Henrik Nielsen (hnielsen at rna) wrote:
: I need to classify some sequence entries from databases into
: Gram-positive (single-membraned, such as B.subtilis) and Gram-negative
: (double-membraned, such as E.coli) bacteria. SWISSPROT, however, does
: not use those terms in the classification, instead it divides
: PROKARYOTA into FIRMICUTES, GRACILICUTES (including ANOXYPHOTOBACTERIA,
: OXYPHOTOBACTERIA, and SCOTOBACTERIA), MENDOSICUTES (= ARCHAEBACTERIA),
: and TENERICUTES (= MYCOPLASMA). Do these groups relate to the Gram +/-
: concept, and if so, how?
: Would it e.g. be safe to say that FIRMICUTES = Gram+ and GRACILICUTES
: (or maybe SCOTOBACTERIA) = Gram- ???
: Answers will be greatly appreciated.
Two very useful resources for prokaryote classification are:
The Ribosomal Database Project at University of Illinois,
You can download a PostScript file of the current tree,
or a plaintext file (more useful for searching).
An article describing RDP was published in one of the
January issues of J.Bacteriology.
NCBI's Entrez database/software incorporates a full taxonomy of living
things now, with a nice tree-oriented browser of the taxonomy. If your
Entrez software doesn't have this, time for an upgrade.
Entrez software is available via ftp from ncbi.nlm.nih.gov.
There is also a WWW version of Entrez available at
Both of these taxonomies use a much broader model than Gram+/Gram-.
Department of Cellular and Developmental Biology
Department of Genetics / HHMI
robison at mito.harvard.edu