Gene Annotation

In this exercise we use advanced bioinformatics tools to derive functional information of E. coli YciE protein.

1. Get the protein sequence for E. coli YciE (accession P21363) from GenBank in FASTA format.
2. Do domain and motif searches using RPS-BLAST http://blocks.fhcrc.org/rpsblast.html
3. Do domain and motif searches using SMART
   http://smart.embl-heidelberg.de/smart/set_mode.cgi?NORMAL=1. Use ``Normal Mode'', check ``outlier homologs'', ``PFAM domains'', ``signal peptides'' and ``internal repeats''.
4. Do another domain search with InterPro http://www.ebi.ac.uk/interpro/
5. Finally, compare the results. Which domains and motifs were detected by all 3 programs and why?
6. Do a functional prediction using STRING http://string.embl.de/ with default settings. What are the predicted interaction partner? What is the evidence for interactions?
7. Do a protein structure prediction (threading analysis) using HHPred
   http://toolkit.tuebingen.mpg.de/hhpred with default settings
8. Take a closer look at the top hit with the most significant E-value. Study the annotation and the quality of the alignment.
9. Explore the PDB (protein data base) entry by clicking the ``PDB'' link. Which functional information can you get from the literature links listed?
10. Download the sequence of chain A in FASTA format: select menu ``Summarize'' -> ``Sequence details'' -> ``Download''
11. Do a refined pairwise alignment of YciE and chain A of the just downloaded protein sequence using AliBee http://www.genebee.msu.su/services/malign_reduced.html.
12. compile the results from each of the predictions. What is your overall conclusion of the function of the protein YciE?