Is there any source to find amino acid composition of different bacteria species?

Question

[m.koohi.m]

I have some bacteria species and want to find their amino acid composition statistics. I am wondering is there any online source that already calculated and published it or I should do that by myself?

Answer 1

[natasha.sernova]

See my answer in this post:

A: where can I get environmental bacteria genome in fasta format (as many as possib

Select your bacteria here:

ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/assembly_summary_genbank.txt

You will get faa.gz-file for each one.

Statistical data you will have to calculate by a different tool.

It was discussed in these posts:

Whole Genome Amino Acid Composition Tool?

Aminoacid Composition Using Biopython

Amino Acid Composition-Graphic Representation

Detecting Different Amino Acid Composition Between Two Bacterial Genomes?

Answer 2

[John]

Amino Acid Composition is a very broad term. To some it means tRNA/codon usage, which is usually best answered with a specific assay.

There's also bioinformaticy-ways to get an estimate of codon usage using the sequenced genome, counting 3mers either for the whole genome, or anchored on the first base of genes with non-overlapping 3mers. But remember this isn't really the same as codon usage as the amount of transcription of each gene is not taken into account. A "weird" gene with "weird" codons that is rarely transcribed would get as much weighting in such a table as a constitutively expressed housekeeping gene.

A long long time ago, I used to get my codon usage tables from http://www.kazusa.or.jp/codon/, which i presume is still relevant. But if you are just looking for a dataset where you can ask "how much of X is there in this organism" where X is some arbitrary fragment of DNA, then the only tool I know that can make use such a dataset is ACGTrie which I wrote and no one uses (not even me), so good luck with that :)

Answer 3

[piet]

The protein content of a given bacterial cell varies substantially with environmental conditions and cell life cycle (whether it is dividing or not). Accordingly its AA composition varies. You can measure the AA composition of a bacterial culture grown under certain conditions, but you cannot calculate it. Maybe you mean codon usage in the genome?

Answer 4

[Naresh]

You can use predictprotein.org.

Where your can see your species of interest amino acid composition.