Strain identifier
BacDive ID: 13164
Type strain: 
Species: Pseudomonas panipatensis
Strain Designation: Esp-1
Strain history: <- R. Lal, Univ. Delhi, Dept. Zoology; Esp-1
NCBI tax ID(s): 428992 (species)
version 8.1 (current version)
General
@ref: 15969
BacDive-ID: 13164
DSM-Number: 21819
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Pseudomonas panipatensis Esp-1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from oil contaminated soil.
NCBI tax id
- NCBI tax id: 428992
- Matching level: species
strain history
- @ref: 15969
- history: <- R. Lal, Univ. Delhi, Dept. Zoology; Esp-1
doi: 10.13145/bacdive13164.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Pseudomonadales
- family: Pseudomonadaceae
- genus: Pseudomonas
- species: Pseudomonas panipatensis
- full scientific name: Pseudomonas panipatensis Gupta et al. 2008
@ref: 15969
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pseudomonadales
family: Pseudomonadaceae
genus: Pseudomonas
species: Pseudomonas panipatensis
full scientific name: Pseudomonas panipatensis Gupta et al. 2008
strain designation: Esp-1
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 32377 | negative | 3.15 µm | 1.1 µm | rod-shaped | yes | |
| 69480 | yes | 97.56 | ||||
| 69480 | negative | 99.996 |
Culture and growth conditions
culture temp
- @ref: 32377
- growth: positive
- type: growth
- temperature: 28-37
- range: mesophilic
culture pH
- @ref: 32377
- ability: positive
- type: growth
- pH: 05-09
- PH range: alkaliphile
Physiology and metabolism
oxygen tolerance
- @ref: 32377
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 32377 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.961 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32377 | 22599 | arabinose | + | carbon source |
| 32377 | 28757 | fructose | + | carbon source |
| 32377 | 28260 | galactose | + | carbon source |
| 32377 | 17234 | glucose | + | carbon source |
| 32377 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 32377 | catalase | + | 1.11.1.6 |
| 32377 | cytochrome oxidase | + | 1.9.3.1 |
| 32377 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
- @ref: 15969
- sample type: oil contaminated soil
- geographic location: Panipat Oil Refinery
- country: India
- origin.country: IND
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Contamination | #Oil (Fuel) |
| #Environmental | #Terrestrial | #Soil |
Safety information
risk assessment
- @ref: 15969
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 15969
- description: Pseudomonas panipatensis strain Esp-1 16S ribosomal RNA gene, partial sequence
- accession: EF424401
- length: 1419
- database: ena
- NCBI tax ID: 428992
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pseudomonas panipatensis CCM 7469 | GCA_900099785 | scaffold | ncbi | 428992 |
| 66792 | Pseudomonas panipatensis strain CCM 7469 | 428992.5 | wgs | patric | 428992 |
| 66792 | Pseudomonas panipatensis Esp-1 | 2706794920 | draft | img | 428992 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 88.122 | yes |
| flagellated | yes | 77.169 | no |
| gram-positive | no | 98.469 | yes |
| anaerobic | no | 98.239 | yes |
| aerobic | yes | 88.341 | no |
| halophile | no | 83.646 | no |
| spore-forming | no | 95.568 | yes |
| glucose-ferment | no | 90.832 | no |
| thermophile | no | 99.643 | yes |
| glucose-util | yes | 90.055 | yes |
External links
@ref: 15969
culture collection no.: DSM 21819, CCM 7469, MTCC 8990
straininfo link
- @ref: 82372
- straininfo: 354319
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 18523175 | Pseudomonas panipatensis sp. nov., isolated from an oil-contaminated site. | Gupta SK, Kumari R, Prakash O, Lal R | Int J Syst Evol Microbiol | 10.1099/ijs.0.65401-0 | 2008 | Bacterial Typing Techniques, Base Sequence, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, India, Molecular Sequence Data, Nucleic Acid Hybridization, *Petroleum, Phenotype, Phylogeny, Pseudomonas/*classification/genetics/*isolation & purification/physiology, RNA, Ribosomal, 16S/chemistry/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Species Specificity | Genetics |
| Phylogeny | 33411665 | Pseudomonas nicosulfuronedens sp. nov., a nicosulfuron degrading bacterium, isolated from a microbial consortium. | Li M, Ma Q, Kong D, Han X, Che J, Zhou Y, Jiang X, Ruan Z, Zhang Q | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004632 | 2021 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, *Microbial Consortia, Phospholipids/chemistry, *Phylogeny, Pseudomonas/*classification/isolation & purification, Pyridines/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sulfonylurea Compounds/*metabolism, Ubiquinone/chemistry | Metabolism |
| Phylogeny | 34705625 | Pseudomonas schmalbachii sp. nov., isolated from the gut of a millipede (Trigoniulus corallinus) from a coconut tree. | Shelomi M, Chen WM, Chen HK, Lee HY, Young CC, Lin SY, Liaw SJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005101 | 2021 | Animals, *Arthropods/microbiology, Bacterial Typing Techniques, Base Composition, Cocos, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, Pseudomonas/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 15969 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21819) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21819 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 32377 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28605 | 28776041 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 82372 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID354319.1 | StrainInfo: A central database for resolving microbial strain identifiers |