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Figure 1 | BMC Genomics

Figure 1

From: A network-based approach to identify substrate classes of bacterial glycosyltransferases

Figure 1

Glycosyltransferase annotation flow. A: Genome-wide annotation of glycosyltransferases (GTs). Glycosyltransferases are predicted by scanning the proteomes of the studied species for GT-specific signatures using Hidden Markov Models (HMM) from SUPERFAMILY, CAZy and Pfam. An additional fold recognition filtering step is applied to only retain those genes containing a three-dimensional fold (inferred by the PGenTHREADER algorithm) with significant homology to folds present in experimentally confirmed GTs (deposited in the SCOP database). B: Predicting GT substrate class and putative mode of action (bottom panel). The local network neighborhood of each query GT (black node) in a functional interaction network (STRING) is used to extract a GT-specific local subnetwork for each query GT. The local subnetwork of a GT comprises predicted functional partners (proteins being functionally related to the query GT). Based on the GO enrichment analysis of these genes in this local subnetwork, the substrate class of the query GT is derived. To gain information on the mode of glycosylation, the GT specific local subnetwork is further annotated with either membrane associations between a query GT and a predicted transmembrane protein (blue edge) and with relations indicative for protein glycosylation (yellow edge).

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