Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities

Table 4 Mean percentage amino acid identity of OMZ 50-m reads with top matches to distinct reference databases (GOS, KEGG, NCBI-nr) and with ribosomal proteins removed

			Percentage identity to reference genes present in^b
	Database^a	Data	DNA+RNA^c	DNA only^d	RNA only	All^e
All data
	GOS	DNA	89.3	82.1	NA	82.8
	GOS	RNA	90.8	NA	87.5	89.3
	KEGG	DNA	67.8	58.3	NA	59.7
	KEGG	RNA	71.0	NA	69.4	69.6
	NR	DNA	71.0	59.8	NA	60.8
	NR	RNA	73.8	NA	72.2	72.7
Without ribosomal proteins^f
	NR	DNA	70.7	59.6	NA	60.6
	NR	RNA	73.6	NA	71.9	72.5

^aBLAST database against which reads were compared. ^bMean percentage identity across all genes identified via BLASTX against NCBI-nr (HSP alignment regions only; bit score cutoff = 50). ^cGenes present in both DNA and RNA datasets, that is, 'expressed' genes. ^dGenes present only in the DNA dataset, that is, 'non-expressed' genes. ^eGenes shared between datasets (in DNA + RNA) plus genes unique to a dataset. ^fRibosome-associated proteins removed manually from datasets. BATS, Bermuda Atlantic Time Series; BLAST, Basic Local Alignment Search Tool; GOS, Global Ocean Sampling; HOT, Hawaii Ocean Time Series; HSP, high-scoring segment pair; KEGG, Kyoto Encyclopedia of Genes and Genomes; NA, not applicable; NR, National Center for Biotechnology Information non-redundant protein database (NCBI-nr); OMZ, oxygen minimum zone.

ISSN: 1474-760X