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As far as I know there is no sensible way to have a chemical compound in fasta. Are you sure that's what you mean? Fasta is used for DNA, RNA or protein.
The chemical compound is a part of a pathway and I want to conclude if my sequences are involved in the pathway or not! If you have any alternate suggestion please help.
I think you need more help than an online forum can offer. Do you have supervision in your institute who can support you in finding logical steps in your project?
It's unclear which data you have and what the aim is of your analysis.
Okay, Thank you.
What pathway is this? If you are looking at something like TCA cycle where the components/genes are well known then you should be able to get those easily.
You say you have sequences then logical thing to do will be a BLAST+ search at NCBI and then to see if you are able to retrieve homologies to genes known to be involved in that pathway.