Pantoea rara

Citation

Formal styling

Pantoea rara Crosby et al., 2023

Effective publication

Crosby et al., 2023

SeqCode status

Valid (SeqCode)

Register List

seqco.de/r:xfaladud (validated)

Canonical URL

https://seqco.de/i:31356

Nomenclature

Rank

Species

Syllabication

ra'ra

Etymology

L. fem. adj. rara, sporadic or uncommon, referring to the sporadic isolation and recovery from disparate sources of members of this species

Nomenclatural type

NCBI Assembly: GCA_002419935.1

Nomenclatural status

Validly published under the SeqCode

Taxonomy

Description

This species consists of the genomes of strain WMus005, isolated from the oral cavity of a wild house mouse (Mus musculus) in the United Kingdom, and the metagenome-assembled genome (MAG) UBA5707 recovered from a metagenomic sample taken from the New York City subway system. Pairwise ANI of the two genomes is over 99% and they thus clearly belong to the same species, with all comparisons to other species below species delineation guidelines. The nomenclatural type for the species is the genome UBA5707^Ts, available under the assembly accession number GCA_002419935.1.

Classification

Bacteria » Pseudomonadota » Gammaproteobacteria » Enterobacterales » Erwiniaceae » Pantoea » Pantoea rara

Parent

Pantoea gtdb

Genomics

Accession

NCBI Assembly:GCA_002419935.1

Type

Metagenome-Assembled Genome (MAG)

Estimated Quality Metrics

• Completeness: 97.87%
• Contamination: 0.36%
• Quality: 96.07

Ribosomal and transfer RNA genes

• 0 16S rRNAs
• 0 23S rRNAs
• tRNAs for 18 amino acids

Sequencing depth

40.92 ×

Source

• BioSample: SAMN06452238
• BioSample: SAMN03271299

Other features

• G+C Content: 54.96%
• Coding Density: 87.81%
• Codon Table: 11
• N50: 464,666 bp
• Contigs: 14
• Largest Contig: 1,392,764 bp
• Assembly Length: 4,248,722 bp
• Ambiguous Assembly Fraction: 0.009%

Submitter comments

Quality assessed with CheckM v. 1. rRNA prediction performed with barrnap v. 0.9, and tRNA prediction performed with tRNAscan-SE v. 2.0.9.

Automated checks

Complete

See additional details

---

Last modified 6 days ago

Metadata

Outside links and data sources

• GTDB Genome: GCA_002419935.1
• GTDB Tree: s__Pantoea rara
• Global Biodiversity Information Facility (GBIF)
• Wikispecies: Pantoea rara (see reference source)

Search sequences

• Seach in NCBI Nucleotide

Local history

• This name was last modified 12 months ago
• Submission process status
• Quality checks before valid publication

Registered by

Palmer, Marike over 1 year ago

Submitted by

Palmer, Marike over 1 year ago

Curators

• Rodriguez-R, Luis M
• Chuvochina, Maria

Endorsed by

Chuvochina, Maria over 1 year ago

Validated by

Rodriguez-R, Luis M 12 months ago

Date of priority

2023-11-15 01:31 PM (UTC)