I wanted a list of all the proteins (amino acid sequences) and their corresponding gene sequences of Vibrio cholerae. I tried to search in patric, but the number of amino acid sequences and gene sequences do not match, as they have provided the whole genome. I need to know if there is a database where all the proteins of Vibrio cholerae and their corresponding gene sequences can be obtained in a single file or in a couple of files. Copy pasting 4000-5000 genome and protein sequences individually from the internet seems cumbersome to me.
You want to go to PATRIC > Data > Download Tool.
From the Taxonomy tree, find Vibrio cholerae, choose Type of annotation as either PATRIC/RefSeq or both, choose the type of file you want (gbk or faa) and download from there.