 24 2
superpathway of ergosterol biosynthesis II 26 9 2
platensimycin biosynthesis 26 6 2
superpathway of ergosterol biosynthesis I 26 3 2
androstenedione degradation II (anaerobic) 27 4 2
superpathway of NAD biosynthesis in eukaryotes 14 11 1
hypoglycin biosynthesis 14 4 1
superpathway of testosterone and androsterone degradation 28 7 2
superpathway of cholesterol degradation I (cholesterol oxidase) 42 8 3
palmitate biosynthesis II (type II fatty acid synthase) 31 22 2
superpathway of cholesterol degradation II (cholesterol dehydrogenase) 47 8 3
superpathway of L-methionine salvage and degradation 16 8 1
cutin biosynthesis 16 1 1
cholesterol degradation to androstenedione I (cholesterol oxidase) 17 2 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 16 1
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 19 3
superpathway of cholesterol biosynthesis 38 3 2
cholesterol degradation to androstenedione II (cholesterol dehydrogenase) 22 2 1
L-tryptophan degradation XI (mammalian, via kynurenine) 23 8 1
superpathway of cholesterol degradation III (oxidase) 49 4 2
aspartate superpathway 25 21 1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered) 26 17 1
superpathway of fatty acids biosynthesis (E. coli) 53 38 2
anaerobic aromatic compound degradation (Thauera aromatica) 27 2 1
palmitate biosynthesis III 29 21 1
superpathway of chorismate metabolism 59 41 2
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis 33 13 1
superpathway of aromatic compound degradation via 3-oxoadipate 35 13 1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate 42 8 1