Fig. 1: Bioinformatic analyses of Sll0485 (KaiA3).

a Multiple sequence alignment and maximum likelihood-inferred phylogenetic reconstruction of KaiA3 and selected KaiA orthologs. The sequences were aligned with Mafft (L-INS-i default parameters, Jalview), trimmed to position 168 of the C-terminus of Synechococcus KaiA and are represented in the Clustalx color code with conservation visibility set to 25%. Marks above the alignment refer to Synechococcus KaiA as a reference. Light green bars and dots indicate residues critical for KaiC interaction, light pink bars and dots represent residues important for dimerization, and light gray blocks outline residues forming α-helices as secondary structures. Aligned sequences were used to infer a maximum likelihood protein tree. The scale bar indicates one substitution per position. Bootstrap values (n = 1000) are displayed on the branches. Bootstrap values of less than 50 are not shown. b Synteny analysis of kaiA1B1C1 compared to kaiA3, kaiB3, and kaiC3 genes for selected bacterial species. Analysis was performed with the online tool SyntTax, a prokaryotic synteny and taxonomy explorer (https://archaea.i2bc.paris-saclay.fr/synttax/; 2020-06-08). Default settings were used for analysis (best match, 10% norm. Blast). c Co-occurrence of KaiA3 with circadian clock proteins in cyanobacteria using pairwise right-sided Fisher’s exact test. Network of significant co-occurring circadian clock factors from Schmelling et al.²⁷, including KaiA3 in Cyanobacteria. The line color corresponds to the level of significance resulting from pairwise Fisher’s exact test. Missing links were those with p-values higher than 0.01. The node size is proportional to the degree of that node.