Strain identifier
BacDive ID: 162985
Type strain: 
Species: Pectobacterium carotovorum subsp. carotovorum
Strain history: IAM 12633 <-- IFO 3380 <-- H. Muko; Natl. Inst. Agro-Environ. Sci., Japan.
NCBI tax ID(s): 555 (subspecies)
version 9.3 (current version)
General
@ref: 67770
BacDive-ID: 162985
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Pectobacterium carotovorum subsp. carotovorum JCM 20699 is a mesophilic, Gram-negative bacterium that was isolated from Soft rot of carrot.
NCBI tax id
- NCBI tax id: 555
- Matching level: subspecies
strain history
- @ref: 67770
- history: IAM 12633 <-- IFO 3380 <-- H. Muko; Natl. Inst. Agro-Environ. Sci., Japan.
doi: 10.13145/bacdive162985.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Enterobacterales
- family: Pectobacteriaceae
- genus: Pectobacterium
- species: Pectobacterium carotovorum subsp. carotovorum
- full scientific name: Pectobacterium carotovorum subsp. carotovorum (Jones 1901) Hauben et al. 1999
synonyms
- @ref: 20215
- synonym: Erwinia carotovora subsp. carotovora
@ref: 67770
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Enterobacterales
family: Pectobacteriaceae
genus: Pectobacterium
species: Pectobacterium carotovorum subsp. carotovorum
full scientific name: Pectobacterium carotovorum subsp. carotovorum (Jones 1901) Hauben 1999
type strain: no
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125438 | negative | 99 |
| 125439 | negative | 99.1 |
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 25
Physiology and metabolism
spore formation
- @ref: 125439
- spore formation: no
- confidence: 97.8
Isolation, sampling and environmental information
isolation
- @ref: 67770
- sample type: Soft rot of carrot
Sequence information
16S sequences
- @ref: 124043
- description: Pectobacterium carotovorum subsp. carotovorum gene for 16S rRNA, partial sequence, strain: NBRC 3380.
- accession: AB680074
- length: 1467
- database: nuccore
- NCBI tax ID: 555
Genome sequences
- @ref: 66792
- description: Pectobacterium carotovorum subsp. carotovorum NBRC 3380
- accession: GCA_024343445
- assembly level: contig
- database: ncbi
- NCBI tax ID: 555
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 99 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 95.254 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 74.104 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 88.55 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 98.083 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 79.979 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 97.8 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 82.1 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 99.1 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | aerobe | 86.5 |
External links
@ref: 67770
culture collection no.: JCM 20699, IAM 12633, IFO 3380, NBRC 3380
straininfo link
- @ref: 113754
- straininfo: 62584
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/ | |
| 113754 | 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-ID62584.1 |
| 124043 | Isabel Schober, Julia Koblitz | Data extracted from sequence databases, automatically matched based on designation and taxonomy | |
| 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 |