Experiment set11IT015 for Agrobacterium fabrum C58

L-(+)-Erythrulose carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + L-(+)-Erythrulose (10 mM), pH=7
Culturing: Agro_ML11, 24-well plate, Aerobic, at 28 (C), shaken=200 rpm
By: Mitchell Thompson on 1/6/22
Media components: 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 9.5 mM Ammonium chloride, 0.276 mM Aluminum potassium sulfate dodecahydrate, 0.0005 mM Calcium chloride, 0.525 mM Magnesium chloride hexahydrate, 50 mM Sodium Chloride, 3e-09 M Ammonium heptamolybdate tetrahydrate, 4e-07 M Boric Acid, 3e-08 M Cobalt chloride hexahydrate, 1e-08 M Copper (II) sulfate pentahydrate, 8e-08 M Manganese (II) chloride tetrahydrate, 1e-08 M Zinc sulfate heptahydrate

Specific Phenotypes

For 9 genes in this experiment

For carbon source L-(+)-Erythrulose in Agrobacterium fabrum C58

For carbon source L-(+)-Erythrulose across organisms

SEED Subsystems

Subsystem	#Specific
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	2
Acetoin, butanediol metabolism	1
Branched-Chain Amino Acid Biosynthesis	1
D-Sorbitol(D-Glucitol) and L-Sorbose Utilization	1
Entner-Doudoroff Pathway	1
Fermentations: Mixed acid	1
Glycolate, glyoxylate interconversions	1
Methylglyoxal Metabolism	1
Peptidoglycan Biosynthesis	1
Photorespiration (oxidative C2 cycle)	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	1
Synechocystis experimental	1
Triacylglycerol metabolism	1
Type IV pilus	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Peptidoglycan biosynthesis
• Glycolysis / Gluconeogenesis
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Lysine degradation
• Arginine and proline metabolism
• Tryptophan metabolism
• Glycerolipid metabolism
• 1- and 2-Methylnaphthalene degradation
• Glyoxylate and dicarboxylate metabolism
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Limonene and pinene degradation
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Valine, leucine and isoleucine biosynthesis
• Lysine biosynthesis
• Histidine metabolism
• Tyrosine metabolism
• beta-Alanine metabolism
• N-Glycan biosynthesis
• O-Glycan biosynthesis
• High-mannose type N-glycan biosynthesis
• O-Mannosyl glycan biosynthesis
• Keratan sulfate biosynthesis
• Lipopolysaccharide biosynthesis
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• Glycerophospholipid metabolism
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - lacto and neolacto series
• Glycosphingolipid biosynthesis - globo series
• Glycosphingolipid biosynthesis - ganglio series
• Pyruvate metabolism
• Naphthalene and anthracene degradation
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• C5-Branched dibasic acid metabolism
• Pantothenate and CoA biosynthesis
• Biotin metabolism
• Retinol metabolism
• Carotenoid biosynthesis - General
• Zeatin biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Flavone and flavonol biosynthesis
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetaldehyde biosynthesis I	1	1	1
ethanol degradation II	3	3	2
glycolate and glyoxylate degradation II	2	2	1
putrescine degradation V	2	2	1
phytol degradation	4	3	2
putrescine degradation I	2	1	1
ethylene glycol degradation	2	1	1
pyruvate fermentation to (R)-acetoin II	2	1	1
pyruvate fermentation to ethanol II	2	1	1
ethanol degradation I	2	1	1
pyruvate fermentation to isobutanol (engineered)	5	4	2
ethanol degradation IV	3	3	1
pyruvate fermentation to (R)-acetoin I	3	3	1
L-leucine degradation III	3	2	1
hypotaurine degradation	3	2	1
L-isoleucine degradation II	3	2	1
L-valine degradation II	3	2	1
ethanol degradation III	3	2	1
putrescine degradation IV	3	2	1
pyruvate fermentation to (S)-acetoin	3	2	1
pyruvate fermentation to ethanol III	3	1	1
pyruvate fermentation to ethanol I	3	1	1
histamine degradation	3	1	1
L-methionine degradation III	3	1	1
glycolate and glyoxylate degradation III	3	1	1
noradrenaline and adrenaline degradation	13	4	4
superpathway of glycol metabolism and degradation	7	4	2
serotonin degradation	7	3	2
L-valine biosynthesis	4	4	1
L-phenylalanine degradation III	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
glycolate and glyoxylate degradation I	4	2	1
L-tyrosine degradation III	4	2	1
phospholipid remodeling (phosphatidylethanolamine, yeast)	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
D-arabinose degradation II	4	1	1
salidroside biosynthesis	4	1	1
putrescine degradation III	4	1	1
cytidine-5'-diphosphate-glycerol biosynthesis	4	1	1
superpathway of (R,R)-butanediol biosynthesis	5	4	1
mitochondrial NADPH production (yeast)	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
octane oxidation	5	2	1
acetylene degradation (anaerobic)	5	1	1
phenylethanol biosynthesis	5	1	1
(S)-propane-1,2-diol degradation	5	1	1
dopamine degradation	5	1	1
ethanolamine utilization	5	1	1
L-isoleucine biosynthesis IV	6	3	1
3-methyl-branched fatty acid α-oxidation	6	3	1
superpathway of 2,3-butanediol biosynthesis	6	2	1
alkane oxidation	6	1	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
3-methylbutanol biosynthesis (engineered)	7	6	1
L-isoleucine biosynthesis III	7	4	1
ceramide degradation by α-oxidation	7	2	1
limonene degradation IV (anaerobic)	7	1	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	6	1
L-isoleucine biosynthesis II	8	5	1
superpathway of ornithine degradation	8	4	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
aromatic biogenic amine degradation (bacteria)	8	1	1
superpathway of branched chain amino acid biosynthesis	17	17	2
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	2
peptidoglycan biosynthesis II (staphylococci)	17	12	2
peptidoglycan biosynthesis V (β-lactam resistance)	17	11	2
photorespiration III	9	6	1
photorespiration I	9	6	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	5	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	3	1
photorespiration II	10	6	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	6	1
peptidoglycan biosynthesis I (meso-diaminopimelate containing)	12	11	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	3	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of L-arginine and L-ornithine degradation	13	8	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	5	1
L-tryptophan degradation V (side chain pathway)	13	1	1
peptidoglycan biosynthesis III (mycobacteria)	15	11	1
mixed acid fermentation	16	9	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	5	1
heterolactic fermentation	18	12	1
superpathway of L-threonine metabolism	18	11	1
superpathway of anaerobic sucrose degradation	19	13	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	10	1
superpathway of N-acetylneuraminate degradation	22	12	1
superpathway of pentose and pentitol degradation	42	16	1