Early terminated transcripts and missing proteins reflect artifacts in bacterial proteomes

The high redundancy of many bacterial proteomes can be used to evaluate proteome quality and identify sequence errors. We have used MMseqs2 clustering with subsequent filtering to identify clusters that contain sequences from at least 50% of the clustered proteomes to build sets of core proteins that include proteins from 95% of the clustered bacteria. These clusters typically capture >80% of proteins in the bacteria. Because these clusters have highly uniform length (the median cluster has >99% of its proteins at the mode length), short (<75% of mode length) or long (>133%) proteins are likely artifacts. Most "outlier" proteins are found in fewer than 10% of clusters, and "high-outlier" clusters are over-represented in a small fraction of proteomes, which often have poor proteome BUSCO fragment scores. Short-outlier proteins are artifacts; at least 80% of short-outlier genomes contain mode-length copies of the protein, which were missed because of frameshifts, termination codons, or initiation codon choice. MMseqs2 clustering with 50% participation provides robust sets of core bacterial proteins and can be used to identify lower-quality proteomes and proteins.