SUMMARY: Life over the past four billion years has been shaped by proteins and their capacity to assemble into three-dimensional conformations. Protein sequence alignments have been the enabling technology for exploring the evolution and functional adaptation of proteins across the tree of life. Recent advancements in scaling the prediction of three-dimensional protein structures from primary sequence alone, revealed that different modes of conservation and function operate on the sequence and structure level. This difference in protein conservation patterns and their underlying functional change that could emerge in suboptimal alignment configurations is often ignored in optimal protein alignment approaches. We introduce EMERALD-UI, an open-source interactive web application which is designed to reveal unexplored biology by visualising stable structural conformations or protein regions hidden in the alternative alignment space. AVAILABILITY: EMERALD-UI is available at https://algbio.github.io/emerald-ui/. The source code of the version described in this manuscript is available at https://github.com/algbio/emerald-ui and archived at Software Heritage: swh: 1: dir: 8b5a70160396d5e9a2e6d015c3b6f1426176d9a4.