Table 1. Protein targets from M. smegmatis with one or more confirmed PUP modifications.

Protein targets with pupylated sequences that have been identified by both methods, ESI QqTOF mass spectrometry analysis and 2D gel analysis, are highlighted in gray. Column annotation: Global MS, peptide index from ESI-QqTOF analysis (Supplementary Table 1); 2D gel, peptide index from 2D gel electrophoresis (Supplementary Table 2); App. MW (calculated), apparent MW versus calculated MW (all targets identified by 2D gel electrophoresis show an apparent MW that exceeds the calculated MW of the same target); Gene locus (M. smegmatis); Detected pupylation peptides, PUP GGE sites are highlighted by superscript; Pupylated lysines, sequence residue numbers; Gene locus (M. tuberculosis) for M. smegmatis genes with identified paralogs in M. tuberculosis; Conservation of lysine pupylation site, based on M. smegmatis/M. tuberculosis sequence alignments of targets genes (data not shown); Functional annotation (M. tuberculosis); Functional categorization (M. tuberculosis), category identifiers have been taken from (Camus et al, 2002). 0, virulence, detoxification, adaptation; 1, lipid metabolism; 2, information pathways; 3, cell wall and cell processes; 7, intermediary metabolism and respiration; 8, proteins of unknown function; 9, regulatory proteins; 10, conserved hypothetic proteins. Target gene clusters, pair or multiple pupylation targets that are encoded from genes with neighboring loci, generally found in joint operons, are indicated I–VI.