How to understand and analyse RNA-seq data (for a beginner)? I am trying to understand expression of a certain protein across Pseudomonas species. I downloaded an SRA file from NCBI and converted it to a fastaq file. I am not able to understand how to interpret and analyse this file. I want to get the mRNA sequence and see which genes are being expressed and find the mRNA of interest.

How do I proceed with getting the mRNA sequences and then for mapping them to genome?
SRA files are raw sequencing data that have been converted to the NCBI storage format. These can be converted to fastq files, e.g. with fastq-dump from the SRAtoolkit. 

Beyond that I suggest you start with the Hitchhiker's GUide to RNA-seq and the DESeq2 workflow to get a background. Be sure to extensively browse the web for vignettes, guides and tutorials. YOu will find helpful resources to get started.