Strain identifier
BacDive ID: 133988
Type strain: 
Species: Albimonas pacifica
Strain Designation: P-50-3
NCBI tax ID(s): 1114924 (species)
version 8.1 (current version)
General
@ref: 31012
BacDive-ID: 133988
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped
description: Albimonas pacifica P-50-3 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from seawater.
NCBI tax id
- NCBI tax id: 1114924
- Matching level: species
doi: 10.13145/bacdive133988.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Paracoccaceae
- genus: Albimonas
- species: Albimonas pacifica
- full scientific name: Albimonas pacifica Li et al. 2013
@ref: 31012
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Albimonas
species: Albimonas pacifica
strain designation: P-50-3
type strain: yes
Morphology
cell morphology
- @ref: 31012
- gram stain: negative
- cell length: 3 µm
- cell width: 1 µm
- cell shape: rod-shaped
- motility: no
pigmentation
- @ref: 31012
- production: no
Culture and growth conditions
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 31012 | positive | growth | 10-40 | |
| 31012 | positive | optimum | 30 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 31012 | positive | growth | 6.0-9.5 | alkaliphile |
| 31012 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 31012
- oxygen tolerance: aerobe
spore formation
- @ref: 31012
- spore formation: no
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 31012 | NaCl | positive | growth | 0-12 % |
| 31012 | NaCl | positive | optimum | 2 % |
metabolite utilization
- @ref: 31012
- Chebi-ID: 17632
- metabolite: nitrate
- utilization activity: +
- kind of utilization tested: reduction
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 31012 | acid phosphatase | + | 3.1.3.2 |
| 31012 | alkaline phosphatase | + | 3.1.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 31012
- sample type: seawater
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
taxonmaps
- @ref: 69479
- File name: preview.99_69250.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_866;96_29745;97_37558;98_48693;99_69250&stattab=map
- Last taxonomy: Albimonas pacifica subclade
- 16S sequence: JN837486
- Sequence Identity:
- Total samples: 5728
- soil counts: 923
- aquatic counts: 4327
- animal counts: 333
- plant counts: 145
Sequence information
16S sequences
- @ref: 31012
- description: Albimonas pacifica strain P-50-3 16S ribosomal RNA gene, partial sequence
- accession: JN837486
- length: 1427
- database: nuccore
- NCBI tax ID: 1114924
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Albimonas pacifica CGMCC 1.11030 | GCA_900113695 | scaffold | ncbi | 1114924 |
| 66792 | Albimonas pacifica strain CGMCC 1.11030 | 1114924.3 | wgs | patric | 1114924 |
| 66792 | Albimonas pacifica CGMCC 1.11030 | 2667527406 | draft | img | 1114924 |
GC content
- @ref: 31012
- GC-content: 69
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 54.444 | yes |
| flagellated | no | 77.719 | yes |
| gram-positive | no | 98.672 | no |
| anaerobic | no | 96.731 | no |
| aerobic | yes | 90.373 | no |
| halophile | no | 56.664 | no |
| spore-forming | no | 93.798 | no |
| glucose-ferment | no | 88.825 | no |
| thermophile | no | 98.291 | no |
| glucose-util | yes | 82.769 | no |
External links
@ref: 31012
culture collection no.: KACC 16527, CGMCC 1.11030
literature
- topic: Phylogeny
- Pubmed-ID: 23606476
- title: Albimonas pacifica sp. nov., isolated from seawater of the Pacific, and emended description of the genus Albimonas.
- authors: Li GW, Zhang XY, Wang CS, Zhang YJ, Xu XW, Liu C, Li H, Liu A, Xu Z, Song XY, Chen XL, Zhou BC, Zhang YZ
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.049742-0
- year: 2013
- mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Pacific Ocean, Phosphatidylcholines/analysis, Phosphatidylglycerols/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/analysis
- topic2: Genetics
Reference
| @id | authors | title | doi/url | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|
| 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 | |||
| 31012 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 27342 | 28776041 | |
| 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 | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | |
| 69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ |