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 12 genes in this experiment
For carbon source Cytidine in Pseudomonas fluorescens SBW25-INTG
For carbon source Cytidine across organisms
SEED Subsystems
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
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 |
| (5Z)-dodecenoate biosynthesis II | 6 | 6 | 2 |
| 2-deoxy-D-ribose degradation I | 3 | 1 | 1 |
| gondoate biosynthesis (anaerobic) | 4 | 4 | 1 |
| octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast) | 12 | 9 | 3 |
| oleate β-oxidation (isomerase-dependent, yeast) | 4 | 2 | 1 |
| fatty acid biosynthesis initiation (mitochondria) | 4 | 2 | 1 |
| palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate) | 9 | 8 | 2 |
| oleate biosynthesis IV (anaerobic) | 14 | 13 | 3 |
| palmitate biosynthesis III | 29 | 21 | 6 |
| pentose phosphate pathway (non-oxidative branch) I | 5 | 5 | 1 |
| superpathway of unsaturated fatty acids biosynthesis (E. coli) | 20 | 18 | 4 |
| fatty acid elongation -- saturated | 5 | 4 | 1 |
| superpathway of fatty acid biosynthesis initiation | 5 | 4 | 1 |
| cis-vaccenate biosynthesis | 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 II (plant peroxisome) | 5 | 4 | 1 |
| fatty acid β-oxidation VII (yeast peroxisome) | 5 | 3 | 1 |
| palmitate biosynthesis II (type II fatty acid synthase) | 31 | 29 | 6 |
| superpathway of fatty acids biosynthesis (E. coli) | 53 | 49 | 10 |
| superpathway of fatty acid biosynthesis I (E. coli) | 16 | 14 | 3 |
| 8-amino-7-oxononanoate biosynthesis I | 11 | 9 | 2 |
| (5Z)-dodecenoate biosynthesis I | 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-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast) | 12 | 4 | 2 |
| 10-cis-heptadecenoyl-CoA degradation (yeast) | 12 | 4 | 2 |
| petroselinate biosynthesis | 6 | 2 | 1 |
| jasmonic acid biosynthesis | 19 | 7 | 3 |
| odd iso-branched-chain fatty acid biosynthesis | 34 | 24 | 5 |
| even iso-branched-chain fatty acid biosynthesis | 34 | 24 | 5 |
| anteiso-branched-chain fatty acid biosynthesis | 34 | 24 | 5 |
| fatty acid β-oxidation VI (mammalian peroxisome) | 7 | 5 | 1 |
| superpathway of fatty acid biosynthesis II (plant) | 43 | 38 | 6 |
| biotin biosynthesis I | 15 | 13 | 2 |
| pentose phosphate pathway | 8 | 8 | 1 |
| streptorubin B biosynthesis | 34 | 20 | 4 |
| 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 |
| mycolate biosynthesis | 205 | 20 | 1 |
| superpathway of mycolate biosynthesis | 239 | 21 | 1 |