Experiment set8IT065 for Ralstonia sp. UNC404CL21Col

Protocatechuic Acid carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + Protocatechuic Acid (10 mM)
Culturing: CL21_ML4_JBEI, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 2.6 generations
By: Allie Pearson on 8/26/19
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 11 genes in this experiment

For carbon source Protocatechuic Acid in Ralstonia sp. UNC404CL21Col

For carbon source Protocatechuic Acid across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	3
Protocatechuate branch of beta-ketoadipate pathway	3
Benzoate degradation	1
Catechol branch of beta-ketoadipate pathway	1
Chloroaromatic degradation pathway	1
Glutathione: Non-redox reactions	1
Homogentisate pathway of aromatic compound degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Benzoate degradation via hydroxylation
• Glutathione metabolism
• Toluene and xylene degradation
• 2,4-Dichlorobenzoate degradation
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
protocatechuate degradation II (ortho-cleavage pathway)	4	4	3
aromatic compounds degradation via β-ketoadipate	9	9	3
D-phenylglycine degradation	3	1	1
toluene degradation III (aerobic) (via p-cresol)	11	7	3
catechol degradation to β-ketoadipate	4	4	1
4-sulfocatechol degradation	4	1	1
4-hydroxy-2-nonenal detoxification	4	1	1
gallate degradation II	5	2	1
pentachlorophenol degradation	10	3	2
mandelate degradation I	5	1	1
catechol degradation III (ortho-cleavage pathway)	6	6	1
4-hydroxymandelate degradation	6	2	1
superpathway of salicylate degradation	7	7	1
4-methylcatechol degradation (ortho cleavage)	7	4	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	18	5
indole-3-acetate degradation II	7	2	1
glutathione-mediated detoxification I	8	3	1
mandelate degradation to acetyl-CoA	18	9	2
glutathione-mediated detoxification II	9	2	1
gliotoxin biosynthesis	9	1	1
superpathway of aerobic toluene degradation	30	9	3
indole glucosinolate activation (intact plant cell)	12	3	1
camalexin biosynthesis	12	2	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	11	2