Genes related to MidnightRain_54 are often called by Glimmer and GeneMark to start near the beginning of strong coding potential, leaving a sizeable gap. But the reading frame is open upstream and can be extended to reduce the gap to ~16 bp to the upstream gene. These upstream starts are conserved across the pham (as of June 2024).

When the upstream starts are chosen, the longer proteins can have hits on HHPred to metallopeptidases (like IrrE) and to helix-turn-helix domain containing proteins.

The location of the called start can influence the alignment. Shorter proteins often match the HTH domain well, but only part of the peptidase domain. Longer proteins match the full peptidase domain, which includes part that is HTH-like.

Try HHPred on proteins of different lengths. If the longer proteins continue to add alignment to metallopeptidases, the longer protein may be the better call.

See the attachment to visualize the alignments.
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