Electronic Supplementary Material (ESI) for Metallomics. This journal is © The Royal Society of Chemistry 2015 Supplementary Table S1. The key enzymes for autotrophic growth in C. metallidurans Name Rmet-‐number Spec. Predicted Mass, (kDa) Determined Mass, (kDa) Activity HOS Rmet_1522 to Rmet_1525 28.7 65.2, 25.4, 23.4, 52.8 = 166.8 62.4±1.8, 26.4±1.3, 24.0±0.6, 54.1±2.5, =235±20a HOP Rmet_1297, Rmet_1298, 67.0 69.0 + 38.6 = 108 148±24a CAX Rmet_1500, Rmet_1501 2.82 8 * (13.6 + 52.5) = 529 475±36a PRK Rmet_1512 0.994 8 * 32.4 = 259 256±11a a Mean value of masses determined by S300 size exclusion chromatography and sucrose gradient centrifugation. HOS, NAD-‐reducing soluble hydrogenase; HOP, membrane-‐bound hydrogenase; CAX, ribulose-‐bis-‐phosphate carboxylase/oxygenase; PRK, phosphoribulokinase. Specific activity in U/mg protein. Supplementary Table S2. Genes expressed differently in AE104 compared to CH34 wild typea Operon Region Name UP Op1321r Rmet_4594 Op1322f Rmet_4595 Op1322f Rmet_4596 Op1322f Rmet_4597 Op0075f Rmet_0260 Op0075f Rmet_0261 Adjacent to CMGI-‐7 Op0335f Rmet_1171 CMGI-‐2 Op0362r Rmet_1251 CMGI-‐1 Op0663f Rmet_2349 Op0671f Rmet_2382 CMGI-‐10 Op0934r Rmet_3353 Gene zntA czcI2 czcC2 czcB2' -‐ coxB tnpA tnp -‐ tnpA tnpA DOWN aut region 1, Region 1, CMGI-‐3 Op0421f Rmet_1491 -‐ Op0422r Rmet_1492 cbbA1 Op0422r Rmet_1493 fbaA Op0422r Rmet_1494 -‐ Op0422r Rmet_1495 -‐ Op0422r Rmet_1496 -‐ Op0422r Rmet_1497 -‐ Op0422r Rmet_1498 cbbO Op0422r Rmet_1499 cbbQ Op0422r Rmet_1500 cbbS Op0422r Rmet_1501 rbcL Q D Description 1.72 2.03 23.34 15.36 2.31 2.08 7.03 4.08 2.44 4.49 2.77 2.88 2.92 5.36 9.68 2.48 2.49 21.74 0.61 1.15 23.38 4.55 Q1LEH0 Heavy metal translocating P-‐type ATPase Q1LEG9 Putative uncharacterized protein Q1LEG8 Outer membrane efflux protein Q1LEG7 Secretion protein HlyD Q1LRT0 Putative transmembrane protein Q1LRS9 Cytochrome c oxidase subunit 2 Q9F8S6 Transposase (Transposase, IS4 family) Q1LNY9 Putative uncharacterized protein Q8GQ59 Putative uncharacterized protein ORF C51 Q1LB62 Integrase, catalytic region Q9F8S6 Transposase (Transposase, IS4 family) 0.13 0.49 0.69 0.43 0.59 0.20 0.63 0.12 0.06 0.08 0.09 3.76 2.07 0.87 1.71 1.51 1.49 2.71 4.01 5.07 5.16 12.53 Q6SKD6 Transposase Q1LNA1 Fructose-‐bisphosphate aldolase Q1LNA0 Putative uncharacterized protein Q1LN99 Putative uncharacterized protein Q1LN98 Putative uncharacterized protein Q1LN97 Putative uncharacterized protein Q1LN96 Putative uncharacterized protein Q1LN95 von Willebrand factor, type A Q1LN94 ATPase associated with various cellular activities, AAA_5 Q1LN93 Ribulose bisphosphate carboxylase small chain Q1LN92 Ribulose bisphosphate carboxylase large chain Op0423f Op0423f Op0424r Op0424r Op0424r Op0424r Op0424r Op0425f Op0425f Op0425f Op0425f Op0425f Op0425f Op0425f Op0425f Op0425f Op0425f Op0425f Op0425f Op0425f Op0425f Op0425f Op0425f Op0425f Op0425f Op0425f Op0426r Op0427f Op0427f Op0427f Op0427f Op0427f Op0427f Op0427f Rmet_1502 Rmet_1503 Rmet_1504 Rmet_1505 Rmet_1506 Rmet_1507 Rmet_1508 Rmet_1509 Rmet_1510 Rmet_1511 Rmet_1512 Rmet_1513 Rmet_1514 Rmet_1515 Rmet_1517 Rmet_1518 Rmet_1519 Rmet_1520 Rmet_1521 Rmet_1522 Rmet_1523 Rmet_1524 Rmet_1525 Rmet_1526 Rmet_1527 Rmet_1528 Rmet_1529 Rmet_1530 Rmet_1531 Rmet_1532 Rmet_1533 Rmet_1534 Rmet_1535 Rmet_1536 -‐ -‐ -‐ -‐ -‐ cbbF1 cbbR -‐ cbbE1 cbbF2 cbbP cbbT1 cbbZ1 cbbG1 cbbY cbbA2 pykA2 cbbJ1 cbbI1 hoxF hoxU hoxY hoxH hoxW hoxI -‐ -‐ -‐ pntA pntB hoxN -‐ hypA hypB 0.04 0.64 0.48 0.12 0.21 0.59 0.41 0.09 0.04 0.08 0.09 0.54 0.12 0.16 0.10 0.07 0.17 0.34 0.13 0.01 0.01 0.00 0.02 0.00 0.00 0.39 0.70 0.35 0.26 0.44 0.77 0.00 0.00 0.01 5.13 4.64 3.26 6.40 5.26 1.57 3.08 5.62 8.48 8.54 5.82 2.53 4.77 5.40 9.03 5.00 9.60 6.95 4.52 4.95 5.14 6.62 8.18 8.28 13.64 7.34 2.67 2.22 5.08 2.92 0.15 7.06 7.12 14.80 Q1LN91 Transcriptional regulator, LysR family Q9RBF5 Ralstonia eutropha insertion sequence IS1090 Q1LN89 Putative uncharacterized protein Q1LN88 ISSod11, transposase Q6SKD6 Transposase Q1LN86 D-‐fructose 1,6-‐bisphosphatase Q1LN85 Transcriptional regulator, LysR family Q1LN84 Putative uncharacterized protein Q1LN83 Ribulose-‐5-‐phosphate 3-‐epimerase Q1LN82 D-‐fructose 1,6-‐bisphosphatase Q1LN81 Phosphoribulokinase Q1LN80 Transketolase Q1LN79 Phosphoglycolate phosphatase Q1LN78 Glyceraldehyde-‐3-‐phosphate dehydrogenase Q1LN76 HAD-‐superfamily hydrolase subfamily IA, variant 3 Q1LN75 Fructose-‐bisphosphate aldolase Q1LN74 Pyruvate kinase Q1LN73 Triosephosphate isomerase Q1LN72 Ribose-‐5-‐phosphate isomerase Q1LN71 Respiratory-‐chain NADH dehydrogenase domain, 51 kDa subunit Q1LN70 Ferredoxin Q1LN69 NADH ubiquinone oxidoreductase, 20 kDa subunit Q1LN68 Nickel-‐dependent hydrogenase, large subunit Q1LN67 HoxW protein Q1LN66 Cyclic nucleotide-‐binding domain (CNMP-‐BD) protein Q1LN65 Alanine dehydrogenase/PNT-‐like protein Q1LB62 Integrase, catalytic region Q1LN63 Alanine dehydrogenase/PNT-‐like protein Q1LN62 Pyridine nucleotide transhydrogenase subunit alpha Q1LN61 NAD(P) transhydrogenase, beta subunit Q1LN60 High-‐affinity nickel-‐transporter Q1LN59 Putative uncharacterized protein Q1LN58 Hydrogenase nickel insertion protein HypA Q1LN57 Hydrogenase accessory protein HypB Op0427f Op0427f Op0427f Op0427f Op0427f Op0427f Op0428r Op0430r Op0431f Op0431f Rmet_1537 Rmet_1538 Rmet_1539 Rmet_1540 Rmet_1541 Rmet_1542 Rmet_1543 Rmet_1545 Rmet_1546 Rmet_1547 hypF hypC hypD hypE hoxX hoxA -‐ -‐ -‐ -‐ Region 2 = CMGI-‐4 Op0847f Rmet_3013 Op0847f Rmet_3014 Op0848r Rmet_3015 Op0848r Rmet_3016 Op0848r Rmet_3017 Op0848r Rmet_3018 Op0848r Rmet_3019 Op0848r Rmet_3020 Op0848r Rmet_3021 Op0848r Rmet_3022 Op0848r Rmet_3023 yodB -‐ hmzS hmzR -‐ virD2 -‐ traF -‐ parG parA Op0848r Op0848r Op0848r Op0848r Op0849f Op0850r Op0850r Op0851f Op0852r Op0852r repA -‐ -‐ -‐ -‐ -‐ -‐ -‐ -‐ parB Rmet_3024 Rmet_3025 Rmet_3026 Rmet_3027 Rmet_3028 Rmet_3029 Rmet_3030 Rmet_3031 Rmet_3032 Rmet_3033 0.01 0.01 0.00 0.00 0.02 0.01 0.29 0.17 0.25 0.31 8.22 13.63 14.76 4.08 5.68 6.68 2.39 3.42 2.48 2.99 Q1LN56 (NiFe) hydrogenase maturation protein HypF Q1LN55 Hydrogenase assembly chaperone hypC/hupF Q1LN54 Hydrogenase expression/formation protein HypD Q1LN53 Hydrogenase expression/formation protein HypE Q1LN52 Formyl transferase-‐like protein Q1LN51 Response regulator receiver domain protein (CheY-‐like) Q1LN50 Stress responsive alpha-‐beta barrel Q1LN48 Putative uncharacterized protein Q1LN47 Transcriptional regulator, LysR family Q1LN46 Putative lipoprotein 0.06 0.16 0.48 0.25 0.26 0.37 1.00 0.68 0.41 0.44 0.61 5.94 4.62 2.64 3.62 2.03 2.26 0.01 0.96 1.39 1.58 1.89 0.87 0.27 0.52 0.23 0.07 0.43 0.15 0.17 0.28 0.85 0.61 1.51 0.82 3.86 12.79 3.32 7.09 3.16 4.14 0.74 Q1LIZ0 Cytochrome B561 A0HB61 Putative uncharacterized protein Q1LIY8 Sensor protein Q1LIY7 Two component transcriptional regulator, winged helix family Q1LIY6 Ferric reductase-‐like transmembrane component-‐like Q1LIY5 Putative uncharacterized protein Q1LIY4 Putative uncharacterized protein Q1LIY3 TraF peptidase. Serine peptidase. MEROPS family S26C A0HB67 Putative uncharacterized protein Q1LIY1 Putative uncharacterized protein A0HB69 Cobyrinic acid a,c-‐diamide synthase A9BTU5 Conserved hypothetical replication initiator and transcription repressor protein Q1LIX8 Putative uncharacterized protein A9BTV1 Putative uncharacterized protein A9BTV2 Putative lipoprotein A9BTV3 Helix-‐turn-‐helix domain protein Q1LIX4 Putative uncharacterized protein Q1LIX3 Putative uncharacterized protein A9BTV5 GCN5-‐related N-‐acetyltransferase A9BTV6 Putative uncharacterized protein A9BTV7 ParB domain protein nuclease Op0852r Op0853f Op0853f Op0854r Op0854r Op0854r Op0854r Op0854r Op0855f Op0855f Op0856r Op0856r Op0856r Rmet_3034 Rmet_3035 Rmet_3036 Rmet_3037 Rmet_3038 Rmet_3039 Rmet_3040 Rmet_3041 Rmet_3042 Rmet_3043 Rmet_3044 Rmet_3045 Rmet_3046 Region 3 = CMGI-‐2 Op0366r Rmet_1274 Op0366r Rmet_1275 Op0366r Rmet_1276 Op0366r Rmet_1277 Op0367f Rmet_1278 Op0368r Rmet_1279 Op0369f Rmet_1280 Op0370r Rmet_1281 Op0370r Rmet_1282 Op0370r Rmet_1283 Op0370r Rmet_1284 Op0370r Rmet_1285 Op0370r Rmet_1286 Op0370r Rmet_1287 Op0370r Rmet_1288 Op0370r Rmet_1289 Op0370r Rmet_1290 Op0370r Rmet_1291 Op0370r Rmet_1292 yupB -‐ -‐ -‐ -‐ -‐ -‐ -‐ -‐ -‐ -‐ int maeB1 -‐ -‐ -‐ -‐ -‐ -‐ tnpA hypE1 hypD1 hypC1 hyoF1 hypB1 hypA1 hoxV -‐ -‐ hoxQ -‐ hypC2 0.61 0.65 0.61 0.32 0.62 0.06 0.14 0.05 0.00 0.10 0.01 0.20 0.47 1.39 5.14 0.72 2.74 3.27 12.37 3.09 6.72 15.97 8.00 7.42 4.74 4.29 A9BTV8 Putative uncharacterized protein pseudo B2UA43 Putative uncharacterized protein Q1LIW7 Putative uncharacterized protein B2UA41 Putative uncharacterized protein B2UA40 Putative uncharacterized protein Q1LIW4 UBA/THIF-‐type NAD/FAD binding fold A9BTW5 Putative uncharacterized protein Q1LIW2 Putative uncharacterized protein B2UA36 Putative uncharacterized protein A9BTW8 Putative uncharacterized protein Q1LIV9 Phage integrase Q1LIV8 Malic enzyme, NAD-‐binding 0.48 0.72 0.60 0.31 0.22 0.28 0.15 0.21 0.55 0.17 0.65 0.12 0.37 0.71 0.09 0.16 0.07 0.14 0.28 1.24 0.80 0.77 1.93 1.13 3.44 5.58 4.05 4.07 2.60 1.79 2.06 1.43 0.97 5.22 5.13 9.33 4.47 5.01 Q1LNW7 Transposase IS66 Q1LNW6 IS66 Orf2 like Q1LNW5 Putative uncharacterized protein Q1LNW4 ATPase component ABC-‐type multidrug transport system Q1LNW3 Transposase Q1LNW2 Putative transposase Q1LNW1 Integrase, catalytic region Q1LNW0 Hydrogenase expression/formation protein HypE Q1LNV9 Hydrogenase expression/formation protein HypD Q1LNV8 Hydrogenase assembly chaperone hypC/hupF Q1LNV7 Hydrogenase maturation protein hypF Q1LNV6 Hydrogenase accessory protein HypB Q1LNV5 Hydrogenase nickel insertion protein HypA Q1LNV4 Putative uncharacterized protein Q1LNV3 HupJ, contains rubredoxin domain Q1LNV2 Rubredoxin Q1LNV1 HupH hydrogenase expression protein Q1LNV0 Hydrogenase-‐1 expression HyaE Q1LNU9 Hydrogenase assembly chaperone hypC/hupF Op0370r Rmet_1293 -‐ Op0370r Op0370r Op0370r Op0370r Op0370r Op0371f Op0372r Op0373f Op0374r Op0374r Op0375f Op0376r Op0376r Op0376r Op0376r Op0376r Op0376r Op0376r Op0376r Op0376r Op0376r Op0376r Op0376r Op0376r Op0376r Op0376r Op0376r Op0376r Op0376r Op0376r Op0376r Op0376r Rmet_1294 Rmet_1295 Rmet_1296 Rmet_1297 Rmet_1298 Rmet_1299 Rmet_1300 Rmet_1301 Rmet_1302 Rmet_1303 Rmet_1304 Rmet_1305 Rmet_1306 Rmet_1307 Rmet_1308 Rmet_1309 Rmet_1310 Rmet_1311 Rmet_1312 Rmet_1313 Rmet_1314 Rmet_1315 Rmet_1316 Rmet_1317 Rmet_1318 Rmet_1319 Rmet_1320 Rmet_1321 Rmet_1322 Rmet_1323 Rmet_1324 Rmet_1325 -‐ -‐ hupE hoxG hoxK -‐ -‐ tnpA -‐ -‐ -‐ patR -‐ -‐ -‐ -‐ -‐ -‐ tmoE tmoD tmoC tmoB tmoA nahJ dmpH mhpE mhpF -‐ dmpC -‐ dmpB hcaD 0.13 2.48 Q1LNU8 HyaD peptidase. Aspartic peptidase. MEROPS family A31 Q1LNU7 Putative plasmid maintenance system antidote protein, XRE 0.16 3.61 family 0.03 4.15 Q1LNU6 Nickel-‐dependent hydrogenase b-‐type cytochrome subunit 0.06 7.77 Q1LNU5 HupE/UreJ protein 0.05 4.48 Q1LNU4 Nickel-‐dependent hydrogenase, large subunit 0.01 6.37 Q1LNU3 Hydrogenase (NiFe) small subunit (HydA) 0.83 1.23 Q1LNU2 Putative uncharacterized protein 0.38 1.71 Q1LNU1 GMC oxidoreductase 1.10 0.58 Q1LNW1 Integrase, catalytic region 0.29 4.74 Q1LNT9 Putative transposase 0.28 2.81 Q1LNT8 Transposase IS3/IS911 0.37 2.06 Q1LNT7 Putative uncharacterized protein 0.19 2.32 Q1LNT6 Sigma-‐54 factor, interaction region 0.34 4.95 A4JW31 Alpha/beta hydrolase fold 0.63 1.74 Q1LNT4 Membrane protein involved in aromatic hydrocarbon degradation 0.32 1.70 Q1LNT3 Alcohol dehydrogenase GroES-‐like protein 0.21 3.07 not annotated 0.42 1.51 not annotated 0.48 1.87 Q1LNT2 Oxidoreductase FAD-‐binding region 0.59 1.30 Q1LNT1 Methane/phenol/toluene hydroxylase 0.24 5.40 Q1LNT0 Monooxygenase component MmoB/DmpM 0.20 7.77 Q1LNS9 Rieske (2Fe-‐2S) region 0.13 3.30 Q1LNS8 Toluene-‐4-‐monooxygenase system B 0.19 4.91 Q1LNS7 Methane/phenol/toluene hydroxylase 0.42 1.37 Q1LNS6 4-‐oxalocrotonate tautomerase family enzyme 0.15 3.27 Q1LNS5 Hydratase/decarboxylase 0.54 2.02 Q1LNS4 Pyruvate carboxyltransferase 0.61 1.24 Q1LNS3 Semialdehyde dehydrogenase, NAD-‐binding 0.50 1.71 Q1LNS2 Hydratase/decarboxylase 0.46 2.42 Q1LNS1 Aldehyde dehydrogenase 0.62 1.68 Q1LNS0 Putative uncharacterized protein 0.31 1.97 Q1LNR9 Catechol 2,3-‐dioxygenase 0.31 2.28 Q1LNR8 Ferredoxin Op0376r Op0376r Op0376r Op0376r Op0376r Op0376r Op0377f Op0377f Op0377f Op0377f Op0377f Op0377f Op0378r Rmet_1326 Rmet_1327 Rmet_1328 Rmet_1329 Rmet_1330 Rmet_1331 Rmet_1332 Rmet_1333 Rmet_1334 Rmet_1335 Rmet_1336 Rmet_1337 Rmet_1338 -‐ -‐ tomA3 -‐ -‐ -‐ -‐ phaB2 -‐ chnA -‐ -‐ -‐ Region 4 Rmet_5689 Rmet_5690 Rmet_5692 Rmet_5693 Rmet_5694 Rmet_5695 Rmet_5696 Rmet_5697 Rmet_5698 Rmet_5710 Rmet_5714 Rmet_5715 Rmet_5716 Rmet_5724 Rmet_5728 Rmet_5729 Rmet_5730 Rmet_5731 pilY1 -‐ -‐ -‐ -‐ -‐ -‐ -‐ -‐ bvgS1 bvgA -‐ -‐ -‐ -‐ -‐ kpsE kpsT Op1698f Op1698f Op1700f Op1700f Op1701r Op1702f Op1702f Op1703r Op1704f Op1708f Op1709r Op1709r Op1710f Op1714f Op1715r Op1715r Op1715r Op1715r 0.58 0.09 0.07 0.31 0.37 0.26 0.24 0.08 0.37 0.12 0.11 0.15 0.28 1.26 3.26 5.40 3.54 1.62 2.51 5.61 6.16 1.56 7.40 4.77 6.06 3.05 0.07 0.05 0.41 0.22 0.32 0.16 0.16 0.39 0.37 0.48 0.22 0.12 0.12 0.26 0.16 0.25 0.23 0.30 23.92 11.37 1.88 3.43 2.41 3.46 3.10 1.73 3.61 2.06 7.17 4.25 2.33 4.85 2.33 5.76 2.73 6.70 Q1LNR7 Oxidoreductase FAD-‐binding region Q9ANX1 TomA4 Q1LNR5 Methane/phenol/toluene hydroxylase Q1LNR4 Monooxygenase component MmoB/DmpM Q1LNR3 Methane/phenol/toluene hydroxylase Q1LNR2 Phenol hydroxylase subunit Q1LNR1 Putative uncharacterized protein Q1LNR0 Acetoacetyl-‐CoA reductase Q1LNQ9 UspA Q1LNQ8 Short-‐chain dehydrogenase/reductase SDR Q1LNQ7 Transcriptional regulator, LysR family Q1LNQ6 Putative lipoprotein Q1LNQ5 Putative uncharacterized protein Q1LBC8 Putative type 4 fimbrial biogenesis pily1-‐related protein signal peptide Q1LBC7 Putative lipoprotein Q1LBC5 Putative uncharacterized protein Q1LBC4 Putative uncharacterized protein Q1LBC3 Putative uncharacterized protein Q1LBC2 Beta-‐lactamase-‐like protein Q1LBC1 Putative uncharacterized protein Q1LBC0 Putative uncharacterized protein Q1LBB9 Putative uncharacterized protein Q1LBA7 Sensor protein Q1LBA3 Two component transcriptional regulator, LuxR family Q1LBA2 Putative uncharacterized protein Q1LBA1 Putative uncharacterized protein Q1LB93 Sensor protein Q1LB89 Glycosyl transferase, group 1 Q1LB88 Polysaccharide export protein Q1LB87 Chain length determinant protein Q1LB86 ABC transporter related Op1716f Op1716f Op1716f Op1717r Op1717r Op1718f Op1718f Op1720f Op1721r Op1722f Op1723r Op1724f Op1724f Rmet_5735 Rmet_5738 Rmet_5739 Rmet_5742 Rmet_5743 Rmet_5744 Rmet_5745 Rmet_5749 Rmet_5750 Rmet_5751 Rmet_5752 Rmet_5753 Rmet_5754 -‐ -‐ -‐ -‐ -‐ -‐ -‐ -‐ -‐ -‐ -‐ -‐ -‐ Region 5 Op0034r Op0037f Op0038r Op0038r Op0107f Rmet_0133 Rmet_0137 Rmet_0138 Rmet_0139 Rmet_0392 -‐ -‐ -‐ -‐ -‐ radC int int ritC radC parB -‐ -‐ -‐ -‐ virD -‐ Region 6 = CMGI-‐2 Op0357f Rmet_1238 Op0357f Rmet_1239 Op0357f Rmet_1240 Op0357f Rmet_1241 Op0357f Rmet_1242 Op0357f Rmet_1245 Op0358r Rmet_1246 Op035xx Rmet_1247 Op0359f Rmet_1248 Op0363f Rmet_1255 Op0363f Rmet_1259 Op0364r Rmet_1264 0.38 0.26 0.32 0.11 0.38 0.18 0.10 0.07 0.25 0.25 0.14 0.12 0.48 1.67 6.71 4.91 3.12 3.47 2.95 3.46 5.57 4.09 2.12 5.80 5.46 10.58 Q1LB82 KpsF/GutQ family protein Q1LB79 Putative uncharacterized protein Q1LB78 Putative uncharacterized protein Q1LB75 Putative uncharacterized protein Q1LB74 AMP-‐dependent synthetase and ligase Q1LB73 Putative uncharacterized protein Q1LB72 Putative uncharacterized protein Q1LB68 Transcriptional regulator, PadR family Q1LB67 Diguanylate cyclase/phosphodiesterase Q1LB66 Diguanylate cyclase (GGDEF domain) with PAS/PAC sensor Q1LB65 Putative uncharacterized protein Q1LB64 Putative uncharacterized protein Q1LB63 Fumarate hydratase, class II 0.28 0.36 0.37 0.46 0.45 2.49 1.42 2.11 2.87 1.08 Q1LS57 Nuclear export factor GLE1 Q1LS53 Putative uncharacterized protein Q1LS52 Transcriptional regulator, LysR family Q1LS51 Putative uncharacterized protein Q1LRE8 Twin-‐arginine translocation pathway signal 0.35 0.10 0.41 0.27 0.06 0.21 0.44 0.29 0.13 0.48 0.45 0.14 0.86 8.76 2.85 5.52 16.41 3.31 2.88 3.32 7.64 2.76 1.57 3.57 Q1LP02 DNA repair protein RadC Q1LP01 Phage integrase Q1LP00 Phage integrase Q1LNZ9 Phage integrase Q1LNZ8 RadC family protein Q1LNZ5 ParB family protein Q1LNZ4 GCN5-‐related N-‐acetyltransferase Q1LNZ3 Putative uncharacterized protein Q1LNZ2 Transcriptional regulator, XRE family Q1LNY5 Putative uncharacterized protein Q1LNY1 Putative uncharacterized protein Q1LNX7 Integrase, catalytic region Op0364r Op0365f Op0365f Op0365f others Op0153f CMGI-‐2 Op0379f Op0379f CMGI-‐3 Op0413f Op0415f Op0417f Op0431f Rmet_1266 Rmet_1271 Rmet_1272 Rmet_1273 -‐ ritA int int Rmet_0550 Rmet_1350 Rmet_1351 Rmet_1475 Rmet_1477 Rmet_1480 Rmet_1560 -‐ virB10 -‐ -‐ yupB -‐ -‐ Op0565f CMGI-‐1 Op0663f Op0698r Op0716r Op0802r CMGI-‐4 Op0842r Op0842r Op0843f Op0843f Op0878r Op1148f Op1219r Op1314f Op1315r Op1327r Op1327r Rmet_1934 Rmet_2354 Rmet_2529 Rmet_2579 Rmet_2848 Rmet_2987 Rmet_2993 Rmet_2996 Rmet_2997 Rmet_3138 Rmet_4084 Rmet_4291 Rmet_4565 Rmet_4566 Rmet_4607 Rmet_4608 -‐ -‐ -‐ -‐ -‐ -‐ ptxC -‐ -‐ -‐ phoA1 -‐ -‐ -‐ -‐ -‐ 0.43 0.48 0.39 0.38 4.14 0.90 3.82 2.27 0.19 0.16 0.15 0.28 0.45 0.40 0.25 0.50 5.63 7.48 7.53 0.96 5.38 7.14 0.41 0.47 0.39 0.27 0.41 0.40 0.37 0.25 0.25 0.24 0.47 0.45 0.14 0.17 0.28 0.46 1.38 1.55 0.98 1.55 1.84 3.67 4.26 2.66 4.63 0.43 0.68 1.30 1.63 1.68 1.26 1.07 Q1LNX5 Beta-‐lactamase-‐like protein Q1LNX0 Phage integrase Q1LNW9 Phage integrase Q1LNW8 Phage integrase Q1LQZ0 Putative uncharacterized protein Q1LNP3 Conjugation TrbI-‐like protein Q1LNP2 Putative uncharacterized protein Q1LNB8 Putative uncharacterized protein Q1LNB6 Putative uncharacterized protein Q1LNB3 Putative uncharacterized protein Q1LN33 Putative uncharacterized protein Q1LM13 Binding-‐protein-‐dependent transport systems inner membrane component Q8GQ64 Putative uncharacterized protein ORF C46 Q1LKC0 Thiolase Q1LK70 Pirin-‐like protein Q1LJF5 Putative uncharacterized protein Q1LJ16 Putative uncharacterized protein A0HB23 Phosphonate ABC transporter, inner membrane subunit A0HB26 Transcriptional regulator, LysR family A9BTQ2 Putative uncharacterized protein Q1LIL6 2-‐nonaprenyl-‐3-‐methyl-‐6-‐methoxy-‐1,4-‐benzoquinol hydroxylase Q1LFX5 Alkaline phosphatase Q1LFB9 2,3-‐dimethylmalate lyase Q1LEJ9 TonB-‐dependent receptor Q1LEJ8 Putative uncharacterized protein Q1LEF7 TonB-‐dependent copper receptor Q1LEF6 Putative uncharacterized protein Op1521r Rmet_5171 -‐ 0.50 1.60 Q1LCU6 Cold-‐shock DNA-‐binding protein family aCells of wild type strain CH34(pMOL28, pMOL30) and its plasmid-free derivative strain AE104 were cultivated in TMM minerals salts medium without further additions on gluconate to the exponential phase of growth. RNA was isolated, reversely transcribed, labeled and hybridized against a CH34-specific gene array. Provided are the Q-ratios AE104/CH34, red if at least 2-fold down-regulated, green up, bold-faced letters indicate significant differences, letters in italics not significant differences. The D-value for each comparison is also given. This is the distance of both mean values divided by the sum of both deviations. If D>1 the deviation bars do not touch or overlap) the data points are different with a probability in the t-test of > 95%. Three biological repeats for both strains. Genes associated to catabolic metabolic genomic islands (CMGIs) are on a yellow ground with the CMGI number directly above the respective gene(s), operon regions are in a box. Supplementary Table S3. Genes expressed differently in AE104 in the presence of 100 µM Zn(II)a Operon Region Name Up-‐regulated genes Op0027f Rmet_0094 Op0033f Rmet_0131 Op0033f Rmet_0132 Op0039f Rmet_0144 Op0043f Rmet_0151 Op0052r Rmet_0175 Op0066r Rmet_0227 Op0078r Rmet_0272 Op0080r Rmet_0277 Op0083f Rmet_0282 Op0083f Rmet_0283 Op0103f Rmet_0369 Op0103f Rmet_0372 Op0103f Rmet_0379 Op0151f Rmet_0543 Op0151f Rmet_0545 Op0153f Rmet_0550 Op0222r Rmet_0778 Op0243f Rmet_0849 Op0270r Rmet_0967 Op0287f Rmet_1004 Op0287f Rmet_1005 Op0295f Rmet_1024 Op0295f Rmet_1025 Op0295f Rmet_1026 Op0295f Rmet_1027 Op0295f Rmet_1028 Op0295f Rmet_1029 Op0295f Rmet_1030 Gene -‐ -‐ hslU -‐ -‐ -‐ -‐ -‐ nasF -‐ -‐ -‐ -‐ -‐ -‐ -‐ -‐ -‐ -‐ gstI -‐ -‐ -‐ iscS -‐ -‐ hscB hscA -‐ Q_AE104_Zn 2.10 2.22 2.29 2.03 2.62 2.49 2.09 2.64 2.40 2.16 2.41 2.01 2.04 2.03 3.01 3.26 6.66 3.08 2.29 2.08 2.07 2.14 3.26 4.22 4.14 4.06 3.10 2.97 2.84 D 4.17 4.11 4.53 2.02 3.17 4.45 5.04 9.15 0.76 3.97 5.70 3.30 6.87 6.25 0.50 0.57 0.64 4.58 7.96 3.17 6.26 6.22 7.83 10.12 16.89 8.15 7.35 3.68 7.59 Description Q1LS96 Putative uncharacterized protein Q1LS59 ATP-‐dependent protease hslV Q1LS58 Heat shock protein HslVU, ATPase subunit HslU Q1LS46 Methionine biosynthesis MetW Q1LS39 Patatin Q1LS15 5-‐formyltetrahydrofolate cyclo-‐ligase Q1LRW3 Ferredoxin-‐like protein Q1LRR8 RNA polymerase sigma factor Q1LRR3 Putative nitrate transporter protein Q1LRQ8 Peptidase M16-‐like protein Q1LRQ7 Peptidase M16-‐like protein Q1LRH1 ABC transporter-‐like protein Q1LRG8 Import inner membrane translocase, subunit Tim44 Q1LRG1 Putative transmembrane protein Q1LQZ7 Ferredoxin Q1LQZ5 Alcohol dehydrogenase, zinc-‐binding Q1LQZ0 Putative uncharacterized protein Q1LQB2 RNAse G Q1LQ41 17 kDa surface antigen Q1LPS3 Glutathione S-‐transferase-‐like protein Q1LPN6 GrpE protein Q1LPN5 Putative thioredoxin protein Q1LPL6 Transcriptional regulator, BadM/Rrf2 family Q1LPL5 Cysteine desulfurase IscS Q1LPL4 FeS cluster assembly scaffold IscU Q1LPL3 Iron-‐sulfur cluster assembly protein IscA Q1LPL2 Co-‐chaperone Hsc20 Q1LPL1 Chaperone protein hscA homolog Q1LPL0 Ferredoxin, 2Fe-‐2S type Op0295f Op0357f Op0363f Op0370r Op0376r Op0376r Op0376r Op0379f Op0425f Op0425f Op0425f Op0539f Op0539f Op0560r Rmet_1031 Rmet_1242 Rmet_1255 Rmet_1298 Rmet_1315 Rmet_1318 Rmet_1324 Rmet_1350 Rmet_1510 Rmet_1512 Rmet_1518 Rmet_1864 Rmet_1865 Rmet_1920 -‐ -‐ -‐ hoxK tmoB dmpH dmpB trbI cbbE1 cbbP cbbA2 -‐ -‐ -‐ 2.61 2.62 2.18 2.29 2.53 3.95 2.10 2.71 2.31 2.43 2.26 2.15 2.33 2.17 5.89 2.25 2.76 1.40 1.25 1.19 0.59 1.75 1.72 0.83 0.56 4.37 5.50 1.50 Op0565f Op0574r Op0609f Op0621f Op0626r Op0627f Op0628r Op0628r Op0628r Op0628r Op0628r Op0651f Op0656r Op0659f Op0659f Op0659f Op0661f Op0663f Op0669f Rmet_1934 Rmet_1959 Rmet_2111 Rmet_2149 Rmet_2177 Rmet_2178 Rmet_2181 Rmet_2182 Rmet_2183 Rmet_2184 Rmet_2185 Rmet_2280 Rmet_2299 Rmet_2303 Rmet_2304 Rmet_2305 Rmet_2317 Rmet_2354 Rmet_2372 -‐ -‐ -‐ -‐ ppx ppk -‐ pstB pstA pstC pstS -‐ -‐ cadA pbrC2 -‐ -‐ -‐ -‐ 2.19 2.04 2.37 2.21 3.58 4.28 6.00 6.21 6.64 5.88 10.26 2.35 12.67 18.85 22.96 4.42 2.42 2.04 2.69 0.57 4.13 6.64 0.53 2.88 5.76 7.60 5.97 4.14 3.12 5.66 13.55 8.21 5.09 5.39 3.49 3.27 1.16 4.34 Q1LPK9 Putative uncharacterized protein Q1LNZ8 RadC family protein Q1LNY5 Putative uncharacterized protein Q1LNU3 Hydrogenase (NiFe) small subunit (HydA) Q1LNS8 Toluene-‐4-‐monooxygenase system B Q1LNS5 Hydratase/decarboxylase Q1LNR9 Catechol 2,3-‐dioxygenase Q1LNP3 Conjugation TrbI-‐like protein Q1LN83 Ribulose-‐5-‐phosphate 3-‐epimerase Q1LN81 Phosphoribulokinase Q1LN75 Fructose-‐bisphosphate aldolase Q1LM83 UPF0061 protein Rmet_1864 Q1LM82 Methionine sulfoxide reductase B Q1LM27 Isochorismatase hydrolase Q1LM13 Binding-‐protein-‐dependent transport systems inner membrane component Q1LLY8 ATPase AAA-‐2 Q1LLI6 Putative uncharacterized protein Q1LLE8 Beta-‐lactamase-‐like protein Q1LLC0 Ppx/GppA phosphatase Q1LLB9 Polyphosphate kinase Q1LLB6 Phosphate uptake regulator, PhoU Q1LLB5 Phosphate import ATP-‐binding protein pstB Q1LLB4 Phosphate transport system permease protein 2 Q1LLB3 Phosphate ABC transporter, permease protein PstC Q1LLB2 Periplasmic phosphate binding protein Q1LL17 Putative uncharacterized protein Q8GQ11 Putative integral membrane protein / transporter A7HYL0 Heavy metal translocating P-‐type ATPase Q8GQ15 Lipoprotein signal peptidase Q8GQ16 Putative uncharacterized protein ORF C95 Q1LKY2 Transposase Tn3 Q8GQ64 Putative uncharacterized protein ORF C46 Q8GQ82 Putative uncharacterized protein ORF C28 Op0669f Op0669f Op0694r Op0719f Op0741f Op0742r Op0785f Op0804r Op0826r Op0843f Op0845f Rmet_2373 Rmet_2374 Rmet_2505 Rmet_2583 Rmet_2636 Rmet_2637 Rmet_2793 Rmet_2853 Rmet_2922 Rmet_2997 Rmet_2999 -‐ -‐ -‐ phoD -‐ -‐ -‐ -‐ dnaK -‐ -‐ 2.99 2.51 2.12 2.65 2.09 2.31 2.87 2.25 2.46 3.87 2.67 3.19 6.62 1.19 1.86 8.53 3.65 12.22 1.16 3.04 6.72 1.97 Op0845f Op0845f Op0845f Op0855f Rmet_3000 Rmet_3001 Rmet_3002 Rmet_3042 -‐ -‐ -‐ -‐ 2.82 3.27 2.73 2.36 1.99 4.91 3.14 0.99 Op0878r Op0947f Op0947f Op0947f Op0947f Op0948r Op0950r Op0962r Op0970r Op0975f Op1008f Op1008f Op1009r Op1025r Op1040f Op1064f Op1091r Rmet_3138 Rmet_3407 Rmet_3408 Rmet_3409 Rmet_3410 Rmet_3411 Rmet_3430 Rmet_3456 Rmet_3501 Rmet_3525 Rmet_3620 Rmet_3621 Rmet_3622 Rmet_3677 Rmet_3728 Rmet_3826 Rmet_3903 -‐ -‐ -‐ -‐ -‐ -‐ -‐ -‐ -‐ -‐ degP -‐ -‐ -‐ -‐ -‐ -‐ 5.84 5.87 14.33 12.20 11.76 13.88 2.00 2.91 2.15 2.45 118.07 5.87 2.10 2.47 2.40 3.21 2.13 0.62 8.05 6.58 4.92 4.23 4.33 10.45 5.45 3.50 8.67 8.38 6.03 2.44 4.36 0.83 3.23 2.84 Q8GQ83 Putative uncharacterized protein ORF C27 Q1LKS5 Putative uncharacterized protein Q1LKE4 Uracil-‐DNA glycosylase superfamily Q1LK66 Alkaline phosphatase Q1LK13 Thioredoxin Q1LK12 Hemerythrin-‐like, metal-‐binding Q1LJL0 Putative uncharacterized protein Q1LJF0 Putative uncharacterized protein O33522 Chaperone protein dnaK A9BTQ2 Putative uncharacterized protein Q1LDD1 Propeptide, PepSY amd peptidase M4 Q1LDD2 Undecaprenyl-‐diphosphatase (Phosphoesterase, PA-‐ phosphatase related) Q1LDD3 Putative uncharacterized protein Q1LDD4 Conserved hypothetical signal peptide protein Q1LIW2 Putative uncharacterized protein Q1LIL6 2-‐nonaprenyl-‐3-‐methyl-‐6-‐methoxy-‐1,4-‐benzoquinol hydroxylase Q1LHU7 Glycosyl transferase, family 2 Q1LHU6 Radical SAM Q1LHU5 YdjC-‐like protein Q1LHU4 Putative uncharacterized protein Q1LHU3 Uncharacterized protein UPF0065 Q1LHS4 UPF0102 protein Rmet_3430 Q1LHP8 Transcriptional regulator, MerR family Q1LHK3 ATP synthase I chain Q1LHH9 Heavy metal transport/detoxification protein Q1LH84 Peptidase degP, priplasmic protease Q1LH83 Putative uncharacterized protein Q1LH82 Major facilitator superfamily MFS_1 Q1LH27 Nucleoid protein H-‐NS Q1LGX6 Acyl-‐CoA dehydrogenase-‐like protein Q1LGN0 Putative uncharacterized protein Q1LGF5 Putative uncharacterized protein Op1092f Op1092f Op1092f Op1132f Op1133r Op1134f Op1134f Op1148f Op1148f Op1148f Op1199r Op1202f #NV Op1217r Op1219r Rmet_3904 Rmet_3905 Rmet_3906 Rmet_4025 Rmet_4026 Rmet_4027 Rmet_4028 Rmet_4084 Rmet_4085 Rmet_4086 Rmet_4230 Rmet_4245 Rmet_4246 Rmet_4284 Rmet_4290 -‐ -‐ -‐ -‐ -‐ -‐ -‐ phoA1 phoA2 -‐ -‐ -‐ #NV -‐ -‐ 2.38 2.17 2.28 4.52 25.48 2.92 2.66 6.21 2.94 2.66 2.37 2.72 2.51 2.10 2.10 3.93 2.16 2.78 4.89 6.52 3.64 6.07 1.66 2.48 2.98 1.94 5.36 4.85 5.27 2.11 Op1298f Op1318f Op1320f Op1321r Op1322f Op1322f Op1322f Op1323r Op1398f Op1409r Op1412f Op1412f Rmet_4537 Rmet_4583 Rmet_4593 Rmet_4594 Rmet_4595 Rmet_4596 Rmet_4597 Rmet_4598 Rmet_4807 Rmet_4834 Rmet_4839 Rmet_4840 serA2 -‐ -‐ zntA czcI2 czcC2 czcB2' -‐ -‐ -‐ -‐ -‐ 2.74 2.24 2.06 15.61 4.28 6.01 4.99 3.66 3.85 2.08 4.20 2.52 3.57 3.76 6.14 7.79 6.74 5.24 6.01 3.14 7.37 5.63 3.01 4.30 Op1412f Op1412f Op1452f Op1469r Op1509r Rmet_4841 Rmet_4843 Rmet_4942 Rmet_5005 Rmet_5122 -‐ -‐ gabD -‐ phaC3 2.40 2.10 2.30 2.15 2.42 3.49 3.56 4.44 4.66 5.24 Q1LGF4 Putative serine protein kinase, PrkA Q1LGF3 Putative uncharacterized protein Q1LGF2 SpoVR Q1LG33 Major facilitator superfamily MFS_1 Q1LG32 Putative periplasmic ligand-‐binding sensor protein Q1LG31 Proline iminopeptidase Q1LG30 Putative uncharacterized protein Q1LFX5 Alkaline phosphatase Q1LFX4 Alkaline phosphatase Q1LFX3 Putative signal peptide protein Q1LFI0 Two component transcriptional regulator, LuxR family Q1LFG5 Transcriptional regulator, LysR family Q1LFG4 Putative uncharacterized protein Q1LFC6 Entericidin EcnAB Q1LFC0 Transcriptional regulator, AraC family Q1LEM4 D-‐isomer specific 2-‐hydroxyacid dehydrogenase, NAD-‐binding Q1LEI1 Extracellular solute-‐binding protein, family 3 Q1LEH1 Polysaccharide deacetylase Q1LEH0 Heavy metal translocating P-‐type ATPase Q1LEG9 Putative uncharacterized protein Q1LEG8 Outer membrane efflux protein Q1LEG7 Secretion protein HlyD B1LRU9 Tn3 family transposase Q1LDV7 Putative uncharacterized protein Q1LDT0 Porin, Gram-‐negative type Q1LDS5 Transcriptional regulator, LacI family Q1LDS4 Putative periplasmic solute-‐binding protein Q1LDS3 Binding-‐protein-‐dependent transport systems inner membrane component Q1LDS1 ABC transporter related Q1LDH2 Succinate semialdehyde dehydrogenase Q1LDA9 Isochorismatase hydrolase Q1LCZ5 Poly-‐beta-‐hydroxybutyrate polymerase-‐like protein Op1509r Op1509r Op1540f Op1571r Op1571r Rmet_5123 Rmet_5124 Rmet_5223 Rmet_5319 Rmet_5320 phaB3 -‐ -‐ -‐ -‐ 2.23 2.49 2.16 2.49 2.44 8.42 7.74 4.57 7.21 5.05 Op1572f Op1573r Op1575r Op1576f Rmet_5321 Rmet_5322 Rmet_5324 Rmet_5325 -‐ -‐ -‐ -‐ 2.37 2.36 2.45 4.10 8.97 4.09 1.32 6.84 Op1576f Op1576f Op1607r Op1620f Op1629r Op1662f Op1695r Op1695r Rmet_5326 Rmet_5327 Rmet_5395 Rmet_5450 Rmet_5485 Rmet_5582 Rmet_5668 Rmet_5670 -‐ -‐ -‐ -‐ -‐ -‐ -‐ -‐ 2.52 3.05 2.22 2.07 2.84 2.16 2.69 2.66 3.78 11.89 2.09 1.12 6.55 12.21 3.77 2.31 Op1696f Op1696f Op1710f Op1715r Op1718f Op1747r Op1748f Op1749r Op1755r Op1766f Rmet_5672 Rmet_5673 Rmet_5716 Rmet_5728 Rmet_5746 Rmet_5801 Rmet_5802 Rmet_5803 Rmet_5814 Rmet_5846 copR2 copS2 -‐ -‐ furB zwf edd1 -‐ -‐ -‐ 2.18 2.12 2.65 2.39 2.05 2.28 2.61 2.90 2.35 2.11 2.52 3.36 7.02 0.49 1.15 5.11 3.82 7.40 4.21 3.74 Q1LCZ4 3-‐oxoacyl-‐[acyl-‐carrier-‐protein] reductase Q1LCZ3 Putative uncharacterized protein Q1LCP4 Putative uncharacterized protein Q1LCE8 Heavy metal efflux pump CzcA Q1LCE7 Secretion protein HlyD Q1LCE6 RND efflux system, outer membrane lipoprotein, NodT Q1LCE5 Sensor protein Q1LCE3 Putative signal peptide protein Q1LCE2 Putative uncharacterized protein Q1LCE1 Two component transcriptional regulator, winged helix family Q1LCE0 Sensor protein Q1LC72 Putative uncharacterized protein Q1LC17 Putative uncharacterized protein Q1LBY2 Putative uncharacterized protein Q1LBN5 Putative membrane protein Q1LBE9 Copper resistance D Q1LBE7 Copper resistance B Q1LBE5 Two component heavy metal response transcriptional regulator, winged helix family Q1LBE4 Sensor protein Q1LBA1 Putative uncharacterized protein Q1LB89 Glycosyl transferase, group 1 Q1LB71 Ferric uptake regulator, Fur family Q1LB16 Glucose-‐6-‐phosphate 1-‐dehydrogenase Q1LB15 6-‐phosphogluconate dehydratase Q1LB14 MscS Mechanosensitive ion channel Q1LB03 Putative uncharacterized protein Q1LAX1 Putative uncharacterized protein 0.58 3.25 Q1LSG5 Putative uncharacterized protein Q1LSC8 Putative uncharacterized protein Down-‐regulated genes Op0007f Rmet_0025 -‐ Op0019f Rmet_0062 -‐ -‐0.06 0.43 Op0019f Op0019f Op0019f Op0019f Rmet_0063 Rmet_0064 Rmet_0065 Rmet_0066 -‐ -‐ -‐ -‐ 0.29 0.39 0.42 0.47 3.33 3.76 4.07 2.96 Op0019f Op0033f Op0051f Op0051f Op0051f Op0057f Rmet_0067 Rmet_0130 Rmet_0170 Rmet_0171 Rmet_0173 Rmet_0188 -‐ -‐ ahcY -‐ -‐ -‐ 0.49 0.27 0.44 0.42 0.48 0.38 5.02 11.54 6.33 4.85 2.82 2.47 Op0057f Op0057f Rmet_0189 -‐ Rmet_0190 -‐ 0.40 0.39 2.34 2.17 Op0057f Rmet_0191 -‐ 0.36 3.49 Op0057f Op0057f Op0085f Rmet_0192 -‐ Rmet_0193 -‐ Rmet_0294 -‐ 0.45 0.45 0.36 3.40 3.66 3.29 Op0109f Op0109f Op0140r Op0182r Op0197f Op0201f Op0207f Op0224r Op0256r Op0265f Rmet_0400 Rmet_0402 Rmet_0522 Rmet_0657 Rmet_0700 Rmet_0709 Rmet_0733 Rmet_0789 Rmet_0879 Rmet_0920 0.46 0.48 0.35 -‐126.85 0.40 0.42 -‐0.13 0.00 -‐0.29 0.47 4.34 4.44 3.29 0.52 4.82 3.94 0.59 0.58 0.53 3.03 Op0271f Op0290r Rmet_0970 ggt Rmet_1011 -‐ 0.41 0.05 4.88 0.58 gltJ gltL -‐ -‐ dadA2 -‐ -‐ -‐ -‐ -‐ Q1LSC7 Allophanate hydrolase subunit 2 Q1LSC6 UPF0271 protein Rmet_0064 Q1LSC5 Putative uncharacterized protein Q1LSC4 Putative uncharacterized protein Q1LSC3 Pyroglutamyl-‐peptidase I. Cysteine peptidase. MEROPS family C15 Q1LS60 Uncharacterized protein UPF0065 Q1LS20 Adenosylhomocysteinase Q1LS19 Putative uncharacterized protein Q1LS17 TfoX-‐like protein Q1LS02 Pilus assembly protein Q1LS01 Type-‐4 fimbrial biogenesis pilV transmembrane protein Q1LS00 Type-‐4 fimbrial biogenesis transmembrane protein Q1LRZ9 Putative type-‐4 fimbrial biogenesis transmembrane protein Q1LRZ8 Putative type-‐4 fimbrial biogenesis pily1-‐related protein Q1LRZ7 Pilus assembly protein PilE Q1LRP6 Putative uncharacterized protein Q1LRE0 Amino acid ABC transporter, permease protein, 3-‐TM region, His/Glu/Gln/Arg/opine Q1LRD8 ABC transporter-‐related protein Q1LR18 Putative uncharacterized protein Q1LQN3 Putative membrane protein Q1LQJ0 FAD dependent oxidoreductase Q1LQI1 Putative uncharacterized protein Q1LQF7 Histone deacetylase superfamily Q1LQA1 Uncharacterized protein UPF0065 Q1LQ11 Putative uncharacterized protein Q1LPX0 Putative transporter signal peptide protein Q1LPS0 Gamma-‐glutamyltransferase 1. Threonine peptidase. MEROPS family T03 Q1LPM9 Alpha/beta hydrolase fold Op0321f Op0340r Op0342r Op0346r Op0355f Op0355f Op0355f Op0355f Op0355f Op0355f Op0370r Op0427f Op0450r Op0455f Rmet_1123 Rmet_1177 Rmet_1184 Rmet_1195 Rmet_1225 Rmet_1226 Rmet_1227 Rmet_1228 Rmet_1229 Rmet_1231 Rmet_1285 Rmet_1533 Rmet_1612 Rmet_1628 -‐ -‐ -‐ -‐ -‐ -‐ -‐ -‐ livG6 -‐ -‐ -‐ -‐ -‐ -‐0.56 0.21 0.49 0.49 0.35 0.41 0.34 0.45 0.48 0.46 0.49 0.04 0.38 0.26 0.59 0.56 3.80 2.91 17.27 6.03 10.81 4.52 4.22 6.90 0.93 0.58 5.21 6.73 Op0456r Op0486r Op0538r Op0568r Rmet_1629 Rmet_1720 Rmet_1862 Rmet_1943 -‐ -‐ -‐ -‐ 0.49 0.15 0.42 -‐2.10 3.61 0.54 6.31 0.64 Op0596r Rmet_2052 ugpC 0.46 4.71 Op0596r Op0596r Op0630r Op0655f Op0680r Op0695f Op0729f Rmet_2053 Rmet_2055 Rmet_2205 Rmet_2294 Rmet_2429 Rmet_2515 Rmet_2605 0.47 0.49 0.01 0.01 0.30 0.49 0.01 2.10 9.43 0.58 0.58 0.62 2.93 0.58 Op0775f Rmet_2752 -‐ 0.17 3.79 Op0775f Op0806r Rmet_2753 -‐ Rmet_2864 livG2 0.22 0.42 4.79 2.91 ugpE ugpB -‐ -‐ fabD -‐ -‐ Q1LPB7 Extracellular solute-‐binding protein, family 3 Q1LP63 Putative uncharacterized protein Q1LP56 Uncharacterized protein UPF0065 Q1LP45 Sensor protein Q1LP15 Alpha/beta hydrolase fold Q1LP14 Extracellular ligand-‐binding receptor Q1LP13 Inner-‐membrane translocator Q1LP12 Inner-‐membrane translocator Q1LP11 ABC transporter-‐related protein Q1LP09 Probable potassium transport system protein kup Q1LNV6 Hydrogenase accessory protein HypB Q1LN60 High-‐affinity nickel-‐transporter B2UH78 Integrase catalytic region Q1LMW5 Porin, Gram-‐negative type Q1LMW4 Glutathione-‐dependent formaldehyde-‐activating, GFA Q1LMM5 Transcriptional regulator, IclR family Q1LM85 Extracellular ligand-‐binding receptor Q1LM04 Secretion protein HlyD Q1LLP5 sn-‐glycerol-‐3-‐phosphate import ATP-‐binding protein ugpC Q1LLP4 Binding-‐protein-‐dependent transport systems inner membrane component Q1LLP2 Extracellular solute-‐binding protein, family 1 Q1LL92 Lytic transglycosylase, catalytic Q8GQ06 Putative uncharacterized protein ORF C105 Q1LKM0 [Acyl-‐carrier-‐protein] S-‐malonyltransferase Q1LKD4 L-‐lactate transport Q1LK44 2-‐nitropropane dioxygenase, NPD Q1LJQ1 Tripartite ATP-‐independent periplasmic transporter, DctQ component Q1LJQ0 TRAP C4-‐dicarboxylate transport system permease DctM subunit Q1LJD9 ABC transporter-‐related protein Op0806r Op0806r Op0806r Op0813f Op0879f Op0881f Op0900r Op0918r Op0920r Op0920r Op0920r Op0920r Op0920r Op0920r Op0926r Op0926r Op0926r Op0941f Op0941f Op0941f Op0941f Op0941f Op0941f Op0974r Op0974r Op0974r Op0974r Op0974r Op0976r Op0983f Op0985f Op0985f Op0985f Op1026f Rmet_2865 Rmet_2866 Rmet_2867 Rmet_2894 Rmet_3139 Rmet_3144 Rmet_3199 Rmet_3234 Rmet_3262 Rmet_3263 Rmet_3269 Rmet_3270 Rmet_3271 Rmet_3272 Rmet_3309 Rmet_3313 Rmet_3318 Rmet_3389 Rmet_3390 Rmet_3391 Rmet_3392 Rmet_3393 Rmet_3394 Rmet_3516 Rmet_3517 Rmet_3518 Rmet_3519 Rmet_3520 Rmet_3526 Rmet_3543 Rmet_3549 Rmet_3550 Rmet_3552 Rmet_3699 livM2 livH2 livK2 -‐ -‐ -‐ -‐ -‐ gltD gltB -‐ -‐ -‐ -‐ rpmC rpsS -‐ gspL gspM -‐ gspD gspE gspF livM5 livH5 -‐ livF5 livG5 -‐ -‐ tctC tctB -‐ flhA 0.36 0.30 0.34 0.30 0.10 0.07 0.03 0.33 0.39 -‐1.98 0.33 0.30 0.32 0.34 0.49 0.46 -‐3.29 0.48 0.44 0.16 0.50 0.44 0.39 0.39 0.26 0.21 0.40 0.21 0.29 0.36 0.19 0.26 -‐0.06 0.48 3.94 3.31 6.86 13.64 6.12 7.66 0.58 10.96 8.85 0.36 2.77 6.99 2.26 5.32 4.69 3.43 0.53 5.08 6.68 0.77 4.62 5.87 5.46 5.26 7.25 4.98 6.93 5.26 5.52 6.19 5.11 5.34 0.58 2.82 Q1LJD8 Inner-‐membrane translocator Q1LJD7 Inner-‐membrane translocator Q1LJD6 Extracellular ligand-‐binding receptor Q1LJA9 Cold-‐shock DNA-‐binding protein family Q1LIL5 Putative uncharacterized protein Q1LIL0 Porin, Gram-‐negative type Q1LIF5 Conserved hypothetical transmembrane protein Q1LIC0 Porin, Gram-‐negative type Q1LI92 Glutamate synthase (NADH) small subunit Q1LI91 Glutamate synthase (NADH) large subunit Q1LI85 Pilus assembly protein, PilQ Q1LI84 Pilus assembly protein, PilO Q1LI83 Fimbrial assembly Q1LI82 Type IV pilus assembly protein PilM Q1LI45 50S ribosomal protein L29 Q1LI41 30S ribosomal protein S19 Q1LI36 Flavin reductase-‐like, FMN-‐binding Q1LHW5 General secretion pathway L Q1LHW4 General secretion pathway M protein Q1LHW3 Type II secretion system protein N Q1LHW2 Type II and III secretion system protein Q1LHW1 Type II secretion system protein E (GspE) Q1LHW0 General secretion pathway protein F Q1LHI8 Inner-‐membrane translocator Q1LHI7 Inner-‐membrane translocator Q1LHI6 Extracellular ligand-‐binding receptor Q1LHI5 ABC transporter-‐related protein Q1LHI4 ABC transporter-‐related protein Q1LHH8 OmpW Q1LHG1 Twin-‐arginine translocation pathway signal Q1LHF5 Uncharacterized protein UPF0065 Q1LHF4 Conserved hypothetical membrane protein Q1LHF2 Phenylacetic acid degradation-‐related protein Q1LH05 Flagellar biosynthesis protein FlhA Op1042f Op1042f Op1042f Op1066f Op1066f Op1066f Op1086f Op1088f Op1095r Op1115r Op1123r Rmet_3734 Rmet_3735 Rmet_3736 Rmet_3836 Rmet_3837 Rmet_3838 Rmet_3894 Rmet_3900 Rmet_3913 Rmet_3980 Rmet_3998 flgB flgC flgD -‐ -‐ -‐ -‐ -‐ -‐ livH4 -‐ 0.42 0.44 0.44 0.41 0.36 0.40 0.35 0.38 -‐0.08 -‐0.02 -‐0.06 4.19 3.30 3.80 6.85 5.76 5.00 4.68 1.90 0.58 0.57 0.59 Op1128f Op1184f Op1198f Op1219r Op1276f Op1305r Op1314f Op1314f Op1316f Rmet_4019 Rmet_4188 Rmet_4222 Rmet_4287 Rmet_4477 Rmet_4549 Rmet_4564 Rmet_4565 Rmet_4575 surE -‐ -‐ -‐ livM3 uvrA2 metE -‐ -‐ 0.17 0.45 0.47 0.48 0.37 0.19 0.06 0.25 0.38 0.54 5.60 12.52 2.52 4.54 0.56 17.81 1.22 1.19 Op1316f Op1325r Op1362f Op1377r Op1396f Op1417r Op1431r Op1446f Op1466f Op1493r Op1493r Op1493r Rmet_4576 Rmet_4605 Rmet_4721 Rmet_4749 Rmet_4796 Rmet_4857 Rmet_4893 Rmet_4931 Rmet_4994 Rmet_5073 Rmet_5074 Rmet_5075 -‐ -‐ -‐ -‐ -‐ -‐ -‐ -‐ -‐ metE -‐ msuE1 0.02 -‐0.11 0.22 0.32 -‐2.33 0.00 0.49 0.48 0.16 0.17 0.15 0.23 0.58 0.59 4.10 4.21 0.68 0.58 4.02 1.96 5.62 18.51 10.79 8.46 Q1LGX0 Flagellar basal-‐body rod protein FlgB Q1LGW9 Flagellar basal-‐body rod protein FlgC Q1LGW8 Flagellar hook capping protein Q1LGM0 Outer membrane efflux protein Q1LGL9 Secretion protein HlyD Q46VH3 Heavy metal efflux pump CzcA Q1LGG4 Putative uncharacterized protein Q1LGF8 Uncharacterized protein UPF0065 Q1LGE5 Uncharacterized protein UPF0065 Q1LG78 Inner-‐membrane translocator Q1LG60 Putative uncharacterized protein Q1LG39 Exopolyphosphatase / 3'-‐nucleotidase / 5'-‐ nucleotidase Q1LFM1 Transcriptional regulator, TetR family Q1LFI7 Transcriptional regulator, IclR family Q1LFC3 Rare lipoprotein A Q1LET4 Inner-‐membrane translocator Q1LEL2 UvrA family protein Q1LEK0 Methionine synthase (B12-‐independent) Q1LEJ9 TonB-‐dependent receptor Q1LEI9 Acyl-‐CoA dehydrogenase-‐like protein Q1LEI8 Binding-‐protein-‐dependent transport systems inner membrane component Q1LEF9 Sensor protein Q1LE43 Putative uncharacterized protein Q46TY9 HU family DNA-‐binding protein Q1LDW8 Rhs element Vgr protein Q1LDQ7 Putative uncharacterized protein Q1LDM1 Putative uncharacterized protein Q1LDI3 Uncharacterized protein UPF0065 Q1LDC0 Porin, Gram-‐negative type Q1LD41 Putative uncharacterized protein Q1LD40 NADPH-‐dependent FMN reductase Q1LD39 Putative uncharacterized protein Op1517r Op1560f Op1566f Op1566f Op1566f Op1709r Op1719r Op1740f Op1750f Op1759r Op1778f Op1792f Rmet_5152 Rmet_5288 Rmet_5297 Rmet_5298 Rmet_5299 Rmet_5713 Rmet_5748 Rmet_5785 Rmet_5807 Rmet_5821 Rmet_5877 Rmet_5907 -‐ -‐ -‐ fliM fliN -‐ -‐ -‐ -‐ -‐ -‐ -‐ 0.46 0.24 0.44 0.49 0.48 0.49 0.00 -‐0.06 -‐0.01 -‐0.04 0.25 -‐0.01 0.77 7.17 1.73 1.44 1.96 0.88 0.58 0.57 0.58 0.58 4.22 0.58 Q1LCW5 Acyl-‐CoA dehydrogenase-‐like protein Q1LCH9 Porin, Gram-‐negative type Q1LCH0 Flagellar basal body-‐associated protein FliL Q1LCG9 Flagellar motor switch protein FliM Q1LCG8 Flagellar motor switch FliN Q1LBA4 Hpt domain protein Q1LB69 Putative uncharacterized protein Q1LB32 Putative uncharacterized protein Q1LB10 TonB-‐dependent siderophore receptor Q1LAZ6 Putative integrase/recombinase protein Q1LAU0 Extracellular ligand-‐binding receptor Q1LAR0 Putative uncharacterized protein aCells of strain AE104 was confronted with 100 µM zinc chloride for 10 min or not, RNA was isolated, reversely transcribed, labeled and hybridized against a CH34-specific gene array. Provided are the Q-ratios ±Zn for, red if at least 2-fold down-regulated, green up, boldfaced letters indicate significant differences, letters in italics not significant differences. The D-value for each comparison is also given. This is the distance of both mean values divided by the sum of both deviations. If D>1 the deviation bars do not touch or overlap) the data points are different with a probability in the t-test of > 95%. Three biological repeats. Genes in operon regions or adjacent operon regions are in a box. Regions with a gene up- or down-regulated at least four-fold are on a green ground. A yellow ground indicates genes of interest, e.g. hydrogenase genes. Supplementary Table S4. Genes specifically up- or down-regulated in the comparison ∆zupT/AE104 under EDTA and/or zinc stressa. Locus Rmet Gene Regionb Q(∆zupT/AE104) Q(Zn) D(Zn) Q(EDTA) D(EDTA) Description Q(EDTA)≥2 Q(EDTA)≥2, Q(Zn)≤0.5. Rmet_1098 Op0317f Rmet_1099 Op0317f Rmet_1100 cysS Op0317f Rmet_1101 Op0317f Rmet_1102 Op0317f Rmet_1103 allB Op0317f Rmet_1104 Op0318r Rmet_5990 Op1825r Q(EDTA)≥2, Q (Zn)≥2. CMGI-‐3 0.48 0.35 0.46 0.49 17.91 22.52 21.00 14.38 16.54 52.14 6.82 4.34 0.40 1.69 0.49 3.91 0.42 4.33 15.38 13.61 3.35 3.83 6.60 8.54 0.50 1.67 2.83 0.37 2.94 3.02 2.29 2.84 Rmet_1499 cbbQ Rmet_1502 Rmet_1511 cbbF2 Rmet_1521 cbbI1 Op0422r Op0423f Op0425f Op0425f 2.08 4.28 4.16 3.22 5.54 6.65 11.31 3.39 3.15 3.05 2.61 2.87 1.89 2.66 1.65 1.20 Rmet_1522 Rmet_1523 Rmet_1524 Rmet_1525 Rmet_1526 Op0425f Op0425f Op0425f Op0425f Op0425f 4.18 6.99 8.81 7.85 8.57 2.94 4.38 3.62 2.73 3.55 2.84 5.85 6.85 6.77 6.44 3.46 1.59 1.37 1.57 1.80 Op0425f Op0425f Op0427f 8.67 2.67 4.17 3.70 7.24 3.20 5.70 2.38 4.85 1.55 1.84 1.55 hoxF hoxU hoxY hoxH Rmet_1527 Rmet_1528 Rmet_1533 Q1LPE2 Cobalamin synthesis protein, P47K Q1LPE1 UPF0343 protein Rmet_1099 Q1LPE0 Cysteinyl-‐tRNA synthetase Q1LPD9 6-‐pyruvoyl-‐tetrahydropterin synthase-‐like protein Q1LPD8 Carbonic anhydrases/acetyltransferase isoleucine patch superfamily Q1LPD7 Dihydroorotase Q1LPD6 TonB-‐dependent siderophore receptor Q58AN1 Mercury regulatory protein (Transcriptional regulator, MerR family) Q1LN94 ATPase associated with various cellular activities, AAA_5 Q1LN91 Transcriptional regulator, LysR family Q1LN82 D-‐fructose 1,6-‐bisphosphatase Q1LN72 Ribose-‐5-‐phosphate isomerase Q1LN71 Respiratory-‐chain NADH dehydrogenase domain, 51 kDa subunit Q1LN70 Ferredoxin Q1LN69 NADH ubiquinone oxidoreductase, 20 kDa subunit Q1LN68 Nickel-‐dependent hydrogenase, large subunit Q1LN67 HoxW protein Q1LN66 Cyclic nucleotide-‐binding domain (CNMP-‐BD) protein Q1LN65 Alanine dehydrogenase/PNT-‐like protein Q1LN60 High-‐affinity nickel-‐transporter Rmet_1534 Rmet_1535 Rmet_1536 Rmet_1537 Rmet_1538 Rmet_1539 Rmet_1540 Rmet_1541 3.60 9.49 14.26 7.74 7.75 8.31 11.02 6.95 4.92 5.14 5.67 4.98 4.24 4.80 5.08 4.83 Rmet_1542 Op0427f 10.37 7.28 Rmet_6333 Op1926f 5.76 2.73 Rmet_6338 Op1926f 3.57 2.82 Q(EDTA)≥2, Q (Zn) unchanged. CMGI-‐3 Rmet_1498 Op0422r 1.69 1.34 Rmet_1517 Op0425f 1.66 1.01 Rmet_3842 Op1067r 1.46 0.35 Q(EDTA)≤ 0 .5 Q(EDTA)≤0.5, Q(Zn)≥ 2. CMGI-‐1 Rmet_2305 Op0659f 2.34 0.83 Q(EDTA≤0.5, Q(Zn)≤ 0.5. Rmet_0005 Op0002r 0.45 2.21 Rmet_0007 Op0002r 0.43 2.79 Rmet_0022 Op0004r 0.44 2.07 Rmet_0086 Op0024r 0.50 3.60 Rmet_0092 Op0026r 0.33 1.83 Rmet_0093 Op0027f 0.48 1.40 Rmet_0094 Op0027f 0.44 1.64 Rmet_0095 Op0028r 0.33 1.43 Rmet_0097 Op0029f 0.47 4.00 Rmet_0123 Op0032r 0.44 1.64 Rmet_0156 metK Op0045f 0.48 4.19 4.64 3.91 Op0427f Op0427f Op0427f Op0427f Op0427f Op0427f Op0427f Op0427f 11.16 11.88 10.59 9.31 8.36 11.50 11.83 10.76 2.68 3.42 5.50 1.85 4.77 4.21 7.40 6.55 Q1LN59 Putative uncharacterized protein Q1LN58 Hydrogenase nickel insertion protein HypA Q1LN57 Hydrogenase accessory protein HypB Q1LN56 (NiFe) hydrogenase maturation protein HypF Q1LN55 Hydrogenase assembly chaperone hypC/hupF Q1LN54 Hydrogenase expression/formation protein HypD Q1LN53 Hydrogenase expression/formation protein HypE Q1LN52 Formyl transferase-‐like protein Q1LN51 Response regulator receiver domain protein 3.71 (CheY-‐like) 5.94 Q1L9I4 Transposase Tn3 Q5NUU5 Hypothetical general secretion pathway protein A 3.74 (ATPase) ( 2.72 3.81 Q1LN95 von Willebrand factor, type A 1.70 Q1LN76 HAD-‐superfamily hydrolase subfamily IA, variant 3 0.55 Q1LGL6 Putative uncharacterized protein 0.48 Q8GQ16 Putative uncharacterized protein ORF C95 2.27 2.51 3.02 0.49 0.42 0.46 0.21 0.48 0.12 0.26 0.29 0.14 0.47 0.48 0.49 4.29 5.65 10.68 4.36 11.12 1.94 2.26 4.68 2.56 2.39 2.57 Q1LSI5 Twin-‐arginine translocation pathway signal Q1LSI3 Transcriptional regulator, AraC family Q1LSG8 Transcriptional regulator, AraC family Q1LSA4 Rhodanese-‐like protein Q1LS98 Histidine kinase Q1LS97 UPF0391 membrane protein Rmet_0093 Q1LS96 Putative uncharacterized protein Q1LS95 Putative uncharacterized protein Q1LS93 Sporulation related Q1LS67 TonB-‐dependent receptor Q1LS34 S-‐adenosylmethionine synthetase Rmet_0157 Rmet_0160 CMGI-‐7 Op0045f Op0048r 0.44 2.69 0.40 2.26 0.44 0.41 Rmet_0320 Rmet_0361 Rmet_0364 Rmet_0366 Rmet_0372 Rmet_0393 Rmet_0409 Rmet_0410 rplM Rmet_0412 Rmet_0457 Rmet_0483 Rmet_0485 Rmet_0551 Rmet_0585 Rmet_0586 arcB Rmet_0650 Rmet_0651 Rmet_0652 Rmet_0671 pilI Rmet_0744 Rmet_0745 Rmet_0751 rplS Rmet_0795 Rmet_0802 Rmet_0803 Rmet_0804 Op0092r Op0102r 0.46 2.26 0.45 1.65 0.41 0.48 Op0102r Op0103f 0.39 1.42 0.42 2.76 0.19 0.34 Op0103f Op0107f Op0112r Op0113f Op0113f Op0119f Op0129f Op0129f 0.48 0.44 0.38 0.49 0.49 0.34 0.42 0.43 4.02 1.26 2.03 2.50 2.38 1.72 1.93 3.18 0.37 0.48 0.26 0.44 0.48 0.43 0.42 0.49 Op0153f Op0165f Op0165f Op0180r Op0180r Op0180r Op0187f Op0210r Op0211f Op0213f Op0226r 0.48 0.38 0.45 0.27 0.38 0.32 0.40 0.46 0.34 0.49 0.25 3.37 5.16 2.06 1.02 4.44 2.96 6.26 1.06 0.96 3.93 1.21 0.50 0.44 0.38 0.48 0.50 0.43 0.48 0.39 0.30 0.41 0.42 Op0227f Op0228r Op0228r 0.38 2.41 0.34 2.42 0.15 1.81 0.38 0.25 0.08 2.47 Q1LS33 Putative uncharacterized protein 4.85 Q1LS30 Methyl-‐accepting chemotaxis sensory transducer Q5NUU5 Hypothetical general secretion pathway protein A 7.60 (ATPase) 1.24 Q1LRH9 VWA containing CoxE-‐like protein Q1LRH6 Xanthine dehydrogenase, molybdenum binding 10.43 subunit apoprotein 7.49 Q1LRH4 Putative membrane protein Q1LRG8 Import inner membrane translocase, subunit 4.49 Tim44 2.93 Q1LRE7 ABC transporter-‐related protein 8.26 Q1LRD0 50S ribosomal protein L13 2.05 Q1LRC9 30S ribosomal protein S9 2.86 Q1LRC7 Putative uncharacterized protein 1.75 Q1LR83 Aminoglycoside phosphotransferase 5.41 Q1LHY9 Integrase, catalytic region 10.00 Q1LR55 Putative uncharacterized protein Q1LQY9 Hyicolysin. Metallo peptidase. MEROPS family 3.67 M30 4.90 Q1LQV5 Amidinotransferase 4.46 Q1LQV4 Ornithine cyclodeaminase 2.59 Q1LQP0 Peptidase A24A, prepilin type IV 5.38 Q1LQN9 Flp/Fap pilin component 5.86 Q1LQN8 Flp/Fap pilin component 2.39 Q1LQL9 CheW protein 8.88 Q1LQE6 TM2 8.89 Q1LQE5 Putative uncharacterized protein 5.29 Q1LQD9 50S ribosomal protein L19 14.87 Q1LQ95 Inner-‐membrane translocator Q1LQ88 Glycine betaine/L-‐proline transport ATP binding 4.39 subunit 3.36 Q1LQ87 Putative uncharacterized protein 12.37 Q1LQ86 SPFH domain, Band 7 family protein Rmet_0805 Rmet_0816 Rmet_0817 Rmet_0821 Rmet_0861 Rmet_0863 Rmet_0864 Rmet_0865 Rmet_0872 Rmet_0873 Rmet_0880 Rmet_0930 Rmet_0933 Rmet_0934 Rmet_1026 Rmet_1141 Rmet_1142 Rmet_1161 Rmet_1215 CMGI-‐2 Rmet_1251 Rmet_1301 Rmet_1436 CMGI-‐3 Rmet_1465 Rmet_1469 Rmet_1567 Rmet_1571 Rmet_1573 nuoD nuoG nuoH tsf Rmet_1728 Rmet_1932 Rmet_1936 Op0228r Op0230r Op0230r Op0232r Op0247f Op0248r Op0249f Op0249f Op0253f 0.21 0.47 0.46 0.35 0.48 0.41 0.18 0.14 0.47 2.04 2.59 1.56 3.56 13.87 2.45 1.52 1.84 1.61 0.12 0.45 0.34 0.47 0.45 0.14 0.16 0.16 0.46 8.89 8.60 10.80 4.74 4.28 14.25 6.21 8.21 2.26 Op0253f Op0256r Op0267f Op0267f Op0267f Op0295f Op0326r Op0327f Op0333f Op0353f Op0362r Op0373f Op0403f Op0411f Op0412r Op0432r Op0433f Op0433f 0.46 0.47 0.37 0.50 0.37 0.49 0.34 0.36 0.35 0.48 0.44 0.32 0.34 0.47 0.44 0.35 0.42 0.39 2.70 3.15 7.21 3.46 2.34 2.52 2.35 2.67 2.02 3.49 2.23 2.93 11.22 2.16 1.96 4.21 2.23 2.17 0.46 0.49 0.36 0.42 0.37 0.41 0.29 0.44 0.48 0.34 0.30 0.19 0.43 0.34 0.30 0.45 0.43 0.32 6.18 4.29 5.74 8.79 1.90 9.40 6.69 2.59 6.04 4.32 3.88 4.85 3.43 3.41 12.12 4.52 2.76 5.39 Op0489f Op0565f Op0565f 0.40 2.25 0.42 2.70 0.38 2.05 0.31 0.39 0.34 3.54 4.55 7.08 Q1LQ85 Putative uncharacterized protein Q1LQ74 Putative transmembrane protein Q1LQ73 Putative uncharacterized protein Q1LQ69 Phenazine biosynthesis PhzC/PhzF protein Q1LQ29 Putative uncharacterized protein Q1LQ27 Putative uncharacterized protein Q1LQ26 Putative uncharacterized protein Q1LQ25 Putative uncharacterized protein Q1LQ18 Putative uncharacterized protein Q1LQ17 Response regulator receiver domain protein (CheY-‐like) Q1LQ10 Porin, gram-‐negative type Q1LPW0 NADH dehydrogenase I, D subunit Q1LPV7 NADH-‐quinone oxidoreductase Q1LPV6 NADH-‐quinone oxidoreductase subunit H Q1LPL4 FeS cluster assembly scaffold IscU Q1LP99 Transcriptional regulator, GntR family Q1LP98 Type IV pilus assembly PilZ Q1LP79 Translation initiation factor IF-‐3 Q1LP25 Putative uncharacterized protein Q1LNY9 Putative uncharacterized protein Q1LNW1 Integrase, catalytic region Q1LNF7 Elongation factor Ts Q1LNC8 Phage integrase Q1LNC4 TatD-‐related deoxyribonuclease Q1LN26 Transcriptional regulator, TetR family Q1LN22 Putative uncharacterized protein Q1LN20 tRNA-‐adenosine deaminase Q46NG6 General substrate transporter:Major facilitator superfamily MFS_1 Q1LM15 Extracellular solute-‐binding protein, family 5 Q1LM11 Oligopeptide/dipeptide ABC transporter, ATP-‐ Rmet_1954 Rmet_2067 Rmet_2081 Rmet_2131 Rmet_2155 Rmet_2214 Rmet_2218 Rmet_2230 Rmet_2231 Rmet_2232 CMGI-‐1 Rmet_2271 Rmet_2325 Rmet_2331 Rmet_2332 Rmet_2337 Rmet_2343 Rmet_2344 Rmet_2346 Rmet_2349 Rmet_2350 Rmet_2352 Rmet_2354 Rmet_2355 Rmet_2356 Rmet_2357 Rmet_2358 Rmet_2359 Rmet_2360 Rmet_2361 ispD pilL Op0572r Op0600r Op0601f Op0614r Op0621f Op0634r Op0635f Op0638r 0.37 0.48 0.42 0.48 0.31 0.42 0.29 0.41 1.02 5.60 4.26 2.69 2.24 4.28 2.30 2.26 0.49 0.48 0.48 0.36 0.37 0.41 0.18 0.42 2.61 5.33 3.09 5.04 4.31 3.24 11.21 4.71 Op0638r 0.24 3.11 0.19 18.42 Op0638r Op0649f Op0661f Op0661f Op0661f Op0661f Op0662r Op0662r Op0663f Op0663f Op0663f Op0663f Op0663f Op0663f Op0663f Op0663f Op0663f Op0663f Op0663f Op0664r 0.37 0.48 0.36 0.42 0.39 0.48 0.39 0.47 0.46 0.30 0.34 0.39 0.31 0.43 0.41 0.30 0.36 0.43 0.35 0.30 0.46 0.42 0.49 0.50 0.41 0.44 0.25 0.27 0.49 0.31 0.39 0.45 0.41 0.47 0.38 0.50 0.42 0.39 0.25 0.26 2.60 11.21 1.45 1.67 3.13 5.43 16.58 6.66 2.88 4.02 5.92 1.65 1.97 3.06 4.28 2.85 3.93 5.88 4.86 6.05 1.97 5.00 1.52 3.09 2.38 2.04 1.49 1.91 1.41 3.19 1.12 2.56 1.06 2.00 2.55 1.18 3.55 2.06 8.03 1.22 binding protein Q1LLZ3 2-‐C-‐methyl-‐D-‐erythritol 4-‐phosphate cytidylyltransferase Q1LLN0 Polysaccharide deacetylase Q1LLL6 Transcriptional regulator, AsnC family Q1LLG6 DNA helicase/exodeoxyribonuclease V, subunit A Q1LLE2 Cytochrome c, class I Q1LL83 Putative uncharacterized protein Q1LL79 Luciferase-‐like protein Q1LL67 Putative integral membrane protein Q1LL66 ABC transport systems inner membrane component Q1LL65 ABC transport systems inner membrane component Q1LL26 Putative uncharacterized protein Q1LKX4 Putative uncharacterized protein Q1LKW8 Putative secreted protein Q8GQ41 Putative uncharacterized protein ORF C69 A3LCI0 Putative uncharacterized protein Q8GQ53 Putative uncharacterized protein ORF C57 Q8GQ54 Putative excisionase Q8GQ56 Putative uncharacterized protein ORF C54 Q8GQ59 Putative uncharacterized protein ORF C51 Q8GQ60 Putative uncharacterized protein ORF C50 Q8GQ62 Putative uncharacterized protein ORF C48 Q8GQ64 Putative uncharacterized protein ORF C46 Q8GQ65 Putative DNA repair protein RadC Q8GQ66 Putative uncharacterized protein ORF C44 Q8GQ67 Putative uncharacterized protein ORF C43 Q8GQ68 Putative uncharacterized protein ORF C42 Q8GQ69 Putative uncharacterized protein ORF C41 Q8GQ70 Putative uncharacterized protein ORF C40 Q8GQ71 Putative uncharacterized protein ORF C39 Rmet_2362 Rmet_2363 Rmet_2369 Rmet_2370 Rmet_2371 Rmet_2503 Rmet_2525 Rmet_2548 Rmet_2619 Rmet_2621 Rmet_2647 Rmet_2658 Rmet_2683 Rmet_2686 Rmet_2687 Rmet_2758 Rmet_2778 Rmet_2780 Rmet_2798 Rmet_2802 CMGI-‐5 Rmet_2825 Rmet_2826 Rmet_2827 Rmet_2858 zupT fdhC cobQ cobD Rmet_2859 Rmet_2876 Rmet_2883 Rmet_2898 Op0664r Op0664r Op0668r Op0669f Op0669f Op0694r Op0698r Op0707f Op0733f Op0734r Op0748r 0.18 0.47 0.39 0.45 0.44 0.49 0.46 0.44 0.36 0.20 0.27 1.48 1.46 2.99 4.94 1.76 1.97 1.98 2.10 3.54 5.50 1.65 0.08 0.27 0.33 0.42 0.47 0.47 0.49 0.46 0.48 0.23 0.20 17.80 5.37 4.38 3.99 3.60 1.67 3.55 1.86 5.41 4.42 5.04 Op0754r Op0757f Op0757f Op0757f Op0776r 0.36 0.45 0.40 0.27 0.47 2.53 1.44 2.81 3.91 2.76 0.22 0.28 0.35 0.26 0.48 23.80 6.31 3.41 5.16 3.61 Op0782r Op0783f Op0786r Op0788r Op0795f Op0795f 0.43 0.48 0.40 0.23 0.42 0.48 3.43 2.14 2.01 0.68 3.69 1.70 0.49 0.48 0.37 0.48 0.45 0.46 6.67 4.80 6.69 3.85 8.97 7.64 Op0795f 0.37 3.22 0.35 19.84 Op0804r 0.45 3.36 0.47 2.97 Op0804r Op0808r Op0811f Op0815f 0.49 0.20 0.49 0.44 0.49 0.09 0.45 0.50 3.76 30.50 2.37 2.01 1.21 1.56 4.31 3.45 Q8GQ72 Putative uncharacterized protein ORF C38 Q8GQ73 Putative uncharacterized protein ORF C37 Q8GQ79 Similar to metabolite transport protein Q8GQ80 Putative transcriptional activator Q8GQ81 Putative uncharacterized protein ORF C29 Q1LKE6 Glucose-‐methanol-‐choline oxidoreductase Q1LKC4 AMP-‐dependent synthetase and ligase Q1LKA1 Putative uncharacterized protein Q1LK30 Putative uncharacterized protein Q1LK28 Zinc/iron permease Q1LK02 Transcriptional regulator, AsnC family Q0K7X0 Signal transduction protein containing PAS, GGDEF and EAL domains Q1LJX0 Putative transmembrane protein Q1LJW7 Pilus assembly protein PilE Q1LJW6 Pilus assembly protein Fim Q1LJP5 Formate dehydrogenase gamma subunit Q1LJM5 Adenosylcobyric acid synthase (Glutamine-‐ hydrolysing) Q1LJM3 Adenosylcobinamide-‐phosphate synthase Q1LJK5 Transcriptional regulator, GntR family Q1LJK1 Prolipoprotein diacylglyceryl transferase Q1LJH8 Plasmid encoded RepA protein Q1LJH7 Putative uncharacterized protein Q1LJH6 Putative TraY/DotA-‐like type IV secretion system protein Q1LJE5 ABC transport systems inner membrane component Q1LJE4 Substrate-‐binding region of ABC-‐type glycine betaine transporter s Q1LJC7 MscS Mechanosensitive ion channel Q1LJC0 RNA-‐directed DNA polymerase Q1LJA5 Putative uncharacterized protein Rmet_2921 Rmet_3086 Rmet_3087 Rmet_3092 Rmet_3093 Rmet_3097 Rmet_3158 Rmet_3169 Rmet_3187 Rmet_3188 Rmet_3206 Rmet_3213 Rmet_3344 Rmet_3345 CMGI-‐10 Rmet_3358 Rmet_3359 Rmet_3360 Rmet_3361 Rmet_3362 Rmet_3363 Rmet_3365 Rmet_3366 Rmet_3369 Rmet_3370 Rmet_3372 Rmet_3382 Rmet_3594 Rmet_3619 Rmet_3623 Rmet_3625 Rmet_3628 Rmet_3681 Rmet_3682 nrdB cheW aer Op0826r Op0869f Op0870r Op0870r Op0870r Op0872r Op0884r Op0890r Op0896r Op0896r Op0902r Op0906r Op0931f Op0931f Op0935f Op0935f Op0935f Op0935f Op0935f Op0936r Op0936r Op0936r Op0937f Op0937f Op0937f Op0940r Op1000r Op1007r Op1009r Op1009r Op1011r Op1026f Op1026f 0.49 0.33 0.40 0.50 0.48 0.46 0.36 0.48 0.41 0.43 0.41 0.43 0.46 0.45 0.24 0.14 0.36 0.26 0.27 0.48 0.14 0.49 0.43 0.42 0.32 0.41 0.33 0.38 0.42 0.16 0.48 0.45 0.42 3.29 4.07 2.00 2.08 2.88 1.19 1.33 2.43 1.52 2.78 1.44 2.41 2.59 3.10 1.61 1.77 1.98 1.91 1.43 1.69 1.46 1.40 2.08 2.79 3.40 1.75 2.33 2.49 2.38 1.89 1.30 2.74 2.20 0.50 0.09 0.15 0.40 0.35 0.35 0.46 0.48 0.49 0.34 0.39 0.40 0.43 0.29 0.13 0.11 0.17 0.19 0.19 0.48 0.12 0.43 0.43 0.44 0.34 0.38 0.30 0.18 0.28 0.12 0.27 0.35 0.43 3.59 2.82 27.29 11.96 4.61 11.52 3.46 8.29 3.40 4.17 3.20 3.85 5.17 5.63 10.22 5.64 7.63 7.91 6.47 3.96 12.82 3.74 7.71 6.31 2.72 4.14 3.95 4.63 6.46 20.09 7.98 5.09 1.64 Q1LJ82 Chaperone protein dnaJ Q1LIR8 Uncharacterized protein UPF0065 Q1LIR7 Ribonucleotide reductase Q1LIR2 Putative uncharacterized protein Q1LIR1 Cytochrome c assembly protein Q1LIQ7 Putative uncharacterized protein Q1LIJ6 Extracellular solute-‐binding protein, family 5 Q1LII5 Cytochrome d1, heme region Q1LIG7 Putative uncharacterized protein Q1LIG6 Peptidase M61 Q1LIE8 Putative uncharacterized protein Q1LIE1 Cl-‐channel, voltage gated Q1LI10 Putative membrane protein Q1LI09 Putative uncharacterized protein Q1LHZ6 Putative uncharacterized protein Q1LHZ5 UBA/THIF-‐type NAD/FAD binding fold Q1LHZ4 Putative uncharacterized protein Q1LHZ3 Putative uncharacterized protein Q1LHZ2 Putative uncharacterized protein Q1LHZ1 Putative uncharacterized protein Q1LHY9 Integrase, catalytic region Q1LHY8 Putative uncharacterized protein Q1LHY5 Phenylacetate-‐CoA oxygenase, PaaG subunit Q1LHY4 Phenylacetic acid degradation B Q1LHY2 Phenylacetate-‐CoA oxygenase, PaaJ subunit Q1LHX2 Globin Q1LHB0 Putative lipoprotein transmembrane Q1LH85 Transcriptional regulator, MarR family Q1LH81 Transcriptional regulator, MarR family Q1LH79 Putative uncharacterized protein Q1LH76 Putative uncharacterized protein Q1LH23 CheW protein Q1LH22 Methyl-‐accepting chemotaxis sensory transducer, Rmet_3684 Rmet_3691 cheR Op1026f Op1026f 0.42 3.74 0.46 1.69 0.37 0.46 1.62 5.78 Rmet_3693 Rmet_3698 Rmet_3701 Rmet_3702 Rmet_3735 Rmet_3736 Rmet_3737 Rmet_3738 Rmet_3741 Rmet_3744 Rmet_3820 Rmet_3826 Rmet_3832 Rmet_3979 Rmet_4009 Rmet_4010 Rmet_4029 Rmet_4033 Rmet_4054 Rmet_4084 Rmet_4121 Rmet_4123 Rmet_4128 Rmet_4134 Rmet_4135 Rmet_4136 Rmet_4157 Rmet_4159 Rmet_4173 Rmet_4198 Op1026f Op1026f Op1026f Op1026f Op1042f Op1042f Op1042f Op1042f Op1042f Op1042f Op1062f Op1064f Op1065r Op1115r Op1125r Op1125r Op1135r Op1137r Op1141r Op1148f Op1160f Op1162f Op1164f Op1165r Op1165r Op1166f Op1170f Op1170f Op1175r Op1190f 0.46 0.42 0.35 0.24 0.48 0.47 0.49 0.44 0.49 0.44 0.42 0.38 0.45 0.24 0.38 0.47 0.45 0.44 0.43 0.34 0.35 0.34 0.33 0.09 0.39 0.47 0.29 0.37 0.22 0.44 0.48 0.49 0.39 0.45 0.33 0.40 0.46 0.35 0.44 0.38 0.39 0.46 0.34 0.47 0.50 0.49 0.49 0.48 0.50 0.46 0.45 0.35 0.19 0.46 0.39 0.42 0.49 0.48 0.45 0.26 3.73 3.16 4.03 3.48 4.10 3.34 2.93 3.15 4.47 5.63 2.31 1.85 7.83 5.92 2.32 9.25 3.48 4.65 4.40 2.38 2.11 18.41 3.70 4.56 4.61 7.90 5.12 2.85 6.32 3.45 cheB1 flhB flhG fliA flgC flgD flgE flgF flgI flgL livM4 aroK phoA1 pdhA tauD 3.08 2.75 4.08 0.89 0.96 3.08 2.10 2.01 2.33 1.39 1.86 1.52 2.61 1.16 4.28 2.58 2.38 1.36 3.61 2.25 1.55 2.17 2.29 0.62 3.34 4.50 0.98 6.65 0.98 2.35 Pas/Pac sensor Q1LH20 Putative uncharacterized protein Q1LH13 MCP methyltransferase, CheR-‐type Q1LH11 Chemotaxis response regulator protein-‐glutamate methylesterase 1 Q1LH06 Flagellar biosynthetic protein FlhB Q1LH03 Flagellar biosynthesis protein FlhG Q1LH02 RNA polymerase sigma factor Q1LGW9 Flagellar basal-‐body rod protein FlgC Q1LGW8 Flagellar hook capping protein Q1LGW7 Putative uncharacterized protein Q1LGW6 Flagellar basal-‐body rod FlgF Q1LGW3 Flagellar P-‐ring protein Q1LGW0 Flagellin-‐like protein Q1LGN6 Putative cytochrome p450 oxidoreductase Q1LGN0 Putative uncharacterized protein Q1LGM4 Uncharacterized protein UPF0065 Q1LG79 Inner-‐membrane translocator Q1LG49 Putative uncharacterized protein Q1LG48 Shikimate kinase Q1LG29 MscS Mechanosensitive ion channel Q1LG25 Transcriptional regulator, LysR family Q1LG04 Cytochrome C biogenesis protein Q1LFX5 Alkaline phosphatase Q1LFT8 Secretion protein HlyD Q1LFT6 Heavy metal efflux pump CzcA Q1LFT1 Putative uncharacterized protein Q1LFS5 Dehydrogenase, E1 component Q1LFS4 Putative uncharacterized protein Q1LFS3 Taurine catabolism dioxygenase TauD/TfdA Q1LFQ2 Putative lipoprotein Q1LFQ0 Putative transmembrane protein Q1LFN6 Putative uncharacterized protein Q1LFL1 Transcriptional regulator, PadR family Rmet_4203 Rmet_4204 Rmet_4218 Rmet_4279 Rmet_4283 Rmet_4350 Rmet_4351 Rmet_4361 Rmet_4369 Rmet_4414 Rmet_4440 Rmet_4461 Rmet_4465 czcR2 Rmet_4472 Rmet_4489 Rmet_4490 Rmet_4492 Rmet_4493 Rmet_4494 Rmet_4522 Rmet_4587 Rmet_4588 Rmet_4590 arnC Rmet_4591 Rmet_4593 Rmet_4600 Rmet_4601 Rmet_4603 Rmet_4604 Rmet_4606 metY Op1192f Op1192f Op1197r Op1215r Op1217r Op1239r Op1240f 0.45 0.44 0.36 0.47 0.31 0.39 0.46 1.49 3.27 3.01 1.97 0.77 1.63 8.25 0.47 0.39 0.33 0.49 0.50 0.47 0.35 3.80 15.12 26.42 1.67 5.24 2.91 4.00 Op1244f Op1246f Op1257r Op1263r Op1271r 0.43 0.33 0.42 0.34 0.16 2.69 2.23 1.08 3.77 0.62 0.48 0.34 0.50 0.41 0.47 3.89 3.98 11.45 9.67 3.87 Op1274f Op1275r Op1279r Op1279r Op1279r Op1279r Op1279r 0.38 0.32 0.37 0.31 0.46 0.38 0.26 2.78 1.54 3.44 1.99 2.18 1.83 1.37 0.33 0.24 0.40 0.22 0.38 0.17 0.15 5.89 7.49 5.63 6.48 5.45 4.37 6.40 Op1295r Op1320f 0.48 1.65 0.30 3.56 0.39 0.31 3.09 4.88 Op1320f Op1320f Op1320f Op1320f Op1324f Op1324f Op1324f Op1324f Op1326f 0.37 0.28 0.35 0.47 0.27 0.45 0.19 0.17 0.38 0.39 0.40 0.46 0.46 0.18 0.45 0.21 0.13 0.37 6.14 3.38 3.12 3.06 19.44 2.62 6.70 9.07 1.96 4.50 3.32 12.67 10.58 2.31 3.30 3.25 2.56 2.16 Q1LFK6 Uncharacterized protein UPF0065 Q1LFK5 LmbE-‐like protein Q1LFJ1 Lysine exporter protein (LYSE/YGGA) Q1LFD1 Fusaric acid resistance protein conserved region Q1LFC7 Putative uncharacterized protein Q1LF61 UvrD/REP helicase family protein Q1LF60 Putative uncharacterized protein Q1LF50 L-‐carnitine dehydratase/bile acid-‐inducible protein F Q1LF42 Major facilitator superfamily MFS_1 Q1LEZ7 Short-‐chain dehydrogenase/reductase SDR Q1LEX1 Endoribonuclease L-‐PSP Q1LEV0 Putative uncharacterized protein Q1LEU6 Two component heavy metal response transcriptional regulator Q1LEG4 Sulphate transporter Q1LES2 Zonular occludens toxin Q1LES1 Putative uncharacterized protein Q1LER9 Putative uncharacterized protein Q1LER8 Putative uncharacterized protein Q1LER7 Putative uncharacterized protein Q1LEN9 Transcriptional regulator, AraC family with amidase-‐like domain Q1LEH7 Glycosyl transferase, family 39 Q1LEH6 Putative small multidrug resistance transmembrane protein Q1LEH4 Glycosyl transferase, family 2 Q1LEH3 Formyl transferase-‐like protein Q1LEH1 Polysaccharide deacetylase Q1LEG4 Sulphate transporter Q1LEG3 UspA Q1LEG1 Transcriptional regulator, GntR family Q1LEG0 Putative uncharacterized protein Q1LEF8 O-‐acetylhomoserine/O-‐acetylserine sulfhydrylase Rmet_4609 Rmet_4611 Rmet_4613 Rmet_4615 Rmet_4616 Rmet_4617 Rmet_4618 Rmet_4619 Rmet_4623 Rmet_4629 Rmet_4633 Rmet_4635 Rmet_4640 Rmet_4641 Rmet_4642 Rmet_4643 Rmet_4644 Rmet_4645 Rmet_4646 Rmet_4647 Rmet_4648 Rmet_4649 Rmet_4650 Rmet_4662 Rmet_4668 Rmet_4685 Rmet_4700 Rmet_4730 Rmet_4735 Rmet_4754 Rmet_4805 tauD kbl Op1328f Op1328f Op1329r Op1330f Op1330f Op1330f Op1331r 0.36 0.35 0.38 0.36 0.29 0.31 0.31 2.65 3.23 1.67 3.40 3.32 1.92 2.56 0.39 0.39 0.33 0.33 0.32 0.23 0.22 7.82 4.49 10.54 9.84 6.09 5.10 4.65 Op1331r Op1332f Op1334f Op1337r Op1339r Op1341r 0.33 0.42 0.44 0.38 0.29 0.37 1.98 2.50 3.41 2.94 1.72 4.35 0.26 0.49 0.49 0.47 0.47 0.47 5.07 1.66 1.43 4.78 3.10 4.05 Op1341r Op1341r Op1341r Op1341r Op1341r Op1341r Op1342f Op1343r 0.45 0.43 0.37 0.36 0.17 0.40 0.44 0.40 4.33 2.24 2.20 1.73 2.96 4.50 4.12 3.80 0.49 0.49 0.32 0.22 0.08 0.43 0.36 0.35 16.93 1.83 12.30 9.14 3.60 4.53 6.95 5.55 Op1343r Op1344f Op1349r Op1351r Op1355r Op1359r Op1367r Op1369r Op1381r Op1397r 0.34 0.46 0.42 0.39 0.39 0.39 0.35 0.36 0.47 0.42 5.15 3.50 2.24 2.88 2.63 3.89 6.39 3.86 3.05 2.86 0.33 0.48 0.47 0.39 0.50 0.47 0.39 0.48 0.42 0.39 3.79 5.22 2.69 5.81 3.38 3.51 6.57 3.75 11.28 2.10 Q1LEF5 Uncharacterized protein UPF0065 Q1LEF3 Putative uncharacterized protein Q1LEF1 Acyl-‐CoA dehydrogenase-‐like protein Q1LEE9 Transcriptional regulator, GntR family Q1LEE8 Putative uncharacterized protein Q1LEE7 TonB-‐dependent siderophore receptor Q1LEE6 Putative uncharacterized protein Q1LEE5 RND efflux system, outer membrane lipoprotein, NodT Q1LEE1 Putative uncharacterized protein Q1LED5 Transcriptional regulator, AraC family Q1LED1 Taurine catabolism dioxygenase TauD/TfdA Q1LEC9 Sulphate transporter Q1LEC4 Putative uncharacterized protein Q1LEC3 ATP-‐dependent endonuclease of the OLD family-‐ like protein Q1LEC2 Putative uncharacterized protein Q1LEC1 Putative uncharacterized protein Q1LEC0 Carboxymuconolactone decarboxylase Q1LEB9 Uncharacterized protein UPF0065 Q1LEB8 Short-‐chain dehydrogenase/reductase SDR Q1LEB7 Transcriptional regulator, LacI family Q1LEB6 Filamentation induced by cAMP protein Fic Q1LEB5 RND efflux system, outer membrane lipoprotein, NodT Q1LEB4 Putative transcriptional regulator Q1LEA2 Putative uncharacterized protein Q1LE96 NADH/Ubiquinone/plastoquinone (Complex I) Q1LE79 Putative uncharacterized protein Q1LE64 Conserved hypothetical signal peptide protein Q1LE34 Uncharacterised peroxidase-‐related Q1LE29 D-‐galactonate transporter Q1LE10 Glycosyl transferase, family 2 Q1LDV9 2-‐amino-‐3-‐ketobutyrate coenzyme A ligase Rmet_4808 Rmet_4836 Rmet_4875 catD Rmet_4876 Rmet_4881 catA Op1399r Op1411r Op1425r Op1425r Op1428f 0.47 0.37 0.49 0.41 0.50 3.56 1.62 12.74 4.15 1.73 0.33 0.41 0.46 0.33 0.45 5.24 0.83 4.48 2.34 4.43 Rmet_4891 Rmet_4960 Rmet_4962 Rmet_4964 Rmet_4977 Rmet_4978 Rmet_4979 Rmet_4981 Rmet_4982 Rmet_5007 Rmet_5008 Rmet_5011 Rmet_5033 cusA Rmet_5040 Rmet_5079 Rmet_5082 Rmet_5111 Rmet_5112 Rmet_5128 aldB Rmet_5133 Rmet_5172 Rmet_5175 Rmet_5176 Rmet_5177 Rmet_5178 Op1430f Op1457r Op1457r 0.44 1.68 0.33 1.18 0.38 1.57 0.47 0.50 0.42 6.77 4.41 3.37 Op1457r Op1461r 0.42 1.36 0.45 1.81 0.47 0.42 3.34 4.54 Op1461r Op1461r Op1461r Op1461r Op1470f Op1470f 0.27 0.38 0.43 0.35 0.36 0.42 1.17 2.57 2.07 4.46 2.49 2.31 0.12 0.24 0.36 0.34 0.36 0.42 39.35 4.86 4.96 10.49 4.44 2.47 Op1473r Op1480f Op1482f Op1496f Op1496f Op1505r Op1505r Op1513r Op1513r Op1522f Op1522f Op1522f Op1523r Op1524f 0.43 0.38 0.48 0.41 0.44 0.38 0.21 0.46 0.42 0.36 0.37 0.33 0.33 0.49 2.88 3.68 2.36 2.41 2.57 2.51 2.44 5.39 1.81 2.49 1.81 1.05 0.98 1.97 0.44 0.32 0.47 0.37 0.47 0.46 0.17 0.46 0.29 0.43 0.44 0.44 0.36 0.43 6.62 6.53 1.65 5.40 11.07 1.66 8.94 7.48 4.25 2.88 4.14 2.42 3.76 3.86 Q1LDV6 Di-‐haem cytochrome c peroxidase Q1LDS8 Diguanylate phosphodiesterase (EAL domain) Q1LDN9 3-‐oxoadipate enol-‐lactonase Q1LDN8 Uncharacterized protein UPF0065 Q1LDN3 Catechol 1,2-‐dioxygenase Q1LDM3 Sulfite dehydrogenase (Cytochrome) subunit SorA apoprotein Q1LDF4 Pili assembly chaperone Q1LDF2 Diguanylate phosphodiesterase (EAL domain) Q1LDF0 Two component transcriptional regulator, LuxR family Q1LDD7 Sensor protein Q1LDD6 Two component transcriptional regulator, winged helix family Q1LDD5 Putative uncharacterized protein Q1LDD3 Putative uncharacterized protein Q1LDD2 Undecaprenyl-‐diphosphatase Q1LDA7 Putative uncharacterized protein Q1LDA6 CsbD-‐like protein Q1LDA3 Pyridine nucleotide-‐disulphide oxidoreductase dimerisation region Q1LD81 Heavy metal efflux pump CzcA Q1LD74 Transcriptional regulator, GntR family Q1LD38 Putative uncharacterized protein Q1LD35 OmpA/MotB Q1LD06 Thiolase Q1LD05 Putative uncharacterized protein Q1LCY9 Aldehyde dehydrogenase Q1LCY4 Acyl-‐CoA dehydrogenase-‐like protein Q1LCU5 Putative uncharacterized protein Q1LCU2 Putative uncharacterized protein Q1LCU1 Translation initiation factor IF-‐1 3 Q1LCU0 Putative uncharacterized protein Q1LCT9 Putative uncharacterized protein Rmet_5179 Rmet_5185 Rmet_5195 Rmet_5225 Rmet_5230 Rmet_5236 Rmet_5237 Rmet_5238 Rmet_5239 Rmet_5252 Rmet_5253 Rmet_5255 Rmet_5256 Rmet_5263 Rmet_5265 Rmet_5266 Rmet_5300 Rmet_5332 Rmet_5333 Rmet_5352 Rmet_5353 Rmet_5365 Rmet_5376 Rmet_5378 Rmet_5379 Rmet_5380 Rmet_5386 Rmet_5394 Rmet_5426 Rmet_5428 Rmet_5437 Rmet_5467 Rmet_5490 iscS2 fliC2 fliS fliH fliJ fliK fliO hmuT hmuV pobA Op1525r Op1528f Op1532f Op1541r Op1543r Op1544f Op1544f Op1544f Op1544f Op1550f Op1550f Op1550f Op1550f Op1552f Op1552f Op1552f Op1566f Op1578f Op1579r Op1590f 0.48 0.40 0.45 0.36 0.47 0.50 0.44 0.45 0.48 0.49 0.33 0.46 0.46 0.43 0.49 0.32 0.44 0.39 0.25 0.48 3.22 3.36 2.56 2.60 2.88 1.79 2.66 2.83 1.48 3.76 4.61 6.70 3.51 1.47 1.60 0.68 1.05 3.65 1.17 3.24 0.48 0.47 0.50 0.40 0.47 0.37 0.46 0.39 0.40 0.27 0.36 0.40 0.46 0.46 0.47 0.50 0.47 0.50 0.24 0.41 8.34 2.07 1.82 7.06 3.39 3.06 2.19 3.41 3.46 3.48 2.13 4.03 6.43 3.31 3.14 1.87 2.50 3.11 1.31 2.29 Op1590f Op1596f Op1600f Op1600f Op1601r Op1601r Op1603r Op1606f Op1614f Op1615r Op1617r Op1625r Op1631r 0.42 0.34 0.48 0.48 0.44 0.47 0.42 0.38 0.26 0.49 0.43 0.45 0.50 1.64 1.51 1.93 1.65 4.32 2.63 3.17 1.86 1.77 1.51 2.88 2.58 1.95 0.50 0.39 0.47 0.49 0.47 0.47 0.38 0.40 0.40 0.48 0.48 0.35 0.42 5.66 0.83 2.64 1.77 2.48 3.00 7.06 5.16 3.69 4.90 2.55 4.61 6.50 Q1LCT8 Putative uncharacterized protein Q1LCT2 Carbonic anhydrase Q1LCS2 Porin, Gram-‐negative type Q1LCP2 Putative uncharacterized protein Q1LCN7 Aminotransferase, class V Q1LCN1 DegT/DnrJ/EryC1/StrS aminotransferase Q1LCN0 WbnG Q1LCM9 Putative uncharacterized protein Q1LCM8 Phytanoyl-‐CoA dioxygenase Q1LCL5 Flagellin-‐like protein Q1LCL4 Flagellar protein FlaG protein Q1LCL2 Flagellar protein FliS Q1LCL1 Flagellar protein FliT Q1LCK4 Flagellar assembly protein FliH Q1LCK2 Flagellar export FliJ Q1LCK1 Flagellar hook-‐length control protein Q1LCG7 Flagellar biosynthesis protein, FliO Q1LCD5 Sensor protein Q1LCD4 Putative uncharacterized protein Q1LCB5 Putative uncharacterized protein Q1LCB4 Pyridoxamine 5'-‐phosphate oxidase-‐related, FMN-‐ binding Q1LCA2 Transcriptional regulator, LysR family Q1LC91 Periplasmic binding protein Q1LC89 Hemin import ATP-‐binding protein hmuV Q1LC88 Short-‐chain dehydrogenase/reductase SDR Q1LC87 Putative uncharacterized protein Q1LC81 Putative uncharacterized protein Q1LC73 Putative uncharacterized protein Q1LC41 Putative uncharacterized protein Q1LC39 Putative uncharacterized protein Q1LC30 Acyl-‐CoA dehydrogenase-‐like protein Q1LC00 Putative uncharacterized protein Q1LBX7 Monooxygenase, FAD-‐binding Rmet_5497 Rmet_5500 Rmet_5503 Rmet_5515 Rmet_5516 Rmet_5517 Rmet_5521 Rmet_5522 Rmet_5525 Rmet_5526 Rmet_5528 Rmet_5533 Rmet_5539 Rmet_5627 Rmet_5682 Rmet_5685 Rmet_5688 Rmet_5728 Rmet_5762 Rmet_5764 Rmet_5818 Rmet_5821 Rmet_5832 Rmet_5835 Rmet_5850 Rmet_5899 Rmet_5918 Rmet_5937 Rmet_5970 cyp vanB Op1634f Op1636f Op1636f Op1641r Op1641r Op1641r Op1641r Op1641r 0.38 0.44 0.35 0.40 0.45 0.31 0.44 0.45 3.41 1.69 3.36 2.38 2.03 2.17 2.71 2.23 0.45 0.48 0.50 0.46 0.50 0.37 0.46 0.50 5.35 5.01 5.63 3.87 3.19 10.73 2.08 11.07 Op1642f Op1643r Op1643r Op1645r Op1647r Op1679r Op1697r Op1698f Op1698f Op1715r Op1728f Op1729r Op1757r Op1759r 0.44 0.38 0.45 0.24 0.34 0.44 0.43 0.38 0.44 0.37 0.50 0.44 0.44 0.36 2.89 1.73 1.88 1.86 2.95 1.64 2.42 3.58 2.87 2.56 3.69 1.82 1.58 7.99 0.47 0.29 0.42 0.21 0.44 0.49 0.39 0.35 0.49 0.42 0.44 0.47 0.39 0.32 3.50 6.70 4.15 22.47 3.71 3.84 3.44 28.05 4.81 6.37 4.24 4.49 2.77 10.91 Op1764f Op1764f Op1769r Op1787r Op1797r Op1805r Op1817r 0.34 0.43 0.43 0.37 0.45 0.47 0.24 2.16 1.82 1.72 1.89 6.37 2.58 2.11 0.43 0.49 0.48 0.44 0.46 0.46 0.49 3.17 4.98 3.87 2.78 3.25 4.09 1.02 0.45 2.74 0.47 2.59 Rmet_6282 Op1915r Q(EDTA≤0.5, Q(Zn) unchanged. Q1LBX0 Integrase, catalytic region Q1LBW7 Putative uncharacterized protein Q1LBW4 Uncharacterized protein UPF0065 Q1LBV2 Aldehyde dehydrogenase Q1LBV1 Cytochrome P450 Q1LBV0 Ferredoxin Q1LBU6 Enoyl-‐CoA hydratase/isomerase Q1LBU5 Putative uncharacterized protein Q1LBU2 L-‐carnitine dehydratase/bile acid-‐inducible protein F Q1LBU1 Putative uncharacterized protein Q1LBT9 AMP-‐dependent synthetase and ligase Q1LBT4 Nitroreductase Q1LBS8 Putative uncharacterized protein Q1LBJ0 Putative uncharacterized protein Q1LBD5 Secretion protein HlyD Q1LBD2 Pilus assembly protein FimT Q1LBC9 Putative transmembrane protein Q1LB89 Glycosyl transferase, group 1 Q1LB55 Putative uncharacterized protein Q1LB53 Putative uncharacterized protein Q46Q97 Cold-‐shock DNA-‐binding protein family Q1LAZ6 Putative integrase/recombinase protein Q1LAY5 Response regulator receiver domain protein (CheY-‐ like) Q1LAY2 Sugar transferase Q1LAW7 Protein tyrosine phosphatase Q1LAR8 Putative uncharacterized protein Q1LAP9 Transcriptional regulator, IclR family Q1LAN0 Putative uncharacterized protein Q1LAJ7 Heavy metal translocating P-‐type ATPase P37248 Transposase for insertion sequence element IS1086 Rmet_0090 Rmet_0091 Rmet_0096 Rmet_0133 Rmet_0137 Rmet_0138 Rmet_0139 Rmet_0158 Rmet_0170 Rmet_0175 Rmet_0191 Rmet_0192 Rmet_0193 Rmet_0208 Rmet_0227 Rmet_0271 Rmet_0289 Rmet_0310 Rmet_0355 Rmet_0356 Rmet_0359 Rmet_0360 Rmet_0363 Rmet_0365 Rmet_0367 Rmet_0368 Rmet_0369 argS ahcY prs otsB coxM coxS Op0025f 0.86 0.21 0.48 2.69 Op0025f Op0029f Op0034r Op0037f Op0038r Op0038r Op0046r Op0051f Op0052r 0.65 0.64 0.84 0.70 0.80 0.64 0.51 0.63 0.59 0.75 2.58 0.73 0.85 0.70 3.42 2.58 3.47 1.36 0.42 0.43 0.41 0.30 0.29 0.39 0.34 0.49 0.48 3.39 4.56 1.49 1.13 1.22 1.86 4.94 3.11 2.53 Op0057f 0.57 2.02 0.47 2.15 Op0057f Op0057f Op0062r Op0066r Op0077f Op0084r Op0088r Op0101f Op0101f 0.51 0.63 0.56 0.90 0.74 0.81 0.52 0.94 0.59 1.56 1.51 2.47 0.35 0.40 1.66 5.32 0.25 1.96 0.41 0.45 0.48 0.49 0.37 0.40 0.46 0.39 0.42 4.20 4.85 3.21 5.98 1.26 15.86 1.78 4.04 2.88 Op0102r Op0102r Op0102r Op0102r Op0103f Op0103f Op0103f 0.67 0.52 0.54 0.54 0.53 0.80 0.62 7.20 0.84 2.36 3.81 2.71 0.58 1.38 0.39 0.17 0.44 0.44 0.45 0.42 0.43 5.59 7.23 8.01 3.38 5.67 2.99 3.69 Q1LSA0 Two component transcriptional regulator, LuxR family Q1LS99 Response regulator receiver domain protein (CheY-‐ like) Q1LS94 Arginyl-‐tRNA synthetase Q1LS57 Nuclear export factor GLE1 Q1LS53 Putative uncharacterized protein Q1LS52 Transcriptional regulator, LysR family Q1LS51 Putative uncharacterized protein Q1LS32 Aldehyde dehydrogenase Q1LS20 Adenosylhomocysteinase Q1LS15 5-‐formyltetrahydrofolate cyclo-‐ligase Q1LRZ9 Putative type-‐4 fimbrial biogenesis transmembrane protein Q1LRZ8 Putative type-‐4 fimbrial biogenesis pily1-‐related protein Q1LRZ7 Pilus assembly protein PilE Q1LRY2 Transcriptional regulator, GntR family Q1LRW3 Ferredoxin-‐like protein Q1LRR9 Electron transport protein SCO1/SenC Q1LRQ1 Ribose-‐phosphate pyrophosphokinase Q1LRN0 Peptidase C56, PfpI Q1LRI5 HAD-‐superfamily hydrolase subfamily IIB Q1LRI4 Glycoside hydrolase 15-‐related Q1LRI1 Predicted sulfurylase large subunit, molybdopterin cytosine dinucleotide biosynthesis / predicted sulfurylase small subunit, molybdopterin cytosine dinucleotide biosynthesis Q1LRI0 Carbon monoxide dehydrogenase subunit G Q1LRH7 Molybdopterin dehydrogenase, FAD-‐binding Q1LRH5 (2Fe-‐2S)-‐binding Q1LRH3 FAD linked oxidase-‐like protein Q1LRH2 Histidine triad (HIT) protein Q1LRH1 ABC transporter-‐like protein Rmet_0411 Rmet_0452 Rmet_0456 Rmet_0466 Rmet_0673 Rmet_0674 Rmet_0696 Rmet_0697 Rmet_0730 Rmet_0742 Rmet_0748 Rmet_0749 Rmet_0750 Rmet_0752 Rmet_0790 Rmet_0799 Rmet_0800 Rmet_0801 Rmet_0806 Rmet_0807 Rmet_0808 Rmet_0814 Rmet_0818 rpsI rhlE1 recA pilL2 pilA rpsP rimM trmD glnS Rmet_0822 ggt Rmet_0825 Rmet_0828 Rmet_0829 Rmet_0830 Rmet_0833 Op0113f Op0118r Op0119f Op0123f Op0187f Op0188r Op0196r Op0196r Op0205f Op0210r Op0213f Op0213f Op0213f Op0213f Op0225f 0.67 0.56 0.58 0.67 0.65 0.68 0.79 0.62 0.69 0.55 0.96 0.59 0.77 0.53 0.61 3.01 1.90 2.17 1.25 1.60 1.01 0.29 1.18 1.15 2.51 0.31 1.08 0.79 3.22 1.14 0.47 0.43 0.42 0.43 0.45 0.49 0.43 0.41 0.49 0.50 0.42 0.35 0.36 0.44 0.45 3.15 9.44 3.90 3.18 3.07 3.22 2.02 7.21 3.45 14.63 8.79 4.64 5.53 4.87 3.97 Op0227f 0.63 0.89 0.23 6.98 Op0227f 0.67 1.47 0.31 11.81 Op0227f Op0229f Op0229f Op0229f Op0230r Op0230r 0.52 0.51 0.52 0.56 0.52 0.60 2.65 2.56 2.51 1.61 3.33 1.58 0.33 0.43 0.42 0.47 0.48 0.49 15.86 2.77 4.74 3.42 3.73 4.54 Op0232r Op0234r Op0236r Op0236r 0.54 0.67 0.55 0.52 1.79 6.36 2.02 2.00 -‐0.37 0.49 0.50 0.42 0.60 18.72 3.92 9.06 Op0236r Op0238r 0.67 2.55 0.59 1.70 0.44 0.46 1.54 4.69 Q1LRC8 Putative uncharacterized protein Q1LR88 PhoH-‐like protein Q1LR84 DEAD/DEAH box helicase-‐like protein Q1LR74 Protein recA Q1LQL7 CheA signal transduction histidine kinases Q1LQL6 Major facilitator superfamily MFS_1 Q1LQJ4 Putative uncharacterized protein Q1LQJ3 Pilus assembly protein major pilin PilA Q1LQG0 Uracil-‐xanthine permease Q1LQE8 Radical SAM Q1LQE2 SSU ribosomal protein S16P Q1LQE1 Ribosome maturation factor rimM Q1LQE0 tRNA (guanine-‐N(1)-‐)-‐methyltransferase Q1LQD8 NUDIX hydrolase Q1LQA0 Putative uncharacterized protein Q1LQ91 ABC transport systems inner membrane component Q1LQ90 Substrate-‐binding region of ABC-‐type glycine betaine transporter Q1LQ89 ABC transport systems inner membrane component Q1LQ84 Putative uncharacterized protein Q1LQ83 Class II aldolase/adducin-‐like protein Q1LQ82 4-‐oxalocrotonate tautomerase family enzyme Q1LQ76 Putative uncharacterized protein Q1LQ72 Glutaminyl-‐tRNA synthetase Q1LQ68 Gamma-‐glutamyltransferase 2. Threonine peptidase. Q1LQ65 Putative uncharacterized protein Q1LQ62 Uncharacterized protein UPF0065 Q1LQ61 Putative transmembrane protein Q1LQ60 L-‐carnitine dehydratase/bile acid-‐inducible protein F Q1LQ57 Transcriptional regulator, GntR family Rmet_0834 Rmet_0860 Rmet_0862 Rmet_0894 Rmet_0918 Rmet_0921 Rmet_0922 Rmet_0925 Rmet_0926 Rmet_0928 Rmet_0929 Rmet_0931 Rmet_0932 Rmet_0935 gudD tpiA secG nuoB nuoC nuoE nuoF nuoI Op0239f Op0247f Op0248r Op0259f Op0263f Op0265f Op0266r Op0267f Op0267f Op0267f Op0267f Op0267f Op0267f Op0267f 0.52 0.55 0.69 0.71 0.63 0.53 0.71 0.85 0.87 0.74 0.71 0.54 0.64 0.59 2.53 5.41 0.31 3.19 3.51 1.67 1.56 0.56 0.43 1.89 2.05 2.22 0.80 2.97 0.49 0.43 0.40 0.46 0.45 0.45 0.42 0.46 0.44 0.35 0.37 0.38 0.50 0.48 1.72 5.79 4.29 3.68 3.70 4.65 4.05 7.77 5.68 3.39 4.12 8.82 1.69 3.81 Rmet_0936 nuoJ Op0267f 0.66 0.79 0.49 5.27 Rmet_0938 nuoL Op0267f 0.67 1.24 0.47 2.93 Rmet_0939 Rmet_1024 Rmet_1025 Rmet_1027 Rmet_1028 Rmet_1029 Rmet_1030 Rmet_1031 Rmet_1053 Rmet_1054 Rmet_1140 Op0267f Op0295f Op0295f Op0295f Op0295f Op0295f Op0295f Op0295f Op0301f Op0301f Op0326r 0.57 0.60 0.57 0.64 0.69 0.71 0.66 0.86 0.60 0.77 0.62 1.40 0.94 1.54 1.04 0.76 1.69 0.95 0.15 4.87 1.46 2.33 0.47 0.40 0.45 0.47 0.47 0.45 0.43 0.49 0.49 0.49 0.49 5.87 4.95 3.50 3.28 6.70 3.28 10.86 5.18 3.80 4.32 3.32 Op0333f Op0333f Op0333f 0.53 1.98 0.63 2.97 0.62 4.10 0.30 0.48 0.42 1.99 13.82 14.25 leuA rpsO nuoM iscS hscB hscA kdsA Rmet_1160 thrS Rmet_1162 rpmI Rmet_1163 rplT Q1LQ56 D-‐glucarate dehydratase Q1LQ30 Putative uncharacterized protein Q1LQ28 Putative uncharacterized protein Q1LPZ6 Transcriptional regulator, LysR family Q1LPX2 2-‐isopropylmalate synthase Q1LPW9 30S ribosomal protein S15 Q1LPW8 Putative uncharacterized protein Q1LPW5 Triosephosphate isomerase Q1LPW4 Protein translocase subunit secG Q1LPW2 NADH-‐quinone oxidoreductase subunit B Q1LPW1 NADH-‐quinone oxidoreductase subunit C Q1LPV9 NADH-‐quinone oxidoreductase, E subunit Q1LPV8 NADH-‐quinone oxidoreductase, F subunit Q1LPV5 NADH-‐quinone oxidoreductase subunit I Q1LPV4 NADH-‐ubiquinone/plastoquinone oxidoreductase, chain 6 Q1LPV2 Proton-‐translocating NADH-‐quinone oxidoreductase, chain L Q1LPV1 Proton-‐translocating NADH-‐quinone oxidoreductase, chain M Q1LPL6 Transcriptional regulator, BadM/Rrf2 family Q1LPL5 Cysteine desulfurase IscS Q1LPL3 Iron-‐sulfur cluster assembly protein IscA Q1LPL2 Co-‐chaperone Hsc20 Q1LPL1 Chaperone protein hscA homolog Q1LPL0 Ferredoxin, 2Fe-‐2S type Q1LPK9 Putative uncharacterized protein Q1LPI7 2-‐dehydro-‐3-‐deoxyphosphooctonate aldolase Q1LPI6 Putative uncharacterized protein Q1LPA0 FAD dependent oxidoreductase Q1LP80 Threonyl-‐tRNA synthetase / Ser-‐tRNA(Thr) hydrolase Q1LP78 50S ribosomal protein L35 Q1LP77 50S ribosomal protein L20 Rmet_1212 Rmet_1213 Rmet_1216 Rmet_1217 Rmet_1363 Rmet_1419 Rmet_1435 Rmet_1437 CMGI-‐3 Rmet_1463 Rmet_1466 Rmet_1468 Rmet_1470 Rmet_1471 Rmet_1472 Rmet_1473 Rmet_1474 Rmet_1572 Rmet_1576 Rmet_1732 Rmet_1812 Rmet_1834 Rmet_1931 Rmet_1946 Rmet_1973 Rmet_1981 Rmet_1982 Rmet_1983 Rmet_2024 Rmet_2033 Rmet_2039 Rmet_2044 Rmet_2133 Rmet_2136 Op0352r pyrD Op0352r aat Op0354r Op0354r Op0383f Op0398r rpsB Op0403f pyrH Op0403f guaA Op0409f Op0411f Op0412r Op0412r Op0412r Op0412r Op0412r Op0412r ptpS Op0433f Op0434r Op0491f Op0526r Op0533f amaB-‐2 Op0564r Op0570r pitA Op0576r Op0577f Op0577f Op0578r Op0592r Op0594r Op0596r ccoN Op0596r Op0614r Op0615f 0.51 0.83 0.53 0.79 0.67 0.63 0.77 0.51 0.70 0.56 0.55 0.71 0.60 0.63 0.58 0.56 0.53 0.73 0.52 0.66 0.62 0.55 0.51 0.64 0.59 0.59 0.78 0.88 1.06 0.73 0.72 0.82 0.54 1.06 0.65 4.26 0.85 1.53 1.43 0.55 2.21 1.98 1.59 2.01 0.62 1.22 0.80 1.25 3.18 2.20 0.69 2.34 1.22 1.37 5.23 4.55 1.76 2.77 4.39 1.20 0.23 0.55 0.74 1.66 0.48 2.28 0.46 0.48 0.47 0.42 0.42 0.47 0.37 0.49 0.45 0.42 0.36 0.39 0.36 0.35 0.27 0.26 0.40 0.45 0.43 0.48 0.49 0.49 0.43 0.43 0.39 0.37 0.41 0.49 0.43 0.50 0.48 0.45 0.48 5.31 3.37 14.56 4.14 1.17 2.29 10.15 8.39 6.62 4.13 9.30 5.62 7.37 33.59 6.24 13.76 5.03 8.07 8.92 6.21 3.48 11.59 10.12 89.36 3.64 4.28 11.84 2.46 8.01 3.31 11.06 6.20 4.09 Q1LP28 Aldo/keto reductase Q1LP27 Dihydroorotate dehydrogenase Q1LP24 Leucyl/phenylalanyl-‐tRNA-‐-‐protein transferase Q1LP23 NUDIX hydrolase Q1LNN0 Putative signal peptide protein Q1LNH4 Modification methylase, HemK family Q1LNF8 30S ribosomal protein S2 Q1LNF6 Uridylate kinase Q1LND0 GMP synthase (Glutamine-‐hydrolyzing) Q1LNC7 Putative uncharacterized protein Q1LNC5 Phage transcriptional regulator, AlpA Q1LNC3 Putative uncharacterized protein Q1LNC2 Putative uncharacterized protein Q1LNC1 KAP P-‐loop Q1LNC0 Retron reverse transcriptase Q1LNB9 Putative uncharacterized protein Q1LN21 Putative uncharacterized protein Q1LN17 Putative proline-‐rich protein Q1LML5 Transcriptional regulator, AraC family Q1LMD5 Rieske (2Fe-‐2S) region Q1LMB3 Transcriptional regulator, GntR family Q1LM16 Amidase, hydantoinase/carbamoylase Q1LM01 Putative transmembrane protein Q1LLX4 Phosphate transporter Q1LLW6 LexA repressor Q1LLW5 Putative uncharacterized protein Q1LLW4 Putative uncharacterized protein Q1LLS3 GTP-‐binding protein TypA Q1LLR4 UPF0090 protein Rmet_2033 Q1LLQ8 Putative uncharacterized protein Q1LLQ3 Cytochrome c oxidase, cbb3-‐type, subunit I Q1LLG4 Putative uncharacterized protein Q1LLG1 Putative uncharacterized protein Rmet_2137 Rmet_2138 Rmet_2139 Rmet_2141 Rmet_2174 Rmet_2177 Rmet_2193 Rmet_2194 Rmet_2195 Rmet_2210 Rmet_2212 Rmet_2264 Rmet_2265 Rmet_2266 Rmet_2273 Rmet_2274 Rmet_2286 Rmet_2300 Rmet_2339 Rmet_2340 Rmet_2341 Rmet_2342 Rmet_2424 Rmet_2432 Rmet_2433 Rmet_2441 Rmet_2454 Rmet_2461 Rmet_2484 Rmet_2485 Rmet_2486 Rmet_2487 Rmet_2547 Rmet_2564 ppx carB carA fumA murI rpmF moaA sdhA sdhD sdhC Op0615f Op0615f Op0615f Op0617f Op0625f Op0626r Op0630r Op0630r Op0630r Op0632r Op0633f Op0645f Op0646r Op0647f Op0649f Op0649f Op0654r Op0656r Op0662r Op0662r Op0662r Op0662r Op0680r Op0680r Op0680r Op0683f Op0685f Op0688r Op0688r Op0688r Op0688r Op0688r Op0707f Op0709f 0.90 0.83 0.52 0.64 0.56 0.54 0.71 0.72 0.61 0.65 0.59 0.90 0.73 0.61 0.65 1.08 0.90 0.50 0.54 0.64 0.62 0.64 0.87 1.08 0.67 0.73 0.60 0.55 0.90 0.84 0.69 0.71 0.72 0.57 0.53 1.82 4.50 4.32 1.13 1.16 0.85 0.89 1.58 1.06 2.44 0.45 1.27 1.79 2.66 0.66 0.23 2.18 1.38 1.18 1.29 0.92 0.41 0.17 0.77 2.47 0.92 0.84 0.16 0.26 1.00 1.58 1.31 0.86 0.47 0.46 0.40 0.43 0.44 0.37 0.43 0.47 0.32 0.47 0.46 0.50 0.48 0.50 0.50 0.47 0.44 0.48 0.44 0.45 0.38 0.38 0.47 0.46 0.29 0.50 0.47 0.44 0.45 0.36 0.28 0.38 0.50 0.37 6.93 4.61 4.60 15.96 4.00 5.00 3.54 12.73 8.25 1.73 5.20 1.69 3.85 2.56 12.19 3.21 2.42 3.83 12.29 5.40 10.01 4.14 5.34 3.97 6.15 3.46 2.02 1.40 3.01 6.78 6.73 5.48 2.79 5.09 Q1LLG0 50S ribosomal protein L31 type B Q1LLF9 Putative inner membrane transmembrane protein Q1LLF8 MATE efflux family protein Q1LLF6 Patatin Q1LLC3 Translation initiation factor IF-‐1 1 Q1LLC0 Ppx/GppA phosphatase Q1LLA4 Carbamoyl-‐phosphate synthase large subunit Q1LLA3 Lysine exporter protein (LYSE/YGGA) Q1LLA2 Carbamoyl-‐phosphate synthase small subunit Q1LL87 Putative uncharacterized protein Q1LL85 UspA Q1LL33 Putative uncharacterized protein Q1LL32 Putative uncharacterized protein Q1LL31 Putative uncharacterized protein Q1LL24 Fumarase Q1LL23 Glutamate racemase Q1LL11 Putative uncharacterized protein Q1LKZ7 Putative uncharacterized protein Q8GQ48 Putative uncharacterized protein ORF C62 Q8GQ49 Putative uncharacterized protein ORF C61 Q1LKV8 Putative uncharacterized protein A0H9A7 AAA ATPase, central region Q1LKM5 Anti sigma-‐E protein RseA Q1LKL7 50S ribosomal protein L32 Q1LKL6 Putative uncharacterized protein Q1LKK8 GTP cyclohydrolase subunit MoaA Q1LKJ5 Lysine exporter protein (LYSE/YGGA) Q1LKI8 Colicin V production protein Q1LKG5 Succinate dehydrogenase subunit A Q1LKG4 Succinate dehydrogenase subunit D Q1LKG3 Succinate dehydrogenase subunit C Q1LKG2 Putative uncharacterized protein Q1LKA2 Proline hydroxylase-‐like protein Q1LK85 DEAD/DEAH box helicase-‐like protein Rmet_2567 Rmet_2579 Rmet_2618 Rmet_2685 Rmet_2694 ribH Rmet_2704 trmB Rmet_2723 Rmet_2740 pyrB Rmet_2771 Rmet_2796 Rmet_2860 Rmet_2870 rpmB Rmet_2871 rpmG Rmet_2872 nadB Op0711f Op0716r Op0733f 0.61 0.64 0.53 6.69 0.65 0.81 0.45 0.35 0.50 Op0757f Op0759f Op0765f Op0770r Op0772r Op0778r Op0786r Op0804r Op0807f Op0807f Op0807f 0.60 0.57 0.63 0.64 0.66 0.52 0.65 0.76 1.17 0.89 0.71 1.89 3.78 1.24 1.42 1.03 2.46 0.89 0.62 0.14 0.21 1.31 0.43 0.49 0.47 0.45 0.48 0.48 0.43 0.48 0.46 0.45 0.45 Rmet_2873 Rmet_2874 Rmet_2877 Rmet_2882 Rmet_2897 Rmet_2903 Rmet_3050 Rmet_3070 Rmet_3084 Rmet_3085 Rmet_3105 Rmet_3106 Rmet_3108 Rmet_3109 Op0808r Op0808r Op0808r Op0810r Op0815f Op0819f Op0858r Op0861f Op0867f Op0868r Op0874r Op0874r Op0875f Op0875f 0.72 0.57 0.69 0.57 0.61 0.71 0.53 0.89 0.65 0.50 1.14 1.16 0.54 0.66 1.05 1.24 1.14 3.36 0.69 0.83 2.52 0.16 1.16 2.25 0.27 0.72 3.66 1.83 0.44 0.33 0.41 0.49 0.28 0.44 0.49 0.48 0.22 0.16 0.39 0.46 0.47 0.48 Op0875f Op0876r Op0876r 0.73 1.74 0.53 2.60 0.63 1.15 0.46 0.47 0.47 nadC nadA pyrF rdgC rpmA rplU Rmet_3110 Rmet_3114 Rmet_3115 3.40 Q1LK82 Integral membrane protein TerC 3.34 Q1LK70 Pirin-‐like protein 4.31 Q1LK31 Rieske (2Fe-‐2S) region Q1LJW8 Putative type 4 fimbrial biogenesis PilY1-‐related 3.13 protein 3.67 Q1LJV9 6,7-‐dimethyl-‐8-‐ribityllumazine synthase 2.97 Q1LJU9 tRNA (guanine-‐N(7)-‐)-‐methyltransferase 5.13 Q1LJT0 Polysaccharide biosynthesis protein CapD 2.46 Q1LJR3 Aspartate carbamoyltransferase 2.83 Q1LJN2 Putative uncharacterized protein 2.34 Q1LJK7 Uncharacterized protein UPF0065 11.11 Q1LJE3 NAD-‐dependent epimerase/dehydratase 2.41 Q1LJD3 50S ribosomal protein L28 2.37 Q1LJD2 50S ribosomal protein L33 4.39 Q1LJD1 L-‐aspartate oxidase Q1LJD0 Nicotinate-‐nucleotide pyrophosphorylase 5.36 (Carboxylating) 7.74 Q1LJC9 Quinolinate synthetase A 3.26 Q1LJC6 Fmu (Sun) 2.81 Q1LJC1 Putative uncharacterized protein 2.51 Q1LJA6 Putative uncharacterized protein 5.78 Q1LJA0 Putative uncharacterized protein 6.45 Q1LIV4 Orotidine 5'-‐phosphate decarboxylase 3.13 Q1LIT4 17 kDa surface antigen 5.47 Q1LIS0 Putative exonuclease, RdgC 9.60 Q1LIR9 Alcohol dehydrogenase, zinc-‐binding 6.65 Q1LIP9 50S ribosomal protein L27 5.57 Q1LIP8 50S ribosomal protein L21 2.86 Q1LIP6 Type II secretion system protein E 4.04 Q1LIP5 Type II secretion system protein Q1LIP4 Type 4 prepilin peptidase 1. Aspartic peptidase. 7.65 MEROPS family A24A 2.25 Q1LIP0 Oligopeptide transporter OPT 4.33 Q1LIN9 NUDIX hydrolase Rmet_3151 Rmet_3153 Rmet_3154 Rmet_3178 trpE Rmet_3179 trpG Rmet_3200 hemA Rmet_3201 prfA Rmet_3205 ubiX Rmet_3209 Rmet_3252 Rmet_3274 mrcA Rmet_3284 Rmet_3297 secY Rmet_3298 rplO Rmet_3301 rplR Rmet_3302 rplF Rmet_3303 rpsH Rmet_3304 rpsN Rmet_3305 rplE Rmet_3306 rplX Rmet_3307 rplN Rmet_3314 rplB Rmet_3317 rplC Rmet_3324 Rmet_3336 rplJ Rmet_3337 rplA Rmet_3338 rplK Rmet_3339 nusG Rmet_3340 secE Rmet_3346 CMGI-‐10 Rmet_3350 Op0882r Op0883f 0.55 1.92 0.70 1.06 0.38 0.49 Op0884r Op0893f Op0893f Op0901f Op0901f Op0901f Op0903f 0.66 0.66 0.55 0.84 0.64 0.59 0.52 2.07 0.76 7.54 0.39 3.19 1.49 1.47 0.49 0.34 0.43 0.48 0.47 0.46 0.47 Op0918r Op0921f Op0924r Op0926r Op0926r Op0926r Op0926r Op0926r Op0926r Op0926r Op0926r Op0926r Op0926r Op0926r Op0928r Op0930r Op0930r Op0930r Op0930r Op0930r Op0932r Op0932r 0.70 0.63 0.88 0.85 0.91 0.95 0.61 0.89 1.32 1.51 0.96 0.82 1.25 1.07 1.30 0.99 0.92 1.17 1.02 0.90 0.71 0.63 1.44 2.40 0.37 0.21 0.11 0.05 0.51 0.12 0.28 0.44 0.04 0.29 0.23 0.08 0.29 0.02 0.16 0.19 0.04 0.63 0.75 1.28 0.49 0.46 0.48 0.48 0.49 0.48 0.37 0.44 0.46 0.44 0.28 0.26 0.50 0.46 0.43 0.48 0.43 0.39 0.37 0.45 0.43 0.43 12.48 Q1LIK3 Molybdopterin oxidoreductase 2.33 Q1LIK1 Extracellular ligand-‐binding receptor Q1LIK0 Oligopeptide/dipeptide ABC transporter, ATP-‐ 2.94 binding protein 2.79 Q1LIH6 Anthranilate synthase, component I 37.90 Q1LIH5 Anthranilate synthase, component II 3.10 Q1LIF4 Glutamyl-‐tRNA reductase 6.55 Q1LIF3 Peptide chain release factor 1 1.72 Q1LIE9 3-‐octaprenyl-‐4-‐hydroxybenzoate carboxy-‐lyase 3.36 Q1LIE5 Transcriptional regulator, AsnC family Q1LIA2 ABC-‐type multidrug transport system permease 3.38 component 2.87 Q1LI80 Penicillin-‐binding protein 1A 6.82 Q1LI70 Cytochrome c, class I 4.13 Q1LI57 Preprotein translocase secY subunit 5.47 Q1LI56 50S ribosomal protein L15 4.50 Q1LI53 50S ribosomal protein L18 6.95 Q1LI52 50S ribosomal protein L6 7.95 Q1LI51 30S ribosomal protein S8 4.68 Q1LI50 SSU ribosomal protein S14P 5.27 Q1LI49 50S ribosomal protein L5 6.66 Q1LI48 50S ribosomal protein L24 8.11 Q1LI47 50S ribosomal protein L14 4.25 Q1LI40 50S ribosomal protein L2 2.90 Q1LI37 50S ribosomal protein L3 10.18 Q1LI13 Elongation factor Tu 4.10 Q1LI18 50S ribosomal protein L10 7.16 Q1LI17 50S ribosomal protein L1 5.33 Q1LI16 50S ribosomal protein L11 7.51 Q1LI15 Transcription antitermination protein nusG 8.54 Q1LI14 Protein translocase subunit secE/sec61 gamma 8.28 Q1LI08 UspA 3.69 Q1LI04 Putative uncharacterized protein Rmet_3353 Rmet_3380 Rmet_3381 gspC Rmet_3396 Rmet_3426 Rmet_3427 Rmet_3428 Rmet_3480 gcvT Rmet_3545 Rmet_3612 Rmet_3614 Rmet_3617 Rmet_3618 Rmet_3620 Rmet_3621 Rmet_3622 Rmet_3624 Rmet_3626 Rmet_3678 Rmet_3680 Rmet_3683 Rmet_3689 cheA Rmet_3690 cheW Rmet_3692 Rmet_3695 Rmet_3703 Rmet_3721 Rmet_3734 Rmet_3739 cheD cheZ flgB flgG Op0934r 0.67 1.21 0.49 Op0940r Op0940r Op0943f 0.67 0.88 0.59 1.09 0.81 1.13 0.48 0.38 0.49 Op0950r Op0950r Op0950r Op0969f Op0983f Op1004r Op1004r Op1006f Op1007r Op1008f Op1008f Op1009r Op1009r 0.62 0.62 0.60 0.56 0.58 0.66 0.80 0.56 0.52 0.62 0.77 0.74 0.54 2.95 1.76 3.33 1.52 4.20 0.82 0.72 4.10 1.44 2.14 0.97 0.50 4.25 0.49 0.48 0.48 0.43 0.46 0.49 0.49 0.34 0.27 0.39 0.49 0.35 0.43 Op1009r Op1026f 0.56 2.68 0.51 1.67 0.41 0.46 Op1026f Op1026f Op1026f Op1026f 0.54 0.50 0.61 0.52 2.80 1.72 2.19 2.24 0.44 0.42 0.49 0.49 Op1026f Op1026f Op1026f Op1035r Op1042f Op1042f 0.62 0.57 0.51 0.56 0.51 0.51 1.72 2.38 1.93 1.60 1.03 1.25 0.50 0.50 0.47 0.49 0.33 0.41 20.36 Q9F8S6 Transposase (Transposase, IS4 family) Q1LHX4 Putative signal transduction protein with EFhand 3.47 domain 4.27 Q1LHX3 Putative uncharacterized protein 12.24 Q1LHV8 Pyruvate ferredoxin/flavodoxin oxidoreductase Q1LHS8 Sulfide dehydrogenase (Flavocytochrome), 10.10 flavoprotein subunit 4.69 Q1LHS7 Cytochrome c, class I 2.79 Q1LHS6 Transport-‐associated 3.74 Q1LHM4 Aminomethyltransferase 3.69 Q1LHF9 UMUC-‐like DNA-‐repair protein 0.95 Q1LH92 Methyltransferase type 11 4.64 Q1LH90 UPF0161 protein Rmet_3614 5.76 Q1LH87 Excinuclease ABC, C subunit-‐like protein 4.44 Q1LH86 OsmC-‐like protein 36.02 Q1LH84 Peptidase S1C, Do 3.85 Q1LH83 Putative uncharacterized protein 5.41 Q1LH82 Major facilitator superfamily MFS_1 4.38 Q1LH80 Transglutaminase-‐like protein Q1LH78 ATPase associated with various cellular activities, 4.35 AAA_3 3.47 Q1LH26 Methyl-‐accepting chemotaxis sensory transducer Q1LH24 Response regulator receiver domain protein 8.51 (CheY-‐like) 2.95 Q1LH21 Methyl-‐accepting chemotaxis sensory transducer 3.26 Q1LH15 CheA signal transduction histidine kinases 7.65 Q1LH14 CheW protein Q1LH12 Probable chemoreceptor glutamine deamidase 4.13 cheD 2.96 Q1LH09 Chemotaxis phosphatase, CheZ 1.86 Q1LH01 Flagellar FlhE 3.11 Q1LGY3 Uncharacterized protein UPF0065 4.84 Q1LGX0 Flagellar basal-‐body rod protein FlgB 3.53 Q1LGW5 Flagellar basal-‐body rod FlgG Rmet_3740 flgH Op1042f 0.51 1.72 0.45 Rmet_3742 Rmet_3894 Rmet_3904 Rmet_4119 Rmet_4127 Rmet_4199 Rmet_4206 Rmet_4245 Rmet_4246 Rmet_4426 Rmet_4433 Rmet_4464 Rmet_4466 Rmet_4524 Rmet_4561 Rmet_4565 Rmet_4566 Rmet_4592 Rmet_4594 Rmet_4602 Op1042f Op1086f Op1092f Op1160f Op1163r Op1190f Op1192f Op1202f #NV Op1259r Op1262f Op1273r Op1274f Op1297r Op1311r Op1314f Op1315r Op1320f Op1321r Op1324f 0.51 0.72 0.54 0.60 0.66 0.59 0.61 0.56 0.71 0.65 0.55 0.62 0.50 0.54 0.55 0.58 0.62 0.52 0.58 0.51 2.12 0.82 1.58 1.37 0.70 16.36 2.70 5.31 2.28 2.13 2.83 1.60 3.33 1.55 2.55 2.13 2.06 6.40 2.41 3.64 0.46 0.48 0.44 0.21 0.42 0.48 0.48 0.41 0.44 0.50 0.49 0.48 0.49 0.38 0.42 0.25 0.30 0.42 0.48 0.46 Op1333r Op1386f Op1388f Op1396f Op1398f Op1400f Op1419r Op1427r Op1431r Op1455r Op1460f 0.51 0.53 0.63 0.64 0.61 0.55 1.90 0.54 0.63 0.52 0.61 3.99 1.16 3.62 1.64 2.18 1.48 2.95 1.69 3.12 1.47 1.15 0.50 0.45 0.39 0.50 0.50 0.49 0.49 0.49 0.47 0.48 0.45 Rmet_4627 Rmet_4761 Rmet_4775 Rmet_4802 Rmet_4806 Rmet_4809 Rmet_4864 Rmet_4880 Rmet_4893 Rmet_4954 Rmet_4975 flgJ czcS2 zntA acpA 2.77 Q1LGW4 Flagellar L-‐ring protein Q1LGW2 Mannosyl-‐glycoprotein endo-‐beta-‐N-‐ 7.29 acetylglucosamidase 1.49 Q1LGG4 Putative uncharacterized protein 1.68 Q1LGF4 Putative serine protein kinase, PrkA 8.14 Q1LFU0 Putative uncharacterized protein 8.42 Q1LFT2 Putative uncharacterized protein 5.57 Q1LFL0 FAD-‐binding 9, siderophore-‐interacting 4.82 Q1LFK3 Transcriptional regulator, LysR family 6.34 Q1LFG5 Transcriptional regulator, LysR family 4.58 Q1LFG4 Putative uncharacterized protein 3.24 Q1LEY5 MmgE/PrpD family protein 2.65 Q1LEX8 Uncharacterized protein UPF0065 2.68 Q1LEU7 Putative uncharacterized protein 11.93 Q1LEU5 Sensor protein 6.02 Q1LEN7 Negative transcriptional regulator 1.82 Q1LEK3 Transcriptional regulator, AsnC family 1.34 Q1LEJ9 TonB-‐dependent receptor 1.35 Q1LEJ8 Putative uncharacterized protein 3.91 Q1LEH2 NAD-‐dependent epimerase/dehydratase 3.72 Q1LEH0 Heavy metal translocating P-‐type ATPase 6.10 Q1LEG2 Transcriptional regulators, TraR/DksA family Q1LED7 Two component transcriptional regulator, LuxR 2.43 family 5.60 Q1LE03 Putative uncharacterized protein 8.91 Q1LDY9 Extracellular ligand-‐binding receptor 3.11 Q1LDW2 Putative uncharacterized protein 8.75 Q1LDV8 Transcriptional regulator, XRE family 2.12 Q1LDV5 Phosphoesterase 1.08 Q1LDQ0 Putative uncharacterized protein 21.77 Q1LDN4 Transcriptional regulator, LysR family 2.94 Q1LDM1 Putative uncharacterized protein 2.65 Q1LDG0 Transcriptional regulator, GntR family 4.34 Q1LDD9 Resolvase-‐like protein Rmet_4976 Rmet_5005 Rmet_5006 Rmet_5076 Rmet_5077 Rmet_5080 Rmet_5081 Rmet_5140 Rmet_5213 Rmet_5297 Rmet_5301 Rmet_5344 Rmet_5385 Rmet_5427 Rmet_5475 Rmet_5507 Rmet_5534 Rmet_5547 Rmet_5549 Rmet_5572 Rmet_5594 Rmet_5642 Rmet_5686 Rmet_5763 Rmet_5785 Rmet_5816 Rmet_5846 Rmet_5862 Rmet_5868 Rmet_5935 Rmet_6068 Rmet_6335 fliP fliD3 leuC Op1461r Op1469r Op1469r Op1494f Op1495r Op1496f Op1496f Op1515r Op1535r Op1566f Op1566f Op1586f Op1602f Op1614f Op1626f Op1639r Op1645r Op1647r Op1648f Op1657r Op1666f Op1683r Op1698f Op1728f Op1740f Op1756f Op1766f Op1773r Op1777r Op1804f Op1849r 0.60 0.66 0.66 0.56 0.57 0.71 0.53 0.52 0.64 0.58 0.51 0.79 0.59 0.50 0.55 0.52 0.51 0.51 0.51 0.53 0.54 0.50 0.60 0.51 0.53 0.68 0.52 0.52 0.59 0.53 0.51 1.60 1.66 1.94 7.04 2.56 2.01 4.06 1.89 1.92 1.77 3.99 1.25 4.51 1.52 2.25 2.25 3.68 2.26 2.69 1.26 1.97 2.45 1.33 3.31 1.93 0.70 4.86 8.19 1.52 10.26 1.50 0.47 0.46 0.43 0.42 0.32 0.49 0.49 0.43 0.44 0.37 0.47 0.49 0.34 0.47 0.46 0.44 0.41 0.50 0.50 0.44 0.45 0.44 0.44 0.48 0.48 0.33 0.44 0.47 0.45 0.42 0.48 Op1926f 0.54 1.79 0.48 9.15 5.36 7.67 4.24 6.70 2.76 5.25 4.10 4.04 3.64 2.44 1.75 6.40 2.21 2.86 6.69 2.13 3.19 2.44 3.56 3.06 3.92 6.80 5.31 2.54 6.38 3.70 6.21 6.10 4.74 4.87 Q1LDD8 Putative uncharacterized protein Q1LDA9 Isochorismatase hydrolase Q1LDA8 Putative uncharacterized protein A5FF57 Sulfatase A5FF57 Sulfatase Q1LD37 Putative uncharacterized protein Q1LD36 Putative uncharacterized protein Q1LCX7 AMP-‐dependent synthetase and ligase Q1LCQ4 Transcriptional regulator, GntR family Q1LCH0 Flagellar basal body-‐associated protein FliL Q1LCG6 Flagellar biosynthetic protein FliP Q1LCC3 Putative uncharacterized protein Q1LC82 Putative uncharacterized protein Q1LC40 Putative uncharacterized protein Q1LBZ2 Putative uncharacterized protein Q1LBW0 Acyl-‐CoA dehydrogenase-‐like protein Q1LBT3 2-‐nitropropane dioxygenase, NPD Q1LBS0 Transcriptional regulator, LuxR family Q1LBR8 Ferredoxin Q1LBP5 Dyp-‐type peroxidase Q1LBM3 Putative uncharacterized protein Q1LBH5 Flagellar hook-‐associated 2-‐like protein Q1LBD1 Tfp pilus assembly protein PilV-‐like protein Q1LB54 Putative uncharacterized protein Q1LB32 Putative uncharacterized protein Q1LB01 Cold-‐shock DNA-‐binding protein family Q1LAX1 Putative uncharacterized protein Q1LAV5 Putative signal peptide protein Q1LAU9 3-‐isopropylmalate dehydratase, large subunit Q1LAN2 Methyl-‐accepting chemotaxis sensory transducer Q58AB4 ISRme8aa1 (Transposase IS3/IS911) Q5NUU4 ISRme2 transposase protein (Integrase, catalytic 11.39 region) aCells of strain ∆zupT and its parent AE104 were confronted with 50 µM EDTA or 10 µM zinc chloride until the turbidity reached 100 Klett units, RNA was isolated, reversely transcribed, labeled and hybridized against a CH34-specific gene array. Provided are the Qratios ∆zupT/AE104 for both treatments, red if at least 2-fold down-regulated, green up, bold-faced letters indicate significant differences, letters in italics not significant differences. The D-value for each comparison is also given. This is the distance of both mean values divided by the sum of both deviations. If D>1 the deviation bars do not touch or overlap) the data points are different with a probability in the t-test of > 95%. Three biological repeats for AE104, two for the mutant strain. Genes associated to catabolic metabolic genomic islands (CMGIs) are on a yellow ground and in a box. bAn operon region was defined as adjacent genes in the same direction of transcription without interruption and all genes of the C. metallidurans genome were assigned to operon regions Op0001f on chromosome 1 to Op1929r on pMOL28 with “f” or “r” giving the direction of transcription. Supplementary Table S5. Activity of zupTp and cobW1p promoters as determined with a gfp fusion in trans in various C. metallidurans strainsa. Basal [EDTA] , (µM) 0 1 10 25 50 100 250 500 1000 AE104 2.07 ∆zupT 10.15 1 0.98 1.12 1.14 1.62 2.01 2.63 2.92 2.78 1.00 0.99 1.08 1.09 1.14 1.17 1.23 1.23 1.37 zupTp-gfp ∆e4 ∆e4 ∆zupT 1.72 3.73 1.00 1.00 1.01 1.07 1.55 2.44 3.50 3.75 4.12 1.00 0.98 1.18 1.24 1.26 1.44 1.64 1.73 1.84 ∆zur CH34 7.21 1.89 1.00 0.95 1.03 1.03 1.02 1.02 1.02 1.01 0.96 1.00 0.97 0.94 0.98 1.46 1.81 2.51 2.72 2.63 AE104 ∆zupT 0.81 1.11 1.00 0.94 0.92 0.95 1.06 1.20 1.82 2.76 2.67 1.00 1.02 1.14 1.19 1.30 1.49 1.91 2.61 2.53 cobW1p-gfp ∆e4 ∆e4 ∆zupT 0.74 1.48 1.00 0.88 0.83 0.85 1.01 1.19 1.91 2.89 3.27 1.00 1.08 1.85 1.98 1.97 2.21 2.21 2.18 2.01 ∆zur CH34 5.90 0.87 1.00 0.95 0.95 0.97 0.98 0.97 0.98 0.96 0.93 1.00 0.98 0.97 1.00 0.99 1.20 1.97 3.04 3.16 Basal 2.33 9.66 2.10 3.51 6.51 1.40 0.80 1.15 0.75 1.83 4.97 0.62 [Zn(II)], (µM) 0 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 5 0.95 0.57 0.73 0.49 0.94 0.87 0.89 0.59 0.86 0.35 0.93 0.96 10 0.93 0.48 0.84 0.53 0.90 0.80 0.84 0.60 0.86 0.39 0.94 1.02 25 0.89 0.40 0.98 0.65 0.90 0.76 0.83 0.57 0.95 0.58 1.00 0.91 50 0.88 0.40 1.00 0.68 0.92 0.79 0.83 0.58 1.08 0.53 1.08 0.84 75 0.84 0.41 0.92 0.68 0.88 0.82 0.85 0.70 1.22 0.43 1.07 0.79 100 0.82 0.42 0.82 0.63 0.86 0.81 0.92 0.71 0.98 0.35 0.95 0.61 150 0.80 0.40 0.76 0.66 0.85 0.81 0.91 0.71 0.83 0.32 0.95 0.77 250 0.78 0.42 0.71 0.65 0.85 0.87 0.97 0.72 0.78 0.33 0.99 0.83 500 0.83 0.46 0.71 0.68 0.90 0.90 1.09 0.77 0.66 0.35 0.97 0.87 750 1.01 0.45 0.69 0.64 1.03 0.87 1.27 0.78 0.78 0.35 0.96 0.99 1000 0.97 0.46 0.72 0.64 1.05 0.93 1.05 0.70 0.82 0.33 0.90 1.20 A gfp fusion plasmid was constructed on the basis of plasmid pBBR_MCS2 and designated pBBR-GFP13. Fragments containing the promoter regions of zupT and cobW1 were cloned upstream of the promoterless gfp gene). The resulting plasmids were transferred by conjugation into the C. metallidurans strains CH34 wild type, its plasmid-free derivative AE104, and the AE104 mutants ∆zupT, ∆e4 (∆zntA ∆cadA ∆fieF ∆dmeF), ∆e4 ∆zupT, and ∆zur (= ∆furC). The negative control contained just plasmid pBBR-GFP13. The cells were incubated in TMM containing various concentrations of EDTA or zinc chloride and the specific activity of the GFP fluorescence was calculated in nmol per µg dry weight. There was no difference of the specific activities from the negative controls, which always gave 11.27±3.97 nmol/µg. To obtain the basal expression levels, the specific fluorescence activity coming from the promoter fusions were divided by this background value coming from the negative controls and the D-value was calculated as a measure of significance (D = absolute distance of the mean values divided by the sum of the deviations, if D>1, the differences are significant if n ≥ 3). Bold basal values indicate D > 1, green and bold values additionally a ratio > 2. Since the values resulting from cultures incubated without added zinc should be similar to those coming from cultures without added EDTA, another control for the integrity of the data was obtained. Secondly, all values coming from cultures with added zinc or EDTA were compared to the respective basal levels, indicating up- or down-regulation. Again, D > 1 is indicated by bold-faced numbers, green means more than 2-fold up-regulation and red more than 2-fold down-regulation with respect to the associated basal level value obtained for TMM without additions. Repeats (n) between 3 and 14. Supplementary Figure S1. Comparison of transcriptome and proteome data. The spot densities from a gene array experiment with strain AE104 cells (n = 3, overall density of the array normalized to 10,000 arbitrary gene-specific and intergenic RNAs per cell) cultivated in TMM without additions were compared to the number of proteins per cell obtained from the same strain cultivated under the same conditions. Deviation bars for both axis are given. The position of a few proteins versus their gene array signals are labeled.
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