First check in the NCBI database. You seem to be interested in the protein sequence because you mention CDS. The NCBI protein database gives you several sequences (see link: https://www.ncbi.nlm.nih.gov/protein/?term=RpoD+gene+Pseudomonas+T-strains). Once you have a sequence you should blast it against against the protein database (BlastP), or against the nucleotide database (tblastn) to collect all possible sequence candidates. Align the sequences and create a tree. I you need help, contact me

Fred R. Opperdoes many thanks for the answer. The link you provided is not accessible to me. Regarding my query: I have a list of Pseudomonas species (50 species) and for all those 50 species, I would like to collect sequence of their rpoD gene and then futher wants to create a Phylogenetic tree using MEGA. I have already prepared a tree using their 16sRNA sequence and now I want to compare the trees using rpoD (house keeping gene) sequences. I find it hard to find the sequence of those 50 strains using NCBI. Or to say I am not so familiar with NCBI search system. Could you tell me how to search for this gene? or if there is any other database available which is much more easier than NCBI complications?

Regards,

Timsy

Dear Timsy

Here follows a small tutorial of how to proceed.

Select one of the sequences such as the DNA-directed RNA polymerase subunit D, partial [Pseudomonas sp. IBP-A36]. You find it here.

https://www.ncbi.nlm.nih.gov/protein/AFK74444.1

AFK74444.1 DNA-directed RNA polymerase subunit D, partial [Pseudomonas sp. IBP-A36]

ILAEYQRVVSEGGRLSDILSGYIDPDDGSVPAEEVELDLKDSAGAKAKDDEEEDEESEDDSEDEGDGGPD

PEEAARRFGLVADQLDKTKKALKKHGRGSKQADAEMLALAELFMPIKLVPKQFDVLVARVRDALDQVRRQ

ERAIMQLCVRDARMPRADFLRLFPGQETDESWINGVLKAKPKYAEALERVKDDVIRNQQKLSALESNVDL

KVAEIKDIQT

Download the sequence in fasta format by clicking in the upper-left hand corner on Genpept to change the format to fasta (text) and copy the sequence.

Now go to the NCBI blast facility (https://blast.ncbi.nlm.nih.gov/Blast.cgi) and select "protein blast". Paste the protein sequence into the text window.

Select as database non-redundant protein sequences (nr),

organism: Pseudomonas sp. 2_1_26 (taxid:287);

Algorithm Quick BlastP and

start the blast search.

After one or two minutes you get a new page producing a list with 100 homologous Pseudomonas sequences.

You can read the individual descriptions, visualize the alignments and you can download them all at once, or make a selection of the most relevant sequences, make an multiple alignment or even create a phylogenetic tree.

Once you have seen all this you can import your sequences into MEGA or into any other alignment and tree creating package of your choice.

I hope this is what you wanted.

Good luck,

Fred

Timsy --

Dear Timsy

In the link you can have access to a large number of sequences of the RpoD Pseudomonas' gene.

https://bacteria.ensembl.org/Multi/Search/Results?page=2;q=RpoD%20Pseudomonas;species=all;collection=all;site=ensemblunit

Other database available :https://bacteria.ensembl.org

I hope it is useful

Good luck

Fred R. Opperdoes I thank you very much for taking out time to explain in detail and for your kind paitence. Yes, it was very helpful to know :)

Best Regards,

Timsy

Maura Lina Rojas Pirela Thank you very much the links, it did really save my time alot and it was quite easy :)

Best regards,

Timsy