So, something's been bugging me all night. I'm doing a literature review on the polyester synthase and a group of related proteins. Coming to the molecular aspect, I encounter the terms "N-terminal / C-terminal regions" often.
How do we (or in the near future, I) determine / decide where the N-terminal or C-terminal spans?
The first thought that came into my mind was a multiple alignment with the same protein in other organisms. But that’s only useful for those having a conserved N or C regions. What more, this particular group of protein has a “non-conserved N-terminal region” while the alpha/beta hydrolase fold domain is conserved in part of the C-terminal (see below).
The regions based on the protein of the model organism. (conserved region in blue)
Until now, only the protein in the model organism is well-studied and annotated. So, another way is to align the amino acid sequence from the model together with those from other organisms. Where the C-terminal begins (aspartate 99), that position will be a benchmark of sort to the other query sequence. Still, I felt this isn’t very convincing.
Waitiing for some feedbacks / suggestions / pointers regarding this.
Edited by dreamchaser_jc, 10 February 2012 - 01:49 AM.