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Egaibacter danicusTs

Citation

Formal styling
Egaibacter danicusTs 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:44120

Nomenclature

Rank
Species
Syllabication
da'ni.cus
Etymology
L. masc. adj. danicus, Danish
Nomenclatural type
NCBI Assembly: GCA_016707075.1
Nomenclatural status
Validly published under the SeqCode

Taxonomy

Description
Bacterium found in activated sludge.
Genome-wide gene annotation suggested the potential for full glycolysis, pentose phosphate pathway, citric acid cycle and glyoxylate pathway.
Glucose uptake of via the gtsABC+malK transporter was also predicted.
Can utilize branched chain amino acids (livFGHKM).
Predicted to convert acetate to acetyl-CoA via acetyl-CoA synthetase, acs.
Potential to reduce nitrate with narGHI along with the reduction of nitrate to nitric oxide with nirS. 
Classification
Bacteria » Pseudomonadota » Betaproteobacteria » Burkholderiales » Burkholderiaceae » Egaibacter » Egaibacter danicusTs
Parent
Egaibacter

Genomics

Accession
NCBI Assembly:GCA_016707075.1
Type
Metagenome-Assembled Genome (MAG)
Estimated Quality Metrics
  • Completeness: 98.01%
  • Contamination: 4.13%
  • Quality: 77.36
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
11.1 ×
Source
Other features
  • G+C Content: 58.9%
  • Coding Density: 90.48%
  • Codon Table: 11
  • N50: 413,670 bp
  • Contigs: 32
  • Largest Contig: 659,705 bp
  • Assembly Length: 4,340,715 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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