1. The Bryostatin gene sequence was obtained using Entrez to search the Genbank databases.
Results show 3 hits, the correct one is accession id: DQ889942 Candidatus Endobugula sertula isolate DEEP transposase-like protein gene, complete cds; bryostatin PQRS gene cluster, complete. Not much information is available about this gene in the database. There is no Entrez Gene or REFSEQ records.

2. For further analysis to find out more about this gene, the gene sequence, bryostatin.txt was extracted in FASTA format.

3. We used the gene sequence to:

• find possible matches to the chromosomal location in the model organisms available
• derive open reading frames (ORF) using NCBI ORF Finder
• translate into protein sequence

Results:

Searching against the UCSC Genome browser has found the best match in the Drosophila's chromosome 2L and 2R.

Clicking on the browser leads you to more information from databases such as

• Entrez Gene (links to interaction information and Pubmed articles)
• Unigene (Gene expression profile )

The NCBI's ORF Finder found several open reading frames. CDS position 2199..4052 Frame +3 was translated into its protein sequence, BryP.txt

4.The protein sequence was used to search against the EXPASY databases using BLAST to find similar proteins.

Results show the best match comes from BRYP with accession id: Accession number A2CLL7 from the TREMBL database. Swissprot provides additional predicted information from other databases such as its protein family and links to structure information.

5. CLUSTALW was used to find out if BRYP has conserved residues by comparing it to sequences from other similar proteins, msa.txt

6. Garnier (Web EMBOSS) was used to predict the secondary structure of the protein sequence.

Results

The multiple sequence alignment show shows the following conserved residues:

The secondary prediction from Garnier shows the following:

FPGQGSQ (position 7 to 13) - coil

TQFTQPALY (position 55 to 63) - beta sheet

AGHSLGEYNAL (position 85 to 95) - coil

FHSRYM (position 191 to 197) - helix

VISNF (position 219 to 222) - beta sheet