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cdanielmachado
GPR information is missing in output file
Hi. I am new to all this work. I used CarveMe for making a metabolic model from protein fasta file. I used the following code. $ carve genome.faa --output model.xml, from the documentation. The fasta file was consist of locus tags and their protein sequences. The result I got should have locus tags in the column GPR but the column is empty. (I converted the sbml file to excel file for data visualization). Kindly help me to solve this problem.
yes I can but here in reply the file format is not supported. Kindly send me your email address so I could send it there.
If you run with -v you will see the error message: The input genome did not match sufficient genes/reactions in the database.
There is something strange with your fasta file, most of the proteins have a really short AA sequence. Was this fasta file built from a fully assembled genome? Also, do you know which organism is this?
This organism does not have a GBK file. I used automatic pipe lines for annotation of the whole genome. It is a bacteria. The fasta file is from the automatic annotation proteine seq.
On Thu, Jul 8, 2021 at 4:22 PM Daniel Machado @.***> wrote:
If you run with -v you will see the error message: The input genome did not match sufficient genes/reactions in the database.
There is something strange with your fasta file, most of the proteins have a really short AA sequence. Was this fasta file built from a fully assembled genome? Also, do you know which organism is this?
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Maybe you can run it in eggnog-mapper and see how many metabolic enzymes it predicts: http://eggnog-mapper.embl.de/
Or try to run a reconstruction with modelSEED: https://modelseed.org/