Experiment set1S459 for Parabacteroides merdae CL09T00C40

D-Xylose 10 mg/mL carbon source

Group: carbon source
Media: Varel_Bryant_medium + D-Xylose (10 mg/mL)
Culturing: Pmerdae_CL09T00C40_ML3, 96 deep-well microplate; 1.2 mL volume, Anaerobic, at 37 (C), shaken=0 rpm
By: Surya on 1/10/25
Media components: 15 uM Hemin, 134 uM L-Methionine, 15 uM Iron (II) sulfate heptahydrate, 8.25 mM L-Cysteine, 23.8 mM Sodium bicarbonate, Mineral 3B solution (6.6 mM Potassium phosphate monobasic, 15.4 mM Sodium Chloride, 98 uM Magnesium chloride hexahydrate, 176.5 uM Calcium chloride dihydrate, 4.2 uM Cobalt chloride hexahydrate, 50.5 uM Manganese (II) chloride tetrahydrate, 9.3 mM Ammonium chloride, 1.75 mM Sodium sulfate)

Specific Phenotypes

For 7 genes in this experiment

For carbon source D-Xylose in Parabacteroides merdae CL09T00C40

For carbon source D-Xylose across organisms

SEED Subsystems

Subsystem	#Specific
Xylose utilization	2
NAD regulation	1
Na+ translocating decarboxylases and related biotin-dependent enzymes	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pentose and glucuronate interconversions
• Fructose and mannose metabolism
• Arginine and proline metabolism
• Pyruvate metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
D-xylose degradation I	2	2	2
xylitol degradation I	2	1	1
D-arabinitol degradation I	2	1	1
methylgallate degradation	6	2	1
protocatechuate degradation I (meta-cleavage pathway)	8	3	1
superpathway of glucose and xylose degradation	17	16	2
superpathway of vanillin and vanillate degradation	10	3	1
syringate degradation	12	3	1
superpathway of pentose and pentitol degradation	42	7	2