Experiment set4H33 for Shewanella oneidensis MR-1

Compare to:

Cytidine carbon source replicate 2

Group: carbon source
Media: ShewMM_noCarbon + Cytidine (10 mM), pH=7
Culturing: MR1_ML3, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 4.3 generations
By: Adam on 8/18/2013
Media components: 1.5 g/L Ammonium chloride, 1.75 g/L Sodium Chloride, 0.61 g/L Magnesium chloride hexahydrate, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)

Specific Phenotypes

For 11 genes in this experiment

For carbon source Cytidine in Shewanella oneidensis MR-1

For carbon source Cytidine across organisms

SEED Subsystems

Subsystem #Specific
CO2 uptake, carboxysome 2
Allantoin Utilization 1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate) 1
D-galactarate, D-glucarate and D-glycerate catabolism 1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria 1
Glycine and Serine Utilization 1
Murein hydrolase regulation and cell death 1
Pentose phosphate pathway 1
Photorespiration (oxidative C2 cycle) 1
Serine-glyoxylate cycle 1
Transcription initiation, bacterial sigma factors 1

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
pyrimidine ribonucleosides degradation 2 2 2
pyrimidine deoxyribonucleosides degradation 3 3 2
pyrimidine ribonucleosides salvage II 2 2 1
putrescine degradation I 2 1 1
2-O-α-mannosyl-D-glycerate degradation 2 1 1
putrescine degradation V 2 1 1
superpathway of pyrimidine ribonucleosides degradation 5 2 2
superpathway of pyrimidine deoxyribonucleosides degradation 6 6 2
pentose phosphate pathway (oxidative branch) I 3 3 1
pyrimidine ribonucleosides salvage I 3 3 1
putrescine degradation IV 3 2 1
glycolate and glyoxylate degradation I 4 3 1
D-glucarate degradation I 4 2 1
D-galactarate degradation I 4 2 1
L-arginine degradation IX (arginine:pyruvate transaminase pathway) 4 1 1
L-arginine degradation VIII (arginine oxidase pathway) 4 1 1
pyrimidine deoxyribonucleosides salvage 5 4 1
superpathway of D-glucarate and D-galactarate degradation 5 2 1
superpathway of glycol metabolism and degradation 7 5 1
pentose phosphate pathway 8 8 1
superpathway of ornithine degradation 8 6 1
2-deoxy-D-ribose degradation II 8 4 1
superpathway of pyrimidine deoxyribonucleoside salvage 9 8 1
photorespiration III 9 7 1
photorespiration I 9 7 1
Entner-Doudoroff pathway II (non-phosphorylative) 9 5 1
superpathway of pyrimidine ribonucleosides salvage 10 10 1
photorespiration II 10 8 1
nucleoside and nucleotide degradation (archaea) 10 4 1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation 11 6 1
formaldehyde assimilation I (serine pathway) 13 8 1
superpathway of L-arginine and L-ornithine degradation 13 8 1
superpathway of glucose and xylose degradation 17 14 1
superpathway of microbial D-galacturonate and D-glucuronate degradation 31 6 1