Experiment set2IT050 for Agrobacterium fabrum C58

2-Keto-D-gluconic acid hemicalcium salt hydrate carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + 2-Keto-D-gluconic acid hemicalcium salt hydrate (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 10 genes in this experiment

For carbon source 2-Keto-D-gluconic acid hemicalcium salt hydrate in Agrobacterium fabrum C58

For carbon source 2-Keto-D-gluconic acid hemicalcium salt hydrate across organisms

SEED Subsystems

Subsystem	#Specific
D-gluconate and ketogluconates metabolism	2
Entner-Doudoroff Pathway	2
D-Galacturonate and D-Glucuronate Utilization	1
Deoxyribose and Deoxynucleoside Catabolism	1
Glycine and Serine Utilization	1
Pentose phosphate pathway	1
Pyridoxin (Vitamin B6) Biosynthesis	1
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	1
Serine Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pentose phosphate pathway
• Pentose and glucuronate interconversions
• Glycine, serine and threonine metabolism
• Glutathione metabolism
• Lipopolysaccharide biosynthesis
• Nicotinate and nicotinamide metabolism
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
D-gluconate degradation	1	1	1
L-serine biosynthesis I	3	3	1
L-idonate degradation	3	3	1
pentose phosphate pathway (oxidative branch) I	3	3	1
sorbitol biosynthesis II	3	3	1
L-cysteine biosynthesis IX (Trichomonas vaginalis)	3	2	1
D-fructuronate degradation	4	4	1
superpathway of L-serine and glycine biosynthesis I	4	4	1
L-serine biosynthesis II	4	1	1
4-deoxy-L-threo-hex-4-enopyranuronate degradation	5	5	1
D-galacturonate degradation I	5	3	1
superpathway of β-D-glucuronosides degradation	7	5	1
alginate degradation	7	4	1
3,6-anhydro-α-L-galactopyranose degradation	7	4	1
pentose phosphate pathway	8	8	1
ketogluconate metabolism	8	4	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	1
Entner-Doudoroff pathway III (semi-phosphorylative)	9	7	1
superpathway of hexuronide and hexuronate degradation	10	6	1
formaldehyde assimilation I (serine pathway)	13	5	1
superpathway of glucose and xylose degradation	17	16	1
superpathway of microbial D-galacturonate and D-glucuronate degradation	31	22	1