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ProFinder: Candidate constitutive promoter prediction across the bacterial tree for genetic tool development in non-model species

Gautam, A.; Marsh, J. W.

2026-09-24 microbiology
10.64898/2026.09.23.753901 bioRxiv
Show abstract

Reliable constitutive promoters for non-model bacteria are lacking, resulting in a bottleneck for genetic tool development. Existing computational promoter predictors are trained on model Gammaproteobacteria and degrade on phylogenetically distant or compositionally atypical genomes. Here we present ProFinder, a computational method that integrates three biologically informed criteria for promoter prediction: a conserved 98-gene constitutive marker panel, an empirically derived intergenic search window, and a 72-motif {sigma}70 motif catalogue built from diverse lineages. From an input bacterial assembly, ProFinder returns a ranked shortlist of putative constitutive promoters. It matches the precision of full-genome classifiers and is more robust to GC extremes. Applied to 56,742 bacterial genomes spanning 149 phyla, ProFinder returned candidate promoters for 99.76%, delivering a pan-bacterial catalogue of pre-computed constitutive promoter parts to accelerate chassis development across the bacterial tree. ProFinder can be accessed at: https://plabase.cs.uni-tuebingen.de/profinder/.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.