rMLST Klebsiella/Raoultella Species Annotation Server
Please upload a FASTA format file for an assembled bacterial genome.
Approximate scan time per uploaded 5Mb genome is 5 seconds.
Example Genome File (right-click to save): Example
Species=Klebsiella aerogenes (GCA_000534255.1).
Klebsiella/Raoultella rMLST Nucleotide Identity (rMLST-NI) Scan
- The input genome is scanned against the DNA sequences of rMLST loci found in the 17 Klebsiella/Raoultella type strains using BLASTN.
- A 'local' nucleotide identity between the query genome and each type strain is calculated across all rMLST loci in the rMLST profile (excludes paralogous loci).
- Nucleotide identity thresholds for each type strain have been empirically determined from rMLST-NI scans between a dataset of Klebsiella/Raoultella representative isolates with verified species annotations.
- For each type strain, threshold A is the lowest value observed for any member of the same species and threshold B is the highest value observed for any member of a different species.
- This translates into three species confidence categories as follows:
- High Species Confidence (Green) = Observed rMLST-NI is typical of isolates with the same species (above threshold A).
- Intermediate Species Confidence (Amber) = Observed rMLST-NI is outside the range currently observed for this species (between threshold A and B). This could be a distant member of this species or a new species that is not present in the current library.
- Low Species Confidence (Red) = Observed rMLST-NI is well outside the range currently observed for this species (below threshold B).
Klebsiella/Raoultella Library Information
Created using 17 Klebsiella/Raoultella type strain isolates obtained from the NCBI Assembly database (March 2021).
| NCBI Assembly Genome | Isolate Name | Species |
|---|---|---|
| GCA_000215745.1 | KCTC 2190 | Klebsiella aerogenes |
| GCA_900978845.1 | SB5857 | Klebsiella africana |
| GCA_900200035.1 | 06D021 | Klebsiella grimontii |
| GCA_003261575.2 | WCHKl090001 | Klebsiella huaxiensis |
| GCA_005860775.1 | TOUT106 | Klebsiella indica |
| GCA_002925905.1 | DSM 25444 | Klebsiella michiganensis |
| GCA_001598695.1 | NBRC 105695 | Klebsiella oxytoca |
| GCA_902158725.1 | SB6412 | Klebsiella pasteurii |
| GCA_000281755.1 | DSM 30104 | Klebsiella pneumoniae |
| GCA_000751755.1 | 01A030 | Klebsiella quasipneumoniae |
| GCA_002269255.1 | KPN1705 | Klebsiella quasivariicola |
| GCA_902158555.1 | SB6411 | Klebsiella spallanzanii |
| GCA_000828055.2 | DSM 15968 | Klebsiella variicola |
| GCA_006711645.1 | DSM 102253 | Raoultella electrica |
| GCA_001598295.1 | NBRC 105727 | Raoultella ornithinolytica |
| GCA_000735435.1 | ATCC 33531 | Raoultella planticola |
| GCA_900706855.1 | NCTC13038 | Raoultella terrigena |
Datafiles used by the server
These files are for academic non-commercial use only (right-click to save). Allele sequences are obtained from the Ribosomal MLST database. Terms and conditions of usage are found on the rMLST website.
Allelic profiles for 17 Klebsiella/Raoultella type strains
Nucleotide identity thresholds (server)
Nucleotide identity thresholds (original)
James Bray