Since the most important findings of this paper, the identification of the YoqW and ImuB-C domains, was based on genome context analyses, one is left wondering about the easy reproducibility of the finding, given that this is an in-house package.
In SEED large homology-based protein families are broken into isofunctional subfamilies ('functional roles') based on genome context, functional context, phyletic profiling, shared regulatory sites, and other homology-independent clues.
The strategy for constructing the phylogenetic tree based on genome context was a newly developed system in evolutionary research [23].
As alternatives to analytical tools relying on sequence similarity, there are tools based on genome context.
Members of these transporter families in sequenced genomes were identified by homology searches and the function of each protein was predicted based on genome context (see Methods).
As we have previously stated, the fidelity of functional predictions based on genome context methods greatly improves with larger numbers of available genomes.
The associations are derived from high-throughput experimental data, from the mining of databases and literature and from predictions based on genome context analysis.
Manual curation of the identified Shewanella FIGfams using the SEED and other genomic resources and tools (see below) rejected many of them as well as identified some additional candidate FIGfams based on genome context analysis.
Based on genome context and distant homology analysis we have predicted the gene araY, which is similar to D-xylose 1-dehydrogenase from Caulobacter crescentus (45% similarity), to be the missing L-arabinose 1-dehydrogenase.
Based on genome context (co-localization and/or presence of a B12 riboswitch) and protein similarity analyses, only 12.5% of sequenced COG0523 from the SEED are true CobW proteins and assigned to the cobalamin biosynthesis pathway.
