Experiment set2IT057 for Agrobacterium fabrum C58

D-Saccharic acid potassium salt carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + D-Saccharic acid potassium salt (5 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 34 genes in this experiment

For carbon source D-Saccharic acid potassium salt in Agrobacterium fabrum C58

For carbon source D-Saccharic acid potassium salt across organisms

SEED Subsystems

Subsystem	#Specific
D-Galacturonate and D-Glucuronate Utilization	2
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	2
Ammonia assimilation	1
Branched-Chain Amino Acid Biosynthesis	1
Chitin and N-acetylglucosamine utilization	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
D-Sorbitol(D-Glucitol) and L-Sorbose Utilization	1
D-galactarate, D-glucarate and D-glycerate catabolism	1
D-ribose utilization	1
Deoxyribose and Deoxynucleoside Catabolism	1
Glutamine synthetases	1
Histidine Degradation	1
Homogentisate pathway of aromatic compound degradation	1
Inositol catabolism	1
Peptidoglycan Biosynthesis	1
Proline, 4-hydroxyproline uptake and utilization	1
Pyruvate Alanine Serine Interconversions	1
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	1
Xylose utilization	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Ascorbate and aldarate metabolism
• Arginine and proline metabolism
• Glycerophospholipid metabolism
• Nitrogen metabolism
• Galactose metabolism
• Puromycin biosynthesis
• Glutamate metabolism
• Alanine and aspartate metabolism
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine biosynthesis
• Lysine degradation
• Phenylalanine metabolism
• Benzoate degradation via hydroxylation
• Aminophosphonate metabolism
• Cyanoamino acid metabolism
• D-Arginine and D-ornithine metabolism
• D-Alanine metabolism
• Nucleotide sugars metabolism
• Streptomycin biosynthesis
• Inositol phosphate metabolism
• alpha-Linolenic acid metabolism
• Trinitrotoluene degradation
• Pantothenate and CoA biosynthesis
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Caprolactam degradation
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
phosphatidylcholine biosynthesis V	3	3	3
D-alanine degradation	1	1	1
L-asparagine degradation I	1	1	1
L-glutamine biosynthesis I	1	1	1
D-glucarate degradation II	3	3	2
D-galactarate degradation II	3	3	2
glycine betaine biosynthesis II (Gram-positive bacteria)	2	2	1
D-galactose degradation II	2	2	1
ammonia assimilation cycle I	2	2	1
glycine betaine biosynthesis I (Gram-negative bacteria)	2	2	1
choline degradation I	2	2	1
pyruvate fermentation to acetate VIII	2	1	1
ammonia assimilation cycle II	2	1	1
pseudouridine degradation	2	1	1
D-galacturonate degradation II	5	5	2
D-glucuronate degradation II	5	5	2
phosphatidylcholine biosynthesis III	5	2	2
choline-O-sulfate degradation	3	3	1
ammonia assimilation cycle III	3	3	1
superpathway of ammonia assimilation (plants)	3	2	1
L-asparagine degradation III (mammalian)	3	2	1
L-aspartate degradation III (anaerobic)	3	2	1
L-carnitine degradation II	3	2	1
L-aspartate degradation II (aerobic)	3	2	1
L-lyxonate degradation	3	1	1
L-valine biosynthesis	4	4	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	6	2
1,2-dichloroethane degradation	4	3	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
trans-4-hydroxy-L-proline degradation II	4	2	1
cytosolic NADPH production (yeast)	5	4	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
mitochondrial NADPH production (yeast)	5	3	1
D-xylose degradation III	5	2	1
D-xylose degradation V	5	2	1
N-(1-deoxy-D-fructos-1-yl)-L-asparagine degradation	5	2	1
myo-inositol degradation II	5	1	1
phosphatidylcholine biosynthesis IV	5	1	1
D-arabinose degradation III	6	3	1
L-isoleucine biosynthesis IV	6	3	1
L-arabinose degradation III	6	2	1
superpathway of phosphatidylcholine biosynthesis	12	2	2
L-isoleucine biosynthesis I (from threonine)	7	7	1
myo-inositol degradation I	7	6	1
L-isoleucine biosynthesis III	7	4	1
L-glutamate and L-glutamine biosynthesis	7	4	1
L-isoleucine biosynthesis II	8	5	1
superpathway of branched chain amino acid biosynthesis	17	17	2
L-arginine biosynthesis II (acetyl cycle)	10	10	1
myo-, chiro- and scyllo-inositol degradation	10	6	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of phospholipid biosynthesis II (plants)	28	12	2
superpathway of microbial D-galacturonate and D-glucuronate degradation	31	22	2
superpathway of L-threonine metabolism	18	11	1
streptomycin biosynthesis	18	3	1
superpathway of pentose and pentitol degradation	42	16	2