Table 1. Characteristics of the calibrated SRE-specific profiles included with SigmoID.a.
| Regulatory protein | Binding site length/ information content | Number of binding sites used for profile construction | Source of the original binding site data | |
|---|---|---|---|---|
| Original | Final | |||
| ArcA | 15/16.9 | 19/21.0 | 33 | Ravcheev (2009) |
| ArgR | 18/17.8 | 24/23.2 | 24 | RegPrecise |
| AscG | 20/30.4 | 20/23.3 | 7 | RegPrecise |
| BaeR | 20/26.2 | 27/30.4 | 13 | Nishino, Honda & Yamaguchi (2005) |
| CpxR | 15/15.0 | 15/20.3 | 16 | RegulonDB |
| CRP | 16/10.2 | 24/15.8 | 100 | RegPrecise |
| FliA | 27/23.5 | 26/23.5 | 96 | Ide, Ikebe & Kutsukake (1999) |
| FNR | 14/12.4 | 22/20.7 | 34 | RegulonDB |
| FruR | 16/17.8 | 18/19.4 | 25 | RegPrecise |
| Fur | 19/20.2 | 23/18.8 | 98 | RegPrecise |
| GalR | 20/24.0 | 18/19.5 | 39 | RegPrecise |
| HrpL | 28/19.0 | 31/25.9 | 63 | McNally et al. (2011) |
| KdgR | 21/22.1 | 25/22.4 | 85 | Rodionov (2004) |
| LexA | 20/20.3 | 20/21.2 | 34 | RegPrecise |
| MetJ | 16/20.2 | 24/23.9 | 21 | RegPrecise |
| MetR | 15/17.3 | 21/19.2 | 18 | RegPrecise |
| NarP | 16/17.9 | 18/17.6 | 54 | RegPrecise |
| NifA | 16/14.6 | 18/19.5 | 18 | RegPrecise |
| NsrR | 19/27.9 | 19/23.2 | 20 | RegPrecise |
| NtrC | 17/22.0 | 17/17.8 | 56 | RegPrecise |
| OxyR | 17/13.3 | 15/18.1 | 19 | Seo et al. (2015) |
| PhoP1 | 19/24.4 | 16/20.4 | 24 | Harari et al. (2010) |
| PhoP2 | 19/16.4 | 16/20.3 | 31 | Harari et al. (2010) |
| PmrA | 20/23.1 | 19/22.5 | 19 | Ogasawara et al. (2012) |
| PurR | 16/18.4 | 16/17.6 | 23 | RegPrecise |
| RcsB | 14/19.6 | 18/17.4 | 39 | Andresen et al. (2010) |
| RhaS | 51/42.7 | 51/40.2 | 21 | RegPrecise |
| Rob | 17/15.6 | 20/22.7 | 45 | RegulonDB |
| RpoE | 27/18.4 | 30/20.3 | 57 | Rhodius et al. (2006) |
| RpoH1 | 28/27.5 | 33/29.6 | 20 | Nonaka et al. (2006) |
| RpoH2 | 29/24.7 | 30/30.8 | 19 | Nonaka et al. (2006) |
| RpoN | 16/14.7 | 16/21.8 | 105 | Barrios, Valderrama & Morett (1999) |
| RpoS | 26/22.8 | 35/22.9 | 25 | RegulonDB |
| SlyA | 12/10.7 | 20/19.2 | 55 | Stapleton et al. (2002), Haque et al. (2009) and McVicker et al. (2011) |
| UxuR | 18/27.6 | 22/23.7 | 17 | RegPrecise |
Notes.
a
The table does not include the data on additional 9 profiles for TFs controlling just one or very few operons. These profiles are still distributed with SigmoID.