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Rhodoferax odensensis

Citation

Formal styling
Rhodoferax odensensis Petersen et al., 2025
Effective publication
Petersen et al., 2025
SeqCode status
Valid (SeqCode)
Register List
seqco.de/r:ftcpaei9 (validated)
Canonical URL
https://seqco.de/i:44116

Nomenclature

Rank
Species
Syllabication
o.den.sen'sis
Etymology
N.L. masc. adj. odensensis, pertaining to Odense, a city in Denmark where the original sample was collected
Nomenclatural type
NCBI Assembly: GCA_016718405.1
Nomenclatural status
Validly published under the SeqCode

Taxonomy

Description
acterium found in activated sludge.
Genome-wide gene annotation suggested the potential for full glycolysis, pentose phosphate pathway, citric acid cycle and glyoxylate pathway.
Can utilize branched chain amino acids (livFGHKM).
Predicted to convert acetate to acetyl-CoA via acetyl-CoA synthetase, acs, acetate kinase, ackA, and phosphate acetyltransferase, pta.
Potential to reduce nitrate to nitric oxide with nirS. Lastly it also had nitrous oxide reductase, nosZ predicted.
Classification
Bacteria » Pseudomonadota » Betaproteobacteria » Burkholderiales » Comamonadaceae » Rhodoferax » Rhodoferax odensensis
Parent
Rhodoferax

Genomics

Accession
NCBI Assembly:GCA_016718405.1
Type
Metagenome-Assembled Genome (MAG)
Estimated Quality Metrics
  • Completeness: 96.27%
  • Contamination: 1.17%
  • Quality: 90.42
Ribosomal and transfer RNA genes
  • 1 16S rRNA (up to 100.0%)
  • 1 23S rRNA (up to 100.0%)
  • tRNAs for 19 amino acids
Sequencing depth
11.0 ×
Source
Other features
  • G+C Content: 62.67%
  • Coding Density: 89.18%
  • Codon Table: 11
  • N50: 268,872 bp
  • Contigs: 42
  • Largest Contig: 598,754 bp
  • Assembly Length: 4,871,556 bp
  • Ambiguous Assembly Fraction: 0.0%
Submitter comments
The binning in this project followed the mmlong v0.1.2 hybrid-metaflowpipeline after the assembly step. Metagenome contigs were translated into proteins using FragGeneScan v1.31, annotated taxonomically using Kaiju v1.6.0 against the proGenomes database (2017-05-16). DASTool v1.1.1 --search_engine diamond was used to dereplicate and select for the best representative bin. The dereplicated bins in the analysis were checked for completeness and contamination using CheckM --lineage_wf v1.0.11.
Genome taxonomy was determined using GTDB-Tk v1.0.2 and the refseq release 89 (2019-06-19) database, and the dependencies pplacer v1.1, FastANI v1.2, Prodigal v2.6.2, FastTree 2 v1.2, and HMMER v3.1b2.
Automated checks
Complete
See additional details
Last modified 3 months ago

Metadata

Outside links and data sources
Search sequences
Local history
Registered
Over 1 year ago by Fischer Petersen, Jette
Submitted
Over 1 year ago by Fischer Petersen, Jette
Curators
Endorsed
Over 1 year ago by Rodriguez-R, Luis M
Validated
3 months ago by Palmer, Marike
Date of priority
2025-08-28 09:33 AM (UTC)

Publications
1

Citation Title
Petersen et al., 2025, Systematic and Applied Microbiology Diversity and physiology of abundant Rhodoferax species in global wastewater treatment systems
Effective publication


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seqco.de/r:ftcpaei9