GO annotation, enrichment & KEGG pathway in non-model organism

Question

[Olajucan]

Dear,

I performed RNA-seq from non-model organism's RNAs and used Trinity to get de novo assembled contigs.

As I wanted to do GO annotation, enrichment analysis and KEGG pathway analysis,

I used BLAST2GO to do blastx for my ~40,000 contigs.

However, when I ran GO mapping after blastx, I got only ~1,000 GO IDs out of 40,000 contigs.

I think it's too small to represent all my contigs for GO enrichment or KEGG analysis.

Did I make some mistakes?

Any suggestions for my data analysis or other programs will be appreciated.

Thanks.