| mbp |
| ID: | 1405071997 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 370 (366) | ||
| Sequences: | 8687 (6668.7) | ||
| Seq/Len: | 23.735 | ||
| Nf(neff/√len): | 348.6 |
HHblits Results: (2013_03)
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: 23.735).
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 |
| 356_T | 359_E | 4.280 | 1.00 |
| 189_K | 358_D | 4.010 | 1.00 |
| 120_D | 241_N | 3.954 | 1.00 |
| 77_A | 273_K | 3.923 | 1.00 |
| 193_T | 197_D | 3.531 | 1.00 |
| 196_V | 200_K | 3.359 | 1.00 |
| 21_A | 25_K | 3.165 | 1.00 |
| 119_K | 243_G | 3.109 | 1.00 |
| 27_F | 278_E | 3.067 | 1.00 |
| 33_I | 275_L | 2.989 | 1.00 |
| 6_K | 36_T | 2.981 | 1.00 |
| 78_E | 102_K | 2.896 | 1.00 |
| 358_D | 362_K | 2.823 | 1.00 |
| 184_D | 362_K | 2.745 | 1.00 |
| 28_E | 34_K | 2.695 | 1.00 |
| 117_Y | 243_G | 2.677 | 1.00 |
| 26_K | 282_N | 2.603 | 1.00 |
| 122_L | 224_M | 2.544 | 1.00 |
| 278_E | 281_E | 2.502 | 1.00 |
| 26_K | 29_K | 2.469 | 1.00 |
| 98_R | 103_L | 2.465 | 1.00 |
| 128_T | 131_E | 2.447 | 1.00 |
| 133_P | 197_D | 2.433 | 1.00 |
| 22_E | 25_K | 2.413 | 1.00 |
| 272_N | 275_L | 2.411 | 1.00 |
| 25_K | 29_K | 2.396 | 1.00 |
| 362_K | 366_T | 2.344 | 1.00 |
| 137_K | 201_N | 2.342 | 1.00 |
| 134_A | 138_E | 2.298 | 1.00 |
| 355_Q | 363_D | 2.284 | 1.00 |
| 91_P | 95_D | 2.275 | 1.00 |
| 285_L | 288_E | 2.229 | 1.00 |
| 197_D | 201_N | 2.199 | 1.00 |
| 131_E | 134_A | 2.195 | 1.00 |
| 88_K | 304_L | 2.177 | 1.00 |
| 119_K | 123_P | 2.123 | 1.00 |
| 58_D | 272_N | 2.079 | 1.00 |
| 24_G | 28_E | 2.069 | 1.00 |
| 60_I | 267_N | 2.067 | 1.00 |
| 193_T | 357_V | 2.044 | 1.00 |
| 27_F | 33_I | 2.024 | 1.00 |
| 24_G | 279_F | 2.022 | 1.00 |
| 6_K | 34_K | 1.979 | 1.00 |
| 76_L | 265_G | 1.977 | 1.00 |
| 186_A | 190_A | 1.973 | 1.00 |
| 270_S | 273_K | 1.930 | 1.00 |
| 8_V | 36_T | 1.910 | 1.00 |
| 28_E | 31_T | 1.900 | 1.00 |
| 274_E | 278_E | 1.889 | 1.00 |
| 97_V | 263_S | 1.873 | 1.00 |
| 189_K | 357_V | 1.869 | 1.00 |
| 10_W | 50_V | 1.845 | 1.00 |
| 193_T | 358_D | 1.843 | 1.00 |
| 349_N | 355_Q | 1.829 | 1.00 |
| 139_L | 223_A | 1.819 | 1.00 |
| 349_N | 354_R | 1.807 | 1.00 |
| 365_Q | 369_T | 1.805 | 1.00 |
| 266_I | 280_L | 1.795 | 1.00 |
| 59_I | 280_L | 1.794 | 1.00 |
| 359_E | 363_D | 1.788 | 1.00 |
| 51_A | 56_G | 1.739 | 1.00 |
| 25_K | 28_E | 1.738 | 1.00 |
| 80_T | 102_K | 1.710 | 1.00 |
| 134_A | 137_K | 1.710 | 1.00 |
| 24_G | 37_V | 1.698 | 1.00 |
| 350_A | 360_A | 1.693 | 1.00 |
| 190_A | 193_T | 1.680 | 1.00 |
| 137_K | 141_A | 1.676 | 1.00 |
| 121_L | 223_A | 1.674 | 1.00 |
| 148_M | 222_T | 1.667 | 1.00 |
| 33_I | 278_E | 1.660 | 1.00 |
| 117_Y | 245_T | 1.658 | 1.00 |
| 130_E | 133_P | 1.644 | 1.00 |
| 115_L | 245_T | 1.641 | 1.00 |
| 318_A | 322_E | 1.603 | 1.00 |
| 184_D | 365_Q | 1.595 | 1.00 |
| 26_K | 30_D | 1.595 | 1.00 |
| 196_V | 350_A | 1.593 | 1.00 |
| 359_E | 362_K | 1.592 | 1.00 |
| 95_D | 98_R | 1.560 | 1.00 |
| 217_F | 242_Y | 1.558 | 1.00 |
| 127_K | 131_E | 1.554 | 1.00 |
| 42_K | 45_E | 1.536 | 1.00 |
| 27_F | 282_N | 1.526 | 1.00 |
| 130_E | 134_A | 1.514 | 1.00 |
| 133_P | 198_L | 1.483 | 1.00 |
| 350_A | 357_V | 1.468 | 1.00 |
| 115_L | 224_M | 1.460 | 1.00 |
| 209_D | 212_I | 1.444 | 1.00 |
| 362_K | 365_Q | 1.433 | 1.00 |
| 71_A | 104_I | 1.431 | 1.00 |
| 17_Y | 21_A | 1.425 | 1.00 |
| 82_D | 277_K | 1.423 | 1.00 |
| 346_A | 355_Q | 1.422 | 1.00 |
| 137_K | 203_H | 1.406 | 0.99 |
| 363_D | 366_T | 1.405 | 0.99 |
| 355_Q | 360_A | 1.402 | 0.99 |
| 26_K | 291_E | 1.400 | 0.99 |
| 77_A | 268_A | 1.400 | 0.99 |
| 133_P | 137_K | 1.400 | 0.99 |
| 136_D | 224_M | 1.396 | 0.99 |
| 28_E | 32_G | 1.394 | 0.99 |
| 119_K | 241_N | 1.391 | 0.99 |
| 138_E | 142_K | 1.390 | 0.99 |
| 279_F | 283_Y | 1.386 | 0.99 |
| 346_A | 363_D | 1.382 | 0.99 |
| 135_L | 138_E | 1.378 | 0.99 |
| 126_P | 131_E | 1.376 | 0.99 |
| 35_V | 279_F | 1.370 | 0.99 |
| 22_E | 26_K | 1.365 | 0.99 |
| 105_A | 263_S | 1.347 | 0.99 |
| 282_N | 288_E | 1.341 | 0.99 |
| 133_P | 201_N | 1.339 | 0.99 |
| 197_D | 200_K | 1.331 | 0.99 |
| 8_V | 38_E | 1.327 | 0.99 |
| 291_E | 295_K | 1.315 | 0.99 |
| 77_A | 270_S | 1.308 | 0.99 |
| 356_T | 360_A | 1.306 | 0.99 |
| 267_N | 270_S | 1.293 | 0.99 |
| 170_K | 177_D | 1.293 | 0.99 |
| 114_S | 244_V | 1.293 | 0.99 |
| 216_A | 221_E | 1.292 | 0.99 |
| 187_G | 190_A | 1.289 | 0.99 |
| 59_I | 279_F | 1.288 | 0.99 |
| 277_K | 281_E | 1.274 | 0.99 |
| 346_A | 364_A | 1.271 | 0.99 |
| 27_F | 275_L | 1.260 | 0.99 |
| 24_G | 35_V | 1.257 | 0.99 |
| 341_Y | 345_T | 1.247 | 0.99 |
| 58_D | 270_S | 1.239 | 0.98 |
| 266_I | 276_A | 1.235 | 0.98 |
| 363_D | 367_R | 1.233 | 0.98 |
| 189_K | 193_T | 1.231 | 0.98 |
| 105_A | 265_G | 1.229 | 0.98 |
| 59_I | 276_A | 1.227 | 0.98 |
| 46_K | 50_V | 1.219 | 0.98 |
| 78_E | 81_P | 1.218 | 0.98 |
| 140_K | 146_A | 1.218 | 0.98 |
| 266_I | 277_K | 1.217 | 0.98 |
| 161_I | 166_G | 1.211 | 0.98 |
| 164_D | 190_A | 1.204 | 0.98 |
| 121_L | 139_L | 1.198 | 0.98 |
| 114_S | 320_T | 1.197 | 0.98 |
| 345_T | 367_R | 1.194 | 0.98 |
| 88_K | 302_V | 1.181 | 0.98 |
| 290_L | 294_N | 1.180 | 0.98 |
| 170_K | 180_D | 1.179 | 0.98 |
| 118_N | 240_V | 1.174 | 0.98 |
| 133_P | 194_F | 1.174 | 0.98 |
| 349_N | 363_D | 1.169 | 0.97 |
| 268_A | 273_K | 1.158 | 0.97 |
| 194_F | 197_D | 1.154 | 0.97 |
| 108_I | 264_A | 1.152 | 0.97 |
| 286_T | 290_L | 1.149 | 0.97 |
| 97_V | 103_L | 1.143 | 0.97 |
| 279_F | 282_N | 1.142 | 0.97 |
| 27_F | 279_F | 1.141 | 0.97 |
| 122_L | 139_L | 1.140 | 0.97 |
| 130_E | 251_K | 1.136 | 0.97 |
| 194_F | 198_L | 1.131 | 0.97 |
| 322_E | 325_Q | 1.130 | 0.97 |
| 192_L | 350_A | 1.130 | 0.97 |
| 135_L | 224_M | 1.128 | 0.97 |
| 302_V | 305_K | 1.123 | 0.97 |
| 275_L | 278_E | 1.117 | 0.96 |
| 47_F | 60_I | 1.113 | 0.96 |
| 189_K | 361_L | 1.108 | 0.96 |
| 273_K | 277_K | 1.101 | 0.96 |
| 136_D | 203_H | 1.099 | 0.96 |
| 62_W | 265_G | 1.096 | 0.96 |
| 342_A | 367_R | 1.093 | 0.96 |
| 56_G | 267_N | 1.088 | 0.96 |
| 132_I | 147_L | 1.077 | 0.95 |
| 346_A | 349_N | 1.073 | 0.95 |
| 71_A | 99_Y | 1.068 | 0.95 |
| 122_L | 135_L | 1.065 | 0.95 |
| 346_A | 360_A | 1.062 | 0.95 |
| 216_A | 222_T | 1.060 | 0.95 |
| 140_K | 203_H | 1.058 | 0.95 |
| 118_N | 121_L | 1.053 | 0.95 |
| 193_T | 196_V | 1.038 | 0.94 |
| 18_N | 21_A | 1.035 | 0.94 |
| 9_I | 59_I | 1.033 | 0.94 |
| 28_E | 35_V | 1.032 | 0.94 |
| 31_T | 278_E | 1.029 | 0.94 |
| 319_A | 322_E | 1.028 | 0.94 |
| 18_N | 22_E | 1.022 | 0.93 |
| 266_I | 270_S | 1.016 | 0.93 |
| 10_W | 57_P | 1.015 | 0.93 |
| 51_A | 75_L | 1.012 | 0.93 |
| 77_A | 266_I | 1.010 | 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 | |
| 4kegA | 1 | 1 | 100 | 0.11 | Contact Map |
| 3oaiA | 2 | 0.9919 | 100 | 0.113 | Contact Map |
| 3iotA | 3 | 1 | 100 | 0.113 | Contact Map |
| 1y4cA | 1 | 0.9919 | 100 | 0.114 | Contact Map |
| 4egcA | 1 | 1 | 100 | 0.114 | Contact Map |
| 1hsjA | 2 | 1 | 100 | 0.115 | Contact Map |
| 3h4zA | 3 | 1 | 100 | 0.115 | Contact Map |
| 4irlA | 3 | 1 | 100 | 0.116 | Contact Map |
| 3f5fA | 1 | 1 | 100 | 0.116 | Contact Map |
| 3py7A | 1 | 0.9973 | 100 | 0.116 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)