| E coli W3110 ExbB |
| ID: | 1509736522 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 244 (221) | ||
| Sequences: | 3501 (2026.8) | ||
| Seq/Len: | 15.842 | ||
| Nf(neff/√len): | 136.3 |
HHblits Results: (2016_02)
Sequences per length for each position, BEFORE the coverage/gap filter was applied
Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 15.842).
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 135_T | 193_V | 3.496 | 1.00 |
| 42_F | 46_V | 3.431 | 1.00 |
| 41_F | 194_I | 3.381 | 1.00 |
| 86_H | 122_V | 3.342 | 1.00 |
| 67_S | 70_Q | 3.318 | 1.00 |
| 154_N | 176_E | 3.147 | 1.00 |
| 137_G | 192_V | 2.915 | 1.00 |
| 132_Y | 136_I | 2.474 | 1.00 |
| 44_K | 47_E | 2.315 | 1.00 |
| 123_G | 206_K | 2.201 | 1.00 |
| 26_V | 146_F | 2.137 | 1.00 |
| 37_T | 191_A | 2.132 | 1.00 |
| 185_L | 189_I | 2.055 | 1.00 |
| 135_T | 196_N | 1.859 | 1.00 |
| 155_S | 173_G | 1.788 | 1.00 |
| 40_I | 132_Y | 1.781 | 1.00 |
| 30_L | 187_A | 1.738 | 1.00 |
| 121_A | 211_D | 1.665 | 1.00 |
| 157_I | 175_A | 1.621 | 1.00 |
| 34_S | 38_W | 1.604 | 1.00 |
| 27_M | 183_I | 1.594 | 1.00 |
| 130_N | 202_I | 1.563 | 1.00 |
| 31_I | 35_V | 1.527 | 1.00 |
| 142_F | 152_I | 1.500 | 1.00 |
| 19_A | 23_V | 1.496 | 1.00 |
| 122_V | 125_Q | 1.491 | 1.00 |
| 50_N | 54_R | 1.465 | 1.00 |
| 13_W | 17_Q | 1.457 | 1.00 |
| 119_V | 123_G | 1.445 | 1.00 |
| 37_T | 41_F | 1.424 | 1.00 |
| 35_V | 39_A | 1.411 | 1.00 |
| 14_G | 18_H | 1.407 | 0.99 |
| 28_I | 32_L | 1.406 | 0.99 |
| 119_V | 213_A | 1.387 | 0.99 |
| 62_L | 212_V | 1.374 | 0.99 |
| 9_D | 14_G | 1.372 | 0.99 |
| 91_A | 115_L | 1.371 | 0.99 |
| 118_R | 122_V | 1.347 | 0.99 |
| 49_F | 53_R | 1.336 | 0.99 |
| 117_R | 211_D | 1.323 | 0.99 |
| 91_A | 114_R | 1.283 | 0.99 |
| 51_Q | 205_F | 1.282 | 0.99 |
| 197_V | 201_Q | 1.273 | 0.99 |
| 139_I | 193_V | 1.267 | 0.99 |
| 156_F | 173_G | 1.259 | 0.99 |
| 61_L | 65_A | 1.254 | 0.99 |
| 33_A | 143_V | 1.254 | 0.99 |
| 177_A | 181_T | 1.236 | 0.98 |
| 159_I | 165_T | 1.235 | 0.98 |
| 146_F | 186_V | 1.229 | 0.98 |
| 48_F | 202_I | 1.223 | 0.98 |
| 37_T | 133_L | 1.210 | 0.98 |
| 87_L | 209_L | 1.192 | 0.98 |
| 98_S | 110_R | 1.190 | 0.98 |
| 131_G | 200_R | 1.188 | 0.98 |
| 127_G | 210_G | 1.188 | 0.98 |
| 150_W | 176_E | 1.187 | 0.98 |
| 20_D | 24_K | 1.183 | 0.98 |
| 25_C | 29_G | 1.181 | 0.98 |
| 91_A | 95_L | 1.166 | 0.97 |
| 142_F | 188_A | 1.156 | 0.97 |
| 8_T | 14_G | 1.152 | 0.97 |
| 48_F | 205_F | 1.137 | 0.97 |
| 139_I | 171_A | 1.135 | 0.97 |
| 82_S | 85_L | 1.134 | 0.97 |
| 194_I | 198_F | 1.132 | 0.97 |
| 158_G | 169_V | 1.130 | 0.97 |
| 63_A | 92_Q | 1.129 | 0.97 |
| 30_L | 183_I | 1.125 | 0.97 |
| 90_E | 118_R | 1.121 | 0.97 |
| 70_Q | 73_D | 1.112 | 0.96 |
| 36_V | 132_Y | 1.112 | 0.96 |
| 19_A | 27_M | 1.112 | 0.96 |
| 43_S | 47_E | 1.108 | 0.96 |
| 124_R | 204_G | 1.105 | 0.96 |
| 145_L | 188_A | 1.103 | 0.96 |
| 52_K | 201_Q | 1.099 | 0.96 |
| 139_I | 143_V | 1.092 | 0.96 |
| 76_A | 89_N | 1.089 | 0.96 |
| 213_A | 217_L | 1.088 | 0.96 |
| 20_D | 154_N | 1.080 | 0.95 |
| 195_Y | 199_A | 1.073 | 0.95 |
| 137_G | 190_P | 1.069 | 0.95 |
| 58_E | 62_L | 1.062 | 0.95 |
| 59_Q | 63_A | 1.062 | 0.95 |
| 58_E | 88_L | 1.060 | 0.95 |
| 16_Y | 24_K | 1.058 | 0.95 |
| 58_E | 212_V | 1.057 | 0.95 |
| 128_R | 204_G | 1.050 | 0.94 |
| 162_T | 169_V | 1.041 | 0.94 |
| 203_G | 207_A | 1.035 | 0.94 |
| 14_G | 17_Q | 1.035 | 0.94 |
| 46_V | 50_N | 1.029 | 0.94 |
| 73_D | 77_D | 1.028 | 0.94 |
| 30_L | 143_V | 1.028 | 0.94 |
| 138_A | 192_V | 1.021 | 0.93 |
| 66_R | 70_Q | 1.020 | 0.93 |
| 30_L | 34_S | 1.019 | 0.93 |
| 85_L | 88_L | 1.013 | 0.93 |
| 160_A | 175_A | 1.013 | 0.93 |
| 23_V | 180_A | 1.008 | 0.93 |
| 165_T | 175_A | 1.008 | 0.93 |
| 126_M | 202_I | 1.004 | 0.93 |
| 154_N | 157_I | 1.004 | 0.93 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 4tllB | 2 | 0.0123 | 7.6 | 0.96 | Contact Map |
| 1pi7A | 1 | 0.0779 | 4.6 | 0.964 | Contact Map |
| 4o5nB | 1 | 0.2951 | 4.3 | 0.964 | Contact Map |
| 3b5mA | 4 | 0.2787 | 4.2 | 0.964 | Contact Map |
| 4mndA | 1 | 0.2008 | 4 | 0.965 | Contact Map |
| 3hlsA | 8 | 0.2459 | 3.6 | 0.966 | Contact Map |
| 2f95B | 1 | 0.1393 | 3.5 | 0.966 | Contact Map |
| 4bsgB | 1 | 0.3115 | 3.5 | 0.966 | Contact Map |
| 4f4sA | 10 | 0.2664 | 3.3 | 0.966 | Contact Map |
| 4i5sA | 2 | 0.8197 | 3.3 | 0.966 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)