2-Protein sequence homology search.

The EMBL entry U22894 contains the sequence of an amplifiable element AUD1 from Streptomyces lividans. Extract and translate the annotated ORF 4.7 and search for homologous sequences in the protein databases.

Perform the following three database search methods:

Use pairwise sequence comparison programs to verify potential homologies.


  1. Which parts of the hypothetical protein are significantly similar to other sequences in the database?
  2. How many different types of domains does the protein contain?
  3. Is the annotation in EMBL "chitinase homolog" correct ?
Hints & Answers:

2 DNA sequence comparisons.

Compare the promoter regions of the mouse and human interleukin-2 receptor alpha chain genes.

Proceed as follows:

  1. Where are the most conserved sequences located?
  2. What percentage of the upstream regions consist of repetitive elements?
  3. Do you find significant sequence similarity between repetitive elements?
  4. Can you find homologous sequences from other mammalian species using BLAST?
Hints & Answers: