Predicting and identifying microbes and enzymes DNA sequence with metabolic prediction
The first step after sequencing is finding probable genes. After that, genes and their proteins can be classified to belong to protein classes. This is the most what you can do with completely unknown genes. It's possible nowadays to predict the final structure using contact maps (if there is no homologous structure known) but this will still leave you unclear on ligands in many cases. So, the final step is to clarify the function with biochemical lab methods.

So, if you are stuck with a huge sequence, first try to find the genes in it.

http://en.wikipedia.org/wiki/Gene_prediction

For subsequent annotation/classification, I recommend InterPro and PROSITE.

http://www.ebi.ac.uk/Tools/pfa/iprscan/

http://prosite.expasy.org/scanprosite/