TABLE 2.
Analysis of positive fusions
| Fusion | Pfluc | COG | Best hitd | PAO1 match (% identity, % positive substitutions)e |
|---|---|---|---|---|
| Nutrient utilization | ||||
| iiv3 | Pflu5341 | COG0318, acyl-CoA synthetases (AMP-forming)/AMP-acid ligases | Putative ligase; Bordetella parapertussis; E = e−138 | PA3300 (29, 45) |
| iiv11 | Pflu5302 | COG0726, predicted xylanase/chitin deacetylase | Putative saccharide deacetylase; Sinorhizobium meliloti; E = 2e−29 | PA1517 (26, 40) |
| Transport | ||||
| iiv6b | Pflu4867 | COG3633, Na+/serine symporter | Sodium-dicarboxylate symporter family; P. putida KT2440; E = 0.0 | PA2042 (80, 87) |
| iiv15 | Pflu4596 | COG1457, purine-cytosine permease and related proteins | Cytosine/purine/uracil/thiamine/allantoin permease, P. putida KT2440; E = e−174 | PA5099 (35, 53) |
| iiv18 | Pflu5167 | COG3451, type IV secretory pathway, VirB4 components | Conserved hypothetical protein with VirB4 domain; P. putida; E = 0.0 | |
| iiv20a | Pflu0451 | COG0477, permeases of the major facilitator superfamily | Permeases of the major facilitator superfamily; P. syringae pv. syringae; B728a; E = 0.0 | PA0229 (75, 84) |
| Regulation | ||||
| iiv7a | Pflu4942 | COG0642, signal transduction histidine kinase | Signal transduction histidine kinase; Burkholderia fungorum; E = e−121 | PA4886 (45, 62) |
| iiv9a | Pflu2333 | COG1167, MocR family transcriptional regulators | COG1167: transcriptional regulator; P. syringae pv. syringae B728a; E = 0.0 | PA1654 (80, 88) |
| Detoxification and metabolism | ||||
| iiv17 | Pflu4220 | COG0604, NADPH quinone reductase and related Zn-dependent oxidoreductases | Putative oxidoreductase; Streptomyces avermitilis MA-4680; E = e−108 | PA3567 (31, 48) |
| iiv21 | Pflu1840 | COG0315, molybdenum cofactor biosynthesis enzyme | Molybdopterin biosynthetic protein C; P. aeruginosa; E = 5e−60 | PA3918 (75, 86) |
| Hypothetical | ||||
| iiv2 | Pflu5100 | None | None | None |
| iiv24 | None | None | Hypothetical protein; P. putida KT2440; E = 5e−19 | None |
a
This fusion was isolated twice in the IVET screen for soil-induced promoters.
b
The fusion is likely to contain the promoter for Pflu4867. None of this ORF is present in the fusion.
c
Pflu numbers are the NCBI designations for genes identified in the NCBI annotation of the Pf0-1 genome.
d
Database searches were carried out by using Blastx, with the Pflu sequences as queries. Best hit excluding matches to Pf0-1 is shown.
e
Closest match in the P. aeruginosa PA01 genome sequence (http://www.pseudomonas.com).