Experiment set27S413 for Pseudomonas fluorescens SBW25-INTG

Cytidine carbon source

Group: carbon source
Media: MME_noCarbon + Cytidine (10 mM)
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C)
By: Andrew Frank on 1/31/23
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium Chloride, 10 mM Ammonium chloride, 0.41 mM Magnesium Sulfate Heptahydrate, 0.07 mM Calcium chloride dihydrate, MME Trace Minerals (0.5 mg/L EDTA tetrasodium tetrahydrate salt, 2 mg/L Ferric chloride, 0.05 mg/L Boric Acid, 0.05 mg/L Zinc chloride, 0.03 mg/L copper (II) chloride dihydrate, 0.05 mg/L Manganese (II) chloride tetrahydrate, 0.05 mg/L Diammonium molybdate, 0.05 mg/L Cobalt chloride hexahydrate, 0.05 mg/L Nickel (II) chloride hexahydrate)

Specific Phenotypes

For 8 genes in this experiment

For carbon source Cytidine in Pseudomonas fluorescens SBW25-INTG

For carbon source Cytidine across organisms

SEED Subsystems

Subsystem	#Specific
D-ribose utilization	4
Deoxyribose and Deoxynucleoside Catabolism	1
Folate Biosynthesis	1
Fructose utilization	1
Pentose phosphate pathway	1
Pyruvate Alanine Serine Interconversions	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pentose phosphate pathway
• Biosynthesis of plant hormones
• Fatty acid metabolism
• Alanine and aspartate metabolism
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• beta-Alanine metabolism
• alpha-Linolenic acid metabolism
• Propanoate metabolism
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
glycine betaine biosynthesis IV (from glycine)	3	2	2
β-alanine degradation II	2	2	1
ribose phosphorylation	2	1	1
2-deoxy-D-ribose degradation I	3	1	1
oleate β-oxidation (isomerase-dependent, yeast)	4	2	1
pentose phosphate pathway (non-oxidative branch) I	5	5	1
fatty acid β-oxidation II (plant peroxisome)	5	4	1
propanoyl-CoA degradation II	5	4	1
fatty acid β-oxidation V (unsaturated, odd number, di-isomerase-dependent)	5	4	1
fatty acid β-oxidation VII (yeast peroxisome)	5	3	1
(5Z)-dodecenoate biosynthesis II	6	6	1
β-alanine biosynthesis II	6	5	1
methyl ketone biosynthesis (engineered)	6	4	1
6-gingerol analog biosynthesis (engineered)	6	3	1
10-cis-heptadecenoyl-CoA degradation (yeast)	12	4	2
10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast)	12	4	2
jasmonic acid biosynthesis	19	7	3
fatty acid β-oxidation VI (mammalian peroxisome)	7	5	1
pentose phosphate pathway	8	8	1
formaldehyde assimilation II (assimilatory RuMP Cycle)	9	6	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
Rubisco shunt	10	8	1
9-cis, 11-trans-octadecadienoyl-CoA degradation (isomerase-dependent, yeast)	10	5	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	10	1
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	3	1
superpathway of glyoxylate cycle and fatty acid degradation	14	12	1
docosahexaenoate biosynthesis III (6-desaturase, mammals)	14	3	1
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered)	14	2	1
Bifidobacterium shunt	15	12	1
superpathway of glucose and xylose degradation	17	16	1