Experiment set9S141 for Xanthomonas campestris pv. campestris strain 8004

Citric Acid 10mM carbon source

Group: carbon source
Media: CaMM_noCarbon + Citric Acid (10 mM)
Culturing: Xantho_ML2, tube, Aerobic, at 28 (C)
By: Alice on 6-Feb-23
Media components: 10.5 g/L Potassium phosphate dibasic, 4.5 g/L Potassium phosphate monobasic, 1 g/L Ammonium Sulfate, 0.1 mM Calcium chloride, 1 mM Magnesium sulfate, 0.00625 g/L Iron (II) sulfate heptahydrate, 0.0625 g/L EDTA disodium dihydrate, 0.0225 g/L Zinc sulfate heptahydrate, 0.0143 g/L Boric Acid, 0.0063 g/L Manganese (II) chloride tetrahydrate, 0.002 g/L Cobalt chloride hexahydrate, 0.0019 g/L Copper (II) sulfate pentahydrate, 0.0014 g/L Ammonium heptamolybdate tetrahydrate

Specific Phenotypes

For 20 genes in this experiment

For carbon source Citric Acid in Xanthomonas campestris pv. campestris strain 8004

For carbon source Citric Acid across organisms

SEED Subsystems

Subsystem	#Specific
Methionine Biosynthesis	3
Cysteine Biosynthesis	2
Methionine Degradation	2
Trehalose Biosynthesis	2
One-carbon metabolism by tetrahydropterines	1
Oxidative stress	1
Serine-glyoxylate cycle	1
Staphylococcal pathogenicity islands SaPI	1
Terminal cytochrome d ubiquinol oxidases	1
Terminal cytochrome oxidases	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:

• Methionine metabolism
• Lysine biosynthesis
• Lysine degradation
• Arginine and proline metabolism
• Aminophosphonate metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• One carbon pool by folate
• Methane metabolism
• Caprolactam degradation

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
trehalose biosynthesis IV	1	1	1
succinate to cytochrome bd oxidase electron transfer	2	2	1
pyruvate to cytochrome bd oxidase electron transfer	2	2	1
NADH to cytochrome bd oxidase electron transfer I	2	2	1
NADH to cytochrome bd oxidase electron transfer II	2	1	1
trehalose biosynthesis V	3	2	1
molybdenum cofactor biosynthesis	3	1	1
dimethylsulfoniopropanoate biosynthesis III (algae and phytoplankton)	4	1	1
folate transformations I	13	9	2
ethene biosynthesis III (microbes)	7	6	1
L-homomethionine biosynthesis	7	2	1
glycogen biosynthesis III (from α-maltose 1-phosphate)	8	4	1
folate transformations III (E. coli)	9	9	1
reductive acetyl coenzyme A pathway I (homoacetogenic bacteria)	10	3	1
folate transformations II (plants)	11	10	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	19	1