Final answer:
To use the Cell eFP Browser for protein localization, enter the gene identifier or sequence. The E value from a BLAST search helps assess the significance of sequence alignments. Protein localization can also be deduced from known localization signals within the sequence and additional BLAST search results.
Step-by-step explanation:
In order to determine the possible localization of a protein coded by your Landoltia gene using the Cell eFP Browser, you should enter the appropriate gene identifier or sequence into the search box. The database will then display the expression patterns of that particular gene across various cell types and conditions, which can provide insights into where in the cell the protein might be localized.
Understanding E value
The E value is an important metric when comparing your gene sequence against other known sequences using tools like BLAST. It represents the number of times you can expect to find a sequence alignment with a similar score purely by chance in the database being searched. A lower E value indicates a more significant, less likely to occur by chance, alignment; theoretically, the closer it is to zero, the stronger the evidence for biological relevance of the alignment.
Protein Localization Signals
Proteins that are destined for the nucleus, for example, often have nuclear localization signals that are rich in positively charged amino acids such as lysine and proline. These signals facilitate the protein's binding to nuclear transport receptor proteins in the cytosol, a process critical for their correct localization within the cell.
Performing Nucleotide BLAST
To perform a nucleotide BLAST search, you input a sequence such as ATTGCTTCGATTGCA into the query box, specify the species (like human or Homo sapiens), and execute the search. The results will provide you with locations where the entered sequence matches within the genome, which can help deduce gene function and potential protein localization. The graphical interface aids in visually understanding these matches in the context of the genome's structure.