Table 2. Reactions with predicted median flux ratio change of at least 2-fold in biofilm cultures compared to stationary cultures.
| Reaction name | Reaction | Genes | GE ratio a | Flux ratio b | ||
|---|---|---|---|---|---|---|
| Median | Min. | Max. | ||||
| Down-regulated | ||||||
| HHQ synthesis c | 3oxdeACP + anth + h = > ACP + co2 + h2o + hhq | pqsABCD | 0.60 | 0.47 | 0.33 | 0.79 |
| Probable FAD-dependent monooxygenase (PQS synthesis) c | fadh2 + hhq + o2 = > fad + h2o + pqs | pqsH | 0.99 | 0.47 | 0.33 | 0.79 |
| Acyl-ACP:malonyl-ACP C-acyltransferase (decarboxylating) | acACP + h + malACP = > ACP + actACP + co2 | fabB or fabF1 or PA5174 | 0.75 | 0.44 | 0.25 | 0.77 |
| Glutamine transaminase | glu-L + pydx5p = > akg + pyam5p | glyA1 or glyA2 | 0.22 | 0.18 | 0.15 | 0.34 |
| Alanine transaminase | ala-L + pydx5p = > pyam5p + pyr | glyA1 or glyA2 or glyA3 | 0.37 | 0.29 | 0.24 | 0.57 |
| 3-deoxy-D-manno-octulosonic acid transferase | PA_lipidA + ckdo = > PA_KDOlipidA + cmp + h | waaA | 1.13 | 0.23 | 0.08 | 0.74 |
| Phosphate transport via ABC system | atp + h2o + pi[e] = > adp + h + 2 pi | pstABCS | 0.24 | 0.27 | 0.25 | 0.34 |
| L-serine deaminase | ser-L < = > nh4 + pyr | sdaAB | 0.45 | 0.28 | 0.09 | 0.43 |
| O-succinylhomoserine lyase (H2S) | h2s + suchms = > hcys-L + succ | metZ | 0.58 | 0.44 | 0.35 | 0.57 |
| Up-regulated | ||||||
| Psl synthesis c | 3 gdpman + udpg + dtdp6dm = > psl[e] + 3 gdp + udp + dtdp | pslACDEFGHIJKL | 0.88 | 2.87 | 1.22 | 6.86 |
| Anthranilate 1,2-dioxygenase | anth + nadph + 2 h + o2 = > catechol + co2 + nadp + nh3 | antA | 5.64 | 2.48 | 1.90 | 6.01 |
| 3-oxoadipyl-CoA thiolase | coa + oxadpcoa = > accoa + succoa | pcaF | 1.93 | 2.06 | 1.32 | 3.24 |
| Catechol 1,2-dioxygenase | catechol + o2 = > muc | catA | 4.30 | 2.48 | 1.90 | 6.01 |
| 3-oxoadipate enol-lactonase | 5odhf2a + h2o < = > 3oxadp + h | pcaD | 3.16 | 2.06 | 1.32 | 3.24 |
| 3-oxoadipate CoA-transferase | 3oxadp + succoa < = > oxadpcoa + succ | dhcAB | 0.92 | 2.06 | 1.32 | 3.24 |
| NAD(P) transhydrogenase | 2 h[e] + nadh + nadp < = > 2 h + nad + nadph | pntAA and pntB | 1.12 | 3.51 | 1.99 | 4.88 |
| Isochorismate synthase | chor = > ichor | pchA | 6.24 | 3.91 | 3.46 | 4.22 |
| Isochorismate-pyruvate lyase | ichor = > sal + pyr | pchB | 7.86 | 3.91 | 3.46 | 4.22 |
| Pyochelin synthesis pchE | cys-L + atp = > cysamp + ppi | pchE | 8.97 | 3.91 | 3.46 | 4.22 |
| Pyochelin synthesis pchD | sal + atp + h = > salamp + ppi | pchD | 3.30 | 3.91 | 3.46 | 4.22 |
| Pyochelin synthesis pchDG | salamp + cysamp = > hpthiazoline + 2 amp + h2o + h | pchDG | 2.73 | 3.91 | 3.46 | 4.22 |
| Pyochelin synthesis pchEF | hpthiazoline + cysamp = > hpbthiazoline + amp + h2o + h | pchEF | 3.86 | 3.91 | 3.46 | 4.22 |
| Pyochelin synthesis pchGF | hpbthiazoline + nadph + h = > dmpyochelin + nadp | pchGF | 1.94 | 3.91 | 3.46 | 4.22 |
| Pyochelin synthesis pchF | dmpyochelin + amet + h2o = > pyochelin + ahcys + 3 h | pchF | 1.66 | 3.91 | 3.46 | 4.22 |
a GE ratio, gene expression ratio between biofilm and stationary planktonic conditions.
b The median, minimum (Min.), and maximum (Max.) values of the flux ratio of each reaction in the set of simulations carried out using each member of the ensemble of flux distributions.
c Biofilm-related reaction with considerable flux change but no significant gene expression changes.