Hello, I'm newbie in bioinformatics and blast+, need to know how I can extract the complete sequences and aligned in fasta format of selected hits.

I've been using the blastp (version 2.3.0+) standalone tool against a database nr via remote:

blastp -query x1.fasta -remote -db nr -out x1.txt

And now with respect to results, I have read several texts that discriminate good or bad alignment based on their statistical analysis and observation of the alignments,

you are saying about it? It is recommended based on the rule of thumb Suggested by Russell Doolittle or other criteria.

I hope I can suggest some text, tutorial or assistance possible. Thank you