GO classification on denovo transcriptome

[Temima]

I have a list of DE genes from a denovo transcriptome project.
We have each gene annotated with its 2 best BLAST hits.
From looking at the GOseq documentation, it seems I can only use this tool if all my genes come from one of the organisms on the GOseq list.
Is there any tool out there that will let me do enrichment analysis for GO terms and KEGG pathways while using gene IDs from multiple organisms?

Thanks!