Multipe Sequence Alignments:
Probing of the Twilight Zone
Solution

1. Fetching the sequences

• hmga_chite.fasta
• hmgl_trybr.fasta



2. Extracting Homologous Segments


• This dotter contains two types of repeats.
• The fuzzy region is a Lysine rich region. It should be avoided here
• A possible extraction: [hmgl_trybr 190 267 hmgb_chite 1 75]
• Extraction of the three segments:[hmgl_trybr 100 190 hmgl_trybr 190 267 hmgb_chite 1 75]



3. Making an Alignment

• Cut and paste the sequence in the multiple alignment server of your choice
• Here is an alignment of the two segments: [two]
• Here is an alignment of the three segments: [three]
• The difference between the two alignments are obvious:[comparison]



4. Testing the validity of the model

• Add extra sequences to check if they affect the original alignment
• Extra sequences will be found using blast
• Sequences must be as diverse as possible, with key residues well conserved
• Here is an example of a correct alignment [ref_aln]
• Observe that also the sequences are distantly related they remain conserved on key positions



5. CONCLUSION
   Although the similarity between hmga_chite.fasta and hmgl_trybr.fasta is clearly within the twilight zone, the multiple alignment shows that they share key positions of the hmg domain. As a consequence it is quite likely that these parts of the proteins are indeed homologous.