Schematic representation of the analyzed primary scaffoldin CipA and secondary scaffoldins of C. thermocellum DSM1313. CipA was truncated to delete different modules by inserting targetrons at the positions indicated by vertical arrows to generate the mutants indicated in parentheses. Secondary scaffoldins were disrupted by inserting targetrons at sites near the N-terminus of each open reading frame. Three secondary scaffoldins, SdbA, Orf2p, and OlpB, contain an S-layer homology module that anchors the protein to the cell surface, while 7CohII (Clo1313_1487) is a non-anchored scaffoldin with seven repeated CohII modules. The number of CohI modules in CipA was determined according to genome annotation and PCR analysis (Additional file 1) and differs from the previously published number for this strain .