Table 3. GAS genes with negative or positive Z-scores (± 2.0 or higher) to SEGS values. M5005_gene Gene Description Function Z(SEGS ) NFD(SEGS ) Phase Analysis Probe-set Probe M5005_Spy1423 - Hyaluronoglucosaminidase (EC 3.2.1.35) Phage -5.216330076 0.007485969 acute PPA1&2 SpM12_ChORF299-63_at 16 M5005_Spy0504 pepF Oligoendopeptidase F (EC 3.4.24.-) Amino acid metabolism -4.331206282 0.296785995 acute PPA1&2 SpM1_ChORF0606_s_at 10 M5005_Spy1186 - Phage protein Phage -4.323906633 0.305389038 acute PPA1&2 SpM1_ChORF1456_s_at 15 M5005_Spy0871 - Multidrug resistance ABC transporter ATP-binding and permease protein Membrane transport -4.320521915 0.309459061 acute PPA1&2 SpM1_ChORF1149_s_at 9 M5005_Spy0783 ptsD PTS system, mannose/fructose family IID component Carbohydrate metabolism -4.206162395 0.48212507 acute PPA1&2 SpM1_ChORF1060_s_at 13 M5005_Spy1466 - Phage protein Phage -4.196697521 0.499972759 acute PPA1&2 SpM12_ChORF299-14_at 12 M5005_Spy0868 - Hypothetical protein Unknown -4.1030198 0.714393283 acute PPA1&2 SpM1_ChORF1146_s_at 6 M5005_Spy0027 - IMP CYCLOHYDROLASE (EC 3.5.4.10) Nucleotide metabolism -4.042526536 0.897014541 acute PPA1&2 SpM18_ChORF0030_s_at 1 M5005_Spy1540 endoS Endo-beta-N-acetylglucosaminidase F2 precursor (EC 3.2.1.96) Carbohydrate metabolism -3.933430822 0.328559653 acute PPA3 SpM1_ChORF1813_at M5005_Spy0767 - 4-nitrophenylphosphatase (EC 3.1.3.41) Unknown -3.892686026 1.561207204 acute PPA1&2 SpM1_ChORF1043_s_at 12 M5005_Spy0680 - Two-component response regulator Signal transduction -3.858649146 1.767166565 acute PPA1&2 SpM1_ChORF0874_s_at 11 M5005_Spy1818 cadC Cadmium efflux system accessory protein Membrane transport -3.854956463 1.791005758 acute PPA1&2 SpM1_ChORF2163_s_at 6 M5005_Spy0135 - Hypothetical membrane associated protein Unknown -3.775054045 2.38833708 acute PPA1&2 SpM1_ChORF0159_s_at 4 M5005_Spy0101 adhE tRNA binding domain protein Protein synthesis -3.762426541 0.621439274 acute PPA3 SpM18_ChORF0118_s_at M5005_Spy0517 regR Transcriptional regulator, LacI family Information processing -3.718295416 2.922851942 acute PPA1&2 SpM1_ChORF0627_s_at 12 M5005_Spy0537 aspC Aspartate aminotransferase (EC 2.6.1.1) Amino acid metabolism -3.713735557 2.97039385 acute PPA1&2 SpM1_ChORF0650_s_at 12 M5005_Spy0850 pta putative phosphotransacetylase Cellular processing -3.712057722 2.988071055 acute PPA1&2 SpM1_ChORF1128_s_at 2 M5005_Spy0539 - ATP-binding protein (contains P-loop) Membrane transport -3.706946834 3.042534595 acute PPA1&2 SpM1_ChORF0652_s_at 12 M5005_Spy0061 rpsE SSU ribosomal protein S5P Protein synthesis -3.564877715 4.992516532 acute PPA1&2 SpM1_ChORF0069_s_at 1 M5005_Spy0780 - PTS system, mannose/fructose family IIA component Unknown -3.558956355 5.095166371 acute PPA1&2 SpM1_ChORF1057_s_at 4 M5005_Spy1222 int.2 DNA integration/recombination/invertion protein phi5005.2 int Phage -3.528292626 1.437858399 acute PPA3 SpM1_ChORF1488_s_at M5005_Spy1663 - PTS SYSTEM, IIB COMPONENT (EC 2.7.1.69) Carbohydrate metabolism -3.518197772 1.489487779 acute PPA3 SpM1_ChORF1950_s_at M5005_Spy0868 - Hypothetical protein Unknown -3.498271411 6.268403115 acute PPA1&2 SpM1_ChORF1146_s_at 13 M5005_Spy0681 - Two component system histidine kinase (EC 2.7.3.-) Signal transduction -3.470882902 6.877391164 acute PPA1&2 SpM1_ChORF0875_s_at 10 M5005_Spy1654 - Hypothetical protein Unknown -3.466760567 1.780738647 acute PPA3 SpM5_ChORF125g-139_at M5005_Spy0058 rpsH SSU ribosomal protein S8P Protein synthesis -3.453323491 7.296659007 acute PPA1&2 SpM1_ChORF0065_s_at 2 M5005_Spy0764 - Hypothetical protein Unknown -3.451868835 7.332449053 acute PPA1&2 SpM1_ChORF1039_s_at 2 M5005_Spy1685 - D-tyrosyl-tRNA(Tyr) deacylase (EC 3.1.-.-) Protein synthesis -3.432458086 7.826096765 acute PPA1&2 SpyM3_1699_at 15 M5005_Spy1412 nusA N utilization substance protein A Cellular processing -3.424128817 8.047355927 acute PPA1&2 SpM1_ChORF1724_s_at 4 M5005_Spy1695 - Ribosomal protein L11 methyltransferase (EC 2.1.1.-) Protein synthesis -3.38737853 2.336928839 acute PPA3 SpM1_ChORF1988_s_at M5005_Spy1184 - Phage protein Phage -3.380925254 9.292393133 acute PPA1&2 SpM1_ChORF1455_s_at 2 M5005_Spy1519 recG ATP-dependent DNA helicase recG (EC 3.6.1.-) Information processing -3.35546511 10.10845036 acute PPA1&2 SpM1_ChORF1785_s_at 4 M5005_Spy1052 int.1 DNA integration/recombination/invertion protein phi5005.1 int Phage -3.338082749 2.760149795 acute PPA3 SpM18_ChORF1309_s_at M5005_Spy0384 - Surface antigen Virulence -3.311211515 11.68868554 acute PPA1&2 SpM1_ChORF0469_s_at 9 M5005_Spy0466 - Hypothetical phage protein Phage -3.303624186 11.98180002 acute PPA1&2 SpM18_ChORF0632_s_at 13 M5005_Spy1083 - Transcription antiterminator, BglG family / PTS system, mannitol (Cryptic)-specific IIA component (EC 2.7.1.69) Information processing -3.287297784 12.63598108 acute PPA1&2 SpM1_ChORF1325_s_at 12 M5005_Spy1331 - Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) Unknown -3.285825973 3.286280558 acute PPA3 SpM12_ChORF289-26_at M5005_Spy0834 - Zn-dependent alcohol dehydrogenases and related dehydrogenases Unknown -3.28182996 12.86242904 acute PPA1&2 SpM1_ChORF1111_s_at 14 M5005_Spy0223 - GTPase (EC 3.6.1.-) Unknown -3.275939861 13.11060343 acute PPA1&2 SpM1_ChORF0263_s_at 2 M5005_Spy1245 - RNA binding protein Unknown -3.275245713 3.403597214 acute PPA3 SpM1_ChORF1515_s_at M5005_Spy1117 deaD2 ATP-dependent RNA helicase Stress -3.240898929 14.68188904 acute PPA1&2 SpM1_ChORF1369_s_at 8 M5005_Spy0962 - Hypothetical protein Unknown -3.22528854 15.43697381 acute PPA1&2 SpM1_ChORF1252_s_at 7 M5005_Spy0318 pflC Pyruvate formate-lyase activating enzyme (EC 1.97.1.4) Carbohydrate metabolism -3.193399082 17.09327816 acute PPA1&2 SpM1_ChORF0379_s_at 1 M5005_Spy0066 infA Bacterial Protein Translation Initiation Factor 1 (IF-1) Cellular processing -3.167588232 18.55343013 acute PPA1&2 SpM1_ChORF0075_s_at 3 M5005_Spy0058 rpsH SSU ribosomal protein S8P Protein synthesis -3.166716579 18.60470802 acute PPA1&2 SpM1_ChORF0065_s_at 15 M5005_Spy0587 pheS Phenylalanyl-tRNA synthetase alpha chain (EC 6.1.1.20) Protein synthesis -3.165720561 4.869546395 acute PPA3 SpM1_ChORF0768_s_at M5005_Spy1386 - Hypothetical membrane spanning protein Unknown -3.163061351 4.911525008 acute PPA3 SpM1_ChORF1691_s_at M5005_Spy0121 - Acetyl-CoA:acetoacetyl-CoA transferase beta subunit (EC 2.8.3.-) Carbohydrate metabolism -3.153036204 19.42695837 acute PPA1&2 SpM1_ChORF0142_s_at 1 M5005_Spy0264 - Hydrolase (HAD superfamily) Unknown -3.1418665 20.12321039 acute PPA1&2 SpM1_ChORF0309_s_at 9 M5005_Spy1077 glnQ.2 Glutamine transport ATP-binding protein glnQ Membrane transport -3.139799861 20.25454571 acute PPA1&2 SpM1_ChORF1316_s_at 2 M5005_Spy1140 queA S-adenosylmethionine:tRNA ribosyltransferase-isomerase (EC 5.-.-.-) Protein synthesis -3.136894369 20.44053681 acute PPA1&2 SpM1_ChORF1400_s_at 3 M5005_Spy0057 rpsN SSU ribosomal protein S14P Protein synthesis -3.113849697 21.97284948 acute PPA1&2 SpM1_ChORF0064_s_at 5 M5005_Spy1581 - Transcriptional regulator, MerR family Information processing -3.108428234 22.34849834 acute PPA1&2 SpM1_ChORF1863_s_at 10 M5005_Spy0291 - Acetyltransferase (GNAT) family Unknown -3.093317946 23.42713531 acute PPA1&2 SpM1_ChORF0346_s_at 10 M5005_Spy1162 - Hypothetical protein Unknown -3.065782387 25.51771239 acute PPA1&2 SpM1_ChORF1425_s_at 14 M5005_Spy1442 - Phage transcriptional activator Phage -3.048812964 7.066038664 acute PPA3 SpM12_ChORF299-47_s_at M5005_Spy1163 - Transcriptional regulator, biotin repressor family Information processing -3.045289397 27.18423637 acute PPA1&2 SpM1_ChORF1427_s_at 2 M5005_Spy0399 - Hypothetical membrane associated protein Unknown -3.031029316 7.470938877 acute PPA3 SpM1_ChORF0484_s_at M5005_Spy1753 pbp2A Multimodular transpeptidase-transglycosylase PBP 2A Cell wall metabolism -3.016868338 29.66235776 acute PPA1&2 SpM1_ChORF2059_s_at 10 M5005_Spy0517 regR Transcriptional regulator, LacI family Information processing -3.015397193 7.844402513 acute PPA3 SpM1_ChORF0627_at M5005_Spy0038 - Acyltransferase family Unknown -3.00540974 30.71921048 acute PPA1&2 SpM1_ChORF0041_s_at 9 M5005_Spy1064 malC Maltose transport system permease protein malF Membrane transport -3.002107449 31.03017584 acute PPA1&2 SpM1_ChORF1301_at 10 M5005_Spy1235 - PHOSPHOGLUCOMUTASE (EC 5.4.2.2) / PHOSPHOMANNOMUTASE (EC 5.4.2.8) Carbohydrate metabolism -2.98473965 8.627219281 acute PPA3 SpM1_ChORF1503_s_at M5005_Spy1184 - Phage protein Phage -2.924566748 10.37627195 acute PPA3 SpM3_ChORF1109_x_at M5005_Spy0338 - Arsenate reductase family protein Unknown -2.870606323 12.21526168 acute PPA3 SpM1_ChORF0410_s_at M5005_Spy1000 - Phage protein Phage -2.866123237 12.38072212 acute PPA3 SpM49_ChORF7585-41_at Page 1 of 8 Table 3. GAS genes with negative or positive Z-scores (± 2.0 or higher) to SEGS values. M5005_gene Gene Description Function Z(SEGS ) NFD(SEGS ) Phase Analysis Probe-set Probe M5005_Spy0225 - Thiamin pyrophosphokinase (EC 2.7.6.2) Coenzyme and cofactor metabolism -2.801086386 15.02283823 acute PPA3 SpM1_ChORF0265_s_at M5005_Spy0305 - putative phosphoesterase Unknown -2.796292302 15.23659114 acute PPA3 SpM1_ChORF0363_s_at M5005_Spy0242 - ABC transporter ATP-binding protein Coenzyme and cofactor metabolism -2.792643857 15.40111464 acute PPA3 SpM1_ChORF0285_s_at M5005_Spy0824 folK 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase (EC 2.7.6.3) Coenzyme and cofactor metabolism -2.790890806 15.48074054 acute PPA3 SpM1_ChORF1100_s_at M5005_Spy0374 rplK LSU ribosomal protein L11P Protein synthesis -2.756988778 17.09613356 acute PPA3 SpM1_ChORF0460_s_at