Colocation of the genes encoding ABC, TRAP, and TCT transport systems and catabolic pathways for the transported ligand provides a strategy for discovering novel microbial enzymes and pathways. We screened solute-binding proteins (SBPs) for ABC transport systems and identified three that bind d-apiose, a branched pentose in the cell walls of higher plants. Guided by sequence similarity networks (SSNs) and genome neighborhood networks (GNNs), the identities of the SBPs enabled the discovery of four catabolic pathways for d-apiose with eleven previously unknown reactions. The new enzymes include d-apionate oxidoisomerase, which catalyzes hydroxymethyl group migration, as well as 3-oxo-isoapionate-4-phosphate decarboxylase and 3-oxo-isoapionate-4-phosphate transcarboxylase/hydrolase, which are RuBisCO-like proteins (RLPs). The web tools for generating SSNs and GNNs are publicly accessible (http://efi.igb.illinois.edu/efi-est/), so similar ‘genomic enzymology’ strategies for discovering novel pathways can be used by the community.

编码ABC，TRAP和TCT转运系统的基因与转运的配体的分解代谢途径共存，为发现新型微生物酶和途径提供了一种策略。我们筛选了ABC转运系统的溶质结合蛋白（SBPs），并确定了三个结合d- apiose（高等植物细胞壁中的分支戊糖）的蛋白。在序列相似性网络（SSN）和基因组邻域网络（GNN）的指导下，SBP的身份能够发现d- apiose的四种分解代谢途径，并具有11种先前未知的反应。新的酶包括d催化羟甲基迁移的β-油酸酯氧化异构酶，以及3-Ruo-isapionate-4-磷酸脱羧酶和3-oxo-异脂酸酯-4-磷酸转羧酶/水解酶，它们是RuBisCO样蛋白（RLP）。生成SSN和GNN的网络工具是可公开访问的（http://efi.igb.illinois.edu/efi-est/），因此社区可以使用类似的“基因组酶学”策略来发现新途径。