TABLE 1.
Table1 Potential c-di-GMP receptor proteins by SPR assaya
| Protein ID | Predicted function | Score |
|---|---|---|
| 0328 | ATP-binding cassette, subfamily B, bacterial | 1,860.74 |
| 4172 | Histidine kinase | 1,845.72 |
| 4790 | PAS domain S-box protein | 1,839.60 |
| 1890 | Para-aminobenzoate synthetase | 1,831.15 |
| 4943 | Hypothetical protein | 1,829.90 |
| 3747 (FimX) | GGDEF domain-containing protein | 1,818.89 |
| 1886 | Serine hydrolase | 1,791.40 |
| 3639 (PilZ) | PilZ domain-containing protein (13) | 1,740.59 |
| 0705 | pilR two-component system, NtrC family, response regulator PilR | 1,674.38 |
| 4562 | Two-component system response regulator WspR, GGDEF domain containing protein | 1,643.62 |
| 0155 | GGDEF domain-containing protein | 1,617.86 |
| 1020 | 3-Oxoacyl-[acyl-carrier protein] reductase | 1,594.19 |
| 3049 | Peptide chain release factor 3 | 1,583.60 |
| 0691 | ATP-dependent Clp protease ATP-binding subunit ClpB | 1,562.76 |
| 4875 | GGDEF domain-containing protein | 1,561.41 |
| 3688 | GGDEF domain-containing protein | 1,560.77 |
| 0067 | GGDEF domain-containing protein | 1,557.90 |
| 0770 | Type II secretion system ATPase GspE | 1,547.64 |
| 4029 | GGDEF domain-containing protein | 1,474.64 |
| 4656 | MerR family transcriptional regulator, copper efflux regulator | 1,458.28 |
| 3677 | GGDEF domain-containing protein | 1,390.65 |
| 2512 | PAS domain S-box protein | 1,385.58 |
| 5095 | Two-component system, OmpR family, sensor histidine kinase KdpD | 1,384.01 |
| 1158 | GGDEF domain-containing protein | 1,372.03 |
| 4727 (RpfG) | Two-component system, response regulator RpfG, HD-GYP domain containing protein | 1,369.92 |
| 3810 | Biofilm PGA synthesis N-glycosyltransferase PgaC | 1,364.51 |
| 0820 | Hypothetical protein | 1,357.96 |
| 2762 (LchP) | GGDEF and EAL domain-containing protein | 1,338.04 |
| 1363 | Hypothetical protein | 1,325.54 |
| 0229 | Hypothetical protein | 1,310.95 |
| 0910 | Hypothetical protein | 1,284.18 |
| 4558 | Chemotaxis protein methyltransferase WspC | 1,283.28 |
| 4781 | Molecular chaperone GrpE | 1,255.45 |
| 1583 | Type III secretion protein SctV | 1,242.25 |
| 1157 | LysM peptidoglycan-binding domain-containing protein | 1,224.18 |
| 3498 | Two-component system, NarL family, response regulator YdfI | 1,199.31 |
| 4096 | Hydrophobic/amphiphilic exporter-1 (mainly G-bacteria), HAE1 family | 1,179.93 |
| 0440 | Peptidyl-tRNA hydrolase, PTH1 family | 1,166.91 |
| 2012 | Hypothetical protein | 1,041.79 |
| 1012 | Shape-determining protein MreB and related proteins | 1,041.21 |
| 1632 | GGDEF domain-containing protein | 964.89 |
| 4431 | Hypothetical protein | 902.47 |
| 3194 | DMT family transporter | 854.90 |
| 2535 | Hypothetical protein | 809.27 |
| 2784 | Parallel beta-helix repeat protein | 770.13 |
| 0285 | Type IV pilus assembly protein PilY1 | 747.79 |
| 3928 | N-acetyltransferase | 734.80 |
| 1452 | Fatty acyl CoA synthetase | 732.42 |
| 1252 | Hypothetical protein | 658.70 |
| 4774 | Carbamoyl-phosphate synthase small subunit | 647.30 |
| 2394 | Hydrophobic/amphiphilic exporter-1 (mainly G-bacteria), HAE1 family | 631.31 |
| 0606 | Hypothetical protein | 623.39 |
| 1277 | Citrate-Mg2+:H + or citrate-Ca2+:H + symporter, CitMHS family | 614.70 |
| 3555 | Membrane glycosyltransferase | 600.43 |
| 4468 | Gluconate 2-dehydrogenase subunit 3 family protein | 566.59 |
| 2781 | Hypothetical protein | 530.31 |
| 0381 | GTP-binding protein | 507.00 |
| 0031 | DUF1800 domain-containing protein | 491.73 |
| 4429 | 2,3-Dihydroxybenzoate-AMP ligase | 456.72 |
| 4088 | DUF4189 domain-containing protein | 421.99 |
| 3061 | Xanthine dehydrogenase family protein molybdopterin-binding subunit | 400.97 |
| 1499 | TonB-dependent receptor | 343.01 |
| 4605 | Malate dehydrogenase (quinone) | 331.51 |
| 4739 | TonB-dependent receptor | 299.15 |
| 0463 | Membrane protein | 296.08 |
| 0848 (Clp) | CRP/FNR family transcriptional regulator, cyclic AMP receptor protein (27) | 294.43 |
| 0385 | DUF2127 domain-containing protein | 208.03 |
| 3440 | Hypothetical protein | 176.70 |
a
The putative c-di-GMP binding proteins were captured from the whole-cell lysate of OH11 through SPR assay. The score is the probability that the observed match is a random event. We report scores as −10*LOG10(P), where P is the absolute probability. Therefore, the higher the score, the greater the likelihood of this protein being a c-di-GMP receptor. The gray shading represents known c-di-GMP receptor proteins.