Gammaproteobacteria: Pseudomonas putida KT2440
NCBI taxonomy id: 160488
Fitness Experiments
| Group | Conditions | Experiments |
|---|---|---|
| agar plate interaction | 1 | 18 |
| agar plate interaction control | 1 | 3 |
| anaerobic m9 | 1 | 2 |
| carbon source | 151 | 300 |
| control | 1 | 1 |
| dilutelb | 1 | 2 |
| in planta | 10 | 32 |
| lb | 1 | 5 |
| lb outgrowth control | 1 | 3 |
| lb outgrowth control more dilute start | 1 | 3 |
| micoeukaryotes | 1 | 8 |
| microaerobic m9 | 1 | 2 |
| mixed carbon source | 7 | 16 |
| mixed community | 1 | 1 |
| mixed community control | 1 | 1 |
| nitrogen source | 74 | 167 |
| no phage control | 2 | 6 |
| no stress control | 2 | 6 |
| nophagecontrol | 2 | 5 |
| pH | 11 | 50 |
| phage | 4 | 34 |
| phage moi 100 | 1 | 3 |
| phagefrs | 1 | 3 |
| r2a control | 1 | 6 |
| r2a control with 0.2% methanol | 1 | 5 |
| r2a control with 0.2x vogels | 1 | 4 |
| reactor | 1 | 15 |
| reactor_pregrowth | 1 | 7 |
| soil | 26 | 62 |
| stress | 34 | 104 |
| supernatant | 9 | 19 |
| supernatant control:fungal media | 1 | 4 |
| temperature | 4 | 29 |
| temperature shift | 2 | 52 |
| time series | 1 | 10 |
| toxin | 1 | 1 |
Tools
- Build heatmap
- Experiment correlations
- KEGG maps
- KEGG overview map
- SEED subsystems
- MetaCyc pathways
- Curated BLAST for this genome
- GapMind for amino acid biosynthesis or carbon catabolism
- ENIGMA genome browser
Specific Phenotypes
992 genes with specific phenotypes, and 277 with conserved-specific phenotypes.
| Group | # Conditions | # Genes |
|---|---|---|
| agar plate interaction | 1 | 12 |
| agar plate interaction control | 1 | 4 |
| carbon source | 105 | 625 |
| control | 1 | 1 |
| dilutelb | 1 | 14 |
| in planta | 10 | 64 |
| lb | 1 | 1 |
| micoeukaryotes | 1 | 77 |
| microaerobic m9 | 1 | 1 |
| mixed carbon source | 1 | 40 |
| mixed community | 1 | 3 |
| mixed community control | 1 | 1 |
| nitrogen source | 54 | 360 |
| no phage control | 1 | 3 |
| no stress control | 1 | 10 |
| nophagecontrol | 1 | 2 |
| pH | 3 | 43 |
| phage | 4 | 104 |
| phage moi 100 | 1 | 4 |
| phagefrs | 1 | 4 |
| r2a control | 1 | 1 |
| r2a control with 0.2% methanol | 1 | 3 |
| reactor | 1 | 14 |
| reactor_pregrowth | 1 | 5 |
| soil | 15 | 28 |
| stress | 22 | 128 |
| supernatant | 5 | 88 |
| supernatant control:fungal media | 1 | 4 |
| temperature | 2 | 15 |
| temperature shift | 1 | 23 |
| time series | 1 | 2 |
| toxin | 1 | 6 |
Updated Annotations
Updated annotations for 41 genesScaffolds
Downloads
- Fitness values (tab-delimited)
- t scores (tab-delimited)
- Top cofitness for each gene (tab-delimited)
- includes 487 genes with conserved cofitness
- Specific phenotypes (tab-delimited)
- Experiment meta-data (tab-delimited)
- Reannotations (tab-delimited; includes protein sequences)
- Genome sequence (fasta)
- Protein sequences (fasta)
- List of genes (tab-delimited)
Fitness data for 4778 of 5661 genes.