We have loads of different critters co-inhabiting with us, and this can be very useful if you need to publish some papers and progress your career. There are at least 2 ways of doing so.
First, you can do phylogenetic analysis of these and ask questions, such as what is conserved in particular protein? Can we relate these conserved residues to some conserved function? What is not conserved? How is this protein related to other proteins? Can we retrace functional evolution via sequence evolution and vice versa, can we predict some functions for the not yet well studied protein knowing something about its sequence? Gem here is talking about stuff like that.
However, there is a problem with this sort of approach. You end up presenting your data in a format that can be criticized by reviewers or readers, or both. They might wonder about your bootstrap values, accuse you of LBA and in general scoff your alignments and so on. Also, you endup testing your hypotheses, or having them tested by other people, and there is a possibility of being wrong when you test things you predict.
Therefore there is an alternative way of benefiting from the diversity of live in order to produce papers. That would be using heterologous systems. This is how it goes.
You take an interacting protein pair from 2 bugs, A and B. It does not matter what bugs are these. Some bugs. As an example you can take proteins EF-G and RRF which split the ribosome after it has finished making the protein. Then you mix them and see if they can do the job in different combinations (AA, AB, BA and BB). If they all work, then you take bug C, and repeat it until you find a combination that does not work. And if you are not bored, you can take bugs D and F and do it again. So far you produced two papers.
The only question remaining is - did you learn anything? From the evolutionary point of view your result is boring - you have found some sequence co-variation, which results in factors from the same organism working together, but not cooperating with a stranger. This is an obvious result which so far generated no hypotheses (having an alignment on the side could generate one though - looking for the co-variation in the 2 proteins would suggest where the differences are).
And when we talk about alignments, we are talking about multiple ones. Aligning 2 genes from the bugs A and B you study has very little information about the conservation of the differences you are looking at (but this is exactly what is done in the EF-G / RRF paper cited above and in the later paper from the same group working now on IF2 from E. coli and bovine mitochondria - heterologous system strikes again!).
References:
Having a tree to go with alignment will make it all even more informative, cause then you can see the directions of sequence changes, but hey - now we are getting in trouble! We are about to do it properly.
Rao AR, & Varshney U (2001). Specific interaction between the ribosome recycling factor and the elongation factor G from Mycobacterium tuberculosis mediates peptidyl-tRNA release and ribosome recycling in Escherichia coli. The EMBO journal, 20 (11), 2977-86 PMID: 11387230
Seshadri A, Singh NS, & Varshney U (2010). Recycling of the posttermination complexes of Mycobacterium smegmatis and Escherichia coli ribosomes using heterologous factors. Journal of molecular biology, 401 (5), 854-65 PMID: 20561528
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