Experiment set5IT076 for Rhodanobacter denitrificans FW104-10B01

Gly-Glu 20 mM

Group: carbon source
Media: Hans_Basal_Media_plus_0.2x_20AA_mix + Gly-Glu (20 mM)
Culturing: rhodanobacter_10B01_ML12, 96 deep-well microplate; 0.8 mL volume, Aerobic, at 30 (C), shaken=700 rpm
By: Hans Carlson and Trenton Owens on 24-Aug-21
Media components: 0.03 M PIPES sesquisodium salt, 0.1 g/L Potassium Chloride, 0.01 g/L Sodium Chloride, 0.01 g/L Calcium chloride dihydrate, 0.1 g/L Magnesium chloride hexahydrate, 0.1 g/L Sodium sulfate, 0.25 g/L Ammonium chloride, 0.1 g/L Disodium phosphate, 20AA_mix (0.1 mM L-Arginine, 0.1 mM L-Histidine, 0.1 mM L-Lysine, 0.1 mM L-Aspartic Acid, 0.1 mM L-Glutamic acid monopotassium salt monohydrate, 0.1 mM L-Serine, 0.1 mM L-Threonine, 0.1 mM L-Asparagine, 0.1 mM L-Glutamine, 0.1 mM L-Cysteine hydrochloride monohydrate, 0.1 mM Glycine, 0.1 mM L-Proline, 0.1 mM L-Alanine, 0.1 mM L-Valine, 0.1 mM L-Isoleucine, 0.1 mM L-Leucine, 0.1 mM L-Methionine, 0.1 mM L-Phenylalanine, 0.1 mM L-tyrosine disodium salt, 0.1 mM L-Tryptophan), DL vitamins (0.0002 mg/L biotin, 0.0002 mg/L Folic Acid, 0.001 mg/L Pyridoxine HCl, 0.0005 mg/L Riboflavin, 0.0005 mg/L Thiamine HCl, 0.0005 mg/L Nicotinic Acid, 0.0005 mg/L calcium pantothenate, 1e-05 mg/L Cyanocobalamin, 0.0005 mg/L 4-Aminobenzoic acid, 0.0005 mg/L Lipoic acid), Sulfur-free DL minerals (0.0003 g/L Magnesium chloride hexahydrate, 0.00015 g/L Nitrilotriacetic acid disodium salt, 0.0001 g/L Sodium Chloride, 5e-05 g/L Manganese (II) chloride tetrahydrate, 1e-05 g/L Cobalt chloride hexahydrate, 1.3e-05 g/L Zinc chloride, 1e-05 g/L Calcium chloride dihydrate, 1e-05 g/L Iron (II) chloride tetrahydrate, 2.5e-06 g/L Nickel (II) chloride hexahydrate, 2e-06 g/L Aluminum chloride hydrate, 1e-06 g/L copper (II) chloride dihydrate, 1e-06 g/L Boric Acid, 1e-06 g/L Sodium Molybdate Dihydrate, 3e-05 g/L Sodium selenite pentahydrate, 2.5e-05 g/L Sodium tungstate dihydrate)
Growth plate: 2 H9

Specific Phenotypes

For 28 genes in this experiment

For carbon source Gly-Glu in Rhodanobacter denitrificans FW104-10B01

For carbon source Gly-Glu across organisms

SEED Subsystems

Subsystem	#Specific
Oxidative stress	3
Branched-Chain Amino Acid Biosynthesis	1
Campylobacter Iron Metabolism	1
De Novo Purine Biosynthesis	1
Glutathione: Non-redox reactions	1
Heat shock dnaK gene cluster extended	1
Homogentisate pathway of aromatic compound degradation	1
Lysine Biosynthesis DAP Pathway	1
Methionine Biosynthesis	1
Methylglyoxal Metabolism	1
Orphan regulatory proteins	1
Proteolysis in bacteria, ATP-dependent	1
Serine-glyoxylate cycle	1
Threonine and Homoserine Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycine, serine and threonine metabolism
• Lysine biosynthesis
• Biosynthesis of plant hormones
• Purine metabolism
• Methionine metabolism
• Valine, leucine and isoleucine biosynthesis
• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Glycerolipid metabolism
• Glycerophospholipid metabolism
• Pyruvate metabolism
• One carbon pool by folate
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-homoserine biosynthesis	3	3	2
L-methionine degradation II	3	2	2
L-phenylalanine biosynthesis III (cytosolic, plants)	2	2	1
tetrahydrofolate salvage from 5,10-methenyltetrahydrofolate	2	2	1
L-threonine degradation I	6	5	3
monoacylglycerol metabolism (yeast)	4	2	2
L-tyrosine degradation II	2	1	1
L-threonine degradation V	2	1	1
atromentin biosynthesis	2	1	1
L-isoleucine biosynthesis I (from threonine)	7	7	3
superpathway of L-isoleucine biosynthesis I	13	13	5
superpathway of L-threonine biosynthesis	6	6	2
L-tyrosine biosynthesis I	3	3	1
L-phenylalanine biosynthesis I	3	3	1
methylglyoxal degradation VIII	3	2	1
methylglyoxal degradation I	3	2	1
triacylglycerol degradation	3	1	1
L-phenylalanine degradation II (anaerobic)	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
superpathway of L-homoserine and L-methionine biosynthesis	8	6	2
dipicolinate biosynthesis	4	3	1
spermidine biosynthesis II	4	2	1
L-tyrosine degradation III	4	2	1
phospholipid remodeling (phosphatidylethanolamine, yeast)	4	2	1
L-phenylalanine degradation III	4	2	1
L-methionine biosynthesis IV	4	2	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	2
superpathway of S-adenosyl-L-methionine biosynthesis	9	7	2
hypoglycin biosynthesis	14	4	3
5-aminoimidazole ribonucleotide biosynthesis I	5	5	1
L-tyrosine degradation I	5	4	1
superpathway of plastoquinol biosynthesis	5	2	1
ectoine biosynthesis	5	2	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
superpathway of branched chain amino acid biosynthesis	17	17	3
superpathway of 5-aminoimidazole ribonucleotide biosynthesis	6	6	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	11	2
superpathway of L-threonine metabolism	18	13	3
norspermidine biosynthesis	6	2	1
L-lysine biosynthesis III	7	6	1
L-lysine biosynthesis VI	7	6	1
3-dehydroquinate biosynthesis II (archaea)	7	3	1
cremeomycin biosynthesis	7	2	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
superpathway of methylglyoxal degradation	8	4	1
superpathway of polyamine biosynthesis III	8	2	1
grixazone biosynthesis	8	2	1
superpathway of aromatic amino acid biosynthesis	18	18	2
L-lysine biosynthesis I	9	9	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	2
L-lysine biosynthesis II	9	7	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	2	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
rosmarinic acid biosynthesis I	10	1	1
tropane alkaloids biosynthesis	11	2	1
(S)-reticuline biosynthesis I	11	1	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	1
chorismate biosynthesis II (archaea)	12	8	1
aspartate superpathway	25	23	2
superpathway of rosmarinic acid biosynthesis	14	1	1
cyclosporin A biosynthesis	15	2	1
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	4	1
superpathway of purine nucleotides de novo biosynthesis I	21	21	1
platensimycin biosynthesis	26	6	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	1	1
superpathway of chorismate metabolism	59	40	2