| LptG |
| ID: | 1490524758 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 360 (356) | ||
| Sequences: | 5918 (4262.1) | ||
| Seq/Len: | 16.624 | ||
| Nf(neff/√len): | 225.9 |
Jackhmmer Results: (2016_04)
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: 16.624).
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 |
| 193_A | 208_Q | 5.810 | 1.00 |
| 164_E | 174_G | 4.719 | 1.00 |
| 209_V | 225_T | 4.200 | 1.00 |
| 194_T | 207_S | 4.118 | 1.00 |
| 165_R | 173_G | 3.554 | 1.00 |
| 171_E | 194_T | 3.484 | 1.00 |
| 7_L | 92_M | 3.389 | 1.00 |
| 179_A | 188_S | 3.307 | 1.00 |
| 8_D | 101_Q | 2.887 | 1.00 |
| 276_W | 342_L | 2.858 | 1.00 |
| 196_K | 207_S | 2.712 | 1.00 |
| 262_K | 272_Q | 2.646 | 1.00 |
| 198_D | 205_R | 2.600 | 1.00 |
| 255_H | 275_M | 2.418 | 1.00 |
| 131_M | 134_N | 2.412 | 1.00 |
| 82_M | 86_R | 2.377 | 1.00 |
| 6_V | 9_R | 2.341 | 1.00 |
| 80_L | 106_V | 2.320 | 1.00 |
| 188_S | 211_E | 2.318 | 1.00 |
| 19_I | 75_G | 2.272 | 1.00 |
| 171_E | 196_K | 2.252 | 1.00 |
| 205_R | 227_S | 2.241 | 1.00 |
| 9_R | 13_K | 2.222 | 1.00 |
| 181_N | 185_R | 2.170 | 1.00 |
| 203_V | 229_T | 2.063 | 1.00 |
| 110_A | 289_M | 2.051 | 1.00 |
| 205_R | 229_T | 2.043 | 1.00 |
| 13_K | 17_T | 2.022 | 1.00 |
| 225_T | 228_G | 2.016 | 1.00 |
| 274_N | 278_K | 1.900 | 1.00 |
| 75_G | 79_G | 1.873 | 1.00 |
| 287_V | 348_F | 1.841 | 1.00 |
| 277_S | 327_G | 1.778 | 1.00 |
| 103_A | 293_L | 1.777 | 1.00 |
| 12_G | 109_T | 1.763 | 1.00 |
| 127_Q | 131_M | 1.756 | 1.00 |
| 280_F | 342_L | 1.754 | 1.00 |
| 188_S | 213_D | 1.752 | 1.00 |
| 116_L | 120_I | 1.745 | 1.00 |
| 159_N | 179_A | 1.745 | 1.00 |
| 199_P | 202_K | 1.725 | 1.00 |
| 195_A | 206_L | 1.723 | 1.00 |
| 173_G | 194_T | 1.704 | 1.00 |
| 49_A | 53_G | 1.704 | 1.00 |
| 48_D | 51_G | 1.701 | 1.00 |
| 114_V | 286_A | 1.692 | 1.00 |
| 92_M | 97_F | 1.667 | 1.00 |
| 207_S | 227_S | 1.662 | 1.00 |
| 210_D | 224_Q | 1.656 | 1.00 |
| 330_T | 340_G | 1.653 | 1.00 |
| 350_L | 354_W | 1.639 | 1.00 |
| 119_A | 123_W | 1.632 | 1.00 |
| 111_I | 115_L | 1.627 | 1.00 |
| 250_S | 253_G | 1.587 | 1.00 |
| 57_L | 61_P | 1.582 | 1.00 |
| 5_G | 9_R | 1.580 | 1.00 |
| 211_E | 223_S | 1.573 | 1.00 |
| 190_R | 211_E | 1.570 | 1.00 |
| 27_V | 60_V | 1.559 | 1.00 |
| 284_S | 319_F | 1.546 | 1.00 |
| 51_G | 54_M | 1.520 | 1.00 |
| 167_K | 173_G | 1.516 | 1.00 |
| 53_G | 57_L | 1.515 | 1.00 |
| 213_D | 223_S | 1.501 | 1.00 |
| 197_F | 236_P | 1.493 | 1.00 |
| 213_D | 221_T | 1.492 | 1.00 |
| 23_L | 71_A | 1.488 | 1.00 |
| 192_A | 206_L | 1.470 | 1.00 |
| 26_L | 67_F | 1.459 | 1.00 |
| 120_I | 124_V | 1.458 | 1.00 |
| 211_E | 225_T | 1.448 | 1.00 |
| 150_Q | 165_R | 1.439 | 1.00 |
| 42_A | 52_A | 1.431 | 1.00 |
| 14_T | 82_M | 1.426 | 1.00 |
| 172_L | 175_I | 1.425 | 1.00 |
| 115_L | 119_A | 1.422 | 1.00 |
| 172_L | 195_A | 1.420 | 1.00 |
| 83_L | 92_M | 1.412 | 1.00 |
| 58_L | 128_G | 1.403 | 0.99 |
| 134_N | 138_Q | 1.395 | 0.99 |
| 23_L | 64_V | 1.388 | 0.99 |
| 346_A | 350_L | 1.387 | 0.99 |
| 336_P | 339_I | 1.379 | 0.99 |
| 72_A | 285_V | 1.378 | 0.99 |
| 68_F | 117_T | 1.378 | 0.99 |
| 71_A | 75_G | 1.360 | 0.99 |
| 268_A | 272_Q | 1.332 | 0.99 |
| 196_K | 205_R | 1.317 | 0.99 |
| 174_G | 193_A | 1.309 | 0.99 |
| 291_M | 352_S | 1.304 | 0.99 |
| 54_M | 58_L | 1.304 | 0.99 |
| 273_L | 331_L | 1.303 | 0.99 |
| 208_Q | 226_V | 1.299 | 0.99 |
| 190_R | 209_V | 1.296 | 0.99 |
| 327_G | 331_L | 1.291 | 0.99 |
| 106_V | 289_M | 1.289 | 0.99 |
| 31_G | 56_T | 1.286 | 0.99 |
| 269_G | 272_Q | 1.285 | 0.99 |
| 14_T | 83_L | 1.272 | 0.99 |
| 16_F | 20_M | 1.268 | 0.99 |
| 167_K | 171_E | 1.267 | 0.99 |
| 175_I | 195_A | 1.255 | 0.99 |
| 100_M | 104_L | 1.253 | 0.99 |
| 77_L | 312_G | 1.252 | 0.99 |
| 174_G | 191_Y | 1.246 | 0.98 |
| 104_L | 108_K | 1.239 | 0.98 |
| 353_L | 357_M | 1.234 | 0.98 |
| 7_L | 97_F | 1.232 | 0.98 |
| 101_Q | 104_L | 1.231 | 0.98 |
| 346_A | 349_F | 1.228 | 0.98 |
| 198_D | 201_H | 1.227 | 0.98 |
| 65_Q | 121_G | 1.226 | 0.98 |
| 258_V | 275_M | 1.219 | 0.98 |
| 163_I | 172_L | 1.210 | 0.98 |
| 283_L | 345_S | 1.207 | 0.98 |
| 38_Q | 56_T | 1.201 | 0.98 |
| 19_I | 113_L | 1.189 | 0.98 |
| 282_P | 285_V | 1.186 | 0.98 |
| 76_A | 289_M | 1.182 | 0.98 |
| 59_S | 62_K | 1.166 | 0.97 |
| 222_G | 225_T | 1.162 | 0.97 |
| 249_L | 253_G | 1.160 | 0.97 |
| 8_D | 104_L | 1.149 | 0.97 |
| 342_L | 345_S | 1.145 | 0.97 |
| 269_G | 333_Y | 1.145 | 0.97 |
| 22_T | 74_L | 1.142 | 0.97 |
| 73_L | 288_M | 1.132 | 0.97 |
| 92_M | 102_V | 1.127 | 0.97 |
| 58_L | 131_M | 1.124 | 0.97 |
| 23_L | 27_V | 1.112 | 0.96 |
| 223_S | 228_G | 1.100 | 0.96 |
| 246_P | 249_L | 1.097 | 0.96 |
| 34_K | 38_Q | 1.092 | 0.96 |
| 251_I | 255_H | 1.090 | 0.96 |
| 258_V | 268_A | 1.087 | 0.96 |
| 112_P | 115_L | 1.082 | 0.96 |
| 349_F | 353_L | 1.079 | 0.95 |
| 287_V | 349_F | 1.078 | 0.95 |
| 287_V | 352_S | 1.077 | 0.95 |
| 274_N | 277_S | 1.072 | 0.95 |
| 55_Y | 132_A | 1.069 | 0.95 |
| 54_M | 131_M | 1.064 | 0.95 |
| 177_I | 206_L | 1.062 | 0.95 |
| 84_A | 89_L | 1.056 | 0.95 |
| 283_L | 342_L | 1.052 | 0.95 |
| 30_S | 67_F | 1.046 | 0.94 |
| 208_Q | 224_Q | 1.045 | 0.94 |
| 50_L | 54_M | 1.045 | 0.94 |
| 197_F | 204_W | 1.040 | 0.94 |
| 275_M | 279_I | 1.037 | 0.94 |
| 211_E | 228_G | 1.034 | 0.94 |
| 118_M | 122_E | 1.033 | 0.94 |
| 107_M | 110_A | 1.032 | 0.94 |
| 257_Y | 261_L | 1.026 | 0.94 |
| 326_F | 344_P | 1.025 | 0.93 |
| 15_I | 72_A | 1.024 | 0.93 |
| 198_D | 202_K | 1.016 | 0.93 |
| 194_T | 208_Q | 1.014 | 0.93 |
| 122_E | 251_I | 1.011 | 0.93 |
| 191_Y | 210_D | 1.011 | 0.93 |
| 4_F | 8_D | 1.010 | 0.93 |
| 314_S | 318_V | 1.010 | 0.93 |
| 127_Q | 130_Q | 1.009 | 0.93 |
| 259_K | 263_S | 1.007 | 0.93 |
| 11_I | 92_M | 1.004 | 0.93 |
| 181_N | 187_Q | 1.002 | 0.92 |
| 209_V | 226_V | 1.001 | 0.92 |
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 | |
| 4hfiA | 5 | 0.3139 | 5 | 0.967 | Contact Map |
| 4us3A | 1 | 0.2806 | 4.6 | 0.968 | Contact Map |
| 4dx5A | 3 | 0.3972 | 3.9 | 0.969 | Contact Map |
| 2l9uA | 2 | 0.0889 | 3.7 | 0.969 | Contact Map |
| 1i17A | 1 | 0.2944 | 3.6 | 0.969 | Contact Map |
| 4lxjA | 1 | 0.2083 | 3.4 | 0.97 | Contact Map |
| 3zojA | 1 | 0.3194 | 3.2 | 0.97 | Contact Map |
| 3w9iA | 6 | 0.3722 | 3 | 0.971 | Contact Map |
| 3orgA | 4 | 0.175 | 2.8 | 0.971 | Contact Map |
| 4b4aA | 1 | 0.225 | 2.7 | 0.971 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)