Dual-Cys bacteriophytochromes: intermediates in cyanobacterial phytochrome evolution?

This work (Yang et al., \"Dual-Cys bacteriophytochromes: intermediates in cyanobacterial phytochrome evolution?\" in FEBS. J.) involves the characterization of new cyanobacterial phytochrome photoreceptor proteins and engineering chromophore preferences via Cysteine mutagenesis both in those proteins and in known reference proteins. Proteins were characterized using absorption and mass spectrometry, phylogenetic analysis, and X-ray crystallography. The crystal structure is available through the RCSB PDB (PDB ID: 9JRY). All other data are in this deposit., Three types of data are deposited: absorption spectroscopy, mass spectrometry, and phylogeny.
Absorption data were collected at 16°C or 26°C using a Shimadzu UV-1900 spectrophotometer equipped with a TCC-100 temperature controller. Data were exported as text files.
Selected reaction monitoring mass spectrometry (SRM-MS) analysis was conducted using a 1290 Infinity Ⅱ Bio 2D-LC System (Agilent Technologies, USA) connected with a 6495D Triple Quadrupole mass spectrometer (Agilent Technologies, USA) with a Jet-stream electrospray source. The separation was performed on a ZORBAX Eclipse Plus C18 column (ID: 959759-902, length: 150 mm, pore size: 95 Å, particle size: 1.8 μm, column temperature 40℃) (Agilent Technologies, USA) using Mobile Phase A [0.1% (vol/vol) formic acid in water] and Mobile Phase B [0.1% (vol/vol) formic acid in acetonitrile]. The peptides derived from protein digestion were separated using a 30-minute gradient. The gradient started at 3% Mobile Phase B for 4 min, then in..., , # Dual-Cys bacteriophytochromes: intermediates in cyanobacterial phytochrome evolution?

## Description of the Data and file structure

Data are deposited as a gzipped tarball. After extraction, deposited data are in three folders:
I. Phylogeny
II. Mass_Spec
III. Absorption_Spectra

#### I. Phylogeny:

Data are all within a single folder, without subdirectories. A single phylogeny was inferred for this study, and the deposited files are all from this analysis.

Three files are deposited: the original multiple sequence alignment in CLUSTAL format, the input file for PHYML in PHYLIP format after removal of gap-enriched columns, and the final tree with transfer bootstrap expectation values in Newick format. The files are:

DCB_tree.aln (CLUSTAL format)

This is the original alignment, generated in MAFFT using the E-INS-i algorithm (v7.450). After a header indicating the MAFFT version, aligned sequences are presented as interleaved blocks. Each block has a segment of each sequence after ...