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Usage of the EMBOSS package

Entret EMBOSS program package is used to get the full record from the database. Format conversion:
entret :.
In order to obtain information about protein orthologs 1YDM of the genus Bacillus, we will write in a PUTTY terinal following query: :

			entret   sw:YQGN_BAC*
		

Our request, unfortunately shows only one protein structure YQGN of Bacillus subtilis (studied earlier).

Usage of the Uniprot database

Let's try to use Advanced Search in UniprotKB database to find orthologs of our protein. We look for the name of the protein, and only "entries from a complete proteome set", that is, the records from the completely sequenced genomes. In line we write: name: YQGN AND keyword: 181. Database gives us 8 entries. However, we did not specify that the structure of the protein we need is from the genus Bacillus. Fix for this: name: yqgn AND taxonomy: bacillus AND keyword: 181. Now the request gives, what we want and have only 3 entries .. All of these findings, except one (YQGN_BACSU) are in the TrEMBL database: A7Z6Q5_BACA2 and Q65HC6_BACLD. The table shows the comparative characteristics of orthologs.
In the table представлена сравнительная характеристика для ортологов.

Sequence alignment of 3-proteins using Clustal Omega is represented in the file Alignment.txt. Asterisks indicate amino acid residues in the match 3-proteins simultaneously, "." and ":" indicates matches of the two proteins. Based on of the alignment we can conclude conservative regions of amino acid sequences for these proteins, for example, with more than 5 amino acid residues. They are:

		"VCIPKC"
		"GGGYYDRYL" 
		"PHDIPV"
		

Usefull links:

1. Cite about EMBOSS