Strain identifier
BacDive ID: 163051
Type strain: 
Species: Agrobacterium sp.
Strain history: IAM 13943 <-- LMG 27 <-- A. C. Hayward 0363 <-- A. Kerr E27/2.
NCBI tax ID(s): 361 (species)
version 9.3 (current version)
General
@ref: 67770
BacDive-ID: 163051
keywords: genome sequence, Bacteria, mesophilic, Gram-negative
description: Agrobacterium sp. JCM 20994 is a mesophilic, Gram-negative bacterium that was isolated from Soil.
NCBI tax id
- NCBI tax id: 361
- Matching level: species
strain history
- @ref: 67770
- history: IAM 13943 <-- LMG 27 <-- A. C. Hayward 0363 <-- A. Kerr E27/2.
doi: 10.13145/bacdive163051.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Rhizobiaceae
- genus: Agrobacterium
- species: Agrobacterium sp.
- full scientific name: Agrobacterium Conn 1942 (Approved Lists 1980)
@ref: 67770
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Hyphomicrobiales
family: Rhizobiaceae
genus: Agrobacterium
species: Agrobacterium sp.
full scientific name: Agrobacterium sp.
type strain: no
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125438 | negative | 98.5 |
| 125439 | negative | 99.6 |
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 25
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: obligate aerobe
- confidence: 97.8
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 125439 | no | 99.1 |
| 125438 | no | 95.432 |
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Soil
- geographic location: South Australia
- country: Australia
- origin.country: AUS
- continent: Australia and Oceania
Sequence information
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Agrobacterium tumefaciens CFBP5506 | GCA_005144495 | complete | ncbi | 358 |
| 66792 | Agrobacterium tumefaciens strain CFBP5506 | 358.246 | wgs | patric | 358 |
GC content
- @ref: 67770
- GC-content: 60.3
- method: thermal denaturation, midpoint method (Tm)
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 | 96.209 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 95.432 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 86.685 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 100 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 69.853 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 99.1 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 69.5 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 99.6 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 97.8 |
External links
@ref: 67770
culture collection no.: JCM 20994, CFBP 5506, IAM 13943, LMG 27
straininfo link
- @ref: 113819
- straininfo: 460
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/ | |
| 113819 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID460.1 |
| 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 |