Computer-Based Annotation of Putative AraC/XylS-Family Transcription Factors of Known Structure but Unknown Function

Figure 2

Multiple-sequence alignment of the DNA binding domain of 62 AraC/XylS family members with experimental evidence of their biological role. Four proteins found by the structural similarity search and whose function is unknown or poorly characterized were included in this multiple sequence alignment. Each sequence label contains the general functional category, the UniProt accession code, and the protein name. Functional categories are BPI: bacteria-plant interaction; M: metabolism; S: stress response; V: virulence and Unk: unknown. One or two functional categories were assigned. The sequences are sorted according to the tree order (see Figure 3). Secondary structure elements are given at the top (according to MarA (PDB code: 1bl0)). The alignment was plotted with JalView version 2.6.1 [24]. Color legend: light blue: hydrophobic; green: polar and aliphatic; turquois: polar and aromatic; red: basic; purple: acidic; orange: glycine; yellow: proline.