Strain identifier
BacDive ID: 163286
Type strain: 
Species: Hafnia alvei
Strain history: R. Sakazaki 287 <-- ATCC 9760 <-- Parke, Davis & Co.; 04414 <-- NCTC 6578 <-- E. F. Gale strain Cadaveris.
NCBI tax ID(s): 569 (species)
version 9.3 (current version)
General
@ref: 67770
BacDive-ID: 163286
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Hafnia alvei JCM 24184 is a mesophilic, Gram-negative bacterium of the family Hafniaceae.
NCBI tax id
- NCBI tax id: 569
- Matching level: species
strain history
- @ref: 67770
- history: R. Sakazaki 287 <-- ATCC 9760 <-- Parke, Davis & Co.; 04414 <-- NCTC 6578 <-- E. F. Gale strain Cadaveris.
doi: 10.13145/bacdive163286.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Enterobacterales
- family: Hafniaceae
- genus: Hafnia
- species: Hafnia alvei
- full scientific name: Hafnia alvei Møller 1954 (Approved Lists 1980)
@ref: 67770
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Enterobacterales
family: Hafniaceae
genus: Hafnia
species: Hafnia alvei
full scientific name: Hafnia alvei M›ller 1954
type strain: no
Morphology
cell morphology
- @ref: 125438
- gram stain: negative
- confidence: 99.985
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 37
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 125439 | no | 97 |
| 125438 | no | 90.135 |
enzymes
- @ref: 67770
- value: lysine decarboxylase
- ec: 4.1.1.18
Sequence information
16S sequences
- @ref: 67770
- description: Hafnia alvei gene for 16S rRNA, partial sequence, strain: JCM 24184
- accession: AB435601
- length: 512
- database: nuccore
- NCBI tax ID: 569
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Hafnia alvei strain NCTC6578 | 569.80 | wgs | patric | 569 |
| 66792 | Hafnia alvei NCTC 6578 | 2835273707 | draft | img | 569 |
| 67770 | Hafnia alvei NCTC6578 | GCA_900451125 | contig | ncbi | 569 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 99.985 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 95.874 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 90.135 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 61.765 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 99.5 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 74.429 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 97 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 69.7 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 86.5 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 87.2 |
External links
@ref: 67770
culture collection no.: JCM 24184, ATCC 9760, NCTC 6578
straininfo link
- @ref: 114004
- straininfo: 35124
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/ | |
| 114004 | 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-ID35124.1 |
| 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 |