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I'm looking for a database or a systematic way to search for organisms which meet certain criteria. My criteria descending importance are:

  • growth substrate
  • chemolithoautotrophy (on which substrate)
  • overflow metabolite
  • methanogen
  • Nitrogen-fixation

Is there a database / some other means to find this information other than manual digging?

I tried NCBI taxonomy, LINNAEUS, uBio, KEGG, organism-tagger and others, but these don't appear to be capable of this kind of query. They all seem to require the organism name to begin with. But maybe I'm missing something?

thanks for any hints.

Ingvar

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1 Answer 1

Some of the criteria, I guess are difficult to find (Also for my lack of understanding of those terms). For the rest you can search these databases:-

  • Growth substrate: I don't really know what you are asking here — growth rate in minimal media/optimal growth medium ? Nevertheless, see the Media Database
  • Methanogenesis: Ortholog Table - KEGG MODULE M00567
  • Nitrogen fixation: Ortholog Table - KEGG MODULE M00175
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