Experiment set2IT005 for Agrobacterium fabrum C58

L-ascorbate carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + L-ascorbate (10 mM)
Culturing: Agro_ML11, 24-well transparent microplate; Multitron, Aerobic, at 28 (C), shaken=200 rpm
By: Mitchell Thompson on 10/20/20
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 79 genes in this experiment

For carbon source L-ascorbate in Agrobacterium fabrum C58

For carbon source L-ascorbate across organisms

SEED Subsystems

Subsystem	#Specific
Molybdenum cofactor biosynthesis	5
Photorespiration (oxidative C2 cycle)	4
D-gluconate and ketogluconates metabolism	3
Glycolate, glyoxylate interconversions	3
Peptidoglycan Biosynthesis	3
Isobutyryl-CoA to Propionyl-CoA Module	2
Valine degradation	2
4-Hydroxyphenylacetic acid catabolic pathway	1
Allantoin Utilization	1
Aromatic amino acid degradation	1
Bacterial RNA-metabolizing Zn-dependent hydrolases	1
Chitin and N-acetylglucosamine utilization	1
Conenzyme B12 related Hypothetical: Clusters with cobST	1
D-galactarate, D-glucarate and D-glycerate catabolism	1
Deoxyribose and Deoxynucleoside Catabolism	1
Entner-Doudoroff Pathway	1
Flagellar motility	1
Flagellum	1
Formate hydrogenase	1
Glutathione-dependent pathway of formaldehyde detoxification	1
Glycine and Serine Utilization	1
Glycogen metabolism	1
Heat shock dnaK gene cluster extended	1
Homogentisate pathway of aromatic compound degradation	1
Lipid A modifications	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
Orphan regulatory proteins	1
Pentose phosphate pathway	1
Pyridoxin (Vitamin B6) Biosynthesis	1
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	1
Serine Biosynthesis	1
Sex pheromones in Enterococcus faecalis and other Firmicutes	1
Sialic Acid Metabolism	1
Synechocystis experimental	1
Transcription initiation, bacterial sigma factors	1
Trehalose Biosynthesis	1
Triacylglycerol metabolism	1
Type IV pilus	1
ZZ gjo need homes	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pentose phosphate pathway
• Lipopolysaccharide biosynthesis
• Peptidoglycan biosynthesis
• Glyoxylate and dicarboxylate metabolism
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• Tyrosine metabolism
• Nucleotide sugars metabolism
• alpha-Linolenic acid metabolism
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Puromycin biosynthesis
• Lysine degradation
• beta-Alanine metabolism
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Butanoate metabolism
• Methane metabolism
• Nicotinate and nicotinamide metabolism
• Retinol metabolism
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Fatty acid elongation in mitochondria
• Ubiquinone and menaquinone biosynthesis
• C21-Steroid hormone metabolism
• Geraniol degradation
• Bisphenol A degradation
• Tryptophan metabolism
• Glutathione metabolism
• Starch and sucrose metabolism
• N-Glycan biosynthesis
• O-Glycan biosynthesis
• High-mannose type N-glycan biosynthesis
• O-Mannosyl glycan biosynthesis
• Polyketide sugar unit biosynthesis
• Aminosugars metabolism
• Glycosaminoglycan degradation
• Keratan sulfate biosynthesis
• Glycerolipid metabolism
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• Glycerophospholipid metabolism
• Linoleic acid metabolism
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - lacto and neolacto series
• Glycosphingolipid biosynthesis - globo series
• Glycosphingolipid biosynthesis - ganglio series
• 1- and 2-Methylnaphthalene degradation
• Tetrachloroethene degradation
• Trinitrotoluene degradation
• 3-Chloroacrylic acid degradation
• Biotin metabolism
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Zeatin biosynthesis
• Sulfur metabolism
• Caprolactam degradation
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Flavone and flavonol biosynthesis
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450
• Biosynthesis of type II polyketide products
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-idonate degradation	3	3	3
bis(guanylyl molybdenum cofactor) biosynthesis	2	2	2
bis(guanylyl tungstenpterin) cofactor biosynthesis	1	1	1
formate oxidation to CO2	1	1	1
guanylyl molybdenum cofactor biosynthesis	1	1	1
acetaldehyde biosynthesis I	1	1	1
D-gluconate degradation	1	1	1
glycolate and glyoxylate degradation II	2	2	1
glycolate and glyoxylate degradation I	4	2	2
ethanol degradation I	2	1	1
pyruvate fermentation to ethanol II	2	1	1
ketogluconate metabolism	8	4	3
L-serine biosynthesis I	3	3	1
ethanol degradation II	3	3	1
sorbitol biosynthesis II	3	3	1
formaldehyde oxidation II (glutathione-dependent)	3	3	1
benzoyl-CoA biosynthesis	3	3	1
pentose phosphate pathway (oxidative branch) I	3	3	1
L-cysteine biosynthesis IX (Trichomonas vaginalis)	3	2	1
NAD salvage pathway III (to nicotinamide riboside)	3	2	1
2-deoxy-D-ribose degradation I	3	2	1
L-valine degradation II	3	2	1
L-isoleucine degradation II	3	2	1
2-deoxy-α-D-ribose 1-phosphate degradation	3	2	1
L-leucine degradation III	3	2	1
L-methionine degradation III	3	1	1
pyruvate fermentation to ethanol III	3	1	1
pyruvate fermentation to ethanol I	3	1	1
glycolate and glyoxylate degradation III	3	1	1
superpathway of glycol metabolism and degradation	7	4	2
glycogen biosynthesis I (from ADP-D-Glucose)	4	4	1
superpathway of L-serine and glycine biosynthesis I	4	4	1
phytol degradation	4	3	1
L-valine degradation I	8	5	2
L-tyrosine degradation III	4	2	1
D-galactarate degradation I	4	2	1
phospholipid remodeling (phosphatidylethanolamine, yeast)	4	2	1
L-phenylalanine degradation III	4	2	1
D-glucarate degradation I	4	2	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	3	3
salidroside biosynthesis	4	1	1
glycogen biosynthesis II (from UDP-D-Glucose)	4	1	1
oxalate degradation VI	4	1	1
L-serine biosynthesis II	4	1	1
2-methyl-branched fatty acid β-oxidation	14	9	3
adipate degradation	5	5	1
NAD salvage pathway II (PNC IV cycle)	5	4	1
adipate biosynthesis	5	4	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
starch biosynthesis	10	6	2
superpathway of D-glucarate and D-galactarate degradation	5	3	1
propanoyl-CoA degradation II	5	3	1
protein S-nitrosylation and denitrosylation	5	3	1
fatty acid β-oxidation II (plant peroxisome)	5	3	1
D-xylose degradation VI	5	3	1
acrylate degradation I	5	3	1
fatty acid β-oxidation IV (unsaturated, even number)	5	2	1
tRNA-uridine 2-thiolation (thermophilic bacteria)	5	2	1
(S)-propane-1,2-diol degradation	5	1	1
acetylene degradation (anaerobic)	5	1	1
ethanolamine utilization	5	1	1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative)	5	1	1
phenylethanol biosynthesis	5	1	1
oxalate degradation III	5	1	1
L-ascorbate degradation IV	5	1	1
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	6	2
peptidoglycan biosynthesis II (staphylococci)	17	12	3
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	3
superpathway of pyrimidine deoxyribonucleosides degradation	6	5	1
D-arabinose degradation IV	6	4	1
methyl ketone biosynthesis (engineered)	6	3	1
β-alanine biosynthesis II	6	3	1
superpathway of C1 compounds oxidation to CO2	12	5	2
L-arabinose degradation V	6	2	1
noradrenaline and adrenaline degradation	13	4	2
3-methylbutanol biosynthesis (engineered)	7	6	1
superpathway of purine deoxyribonucleosides degradation	7	6	1
NAD salvage pathway I (PNC VI cycle)	7	6	1
L-rhamnose degradation III	7	4	1
fatty acid β-oxidation I (generic)	7	4	1
serotonin degradation	7	3	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	3	1
benzoyl-CoA degradation I (aerobic)	7	3	1
pentose phosphate pathway	8	8	1
L-fucose degradation III	8	5	1
4-hydroxyphenylacetate degradation	8	4	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
glycogen biosynthesis III (from α-maltose 1-phosphate)	8	2	1
peptidoglycan biosynthesis V (β-lactam resistance)	17	11	2
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	1
photorespiration I	9	6	1
photorespiration III	9	6	1
valproate β-oxidation	9	5	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	3	1
phenylacetate degradation I (aerobic)	9	3	1
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	3	1
superpathway of coenzyme A biosynthesis II (plants)	10	7	1
photorespiration II	10	6	1
3-phenylpropanoate degradation	10	4	1
NAD salvage (plants)	11	6	1
superpathway of phenylethylamine degradation	11	3	1
Spodoptera littoralis pheromone biosynthesis	22	4	2
oleate β-oxidation	35	27	3
peptidoglycan biosynthesis I (meso-diaminopimelate containing)	12	11	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	5	1
formaldehyde assimilation I (serine pathway)	13	5	1
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	2	1
L-tryptophan degradation V (side chain pathway)	13	1	1
superpathway of glyoxylate cycle and fatty acid degradation	14	12	1
docosahexaenoate biosynthesis III (6-desaturase, mammals)	14	2	1
peptidoglycan biosynthesis III (mycobacteria)	15	11	1
purine nucleobases degradation I (anaerobic)	15	5	1
mixed acid fermentation	16	9	1
superpathway of glucose and xylose degradation	17	16	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	5	1
heterolactic fermentation	18	12	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
purine nucleobases degradation II (anaerobic)	24	14	1
platensimycin biosynthesis	26	6	1
superpathway of microbial D-galacturonate and D-glucuronate degradation	31	22	1