Sixteen known PAS domains (eight LOV domains and eight PAS domains), which have been shown to be involved in LOV sensing/signalling by biochemical and genetic methods, were identified by a search of the literature (Table S4). Also, six PYP and 25 GAF domains were collected from the Uniprot database (Table S5), and PAS domains in Xcc were screened with bioinformatics tools. Clustering and

phylogeny analysis were used on these domains. The details of the procedure are given in Supporting Information. Thirty-three proteins with PAS domains were identified within the genome of the Xcc 8004 strain. These proteins can be divided into seven classes including eight HK, 10 response regulators (RR) or hybrid HKs, eight GGDEF-characterized proteins, three transcription regulators, two chemotaxis proteins, one phytochrome-like selleckchem ABT263 protein and one methyltransferase, which are shown in Fig. S1. PAS domains were most commonly found at the N-terminus, and no more than four repeats were found in any one protein. PAS domains have a highly conserved structure and frequently interact with a variety of ligands and metabolites with conserved secondary structure, such as FMN, FAD, haeme and hydroxycinnamic

acid (Möglich et al., 2009). To further explore the link between PAS domain structure and function, the secondary structures of all 33 PAS proteins in Xcc 8004 were predicted and shown in Table S3. Sixteen known PAS domains, which have been shown to be involved in LOV sensing/signalling with biochemical and genetic methods, were identified by a search of the literature (Table S4). Our first approach to understand the functional relationships among PAS-domain-containing proteins was to perform a phylogenetic analysis of these domains. As shown in

Fig. 1a, some functionally homogeneous Protein kinase N1 PAS domains were linked together, and some were dispersed. Afterwards, a comparison alignment of the SST of 16 PAS domains was constructed, and the tree is shown in Fig. 1b. Most functionally homogeneous PAS domains were closely linked, such as blue light and oxygen signalling PAS domains. Therefore, clustering analysis of SSTs might facilitate functional analysis of these domains. The GAF domain is a type of protein domain that is found in a wide range of phytochrome proteins from all species (Aravind & Ponting, 1997). The GAF domain is named after some of the proteins in which it occurs: cGMP-specific phosphodiesterases, adenylylcyclases and FhlA. The first structure of a GAF domain solved by Ho and colleagues showed that this domain shared a similar fold with the PAS domain (Ho et al., 2000). Photoactive yellow protein (PYP) is a small bacterial photoreceptor (Sprenger et al., 1993), and is a prototypical PAS domain (Pellequer et al., 1998) involved in photosensory processes in some bacteria, such as purple bacteria (Sprenger et al., 1993; Jiang et al., 1999).

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