I’m currently involved in a research that deals with polysaccharides degradation/utilization by bacteria in the human gut.
I used a tool called pSORTb which predicts the cellular localization of proteins. In the results I get, many enzymes which are known to break polysaccharides are predicted to be intracellular. Because polysaccharides have an enormous molecular weight they cannot enter the cell and so that leads to the conclusion that they are not only degraded but also synthesized by the bacteria. However, based on my biological background, I cannot think of any known *intracellular* polysaccharide synthesized by bacteria, except starch.
So either I am wrong and there are many other bacterial polysaccharides synthesized in the cytoplasm, or pSORTb is giving me false predictions of the enzymes’ cellular localization.
Can anyone help me decide on what is more logical?
Thanks! But as far as I looked, pSORTb is the leading predictor for bacterial protein subcellular localization. Obviously there are some mistakes, but what I was more interested in finding out is if there is knowledge of bacterial polysaccharides other than starch which are intracellular. Any idea?
Examine your assumption that this is a valid protocol. pSORTb bills itself as the leading predictor – there aren;t a whole lot of ’em. So challenge its authors with your disconnect at email@example.com.