I have figured out how to download the fasta of the genomes of microorganisms, for example the botulism bacteria and the spirulina algae. However, I want to find a fasta file for some significant extraction of those genomes - say, some important gene, some mutation, some protein that occurs in a microorganisms genome. What should I look for, and how can I find it in genbank?
You can use already available tools to extract information from available database. For finding specific genes, use this. For protein, use this. There are lot more tools. Just explore NCBI, EMBL or DDBJ sites. All information is self explanatory. If you want specialized information for specific organism, you can use specialized database ( like Flybase for flies, SGD for common yeast, EnsemblBacteria for bacteria and archaea or HGMD for human mutations. Best way is to search in Google. You will get everything you want :D
I guess you have found the Genome entry of your favourite genomes in Genbank and got the FastA.
Dexter is completely right, you can just search your genes in the databases and filter them for your genomes of interest.
Another possibility is to get the GenBank-formated file "GenBank (full)", instead of the FastA, then use a Genome Browser (for example Artemis) which allows you to search for genes/proteins in a genome and save them as separate FastA files.
Generally it is a good thing to get the GenBank format file for an organism you are interested in, as you can extract the complete genome sequence as FastA easily, but also keep all the other information you might need later.