This second kind of analysis is done by lining up lots of known binding sites for a particular protein, comparing them position by position, and so finding out which letter is most likely to occur at which position, and how probable it is that a different letter may sometimes crop up instead.
This binding process stimulates production of a protein called interleukin-10 (IL-10) that acts as an anti-inflammatory compound and which helps keep the immune system's response to the infection in check.