Linux based tool:

You can try GeneSCF (no installation required and simple to use).

Note: GeneSCF tool is GENE based, not protein based tool. If you got Uniprot Ids convert then to Entrez Gene (GeneIDs)/Gene name using http://www.uniprot.org/uploadlists/ . Then use it as input for GeneSCF.

KEGG pathway analysis for Brassica napus ( bna ) using GeneSCF:

./geneSCF -m=update -i=INPUTgene.list --gtype=gid -db=KEGG -o=/ExistingOUTPUTfolder/ -org=bna --plot=yes --background=1000

Input file (INPUTgene.list):

List of genes to be used for enrichment analysis in a plain text file (one per line).

Parameters to be changed according to your analysis:

--background=1000 (Please change this to total number of genes taken in your analysis/annotation)

--gtype=gid ('gid', for NCBI entrez gene ids and 'sym' for official gene symbols)

-o=/ExistingOUTPUTfolder/ (Folder where the output to be stored- NOT file name)

Web based tool:

Since GeneSCF uses geneontology.org as source, it does not cover ontology terms for Brassica napus but you can try this web based tool,

http://bioinfo.cau.edu.cn/agriGO/analysis.php

I hope this helps !