Experiment set16IT025 for Klebsiella michiganensis M5al

Compare to:

rhizosphere EcoFAB sample 3; outgrowth in LB

Group: rhizosphere
Media:
Culturing: Koxy_ML2a, EcoFAB
By: Dawn Chiniquy on 4-Apr-19

Specific Phenotypes

For 83 genes in this experiment

SEED Subsystems

Subsystem #Specific
Acetyl-CoA fermentation to Butyrate 2
Butanol Biosynthesis 2
D-ribose utilization 2
Isoleucine degradation 2
L-fucose utilization 2
Maltose and Maltodextrin Utilization 2
Sucrose utilization 2
Valine degradation 2
Allantoin Utilization 1
Anaerobic respiratory reductases 1
Aromatic amino acid degradation 1
Beta-Glucoside Metabolism 1
Calvin-Benson cycle 1
D-Galacturonate and D-Glucuronate Utilization 1
DNA-binding regulatory proteins, strays 1
DNA-replication 1
Glycine and Serine Utilization 1
Glycine cleavage system 1
Heat shock dnaK gene cluster extended 1
Homogentisate pathway of aromatic compound degradation 1
Isobutyryl-CoA to Propionyl-CoA Module 1
Ketoisovalerate oxidoreductase 1
L-Arabinose utilization 1
L-fucose utilization temp 1
L-rhamnose utilization 1
Nitrosative stress 1
Oxidative stress 1
Phosphate metabolism 1
Photorespiration (oxidative C2 cycle) 1
Plastoquinone Biosynthesis 1
Polyhydroxybutyrate metabolism 1
Protein degradation 1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 1
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization 1
Rrf2 family transcriptional regulators 1
Stringent Response, (p)ppGpp metabolism 1
TCA Cycle 1
Thioredoxin-disulfide reductase 1
Tocopherol Biosynthesis 1
n-Phenylalkanoic acid degradation 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
pseudouridine degradation 2 2 2
acetate and ATP formation from acetyl-CoA III 1 1 1
fatty acid β-oxidation III (unsaturated, odd number) 1 1 1
acetate conversion to acetyl-CoA 1 1 1
fatty acid β-oxidation I (generic) 7 6 5
benzoyl-CoA biosynthesis 3 3 2
starch degradation IV 3 2 2
fatty acid β-oxidation IV (unsaturated, even number) 5 3 3
oleate β-oxidation 35 32 19
starch degradation III 4 4 2
oleate β-oxidation (thioesterase-dependent, yeast) 2 2 1
pyruvate fermentation to butanol II (engineered) 6 4 3
pyruvate fermentation to hexanol (engineered) 11 8 5
adipate degradation 5 5 2
adipate biosynthesis 5 4 2
fatty acid β-oxidation II (plant peroxisome) 5 3 2
glutaryl-CoA degradation 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
superpathway of acetate utilization and formation 3 3 1
glycine biosynthesis II 3 3 1
ethanol degradation II 3 3 1
ethanol degradation IV 3 3 1
glycine cleavage 3 3 1
fatty acid salvage 6 5 2
L-isoleucine degradation I 6 4 2
propanoate fermentation to 2-methylbutanoate 6 4 2
L-isoleucine biosynthesis V 3 2 1
ethanol degradation III 3 2 1
valproate β-oxidation 9 5 3
methyl ketone biosynthesis (engineered) 6 3 2
plastoquinol-9 biosynthesis I 3 1 1
oleate β-oxidation (reductase-dependent, yeast) 3 1 1
pyruvate fermentation to butanoate 7 4 2
benzoyl-CoA degradation I (aerobic) 7 3 2
fatty acid β-oxidation VI (mammalian peroxisome) 7 3 2
D-arabinose degradation II 4 4 1
gallate degradation I 4 4 1
L-fucose degradation I 4 4 1
allantoin degradation to ureidoglycolate II (ammonia producing) 4 4 1
chitin deacetylation 4 3 1
L-valine degradation I 8 4 2
pyruvate fermentation to butanol I 8 4 2
oleate β-oxidation (isomerase-dependent, yeast) 4 1 1
phenylacetate degradation I (aerobic) 9 9 2
superpathway of Clostridium acetobutylicum acidogenic fermentation 9 6 2
benzoate biosynthesis I (CoA-dependent, β-oxidative) 9 4 2
allantoin degradation to glyoxylate II 5 5 1
allantoin degradation to glyoxylate III 5 5 1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered) 5 4 1
enterobacterial common antigen biosynthesis 5 4 1
L-tyrosine degradation I 5 4 1
gallate degradation II 5 4 1
3-phenylpropanoate degradation 10 6 2
L-glutamate degradation V (via hydroxyglutarate) 10 6 2
lactate biosynthesis (archaea) 5 3 1
9-cis, 11-trans-octadecadienoyl-CoA degradation (isomerase-dependent, yeast) 10 4 2
benzoate biosynthesis III (CoA-dependent, non-β-oxidative) 5 2 1
superpathway of plastoquinol biosynthesis 5 2 1
2-methylcitrate cycle I 5 2 1
4-hydroxybenzoate biosynthesis III (plants) 5 2 1
superpathway of phenylethylamine degradation 11 11 2
ppGpp metabolism 6 6 1
methylgallate degradation 6 4 1
L-isoleucine biosynthesis IV 6 4 1
L-glutamate degradation VII (to butanoate) 12 7 2
nucleoside and nucleotide degradation (halobacteria) 6 3 1
2-methylcitrate cycle II 6 2 1
6-gingerol analog biosynthesis (engineered) 6 2 1
superpathway of bitter acids biosynthesis 18 3 3
lupulone and humulone biosynthesis 6 1 1
colupulone and cohumulone biosynthesis 6 1 1
adlupulone and adhumulone biosynthesis 6 1 1
β-alanine biosynthesis II 6 1 1
superpathway of Clostridium acetobutylicum solventogenic fermentation 13 7 2
1-butanol autotrophic biosynthesis (engineered) 27 19 4
superpathway of glyoxylate cycle and fatty acid degradation 14 11 2
vitamin E biosynthesis (tocopherols) 7 1 1
Spodoptera littoralis pheromone biosynthesis 22 3 3
L-tryptophan degradation III (eukaryotic) 15 4 2
partial TCA cycle (obligate autotrophs) 8 7 1
superpathway of allantoin degradation in plants 8 7 1
glycerol degradation to butanol 16 12 2
protocatechuate degradation I (meta-cleavage pathway) 8 6 1
2-methylpropene degradation 8 2 1
crotonate fermentation (to acetate and cyclohexane carboxylate) 16 3 2
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation 17 9 2
benzoate fermentation (to acetate and cyclohexane carboxylate) 17 3 2
allantoin degradation IV (anaerobic) 9 8 1
TCA cycle VI (Helicobacter) 9 7 1
reductive glycine pathway of autotrophic CO2 fixation 9 6 1
TCA cycle VII (acetate-producers) 9 6 1
3-hydroxypropanoate/4-hydroxybutanate cycle 18 10 2
L-phenylalanine degradation IV (mammalian, via side chain) 9 5 1
toluene degradation VI (anaerobic) 18 3 2
cis-geranyl-CoA degradation 9 1 1
TCA cycle I (prokaryotic) 10 9 1
Rubisco shunt 10 9 1
superpathway of enterobacterial common antigen biosynthesis 10 9 1
superpathway of vanillin and vanillate degradation 10 7 1
superpathway of coenzyme A biosynthesis II (plants) 10 5 1
methyl tert-butyl ether degradation 10 2 1
gallate degradation III (anaerobic) 11 5 1
superpathway of glyoxylate bypass and TCA 12 11 1
superpathway of fucose and rhamnose degradation 12 11 1
syringate degradation 12 6 1
10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast) 12 2 1
10-cis-heptadecenoyl-CoA degradation (yeast) 12 2 1
androstenedione degradation I (aerobic) 25 7 2
Calvin-Benson-Bassham cycle 13 10 1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered) 26 19 2
platensimycin biosynthesis 26 6 2
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase) 13 2 1
androstenedione degradation II (anaerobic) 27 4 2
peptidoglycan recycling I 14 14 1
superpathway of testosterone and androsterone degradation 28 7 2
superpathway of cholesterol degradation I (cholesterol oxidase) 42 9 3
docosahexaenoate biosynthesis III (6-desaturase, mammals) 14 2 1
superpathway of cholesterol degradation II (cholesterol dehydrogenase) 47 9 3
oxygenic photosynthesis 17 11 1
cholesterol degradation to androstenedione I (cholesterol oxidase) 17 2 1
cholesterol degradation to androstenedione II (cholesterol dehydrogenase) 22 2 1
superpathway of cholesterol degradation III (oxidase) 49 4 2
ethene biosynthesis V (engineered) 25 18 1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass 26 25 1
superpathway of pentose and pentitol degradation 42 21 1