It depends on what you are looking for and what kind of database you use.
Sequences for already well characterized proteins tend to be useful in most cases. However due to the automated pipelines that are used nowadays errors could still be there. Swissprot, for instance is a better curated database, yet with overall fewer sequences.
As a rule of thumb reality checking with well-characterized reference genomes are helpful, especially with regards to functional assignments.
But again, it really depends on what you are looking for (e.g. single protein vs whole genome analyses, intergenic regions etc.)