Gene official symbols and uncharacterised genes in the Salmonella annotations

Question

[robjohn7000]

Hi,

I have a confusing issue with the folloing genes and their annotations:

SL0010 conserved hypothetical protein
SL0430 hypothetical major facilitator family transport protein
SL0471 integral membrane protein AefA
SL0501 putative membrane protein

The following genes have "hypothetical.....", "conserved hypothetical.....", "integral membrane protein AefA" and "putative......." in the Salmonella genome annotations.

My question is: Is it correct to assume that these genes do not have common official gene names such "acnB" because they are uncharacterised, and instead have SL####?

Thanks

Answer 1

[predeus]

Unfortunately, it is never safe to assume such things with bacterial gene names.

In your own list, SL0471 is identified as aefA - this should be its name, unless there's one that is used more often.

SL identifiers are from SL1344 strain. You can take another 10-20 reference strains from NCBI and run Roary pan-genome analysis on it, and then you'll have a pretty good idea if the genes you are interested in have proper names, etc.