Neethu Shah, Rosmarie Gaupp, Hideaki Moriyama, Kent M. Eskridge, Etsuko N. Moriyama, and Greg A. Somerville (submitted) "Reductive evolution and the loss of PDC/PAS domains from the genus Staphylococcus" — Supplementary data — Supplementary tables and figures included with the manuscript Additional file 1 (Excel file) Additional file 2 (pdf file) Additional file 3 (Excel file) Additional file 4 (pdf file, Figure S2 and S3) HMM data used for HHblits and HHsearch HHblits I (Gram positive, gzip file, ~9GB) HHblits II (Gram positive, gzip file, ~8GB) HHblits III (Gram positive, gzip file, ~6GB) HHblits IV (Gram positive, gzip file, ~5GB) HHblits V (Gram negative, gzip file, ~10GB) HHblits VI (Gram negative, gzip file, ~7GB) HHseach I (Gram positive, gzip file, ~2GB) HHseach II (Gram negative, gzip file, ~2GB) PDB HMMs (gzip file) PAS/PDC alignments PAS domains alignment (png file) PDC domains alignment (png file) 16sDNA alignment (text file)

PAS/PDC containing proteins (FASTA format) Gram positive Clostridium difficile 630 Clostridium acetobutylicum ATCC 824 Clostridium botulinum ATCC 3502 Enterococcus faecium DO Enterococcus faecalis V583 Lactobacillus casei ATCC 334 Lactococcus lactis subsp. cremoris MG1363 Streptococcus pneumoniae D39 Streptococcus pyogenes MGAS10270 Streptococcus agalactiae 260 V/R Listeria monocytogenes EGD-e Bacillus subtilis strain 168 Bacillus cereus ATCC 10987 Bacillus anthracis CDC 684 Bacillus megaterium QM B1551 Macrococcus caseolyticus JCSC5402 Staphylococcus saprophyticus ATCC 15305 Staphylococcus lugdunensis HKU09-01 Staphylococcus haemolyticus JCSC1435 Staphylococcus epidermidis ATCC 12228 Staphylococcus aureus USA300_TCH1516 Staphylococcus aureus COL Staphylococcus pseudintermedius HKU10-03 Staphylococcus carnosus TM300 TM300 Streptomyces coelicolor A3(2) Micrococcus luteus NCTC 2665 Mycobacterium tuberculosis CDC1551 Mycobacterium smegmatis MC2 155 Mycobacterium leprae TN Corynebacterium diphtheriae NCTC 13129 Corynebacterium glutamicum ATCC 13032 Bifidobacterium animalis lactis AD011

Gram negative Bradyrhizobium sp BTAi1 Agrobacterium tumefaciens C58 Bartonella henselae Houston-1 Vibrio cholerae MJ-1236 Klebsiella pneumoniae 342 Salmonella enterica arizonae serovar str. RSK2980 Shigella flexneri 2a str. 2457T Pseudomonas aeruginosa PAO1 Yersinia pestis CO92 Escherichia coli K-12 substr. MG1655 Helicobacter pylori 83 Neisseria meningitidis MC58 Leptospira biflexa serovar Patoc strain Treponema pallidum pallidum SS14 pallidum SS14 Synechococcus sp CC9311 Nostoc punctiforme PCC 73102 PCC 73102 All the PAS/PDC containing proteins