Table 1.
Growth impaired hypothetical proteins.
| VMM INSeq Data | TY INSeq Data | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Locus | Growth phenotype | N | Insertion density | Average read depth | Gene state | N | Insertion density | Average read depth | Gene state | Riley key | Annotation | |
| CORE FUNCTIONAL GENOME HYPOTHETICAL PROTEINS | ||||||||||||
| RL1763 | GI | 2 | 0 | 0 | ES | 2 | 0 | 0 | ES | 0.0.0 | Hypothetical protein | |
| RL2220 | GI | 7 | 0.57 | 29.75 | ES | 7 | 0.57 | 30.25 | ES | 0.0.0 | Hypothetical protein | |
| RL2402 | GI | 13 | 0.46 | 13.5 | GD | 13 | 0.46 | 11.33 | GD | 0.0.0 | Hypothetical protein | |
| RL2581 | GI | 6 | 0 | 0 | ES | 6 | 0.33 | 1.5 | ES | 0.0.0 | Hypothetical protein | |
| RL4714 | GI | 1 | 0 | 0 | ES | 1 | 1 | 2 | GD | 0.0.0 | Hypothetical protein | |
| RL0128 | GI | 8 | 0.13 | 1 | ES | 8 | 0 | 0 | ES | 0.0.1 | Conserved hypothetical protein | |
| RL0393 | GI | 8 | 0.38 | 9.33 | GD | 8 | 0.5 | 4.25 | GD | 0.0.1 | Conserved hypothetical protein | |
| RL0412 | GI | 10 | 0 | 0 | ES | 10 | 0 | 0 | ES | 0.0.1 | Conserved hypothetical protein | |
| RL0548 | GI | 7 | 0 | 0 | ES | 7 | 0.14 | 2 | ES | 0.0.1 | Conserved hypothetical protein | |
| RL0612 | GI | 2 | 0 | 0 | ES | 2 | 0 | 0 | GD | 0.0.1 | Conserved hypothetical protein | |
| RL0620 | GI | 7 | 0 | 0 | GD | 7 | 0 | 0 | GD | 0.0.1 | Conserved hypothetical protein | |
| RL1432 | GI | 5 | 0.2 | 7 | ES | 5 | 0.6 | 4.33 | GD | 0.0.1 | Conserved hypothetical protein | |
| RL1566 | GI | 11 | 0.18 | 5 | ES | 11 | 0 | 0 | ES | 0.0.1 | Conserved hypothetical protein | |
| RL2245 | GI | 8 | 0.13 | 22 | ES | 8 | 0.25 | 30 | GD | 0.0.1 | Conserved hypothetical protein with RimI domain, putative N-acetyltransferase | |
| RL3754 | GI | 6 | 0.17 | 8 | ES | 6 | 0 | 0 | ES | 0.0.1 | Conserved hypothetical protein | |
| RL3757 | GI | 5 | 0.6 | 16 | GD | 5 | 0.4 | 33.5 | ES | 0.0.1 | Conserved hypothetical protein | |
| RL3762 | GI | 14 | 0 | 0 | ES | 14 | 0.07 | 1 | ES | 0.0.1 | Conserved hypothetical exported protein | |
| RL4061 | GI | 10 | 0 | 0 | ES | 10 | 0.3 | 1.67 | GD | 0.0.1 | Conserved hypothetical protein | |
| RL4324 | GI | 1 | 0 | 0 | ES | 1 | 0 | 0 | GD | 0.0.1 | Conserved hypothetical exported protein | |
| RL4434 | GI | 3 | 0 | 0 | ES | 3 | 0 | 0 | GD | 0.0.1 | Conserved hypothetical protein | |
| RL4437 | GI | 8 | 0 | 0 | GD | 8 | 0.13 | 2 | GD | 0.0.1 | Conserved hypothetical protein | |
| RL4733 | GI | 8 | 0 | 0 | ES | 8 | 0 | 0 | ES | 0.0.1 | Conserved hypothetical protein | |
| RL0126 | GI | 8 | 0 | 0 | ES | 8 | 0.13 | 3 | ES | 0.0.2 | Conserved hypothetical protein | |
| RL0144 | GI | 5 | 0 | 0 | ES | 5 | 0 | 0 | ES | 0.0.2 | Conserved hypothetical protein | |
| RL0456A | GI | 4 | 0 | 0 | NE | 4 | 0 | 0 | NE | 0.0.2 | Conserved hypothetical protein | |
| RL0619 | GI | 4 | 0.25 | 1 | GD | 4 | 0.25 | 1 | GD | 0.0.2 | Conserved hypothetical protein | |
| RL0626 | GI | 13 | 0.46 | 12.67 | GD | 13 | 0.62 | 14.25 | GD | 0.0.2 | Conserved hypothetical protein | |
| RL0936 | GI | 30 | 0.07 | 1 | ES | 30 | 0.17 | 2 | GD | 0.0.2 | Conserved hypothetical protein (TPR repeat family) | |
| RL1094 | GI | 17 | 0.12 | 8 | ES | 17 | 0.18 | 5.33 | ES | 0.0.2 | Conserved hypothetical protein | |
| RL1116 | GI | 9 | 0.11 | 18 | ES | 9 | 0.11 | 39 | ES | 0.0.2 | Conserved hypothetical protein | |
| RL1569 | GI | 21 | 0.05 | 1 | ES | 21 | 0.14 | 1 | ES | 0.0.2 | Conserved hypothetical protein | |
| RL1598 | GI | 6 | 0 | 0 | ES | 6 | 0.17 | 1 | GD | 0.0.2 | Conserved hypothetical protein | |
| RL1706 | GI | 3 | 0 | 0 | ES | 3 | 0 | 0 | GD | 0.0.2 | Conserved hypothetical protein in NADH-ubiquinone oxidoreductase region | |
| RL2034 | GI | 8 | 0.5 | 3.75 | GD | 8 | 0.38 | 1 | ES | 0.0.2 | Conserved hypothetical protein | |
| RL2042 | GI | 29 | 0.28 | 8.5 | ES | 29 | 0.17 | 5.4 | GD | 0.0.2 | Conserved hypothetical protein | |
| RL2056 | GI | 5 | 0.2 | 1 | GD | 5 | 0.2 | 2 | GD | 0.0.2 | Conserved hypothetical protein | |
| RL2207 | GI | 6 | 0.17 | 1 | ES | 6 | 0.17 | 2 | GD | 0.0.2 | Conserved hypothetical protein | |
| RL2232 | GI | 11 | 0.09 | 1 | ES | 11 | 0 | 0 | ES | 0.0.2 | Conserved hypothetical protein | |
| RL2584 | GI | 9 | 0 | 0 | ES | 9 | 0.11 | 2 | ES | 0.0.2 | Conserved hypothetical protein | |
| RL2697 | GI | 5 | 0.2 | 21 | ES | 5 | 0.2 | 22 | ES | 0.0.2 | Conserved hypothetical exported protein | |
| RL3259 | GI | 1 | 0 | 0 | NE | 1 | 0 | 0 | NE | 0.0.2 | Conserved hypothetical protein | |
| RL3314 | GI | 8 | 0 | 0 | ES | 8 | 0 | 0 | ES | 0.0.2 | Conserved hypothetical protein | |
| RL3464 | GI | 15 | 0.27 | 1.5 | GD | 15 | 0.53 | 2.63 | GD | 0.0.2 | Conserved hypothetical protein | |
| RL3948A | GI | 31 | 0.06 | 2 | ES | 31 | 0.16 | 1 | ES | 0.0.2 | Conserved hypothetical protein | |
| RL3967 | GI | 19 | 0 | 0 | ES | 19 | 0.53 | 3.5 | GD | 0.0.2 | Conserved hypothetical protein | |
| RL4037 | GI | 8 | 0.5 | 3.25 | GD | 8 | 0.63 | 6.8 | GD | 0.0.2 | Conserved hypothetical protein | |
| RL4280 | GI | 20 | 0.4 | 2.5 | GD | 20 | 0.25 | 4 | ES | 0.0.2 | Conserved hypothetical protein | |
| RL4523 | GI | 13 | 0.23 | 7.67 | ES | 13 | 0.23 | 12.33 | ES | 0.0.2 | Conserved hypothetical exported protein | |
| RL4562 | GI | 10 | 0.1 | 3 | ES | 10 | 0.1 | 4 | ES | 0.0.2 | Conserved hypothetical exported protein | |
| RL4734 | GI | 14 | 0 | 0 | ES | 14 | 0 | 0 | ES | 0.0.2 | Conserved hypothetical protein | |
| VMM-GROWTH IMPAIRED HYPOTHETICAL PROTEINS | ||||||||||||
| RL0044 | VGI | 13 | 0.62 | 22.88 | ES | 13 | 0.69 | 32.33 | NE | 0.0.0 | Hypothetical protein | |
| RL1117 | VGI | 6 | 0.5 | 15.33 | ES | 6 | 0.67 | 8 | NE | 0.0.0 | Hypothetical protein | |
| RL1628 | VGI | 39 | 0.64 | 8.32 | ES | 39 | 0.67 | 10.35 | NE | 0.0.0 | Hypothetical protein | |
| RL1946 | VGI | 13 | 0.62 | 1.75 | GD | 13 | 0.69 | 3.33 | NE | 0.0.0 | Hypothetical protein | |
| RL2117A | VGI | 33 | 0.76 | 11.36 | ES | 33 | 0.79 | 13.31 | NE | 0.0.0 | Hypothetical protein | |
| RL2154 | VGI | 16 | 0.69 | 7.55 | GD | 16 | 0.75 | 7.25 | NE | 0.0.0 | Hypothetical protein | |
| RL2611 | VGI | 10 | 0.5 | 11.6 | ES | 10 | 0.9 | 14 | NE | 0.0.0 | Hypothetical protein | |
| RL1524 | VGI | 5 | 0.6 | 3.33 | GD | 5 | 0.8 | 9.75 | NE | 0.0.1 | Conserved hypothetical protein | |
| RL3760 | VGI | 7 | 0 | 0 | ES | 7 | 0.29 | 9 | NE | 0.0.1 | Conserved hypothetical protein | |
| RL4043 | VGI | 2 | 0.5 | 2 | ES | 2 | 1 | 29 | NE | 0.0.1 | Conserved hypothetical protein | |
| RL4066 | VGI | 24 | 0.42 | 2.8 | GD | 24 | 0.79 | 9.68 | NE | 0.0.1 | Conserved hypothetical protein | |
| RL0571 | VGI | 3 | 0 | 0 | ES | 3 | 1 | 26.67 | NE | 0.0.2 | Conserved hypothetical protein | |
| RL0960 | VGI | 10 | 0.3 | 1.33 | GD | 10 | 0.5 | 2.6 | NE | 0.0.2 | Conserved hypothetical protein (Sua5 family) | |
| RL1523 | VGI | 4 | 0.25 | 2 | GD | 4 | 1 | 4.25 | NE | 0.0.2 | Conserved hypothetical protein | |
| RL2210 | VGI | 5 | 0.2 | 1 | GD | 5 | 0.4 | 1 | NE | 0.0.2 | Conserved hypothetical protein | |
| RL2289 | VGI | 3 | 0.33 | 1 | GD | 3 | 1 | 19 | NE | 0.0.2 | Conserved hypothetical protein | |
| RL2291 | VGI | 7 | 0.71 | 2 | GD | 7 | 0.86 | 20 | NE | 0.0.2 | Conserved hypothetical protein | |
| RL2527 | VGI | 13 | 0.31 | 8.5 | GD | 13 | 0.69 | 6.78 | NE | 0.0.2 | Conserved hypothetical exported protein | |
| RL4728 | VGI | 13 | 0.23 | 6 | ES | 13 | 0.69 | 6.11 | NE | 0.0.2 | Conserved hypothetical protein | |
| TY-GROWTH IMPAIRED HYPOTHETICAL PROTEINS | ||||||||||||
| RL1527 | TGI | 2 | 1 | 24 | NE | 2 | 1 | 3.5 | GD | 0.0.1 | Conserved hypothetical protein | |
| RL1562 | TGI | 9 | 0.56 | 14.8 | NE | 9 | 0.56 | 16.4 | ES | 0.0.1 | Conserved hypothetical protein | |
| RL1618A | TGI | 17 | 1 | 9.82 | NE | 17 | 0.65 | 2.18 | GD | 0.0.1 | Conserved hypothetical protein | |
| RL2307 | TGI | 4 | 0.75 | 5.67 | NE | 4 | 0.75 | 10 | GD | 0.0.1 | Conserved hypothetical protein | |
| RL4065 | TGI | 3 | 0.67 | 1 | NE | 3 | 0 | 0 | NE | 0.0.1 | Conserved hypothetical protein | |
| RL4716 | TGI | 18 | 1 | 37.17 | NE | 18 | 0.61 | 6.55 | GD | 0.0.1 | Conserved hypothetical exported protein | |
| RL0109 | TGI | 8 | 0.75 | 8.5 | NE | 8 | 0.25 | 2.5 | GD | 0.0.2 | Conserved hypothetical protein | |
| RL0890 | TGI | 16 | 0.81 | 19.54 | NE | 16 | 0.5 | 13.75 | ES | 0.0.2 | Conserved hypothetical protein | |
| RL1526 | TGI | 11 | 0.91 | 34.9 | NE | 11 | 0.64 | 5.43 | GD | 0.0.2 | Conserved hypothetical protein | |
| RL1528 | TGI | 11 | 0.91 | 14.3 | NE | 11 | 0.45 | 7.2 | GD | 0.0.2 | Conserved hypothetical protein | |
| RL2086 | TGI | 6 | 0.83 | 5.8 | NE | 6 | 0.5 | 1.33 | GD | 0.0.2 | Conserved hypothetical exported protein | |
| RL2142 | TGI | 17 | 0.71 | 13.33 | NE | 17 | 0.65 | 17.55 | ES | 0.0.2 | Conserved hypothetical protein | |
| RL2542 | TGI | 2 | 1 | 4.5 | NE | 2 | 0 | 0 | GD | 0.0.2 | Conserved hypothetical protein | |
| RL2625 | TGI | 15 | 0.8 | 9.08 | NE | 15 | 0.47 | 3.71 | GD | 0.0.2 | Conserved hypothetical protein | |
| RL2641 | TGI | 9 | 0.67 | 14 | NE | 9 | 0.56 | 5.8 | GD | 0.0.2 | Conserved hypothetical protein | |
| RL3499 | TGI | 14 | 0.93 | 17.08 | NE | 14 | 0.5 | 2.29 | GD | 0.0.2 | Conserved hypothetical protein | |
| RL3500 | TGI | 18 | 1 | 34.89 | NE | 18 | 0.67 | 5.75 | GD | 0.0.2 | Conserved hypothetical protein | |
| RL3761 | TGI | 14 | 0.93 | 13.23 | NE | 14 | 0.21 | 1 | ES | 0.0.2 | Conserved hypothetical exported protein | |
| RL4016 | TGI | 5 | 0.8 | 27.5 | NE | 5 | 0 | 0 | GD | 0.0.2 | Conserved hypothetical protein | |
| RL4503 | TGI | 4 | 0.75 | 3 | NE | 4 | 1 | 4.75 | GD | 0.0.2 | Conserved hypothetical protein | |
| PLASMID GROWTH IMPAIRED HYPOTHETICAL PROTEINS | ||||||||||||
| pRL100111 | PGI | 38 | 0.45 | 3.18 | GD | 38 | 0.45 | 3.71 | ES | 0.0.0 | Hypothetical protein | |
| pRL70135 | PGI | 17 | 0.47 | 22.75 | ES | 17 | 0.65 | 23 | ES | 0.0.0 | Hypothetical protein | |
| pRL120721 | PGI | 6 | 0.17 | 1 | ES | 6 | 0.33 | 2.5 | ES | 0.0.1 | Conserved hypothetical protein | |
| pRL100012 | PGI | 3 | 0 | 0 | ES | 3 | 0 | 0 | ES | 0.0.2 | Conserved hypothetical protein | |
| pRL110465 | PGI | 8 | 0.13 | 1 | GD | 8 | 0.13 | 2 | GD | 0.0.2 | Conserved hypothetical protein | |
| pRL70167 | PGI | 11 | 0.27 | 11 | ES | 11 | 0.27 | 19 | ES | 0.0.2 | Conserved hypothetical protein | |
| pRL80098 | PGI | 11 | 0.18 | 9.5 | ES | 11 | 0.64 | 8.14 | GD | 0.0.2 | Conserved hypothetical protein | |
| PLASMID/(VMM/TY)-GROWTH IMPAIRED HYPOTHETICAL PROTEINS | ||||||||||||
| pRL100010 | PVGI | 3 | 0.33 | 3 | GD | 3 | 1 | 11.67 | NE | 0.0.2 | Conserved hypothetical protein | |
| pRL100149 | PVGI | 58 | 0.83 | 14.56 | ES | 58 | 0.83 | 18.54 | NE | 0.0.2 | Conserved hypothetical protein | |
| pRL110044 | PVGI | 6 | 0.33 | 1.5 | GD | 6 | 0.83 | 4 | NE | 0.0.2 | Conserved hypothetical protein | |
| pRL110108 | PVGI | 17 | 0.76 | 9.85 | ES | 17 | 0.76 | 13.38 | NE | 0.0.2 | Conserved hypothetical protein | |
| pRL110351A | PTGI | 10 | 0.7 | 9.71 | NE | 10 | 0.6 | 14.67 | ES | 0.0.2 | Conserved hypothetical protein | |
| pRL70166 | PVGI | 9 | 0.33 | 6.33 | ES | 9 | 0.67 | 6.83 | NE | 0.0.2 | Conserved hypothetical protein | |
| pRL90280 | PVGI | 6 | 0.5 | 4.33 | ES | 6 | 0.83 | 6.6 | NE | 0.0.2 | Conserved hypothetical protein | |
| Locus | Growth phenotype | N | Insertion density | Average read depth | Gene state | N | Insertion density | Average read depth | Gene state | Riley key | Annotation | Sequence duplications |
| GROWTH IMPAIRED OR PLASMID GROWTH IMPAIRED HYPOTHETICAL PROTEINS WITH SEQUENCE DUPLICATION | ||||||||||||
| pRL70102 | PGI | 4 | 0 | 0 | ES | 4 | 0 | 0 | ES | 0.0.0 | Hypothetical protein | pRL70102, pRL110582, downstream pRL100152, upstream pRL100166 |
| RL1481 | GI | 6 | 0 | 0 | ES | 6 | 0 | 0 | ES | 0.0.0 | Hypothetical protein | RL1481, 3′-end of RL00456B, 5′-end of RL0457, 3′-end of pRL100088, 5′-end of pRL100089 |
| pRL110342 | PGI | 2 | 0 | 0 | ES | 2 | 0 | 0 | ES | 0.0.0 | Hypothetical protein | upstream pRL100046, upstream RL2679 |
| pRL100089 | PGN | 5 | 0.4 | 5.5 | NE | 5 | 0.6 | 5.33 | NE | 0.0.1 | Conserved hypothetical protein | pRL100089, RL1481 |
| pRL70033 | PGI | 8 | 0 | 0 | ES | 8 | 0 | 0 | ES | 0.0.1 | Conserved hypothetical protein | pRL70033, pRL70047D, pRL70147 |
| pRL70047 | PGI | 6 | 0 | 0 | ES | 6 | 0 | 0 | ES | 0.0.1 | Conserved hypothetical protein | pRL70142, pRL70047 |
| pRL70142 | PGI | 6 | 0 | 0 | ES | 6 | 0 | 0 | ES | 0.0.1 | Conserved hypothetical protein | pRL70142, pRL70047 |
| pRL70179 | PGI | 3 | 0 | 0 | ES | 3 | 0 | 0 | ES | 0.0.1 | Conserved hypothetical protein | pRL70169, pRL70179, PRL100095 |
| pRL120379 | PGI | 35 | 0 | 0 | ES | 35 | 0 | 0 | ES | 0.0.1 | Conserved hypothetical protein | pRL90004, pRL90319, pRL100469, pRL120379 |
| pRL90004 | PGI | 35 | 0 | 0 | ES | 35 | 0 | 0 | ES | 0.0.1 | Conserved hypothetical protein | pRL90004, pRL90319, pRL100469, pRL120379 |
| pRL120650 | PGI | 6 | 0 | 0 | ES | 6 | 0 | 0 | ES | 0.0.1 | Conserved hypothetical protein | RL2139, RL0835, pRL120650 |
| RL0835 | GI | 7 | 0 | 0 | ES | 7 | 0.14 | 21 | ES | 0.0.1 | Conserved hypothetical protein | RL2139, RL0835, pRL120650 |
| RL2139 | GI | 6 | 0 | 0 | ES | 6 | 0 | 0 | ES | 0.0.1 | Conserved hypothetical protein | RL2139, RL0835, pRL120650 |
| pRL110353 | PGN | 4 | 0.25 | 2 | NE | 4 | 0.25 | 3 | NE | 0.0.2 | Conserved hypothetical protein | pRL110353, RL2153 |
| RL2153 | GI | 4 | 0.25 | 3 | GD | 4 | 0.25 | 4 | GD | 0.0.2 | Conserved hypothetical protein | pRL110353, RL2153 |
| pRL100095 | PGI | 2 | 0 | 0 | NE | 2 | 0 | 0 | NE | 0.0.2 | Conserved hypothetical protein | pRL70169, pRL70179, PRL100095 |
| pRL70169 | PGI | 2 | 0 | 0 | ES | 2 | 0 | 0 | ES | 0.0.2 | Conserved hypothetical protein | pRL70169, pRL70179, PRL100095 |
| pRL100469 | PGI | 35 | 0 | 0 | ES | 35 | 0 | 0 | ES | 0.0.2 | Conserved hypothetical protein | pRL90004, pRL90319, pRL100469, pRL120379 |
| pRL90319 | PGI | 35 | 0 | 0 | ES | 35 | 0 | 0 | ES | 0.0.2 | Conserved hypothetical protein, possible fusion protein | pRL90004, pRL90319, pRL100469, pRL120379 |