I have obtained 2 proteobacterial, 1 bacteriodetes and 1 cyanobacterial genome of a metagenome from a lake in Tucuruí, Pará, Brazil. I have the assembled contigs and their annotations.
What tools can I use?
You could try PathwayTools Pathologic to predict from orthology.
The RAST server allows metabolic analysis based on KEGG pathways database, using either automatic or your own annotations http://rast.nmpdr.org
Thanks for the answers. I used de RAST to annotate them. I'll check the metabolic analysis and also try the Pathway Tools.
I was worried about the fact that I couldn't be able to recontruct the pathways because I have only the contigs (instead a complete genome) without knowing their order,
Thanks for the answer, Andrea. I'm trying to request a license for MetaCyc.
You can use Blast2GO too. It is better to have strong background on the pathways from literature so that you can refine the pathways from the bioinformatics result which may not be completely accurate. See our recent paper: De_novo_transcriptomic_analysis_of_hydrogen_production_in_the_green_alga_Chlamydomonas_moewusii_through_RNA-Seq. Good luck!
RAST annotation results can be filtered for metabolic annotations.
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