TABLE 2.
Top 30 most abundant proteins in the vesicle soluble fraction of D. shibae
| Locus tag | Functiona | Subcellular localizationb | Functional category | riBAQc |
||
|---|---|---|---|---|---|---|
| Meand | SD | % | ||||
| Dshi_3361 | Flagellin | Secreted/released | Cell motility | 6.85E−02 | 1.23E−02 | 6.85 |
| Dshi_2138 | Hypothetical protein | Periplasmic protein | Hypothetical protein | 3.50E−02 | 1.60E−03 | 3.50 |
| Dshi_3025 | OmpA/MotB domain protein | OM lipoprotein | Not assigned | 3.03E−02 | 6.74E−03 | 3.03 |
| Dshi_1195 | TRAP transporter solute receptor | Periplasmic protein | Transporter | 3.03E−02 | 9.96E−03 | 3.03 |
| Dshi_2021 | Putative binding protein component of ABC iron transporter | OM-associated/OM β-barrel protein | Iron metabolism | 2.51E−02 | 6.16E−03 | 2.51 |
| Dshi_1111 | Tol-Pal system beta propeller repeat TolB | OM-associated/OM β-barrel protein | Lipid metabolism and cell wall/membrane/envelope biogenesis/integrity | 2.24E−02 | 3.07E−03 | 2.24 |
| Dshi_0318 | Glutamate/glutamine/aspartate/asparagine ABC transporter | Periplasmic protein | Transporter | 2.20E−02 | 5.41E−03 | 2.20 |
| Dshi_2832 | Hypothetical protein | OM lipoprotein | Hypothetical protein | 1.53E−02 | 9.27E−04 | 1.53 |
| Dshi_2784 | Hypothetical protein | OM lipoprotein | Hypothetical protein | 1.44E−02 | 4.66E−03 | 1.44 |
| Dshi_0924 | Sporulation domain protein | OM lipoprotein | Not assigned | 1.29E−02 | 1.46E−03 | 1.29 |
| Dshi_0563 | Iron-regulated protein | Periplasmic protein | Iron metabolism | 1.20E−02 | 5.76E−03 | 1.20 |
| Dshi_1112 | Peptidoglycan-associated lipoprotein | OM lipoprotein | Lipid metabolism and cell wall/membrane/envelope biogenesis/integrity | 1.19E−02 | 8.53E−04 | 1.19 |
| Dshi_1443 | TRAP transporter solute receptor | Periplasmic protein | Transporter | 1.10E−02 | 2.72E−03 | 1.10 |
| Dshi_1299 | OmpW family protein | OM β-barrel protein | Not assigned | 1.07E−02 | 3.87E−03 | 1.07 |
| Dshi_3872 | Hemolysin-type calcium-binding repeat protein | Secreted/released | Not assigned | 9.83E−03 | 5.91E−03 | 0.98 |
| Dshi_2673 | Quinoprotein ethanol dehydrogenase precursor | Periplasmic protein | Carbon and energy metabolism | 9.59E−03 | 1.14E−03 | 0.96 |
| Dshi_3254 | Flagellar basal body L-ring protein | OM lipoprotein | Cell motility | 9.45E−03 | 2.06E−03 | 0.94 |
| Dshi_1128 | OmpA/MotB domain protein | OM lipoprotein | Not assigned | 9.43E−03 | 2.22E−03 | 0.94 |
| Dshi_1522 | Putative periplasmic ligand-binding protein | Periplasmic protein | Transporter | 9.42E−03 | 3.07E−03 | 0.94 |
| Dshi_1622 | Putative hemolysin precursor | Secreted/released | Not assigned | 9.37E−03 | 3.33E−03 | 0.94 |
| Dshi_1483 | Conserved hypothetical protein | OM lipoprotein | Hypothetical protein | 9.19E−03 | 1.59E−03 | 0.92 |
| Dshi_3402 | Neutral zinc metallopeptidase | Secreted/released | Protein fate | 8.99E−03 | 3.61E−03 | 0.90 |
| Dshi_2763 | Hypothetical protein | Intracellular protein | Hypothetical protein | 8.94E−03 | 3.35E−03 | 0.89 |
| Dshi_2343 | Hypothetical protein | OM-associated/OM β-barrel protein | Hypothetical protein | 8.93E−03 | 1.82E−03 | 0.89 |
| Dshi_1564 | Hypothetical protein | OM lipoprotein | Hypothetical protein | 7.91E−03 | 2.69E−03 | 0.79 |
| Dshi_3153 | TRAP transporter, DctP subunit | Periplasmic protein | Transporter | 7.85E−03 | 1.37E−03 | 0.79 |
| Dshi_0872 | Extracellular solute-binding protein family 5 | Periplasmic protein | Transporter | 7.79E−03 | 2.35E−03 | 0.78 |
| Dshi_0274/Dshi_0223 | Translation elongation factor Tu | Intracellular protein | Translation | 7.14E−03 | 2.36E−03 | 0.71 |
| Dshi_0628 | Basic organic compound ABC-transporter | Periplasmic protein | Transporter | 6.94E−03 | 2.72E−03 | 0.69 |
| Dshi_2780 | Hypothetical protein | OM lipoprotein | Hypothetical protein | 6.81E−03 | 1.59E−03 | 0.68 |
a
Description of the gene products based on the D. shibae DFL 12, DSM 16493 genome annotation (NCBI as of 9 May 2018).
b
Subcellular localization of the identified proteins predicted using LocateP v2. OM, outer membrane.
c
riBAQ, relative intensity-based absolute quantification, a normalized measure of molar abundance of a protein calculated by dividing the protein’s iBAQ value by the sum of all noncontaminant iBAQ values of a given sample.
d
The means from three biological replicates are presented.