Genomic environment. Database GO.
Task 1: Obtaining information about the COG, to which my protein belongs.

In the course of this workshop I worked with the protein assigned to me in the 1st semester - carboxylesterase (Xanthomonas citri pv. citri), AC - AKM25432.1.

To begin with, a fasta sequence of protein was introduced into the CDD service window. Then in the results window in the field (top right corner) View -> Full Results.


KOG information:

  • ID: COG0657
  • E-value for assigning a protein to this COG: 3.72e-27
  • Interval: 8-286
  • KOG name: Acetyl esterase/lipase, functional category: Lipid transport and metabolism

COGNAT


With the help of the program COGNAT, an image of the genomic environment of the COGa under consideration was obtained from different organisms.
Project link itself

In the above image on the left are the organisms that consider the genomic environment of the KOG (the type and kind of the organism), on the right is the window with the environment itself (each arrow is a gene, color is marked by genes that run more than a certain number of times (set through Threshold) in the bottom window are all the conservative COGs found by the program.
The program was started with the following parameters:
  • Search for COG - COG0657
  • Neighborhood Size - 7
  • Occurrence Threshold (%) - 20
  • Taxonomy - YES

For the corresponding COG, 3 neighboring squirrels were searched on the left and on the right, those of them were tinted which were found in more than 20% of cases, and the findings were sorted by taxonomy.
As a result, you can see that the genomic environment of the considered KOG does not reveal any conservatism.

GO Database


The assignment of the AKM25432.1 protein from Xanthomonas citri pv. citri to the GO terms.

The best received protein P96402 from Mycobacterium tuberculosis H37Rv has a P-value: 3.7e-20 and is quite similar to my protein, but belongs to another organism

The GO terms, assigned to a protein with the Uniprot ID: P96402:
Aspect GO ID Name of the term Translation of the term name Reliability type code
biological process GO:0046503 lipid catabolic process липидный катаболический процесс IDA
molecular function GO:0004806 triglyceride lipase activity катализ гидролиза триглициридов IDA
Description of the presented reliability codes:
Reliability type code Decryption of reliability type code Explanation
IDA Inferred from Direct Assay The function was confirmed by a study directly

© Popov Nikita 2016