Table 2.
Presence of outer membrane biomarkers in genomes of Verrucomicrobia.
| Verrucomicrobia | Lipopolysaccharide insertion |
OMP insertion and presence |
TonB system |
||
|---|---|---|---|---|---|
| LptD (accession; E-value; identity) | BamA (accession; E-value; identity) | No. of predicted OMP | TonB (accession; E-value; identity) | No. of predicted TonB-dependent receptors OMPdb (HHomp) | |
| Chthoniobacter flavus | ZP_03128876.1 | ZP_03131538.1 | 52 | ZP_03129142.1 | 1 (1) |
| 8E−26; 22% | 5E−41; 26% | 5E−171; 100% | |||
| Methylacidiphilum infernorum V4 | YP_001938690.1 | YP_001939404.1 | 21 | YP_001940656.1 | 3 (3) |
| 4E−12; 31% | 5E−57; 25% | 8E−20 46% | |||
| Pedosphaera parvula Ellin514 | ZP_03630175.1 | ZP_03629305.1 | 41 | ZP_03632618.1 | 2 (2) |
| 3E−28; 23% | 3E−47; 24% | 7E−16; 46% | |||
| Akkermansia muciniphila | YP_001878042.1 | YP_001877660.1 | 20 | YP_001877830.1 | 2 (2) |
| 9E−12; 23% | 1E−42; 26% | 1E−06; 35% | |||
| Opitutus terrae | YP_001820719.1 | YP_001819216.1 | 59 | YP_001820716.1 | 16 (16) |
| 4E−09; 23% | 2E−39; 22% | 1E−15; 41% | |||
| Coraliomargarita akajimensis | YP_003548125.1 | YP_003548772.1 | 46 | YP_003549454.1 | 8 (8) |
| 9E−16; 23% | 3E−45; 28% | 2E−09; 30% | |||
| Verrucomicrobiae bacterium DG1235 | ZP_05056722.1 | ZP_05056601.1 | 68 | ZP_05059160.1 | 23 (23) |
| 3E−05; 22% | 1E−40; 24% | 4E−08; 34% | |||
| Diplosphaera colitermitum TAV2 | – | ZP_03724090.1 | 31 | ZP_03726249.1 | 4 (4) |
| 1E−39; 28% | 3E−07; 39% | ||||
| Opitutaceae sp. TAV1 | ZP_09662317.1 | ZP_09664527.1 | 55 | ZP_09664015.1 | 12 (12) |
| 2E−17; 23% | 6E−47; 24% | 1E−10; 38% | |||
| Opitutaceae sp. TAV5 | ZP_09595552.1 | ZP_09595454.1 | 65 | ZP_09594113.1 | 13 (13) |
| 1E−18; 23% | 5E−47; 24% | 1E−10; 38% | |||
| Verrucomicrobium spinosum | ZP_02927846.1 | ZP_02926363.1 | 156 (21)1 | ZP_02926217.13 | 82 (8) |
| 1E−12; 22% | 8E−51; 25% | 0,021; 39% | |||
LptD, BamA, outer membrane proteins (OMP), TonB, and TonB-dependent receptors were detected in all genomes searched, with one exception; LptD in Diplosphaera colitermitum TAV2.
1OMP numbers for these organisms were predicted using BOMP. Numbers between brackets indicate BLAST hits against known OMP.
2The number of TonB receptors was based on BLAST hits to TonB-dependent receptors.
3Although E-value of this hit was below the cutoff of 1 × 10−6 protein is annotated as a TonB family protein.