Strain identifier
BacDive ID: 16903
Type strain: 
Species: Thermofilum pendens
Strain Designation: Hrk 5
Strain history: <- W. Zillig, Hrk 5
NCBI tax ID(s): 2269 (species)
version 8.1 (current version)
General
@ref: 1088
BacDive-ID: 16903
DSM-Number: 2475
keywords: genome sequence, 16S sequence, Archaea, anaerobe, hyperthermophilic
description: Thermofilum pendens Hrk 5 is an anaerobe, hyperthermophilic archaeon that was isolated from solfataric hot spring.
NCBI tax id
- NCBI tax id: 2269
- Matching level: species
strain history
- @ref: 1088
- history: <- W. Zillig, Hrk 5
doi: 10.13145/bacdive16903.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/thermoproteota
- domain: Archaea
- phylum: Thermoproteota
- class: Thermoprotei
- order: Thermoproteales
- family: Thermofilaceae
- genus: Thermofilum
- species: Thermofilum pendens
- full scientific name: Thermofilum pendens Zillig and Gierl 1983
@ref: 1088
domain: Archaea
phylum: Crenarchaeota
class: Thermoprotei
order: Thermoproteales
family: Thermofilaceae
genus: Thermofilum
species: Thermofilum pendens
full scientific name: Thermofilum pendens Zillig and Gierl 1983
strain designation: Hrk 5
type strain: yes
Culture and growth conditions
culture medium
- @ref: 1088
- name: THERMOFILUM PENDENS MEDIUM (DSMZ Medium 265)
- growth: yes
- link: https://mediadive.dsmz.de/medium/265
- composition: Name: THERMOFILUM PENDENS MEDIUM (DSMZ Medium 265) Composition: Sulfur 10.0 g/l Sucrose 2.0 g/l Yeast extract 2.0 g/l (NH4)2SO4 1.3 g/l Na2S x 9 H2O 0.3 g/l KH2PO4 0.28 g/l MgSO4 x 7 H2O 0.25 g/l CaCl2 x 2 H2O 0.07 g/l FeCl3 x 6 H2O 0.02 g/l Na2B4O7 x 10 H2O 0.0045 g/l MnCl2 x 4 H2O 0.0018 g/l ZnSO4 x 7 H2O 0.00022 g/l CuCl2 x 2 H2O 5e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l VOSO4 x 2 H2O 3e-05 g/l CoSO4 x 7 H2O 1e-05 g/l Polar lipid fraction Distilled water
culture temp
- @ref: 1088
- growth: positive
- type: growth
- temperature: 88
- range: hyperthermophilic
Physiology and metabolism
oxygen tolerance
- @ref: 1088
- oxygen tolerance: anaerobe
Isolation, sampling and environmental information
isolation
- @ref: 1088
- sample type: solfataric hot spring
- geographic location: Hrafutinnuska Landmannulangar
- country: Iceland
- origin.country: ISL
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Thermal spring |
| #Environmental | #Terrestrial | #Volcanic |
| #Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_187154.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_18160;96_68825;97_89468;98_121746;99_187154&stattab=map
- Last taxonomy: Thermofilum pendens subclade
- 16S sequence: X14835
- Sequence Identity:
- Total samples: 32
- aquatic counts: 32
Safety information
risk assessment
- @ref: 1088
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 1088
- description: Thermofilum pendens DNA for 16S and 23S ribosomal RNA, tRNA-Met, and tRNA-Gly
- accession: X14835
- length: 8935
- database: ena
- NCBI tax ID: 2269
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Thermofilum pendens Hrk 5 | GCA_000015225 | complete | ncbi | 368408 |
| 66792 | Thermofilum pendens Hrk 5 | 639633064 | complete | img | 368408 |
GC content
- @ref: 1088
- GC-content: 57.4
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 74.252 | no |
| flagellated | no | 94.696 | no |
| gram-positive | no | 96.264 | no |
| anaerobic | yes | 98.633 | yes |
| halophile | no | 87.044 | no |
| spore-forming | no | 97.129 | no |
| thermophile | yes | 100 | yes |
| glucose-util | yes | 82.728 | no |
| aerobic | no | 97.644 | yes |
| glucose-ferment | yes | 56.468 | no |
External links
@ref: 1088
culture collection no.: DSM 2475
straininfo link
- @ref: 85909
- straininfo: 47619
literature
- topic: Genetics
- Pubmed-ID: 17369313
- title: In silico screening of archaeal tRNA-encoding genes having multiple introns with bulge-helix-bulge splicing motifs.
- authors: Sugahara J, Yachie N, Arakawa K, Tomita M
- journal: RNA
- DOI: 10.1261/rna.309507
- year: 2007
- mesh: Base Sequence, DNA, Archaeal/chemistry/genetics, Endoribonucleases/genetics/metabolism, Genome, Archaeal, *Introns, Molecular Sequence Data, *RNA Splicing, *RNA, Archaeal, RNA, Transfer/*genetics
- topic2: Metabolism
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 1088 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2475) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-2475 | |
| 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 | |
| 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) | |
| 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |
| 85909 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID47619.1 | StrainInfo: A central database for resolving microbial strain identifiers |