Yersinia pestis KIM (biovar Mediaevalis)

Yersinia pestis is the causitive agent of bubonic and pneumonic plague, which has caused widespread loss of human life during recurrent pandemics. We have completed the genome sequence of Y. pestis KIM (biovar Mediaevalis), chosen because it has been widely used in research and is thus more genetically characterized than other strains.

Whole-genome shotgun libraries of Y. pestis KIM10+ were constructed in the M13Janus vector with an insert size of 1.0-2.5 kbp, and in a pBlueScript plasmid vector with an insert size of 5-6 kbp. Clones were sequenced by the method of Sanger on ABI 377 and 3700 instruments, collecting over 85,000 reads.

The completed chromosome sequence (4,600,755 bp; 47.64% G+C) has been annotated and deposited in the public databases (accession number AE009952). In addition, three plasmids are present in Y. pestis KIM: pMT1 (accession number AF074611), pCD1 (accession number AF074612), and pPCP1 (unpublished).


  • W. Deng, V. Burland, G. Plunkett III, A. Boutin, G. F. Mayhew, P. Liss, N. T. Perna, D. J. Rose, B. Mau, S. Zhou, D. C. Schwartz, J. D. Fetherston, L. E. Lindler, R. R. Brubaker, G. V. Plano, S. C. Straley, K. A. McDonough, M. L. Nilles, J. S. Matson, F. R. Blattner, and R. D. Perry (2002) Genome sequence of Yersinia pestis KIM. J Bacteriol 184(16):4601-4611. [PubMed] [full text] [abstract]
  • R.D. Perry, S. C. Straley, J. D. Fetherston, D. J. Rose, J. Gregor, and F. R. Blattner (1998) DNA sequencing and analysis of the low-Ca2+-response plasmid pCD1 of Yersinia pestis KIM5. Infect Immun 66(10):4611-23. [PubMed]
  • L. E. Lindler, G. V. Plano, V. Burland, G. F. Mayhew, and F. R. Blattner (1998) Complete DNA sequence and detailed analysis of the Yersinia pestis KIM5 plasmid encoding murine toxin and capsular antigen. Infect Immun 66(12):5731-42. [PubMed]
  • A. M. Gehring, E. DeMoll, J. D. Fetherston, I. Mori, G. F. Mayhew, F. R. Blattner, C. T. Walsh, and R. D. Perry (1998) Iron acquisition in plague: modular logic in enzymatic biogenesis of yersiniabactin by Yersinia pestis. Chem Biol 5(10):573-86. [PubMed]

Sequence availability

We have placed the annotated genome sequence on our web server (see below). The chromosomal sequence has been processed by NCBI and entered into GenBank as 415 "pieces" (accession numbers AE013601 - AE014015), accessible via Entrez and BLAST. The complete genome as a single entry is also available via the NCBI ftp site.

  • Annotated sequence in GenBank flatfile format: AE009952.gbk
  • Sequence in fasta format: AE009952.fas
  • Sequences of annotated genes (CDS, rRNA, tRNA, misc_RNA) in fasta format: AE009952.fna
  • Sequences of individual proteins in fasta format: AE009952.faa

Table of Y. pestis KIM features

A table of the annotated features (CDS, rRNA, tRNA, misc_RNA, pseudogene, IS elements) in the current Y. pestis KIM sequence has been prepared. The table is a tab-delimited text file in a Zip archive: AE009952 table

Linear map of Y. pestis KIM chromosome

The 10-page map is available as individual pages (.pdf files; see below) or a single Zip archive containing all 10 .pdf pages (10pagemap). The genes are color-coded according to a simplified scheme, shown in the Key on page 10. Backbone (i.e., like E. coli K-12) genes are dark blue. All other genes are classified by function. The map consists of two tiers. The top tier shows color-coded genes, with gene names above, aligned with the left end of the corresponding gene. If no gene name was assigned, the y-number is shown. The second tier shows RNA genes and IS elements. RNAs are pale blue; ribosomal RNA operons are labelled "rRNA" and gene names are shown for miscellaneous stable RNAs. Transfer RNAs are shown as pale blue ticks but are not named as the genes are too small to be distinguished individually. IS designations are shown; partial elements are marked by "p" before the IS name.

  1. 1-500,000 bp
  2. 500,001-1,000,000 bp
  3. 1,000,001-1,500,000 bp
  4. 1,500,001-2,000,000 bp
  5. 2,000,001-2,500,000 bp
  6. 2,500,001-3,000,000 bp
  7. 3,000,001-3,500,000 bp
  8. 3,500,001-4,000,000 bp
  9. 4,000,001-4,500,000 bp
  10. 4,500,001-4,600,755 bp


This project is part of our Bacterial Pathogens Genome Initiative, funded by NIAID.

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