Help with protein sequence of a CDS in gene details

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Help with protein sequence of a CDS in gene details

Nicolás David Franco Sierra
Hello all:

I'm trying to display translation features of a CDS on the gene details page.

My GFF3 file was generated from a gbk file via bp_genbank2gff3.pl script, and looks like this:

CP000560    GenBank    CDS    412    1752    .    +    1    ID=RBAM_000010;Dbxref=GI:154350370;Name=dnaA;Note=COG0593%3B chromosomal replication initiatior protein;codon_start=1;locus_tag=RBAM_000010;product=DnaA;protein_id=ABS72449.1;transl_table=11;translation=length.446
CP000560    GenBank    gene    412    1752    .    +    1    ID=RBAM_000010.gene;Alias=RBAM_000010;Name=dnaA;locus_tag=RBAM_000010
CP000560    GenBank    CDS    1937    3073    .    +    1    ID=RBAM_000020;Dbxref=GI:154350371;eC_number=2.7.7.7;Name=dnaN;Note=smart00480%3B DNA polymerase III (beta subunit);codon_start=1;locus_tag=RBAM_000020;product=DnaN;protein_id=ABS72450.1;transl_table=11;translation=length.378

I have fasta protein sequences at the end of the file. They are named matching with the feature ID, like this:

>RBAM_000010
MENILDLWNQALAQIEKKLSKPSFETWMKSTKAHSLQGDTLTITAPNEFARDW...
>RBAM_000020
MKFTIQKDRLVESVQDVLKAVSSRTTIPILTGIKIVASDEGVSFTGSDSDISI...
>RBAM_000030
MANPISIDTEMITLGQFLKLADVIQSGGMAKWFLSEHEVTVNNEPDNRRGRKL...

In the gene details page I'm getting the "length.#" string instead of the protein sequence. What should I do in my config file in order to get the proper translation in the gene details page?

I really appreciate any help you can provide me.

Sincerely,
Nicolas

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