Has anyone tried using KOFAMSCAN? I feel like the data is useless unless I'm not using it correctly. There are literally SO many KOFAM hits per gene. What are your thoughts on this? Is it because I'm using it on a metagenomics dataset? It doesn't make sense that almost ever gene has so many hits for each gene. Check out the screenshot:
ATP-binding transporters are one of the largest and most promiscuous protein superfamilies - see here. Their overall structure is the same and is different mostly in parts that bind and recognize the substrate. That is a relatively small portion of the protein, so most if not all transporter proteins will have statistically significant hits to a number of HMMs. This is not just the case with KOFAMSCAN - if you translate that region into protein and search against Pfam or any other protein family database, you will get multiple hits as well. The same will be true for methyltransferases, dehydrogenases, alpha/beta hydrolases, SAM-radical enzymes, and many other large and functionally diverse proteins superfamilies.
In your case, top 5 or so hits indicate that this is likely a transporter for a small sugar molecule.
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