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Fig. S1. Alignment of XylS and AraC.

A. Pairwise alignment of XylS and AraC for different alignment strategies. The alignment is numbered according to XylS, and secondary structure is indicated with blue (β-strand) and red (α-helix). The predicted secondary structure for XylS is from the BioInfoBank Meta server.

B. Final consensus alignment for XylS and AraC used for model building. Conserved positions for each subfamily are shown between the sequences. Mutations discussed in the text are indicated with #.

Fig. S2. Score values for alternative alignments. Score values from DComplex, Fastcontact (kcal mol-1) and RPDock (RP score).

A. Interaction score for the XylS dimer (left) and the AraC dimer (right) at different gap lengths.

B. Interaction score for the final α-helix versus the rest of the XylS monomer (left) and same for the AraC monomer (right). See Supporting information text for details.

Fig. S3. Errat scores. Errat scores for (A) initial XylS monomer model, (B) initial XylS dimer model and (C) XylS dimer model after optimization of gap positions, corresponding to the final alignment in Fig. S1. For the dimer model only the first chain is shown.

Fig. S4. Final model. 3D representations of the final model, in two different orientations. The problematic regions from the Errat score in Fig. S3 are indicated with red in the left part of the structure, showing that this mainly affects the extreme parts of the β-barrel. The gap positions are indicated with cyan in the right part of the structure.

Fig. S5. Plasmid map of pTA13. The bla gene is under transcriptional control of the Pm promoter. xylS: gene for the transcriptional activator XylS; trfA: gene for the replicator protein TrfA; kan: gene for kanamycin resistance; oriV: origin for vegetative replication; oriT: origin for conjugational transfer. The NcoI and AgeI restriction sites for exchange of xylS are shown.

Table S1. Primers used in the study.

Table S2. Plasmids used in the study.

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Please note: Wiley Blackwell is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.