The most abundant 'known' pORF clusters included a large number of housekeeping genes.
When comparing the annotation of the top 10 most abundant pORF clusters (>10 non-redundant sequences) found in the Frias-Lopez studies (Table 6) 6 (by PFAM), 7 (by TIGRfam) and 5 (by COG) clusters are found in both studies as abundant clusters (>100 sequences per pORF cluster).
In contrast, the number of average (day and night) observed metagenomic pORF clusters varied little across seasons (spring = 64,161, summer = 62,959 and winter = 60,743).
All pORF clusters with >10 non redundant sequences were annotated by comparison to the PFAM, TIGRfam and COG databases (Table 3).
At the highest level of assembly, comparisons of pORF clusters reveal that 9% and 7.5% of the mRNAs are shared with the relevant metagenome.
This is supported by the annotation of the dominant pORF clusters (with >10 non-redundant sequences, Table 3) and Fig. 2. The most abundant sequence that could be annotated was PF02407, Putative Viral Replication Protein, and the second most abundant was PF00910, RNA helicase, which is thought to be involved in viral infection (Table 3).
Neither of these proteins were identified as being abundant in the dominant pORF clusters (>10 non-redundant sequences) from study by Frias-Lopez et al. [9] which utilised only 1 L sampling volumes and may have reduced stress on the bacteria by reducing the filtration time.
Other abundant pORF clusters (>10 non-redundant sequences) encoded catalases/peroxidises (COG0376), carbamoylphosphate syntheases (COG0458, TIGR01369), excinucleases (COG0178), S-adenosylhomocysteine hydrolase (COG0499, TIGR00936), acetate-CoA ligases (TIGR02188), 26S proteasome subunit P45 family protein (TIGR01242), and elongation factor Tu GTP binding domain (PF00009) (Table 3).
Specifically, comparisons were generated using BLASTN (Table 4) for 3 versions of the two data sets: 1) total sequences, 2) representative ntDNA sequences from each nucleotide cluster and 3) representative sequences from each pORF cluster.
As iJL1678-ME includes more pORFs, this parameter's value had to be reduced by the expressed mass of new protein content.
