research on gene, which tools can i use?

Question

[wizofe]

Hello stars!

I have an assignment on my degree with the description of "providing information on the rpfB gene in the bacterium Mycobacterium tuberculosis". Unfortunately there is not enough information on the tools to be used for gathering this information but there are some hints about the topics e.g.:

• Conservation of this gene/protein across bacteria (both species that are phylogenetically close to Mtb and others)
• Information on the function of this protein based on sequence analysis (e.g. using HHblits to identify homologues in other species).

For those two steps I run a blastp analysis and found some relevant information but I am not sure if that's enough or if there's a better tool to discover that or to do a phylogenetic conservation analysis.

• Information on the likely cellular location of this protein, as evidenced by motifs in the sequence.

*I could find information of the subcellular location of the protein on Uniprot but again no idea how can I prove that or which way I can look for motifs in the sequence *

• Information on any operon that this gene is part of (including conservation of the operon across closely related species). What is the genomic context of this gene (what other genes surround it and are they likely to be part of the same network?)
• Exploring how good is the current annotation of the start codon (could the protein start earlier or later?)

I would appreciate any help/input on choosing the right tools or getting forward to the right direction. Any ideas on how to further explore and discover information about the gene would be valuable as well.

Thanks everybody in advance :) w.

[Kevin Blighe]

Hi Ioannis, have you spent much time researching this yourself? Part of being a really great researcher is having the ability to seek information, critically assess it, and then use what's relevant and what's not.

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As an example, if I wanted to find out about operons in published literature, I would go to a search engine and search for:

ncbi pubmed operon

The first hit from that (Google UK) is: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2776167/

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If I wanted to find out about operon databases, I would search for:

ncbi pubmed operon database

The first hit is: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245079/