Standard numbering schemes
For the N- and C-terminal expansin domains, standard numbering schemes
were introduced to annotate equivalent positions38.
The B. subtilis expansin, Bs EXLX1 (PDB entry 4fer), was
used as the reference sequence for the assignment of standard position
numbers to the sequence entries in the ExED upon alignment against the
respective profile HMM and subsequent transfer of position numbers: For
both expansin domains, the standard positions range from 11 to 105 and
114 to 186. Insertions with respect to the reference sequence, such as
loops, were specified by subsequent decimals. Thus, all position numbers
mentioned herein are based on the reference Bs EXLX1, unless
otherwise stated. Due to insertions in the reference sequence ofBs EXLX1, some regions in the underlying multiple sequence
alignments of the standard numbering schemes appeared inaccurate, i.e.
these regions could not be aligned properly: In the N-terminal expansin
domain, inaccurate positions are from 14.1 to 17, 39.1 to 47, and 104.1
to 105; in the C-terminal expansin domain, inaccurate positions are from
162.1 to 164 and 185.1 to 186.