Strain identifier
BacDive ID: 162365
Type strain: 
Species: Silvimonas sp.
Strain history: T. Iida Avf-YS5.
NCBI tax ID(s): 1301084 (species)
version 9.3 (current version)
General
@ref: 67770
BacDive-ID: 162365
keywords: genome sequence, Bacteria, mesophilic, Gram-negative
description: Silvimonas sp. JCM 19000 is a mesophilic, Gram-negative bacterium of the family Chromobacteriaceae.
NCBI tax id
- NCBI tax id: 1301084
- Matching level: species
strain history
- @ref: 67770
- history: T. Iida Avf-YS5.
doi: 10.13145/bacdive162365.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Neisseriales
- family: Chromobacteriaceae
- genus: Silvimonas
- species: Silvimonas sp.
- full scientific name: Silvimonas Yang et al. 2005
@ref: 67770
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Neisseriales
family: Chromobacteriaceae
genus: Silvimonas
species: Silvimonas sp.
full scientific name: Silvimonas sp.
type strain: no
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125438 | negative | 98.5 |
| 125439 | negative | 98.6 |
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 30
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: obligate aerobe
- confidence: 99.6
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 125438 | no | 90.685 |
| 125439 | no | 96.3 |
Sequence information
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Silvimonas sp. JCM 19000 | GCA_001313065 | contig | ncbi | 1301084 |
| 66792 | Silvimonas sp. JCM 19000 | 1301084.5 | wgs | patric | 1301084 |
| 66792 | Silvimonas sp. JCM 19000 | 2734481929 | draft | img | 1301084 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 98.5 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 93.803 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 90.685 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 52.19 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 97.5 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 73.745 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 96.3 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 60.1 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 98.6 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 99.6 |
External links
@ref: 67770
culture collection no.: JCM 19000
Reference
| @id | authors | title | doi/url |
|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |