| eh test |
| ID: | 1444920757 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 398 (330) | ||
| Sequences: | 11492 (7519.5) | ||
| Seq/Len: | 34.824 | ||
| Nf(neff/√len): | 413.9 |
HHblits Results: (2015_06)
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: 34.824).
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 |
| 150_P | 172_V | 4.362 | 1.00 |
| 187_I | 210_A | 4.330 | 1.00 |
| 380_R | 383_E | 3.975 | 1.00 |
| 346_P | 370_A | 3.491 | 1.00 |
| 127_I | 385_K | 3.175 | 1.00 |
| 100_A | 143_H | 2.959 | 1.00 |
| 341_G | 391_F | 2.917 | 1.00 |
| 367_R | 387_D | 2.773 | 1.00 |
| 188_I | 198_G | 2.769 | 1.00 |
| 187_I | 392_V | 2.766 | 1.00 |
| 114_L | 198_G | 2.448 | 1.00 |
| 185_G | 209_K | 2.369 | 1.00 |
| 187_I | 209_K | 2.362 | 1.00 |
| 141_P | 389_T | 2.358 | 1.00 |
| 177_M | 186_Y | 2.306 | 1.00 |
| 174_D | 205_F | 2.266 | 1.00 |
| 114_L | 173_V | 2.234 | 1.00 |
| 386_T | 390_A | 2.218 | 1.00 |
| 171_R | 204_G | 2.205 | 1.00 |
| 174_D | 201_L | 2.158 | 1.00 |
| 383_E | 387_D | 2.156 | 1.00 |
| 95_T | 156_S | 2.135 | 1.00 |
| 178_K | 207_A | 2.093 | 1.00 |
| 372_G | 380_R | 2.065 | 1.00 |
| 202_G | 211_V | 2.059 | 1.00 |
| 130_L | 385_K | 2.001 | 1.00 |
| 148_S | 153_T | 1.981 | 1.00 |
| 177_M | 182_F | 1.892 | 1.00 |
| 346_P | 371_E | 1.883 | 1.00 |
| 198_G | 211_V | 1.867 | 1.00 |
| 128_L | 146_V | 1.864 | 1.00 |
| 75_R | 78_E | 1.859 | 1.00 |
| 121_F | 148_S | 1.856 | 1.00 |
| 201_L | 208_C | 1.832 | 1.00 |
| 112_A | 177_M | 1.813 | 1.00 |
| 290_P | 293_T | 1.806 | 1.00 |
| 200_L | 204_G | 1.775 | 1.00 |
| 140_L | 389_T | 1.759 | 1.00 |
| 92_E | 175_Q | 1.757 | 1.00 |
| 96_I | 155_S | 1.750 | 1.00 |
| 99_A | 121_F | 1.730 | 1.00 |
| 343_S | 384_L | 1.711 | 1.00 |
| 299_S | 303_L | 1.709 | 1.00 |
| 90_E | 95_T | 1.700 | 1.00 |
| 387_D | 390_A | 1.680 | 1.00 |
| 110_P | 145_V | 1.670 | 1.00 |
| 113_L | 144_L | 1.654 | 1.00 |
| 384_L | 388_L | 1.648 | 1.00 |
| 113_L | 189_Q | 1.646 | 1.00 |
| 98_F | 176_L | 1.643 | 1.00 |
| 167_M | 204_G | 1.639 | 1.00 |
| 190_G | 198_G | 1.627 | 1.00 |
| 110_P | 143_H | 1.625 | 1.00 |
| 210_A | 395_V | 1.614 | 1.00 |
| 149_L | 197_V | 1.598 | 1.00 |
| 130_L | 382_R | 1.592 | 1.00 |
| 121_F | 146_V | 1.587 | 1.00 |
| 97_H | 154_F | 1.580 | 1.00 |
| 369_H | 372_G | 1.580 | 1.00 |
| 382_R | 386_T | 1.579 | 1.00 |
| 354_R | 358_A | 1.576 | 1.00 |
| 88_T | 95_T | 1.569 | 1.00 |
| 369_H | 387_D | 1.556 | 1.00 |
| 367_R | 390_A | 1.533 | 1.00 |
| 173_V | 201_L | 1.513 | 1.00 |
| 112_A | 173_V | 1.507 | 1.00 |
| 174_D | 178_K | 1.498 | 1.00 |
| 109_V | 187_I | 1.495 | 1.00 |
| 89_T | 179_D | 1.487 | 1.00 |
| 189_Q | 388_L | 1.475 | 1.00 |
| 200_L | 203_V | 1.466 | 1.00 |
| 346_P | 368_D | 1.460 | 1.00 |
| 188_I | 201_L | 1.459 | 1.00 |
| 110_P | 182_F | 1.458 | 1.00 |
| 211_V | 340_F | 1.456 | 1.00 |
| 189_Q | 214_N | 1.455 | 1.00 |
| 343_S | 387_D | 1.443 | 1.00 |
| 114_L | 188_I | 1.440 | 1.00 |
| 147_P | 173_V | 1.437 | 1.00 |
| 147_P | 176_L | 1.431 | 1.00 |
| 108_A | 143_H | 1.421 | 1.00 |
| 383_E | 386_T | 1.389 | 0.99 |
| 145_V | 176_L | 1.389 | 0.99 |
| 119_G | 123_E | 1.388 | 0.99 |
| 341_G | 367_R | 1.388 | 0.99 |
| 186_Y | 208_C | 1.386 | 0.99 |
| 114_L | 149_L | 1.368 | 0.99 |
| 73_D | 76_P | 1.363 | 0.99 |
| 168_D | 171_R | 1.362 | 0.99 |
| 111_I | 142_F | 1.341 | 0.99 |
| 343_S | 369_H | 1.337 | 0.99 |
| 291_S | 295_L | 1.336 | 0.99 |
| 174_D | 207_A | 1.335 | 0.99 |
| 113_L | 131_F | 1.307 | 0.99 |
| 122_V | 125_Y | 1.301 | 0.99 |
| 174_D | 186_Y | 1.299 | 0.99 |
| 174_D | 204_G | 1.299 | 0.99 |
| 218_M | 384_L | 1.295 | 0.99 |
| 130_L | 389_T | 1.290 | 0.99 |
| 345_F | 376_A | 1.289 | 0.99 |
| 165_G | 168_D | 1.280 | 0.99 |
| 191_G | 375_F | 1.278 | 0.99 |
| 216_C | 388_L | 1.275 | 0.99 |
| 72_F | 296_E | 1.269 | 0.99 |
| 195_S | 220_A | 1.268 | 0.99 |
| 190_G | 194_G | 1.268 | 0.99 |
| 332_K | 335_Y | 1.257 | 0.99 |
| 195_S | 215_L | 1.250 | 0.99 |
| 348_D | 374_H | 1.248 | 0.99 |
| 142_F | 393_E | 1.242 | 0.98 |
| 201_L | 205_F | 1.242 | 0.98 |
| 115_H | 152_Y | 1.237 | 0.98 |
| 187_I | 216_C | 1.237 | 0.98 |
| 72_F | 77_F | 1.234 | 0.98 |
| 131_F | 385_K | 1.229 | 0.98 |
| 170_A | 200_L | 1.229 | 0.98 |
| 142_F | 187_I | 1.227 | 0.98 |
| 130_L | 133_E | 1.227 | 0.98 |
| 210_A | 216_C | 1.227 | 0.98 |
| 115_H | 147_P | 1.224 | 0.98 |
| 175_Q | 179_D | 1.218 | 0.98 |
| 372_G | 376_A | 1.212 | 0.98 |
| 114_L | 147_P | 1.204 | 0.98 |
| 97_H | 121_F | 1.202 | 0.98 |
| 86_Q | 97_H | 1.188 | 0.98 |
| 296_E | 299_S | 1.180 | 0.98 |
| 177_M | 201_L | 1.171 | 0.98 |
| 358_A | 362_N | 1.171 | 0.98 |
| 347_K | 371_E | 1.168 | 0.97 |
| 142_F | 392_V | 1.166 | 0.97 |
| 116_G | 192_D | 1.166 | 0.97 |
| 371_E | 380_R | 1.165 | 0.97 |
| 176_L | 180_L | 1.165 | 0.97 |
| 182_F | 186_Y | 1.158 | 0.97 |
| 182_F | 185_G | 1.152 | 0.97 |
| 385_K | 389_T | 1.139 | 0.97 |
| 77_F | 80_R | 1.135 | 0.97 |
| 136_T | 139_T | 1.126 | 0.97 |
| 132_R | 144_L | 1.125 | 0.97 |
| 312_H | 315_R | 1.122 | 0.97 |
| 109_V | 209_K | 1.121 | 0.97 |
| 111_I | 144_L | 1.120 | 0.96 |
| 169_N | 313_T | 1.115 | 0.96 |
| 190_G | 195_S | 1.108 | 0.96 |
| 167_M | 200_L | 1.107 | 0.96 |
| 129_Q | 132_R | 1.104 | 0.96 |
| 210_A | 392_V | 1.104 | 0.96 |
| 101_L | 146_V | 1.103 | 0.96 |
| 150_P | 169_N | 1.102 | 0.96 |
| 115_H | 149_L | 1.095 | 0.96 |
| 91_I | 175_Q | 1.092 | 0.96 |
| 94_L | 156_S | 1.080 | 0.95 |
| 94_L | 150_P | 1.078 | 0.95 |
| 111_I | 392_V | 1.069 | 0.95 |
| 126_P | 129_Q | 1.068 | 0.95 |
| 340_F | 364_V | 1.061 | 0.95 |
| 109_V | 185_G | 1.058 | 0.95 |
| 128_L | 144_L | 1.053 | 0.95 |
| 210_A | 391_F | 1.051 | 0.94 |
| 123_E | 377_A | 1.048 | 0.94 |
| 373_G | 379_E | 1.042 | 0.94 |
| 67_K | 292_E | 1.036 | 0.94 |
| 384_L | 387_D | 1.034 | 0.94 |
| 355_S | 358_A | 1.033 | 0.94 |
| 348_D | 351_P | 1.028 | 0.94 |
| 171_R | 175_Q | 1.028 | 0.94 |
| 192_D | 374_H | 1.027 | 0.94 |
| 388_L | 392_V | 1.027 | 0.94 |
| 154_F | 300_L | 1.027 | 0.94 |
| 109_V | 142_F | 1.026 | 0.94 |
| 125_Y | 129_Q | 1.020 | 0.93 |
| 145_V | 180_L | 1.019 | 0.93 |
| 202_G | 336_I | 1.001 | 0.92 |
| 118_P | 192_D | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 3g02A | 2 | 0.9749 | 100 | 0.172 | Contact Map |
| 4qa9A | 1 | 0.9472 | 100 | 0.243 | Contact Map |
| 4qlaA | 2 | 0.9774 | 100 | 0.248 | Contact Map |
| 1ehyA | 4 | 0.6834 | 100 | 0.574 | Contact Map |
| 4inzA | 2 | 0.701 | 100 | 0.597 | Contact Map |
| 5bovA | 4 | 0 | 100 | 0.6 | Contact Map |
| 3r40A | 2 | 0.706 | 100 | 0.601 | Contact Map |
| 4psuA | 1 | 0.706 | 100 | 0.611 | Contact Map |
| 3qyjA | 2 | 0.7035 | 100 | 0.612 | Contact Map |
| 3oosA | 1 | 0.6859 | 100 | 0.614 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)