Experiment set2S105 for Rhodanobacter denitrificans MT42

Compare to:

R2A_PIPES pH 4.25

Group: pH
Media: R2A, pH=4.3
Culturing: Rhodanobacter_MT42_ML2, 96 well deep well block, Aerobic, at 23 (C), shaken=700 rpm
By: Hans and Hira on 1/10/25
Media components: 0.5 g/L Bacto Peptone, 0.5 g/L casamino acids, 0.5 g/L Yeast Extract, 0.5 g/L D-Glucose, 0.5 g/L Starch, 0.3 g/L Potassium phosphate dibasic, 0.05 g/L Magnesium Sulfate Heptahydrate, 0.3 g/L Sodium pyruvate

Specific Phenotypes

For 46 genes in this experiment

SEED Subsystems

Subsystem #Specific
Arginine and Ornithine Degradation 1
Cobalt-zinc-cadmium resistance 1
DNA Repair Base Excision 1
DNA repair, bacterial 1
Hfl operon 1
Lipid A modifications 1
Maltose and Maltodextrin Utilization 1
Multidrug Resistance Efflux Pumps 1
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon) 1
Oxidative stress 1
Pentose phosphate pathway 1
Photorespiration (oxidative C2 cycle) 1
Polyadenylation bacterial 1
Polysaccharide deacetylases 1
Predicted carbohydrate hydrolases 1
Proline, 4-hydroxyproline uptake and utilization 1
Respiratory dehydrogenases 1 1
Thioredoxin-disulfide reductase 1
Trehalose Biosynthesis 1
Trehalose Uptake and Utilization 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
maltose degradation 2 2 2
L-glutamine degradation I 1 1 1
glutaminyl-tRNAgln biosynthesis via transamidation 4 3 3
L-asparagine biosynthesis III (tRNA-dependent) 4 3 3
trehalose degradation IV 3 3 2
L-glutamate biosynthesis I 2 2 1
kojibiose degradation 2 1 1
trehalose degradation III 2 1 1
L-cysteine degradation II 3 3 1
UTP and CTP de novo biosynthesis 3 3 1
ammonia assimilation cycle III 3 3 1
L-arginine degradation I (arginase pathway) 3 3 1
D-serine degradation 3 3 1
L-serine degradation 3 3 1
pentose phosphate pathway (oxidative branch) I 3 3 1
L-proline degradation I 3 2 1
L-methionine degradation II 3 2 1
L-tryptophan degradation II (via pyruvate) 3 2 1
UTP and CTP dephosphorylation II 3 1 1
superpathway of pyrimidine nucleobases salvage 4 4 1
ethene biosynthesis II (microbes) 4 1 1
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis 5 2 1
L-threonine degradation I 6 5 1
L-methionine biosynthesis II 6 5 1
L-isoleucine biosynthesis I (from threonine) 7 7 1
L-glutamate and L-glutamine biosynthesis 7 6 1
UTP and CTP dephosphorylation I 7 5 1
glycine betaine degradation III 7 4 1
pentose phosphate pathway 8 8 1
L-citrulline biosynthesis 8 6 1
glycine betaine degradation I 8 4 1
L-mimosine degradation 8 4 1
glutathione-mediated detoxification I 8 3 1
superpathway of pyrimidine ribonucleotides de novo biosynthesis 9 9 1
photorespiration III 9 5 1
photorespiration I 9 5 1
superpathway of pyrimidine ribonucleosides salvage 10 7 1
superpathway of L-citrulline metabolism 12 8 1
superpathway of L-isoleucine biosynthesis I 13 13 1
hypoglycin biosynthesis 14 4 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II 15 13 1
superpathway of branched chain amino acid biosynthesis 17 17 1
superpathway of glucose and xylose degradation 17 14 1
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis 18 18 1
superpathway of L-threonine metabolism 18 13 1
purine nucleobases degradation II (anaerobic) 24 9 1
superpathway of histidine, purine, and pyrimidine biosynthesis 46 44 1