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We found that seven of the 15 proteins with multiple domain hits were encoded by contigs mainly built from sample 1 reads, four from Burkholderia and two from Shewanella.
Additionally we could confirm the proposed annotation of further proteins, 197 proteins with multiple domain hits and 146 proteins with single domain hits, that were marked as hypothetical, putative, probable or predicted PKS or PKS I.
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There can be multiple matches across a query, i.e. protein domain hits, and these are returned by phmmer as a table of per-domain hits.
The domain hits with an e-value< = 0.01 were kept.
Among the weak, conserved domain hits was an RRM_1 domain we found in Ssp2.
Annotations of the best BLASTX hits and domain hits are summarized in Table 2.
There may now be additional domain hits defined as the 'B' domain hits.
We did not use any regions with overlapping Pfam domains for the evaluation and also completely excluded regions with insignificant domain hits, i.e. hits below gathering threshold.
There were four A domain hits: A1 = ABC_ATPase, A2 = SEcA_PP_bind, A3 = SecA_SW, A4 = SecA_C and two B domain hits (B1 = IFT20 and B2 = ABC_ATPase).
We find 11 new multiple domain proteins.
Understand the value of multiple domain names.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com