Experiment set2S106 for Rhodanobacter denitrificans MT42
R2A_PIPES pH 4.25
Group: pHMedia: 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
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Starch and sucrose metabolism
- Glutamate metabolism
- Glycine, serine and threonine metabolism
- Arginine and proline metabolism
- Nucleotide sugars metabolism
- Aminoacyl-tRNA biosynthesis
- Ascorbate and aldarate metabolism
- Ubiquinone and menaquinone biosynthesis
- Puromycin biosynthesis
- Alanine and aspartate metabolism
- Tryptophan metabolism
- Benzoxazinone biosynthesis
- Selenoamino acid metabolism
- Glycosaminoglycan degradation
- Glycerolipid metabolism
- alpha-Linolenic acid metabolism
- Glyoxylate and dicarboxylate metabolism
- Trinitrotoluene degradation
- Porphyrin and chlorophyll metabolism
- Diterpenoid biosynthesis
- Carotenoid biosynthesis - General
- Alkaloid biosynthesis I
- Insect hormone biosynthesis
- Biosynthesis of siderophore group nonribosomal peptides
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 |
| L-asparagine biosynthesis III (tRNA-dependent) | 4 | 3 | 3 |
| glutaminyl-tRNAgln biosynthesis via transamidation | 4 | 3 | 3 |
| trehalose degradation IV | 3 | 3 | 2 |
| L-glutamate biosynthesis I | 2 | 2 | 1 |
| trehalose degradation III | 2 | 1 | 1 |
| kojibiose degradation | 2 | 1 | 1 |
| β-alanine degradation III | 2 | 1 | 1 |
| ammonia assimilation cycle III | 3 | 3 | 1 |
| L-arginine degradation I (arginase pathway) | 3 | 3 | 1 |
| L-proline degradation I | 3 | 2 | 1 |
| ethene biosynthesis II (microbes) | 4 | 1 | 1 |
| uracil degradation III | 5 | 3 | 1 |
| L-glutamate and L-glutamine biosynthesis | 7 | 6 | 1 |
| L-citrulline biosynthesis | 8 | 6 | 1 |
| photorespiration I | 9 | 5 | 1 |
| photorespiration III | 9 | 5 | 1 |
| superpathway of L-citrulline metabolism | 12 | 8 | 1 |
| 3-hydroxypropanoate cycle | 13 | 7 | 1 |
| glyoxylate assimilation | 13 | 5 | 1 |
| 3-hydroxypropanoate/4-hydroxybutanate cycle | 18 | 10 | 1 |
| superpathway of the 3-hydroxypropanoate cycle | 18 | 7 | 1 |