As you've seen, when aligning two sequences, the alignment can be either global or local. While the global alignment always includes both sequences from beginning to end, the local alignment can cover just a shorter stretch of the full sequences.
The two proteins O77266 and O69363 both contain a Rieske [2Fe-2S] domain but have otherwise unrelated sequences. Download the sequences from their ``Niceprot pages'' (look for the ``in fasta format'' link) and do both a global and a local alignment with the programs needle and water respectively.
Compare the resulting
alignments and discuss the biological meaning
of
these.
Hint:Look at the Rieske domain locations:
O77266
O69363
Credit to Olof Karlberg, Dept. Mol. Evol., Uppsala