| 1dmb |
| ID: | 1466421678 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 370 (366) | ||
| Sequences: | 19339 (12663.6) | ||
| Seq/Len: | 52.839 | ||
| Nf(neff/√len): | 661.9 |
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: 52.839).
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 |
| 77_A | 273_K | 3.876 | 1.00 |
| 120_D | 241_N | 3.838 | 1.00 |
| 189_K | 358_D | 3.761 | 1.00 |
| 356_T | 359_E | 3.509 | 1.00 |
| 196_V | 200_K | 3.355 | 1.00 |
| 6_K | 36_T | 3.354 | 1.00 |
| 119_K | 243_G | 3.274 | 1.00 |
| 78_E | 102_K | 3.206 | 1.00 |
| 193_T | 197_D | 3.204 | 1.00 |
| 358_D | 362_K | 2.915 | 1.00 |
| 33_I | 275_L | 2.871 | 1.00 |
| 21_A | 25_K | 2.766 | 1.00 |
| 117_Y | 243_G | 2.756 | 1.00 |
| 128_T | 131_E | 2.741 | 1.00 |
| 133_P | 197_D | 2.739 | 1.00 |
| 27_F | 278_E | 2.704 | 1.00 |
| 6_K | 34_K | 2.623 | 1.00 |
| 197_D | 201_N | 2.601 | 1.00 |
| 26_K | 29_K | 2.569 | 1.00 |
| 122_L | 224_M | 2.561 | 1.00 |
| 362_K | 366_T | 2.557 | 1.00 |
| 28_E | 34_K | 2.555 | 1.00 |
| 193_T | 357_V | 2.484 | 1.00 |
| 137_K | 201_N | 2.477 | 1.00 |
| 134_A | 138_E | 2.454 | 1.00 |
| 98_R | 103_L | 2.368 | 1.00 |
| 365_Q | 369_T | 2.347 | 1.00 |
| 137_K | 141_A | 2.288 | 1.00 |
| 80_T | 102_K | 2.257 | 1.00 |
| 355_Q | 363_D | 2.253 | 1.00 |
| 286_T | 289_G | 2.227 | 1.00 |
| 22_E | 25_K | 2.218 | 1.00 |
| 186_A | 190_A | 2.215 | 1.00 |
| 25_K | 29_K | 2.198 | 1.00 |
| 24_G | 28_E | 2.184 | 1.00 |
| 131_E | 134_A | 2.177 | 1.00 |
| 26_K | 283_Y | 2.176 | 1.00 |
| 184_D | 362_K | 2.173 | 1.00 |
| 272_N | 275_L | 2.168 | 1.00 |
| 349_N | 354_R | 2.154 | 1.00 |
| 58_D | 272_N | 2.095 | 1.00 |
| 8_V | 36_T | 2.092 | 1.00 |
| 42_K | 45_E | 2.075 | 1.00 |
| 278_E | 281_E | 2.058 | 1.00 |
| 190_A | 193_T | 2.041 | 1.00 |
| 91_P | 95_D | 2.036 | 1.00 |
| 119_K | 123_P | 2.028 | 1.00 |
| 359_E | 363_D | 1.968 | 1.00 |
| 134_A | 137_K | 1.946 | 1.00 |
| 139_L | 223_A | 1.931 | 1.00 |
| 274_E | 278_E | 1.923 | 1.00 |
| 291_E | 295_K | 1.921 | 1.00 |
| 82_D | 277_K | 1.913 | 1.00 |
| 349_N | 355_Q | 1.907 | 1.00 |
| 24_G | 279_F | 1.903 | 1.00 |
| 26_K | 292_A | 1.886 | 1.00 |
| 117_Y | 245_T | 1.863 | 1.00 |
| 121_L | 223_A | 1.844 | 1.00 |
| 127_K | 131_E | 1.832 | 1.00 |
| 115_L | 245_T | 1.825 | 1.00 |
| 189_K | 357_V | 1.796 | 1.00 |
| 130_E | 133_P | 1.791 | 1.00 |
| 359_E | 362_K | 1.763 | 1.00 |
| 60_I | 267_N | 1.747 | 1.00 |
| 209_D | 212_I | 1.743 | 1.00 |
| 27_F | 33_I | 1.734 | 1.00 |
| 133_P | 137_K | 1.717 | 1.00 |
| 119_K | 241_N | 1.717 | 1.00 |
| 25_K | 28_E | 1.714 | 1.00 |
| 350_A | 360_A | 1.708 | 1.00 |
| 266_I | 280_L | 1.707 | 1.00 |
| 193_T | 358_D | 1.686 | 1.00 |
| 189_K | 193_T | 1.684 | 1.00 |
| 24_G | 37_V | 1.683 | 1.00 |
| 22_E | 26_K | 1.666 | 1.00 |
| 26_K | 30_D | 1.663 | 1.00 |
| 138_E | 142_K | 1.661 | 1.00 |
| 216_A | 221_E | 1.661 | 1.00 |
| 71_A | 104_I | 1.651 | 1.00 |
| 130_E | 134_A | 1.641 | 1.00 |
| 121_L | 139_L | 1.639 | 1.00 |
| 363_D | 367_R | 1.636 | 1.00 |
| 28_E | 31_T | 1.622 | 1.00 |
| 115_L | 224_M | 1.618 | 1.00 |
| 31_T | 278_E | 1.618 | 1.00 |
| 196_V | 350_A | 1.607 | 1.00 |
| 363_D | 366_T | 1.601 | 1.00 |
| 97_V | 263_S | 1.586 | 1.00 |
| 95_D | 98_R | 1.576 | 1.00 |
| 76_L | 265_G | 1.570 | 1.00 |
| 346_A | 363_D | 1.569 | 1.00 |
| 51_A | 56_G | 1.534 | 1.00 |
| 27_F | 279_F | 1.533 | 1.00 |
| 77_A | 268_A | 1.513 | 1.00 |
| 133_P | 198_L | 1.498 | 1.00 |
| 355_Q | 360_A | 1.492 | 1.00 |
| 4_E | 34_K | 1.488 | 1.00 |
| 287_D | 291_E | 1.484 | 1.00 |
| 148_M | 222_T | 1.475 | 1.00 |
| 270_S | 273_K | 1.475 | 1.00 |
| 194_F | 197_D | 1.450 | 1.00 |
| 133_P | 201_N | 1.445 | 1.00 |
| 126_P | 131_E | 1.441 | 1.00 |
| 268_A | 273_K | 1.435 | 1.00 |
| 133_P | 194_F | 1.433 | 1.00 |
| 346_A | 355_Q | 1.415 | 1.00 |
| 362_K | 365_Q | 1.411 | 1.00 |
| 217_F | 242_Y | 1.408 | 1.00 |
| 187_G | 190_A | 1.406 | 0.99 |
| 350_A | 357_V | 1.403 | 0.99 |
| 78_E | 81_P | 1.391 | 0.99 |
| 27_F | 275_L | 1.389 | 0.99 |
| 33_I | 278_E | 1.383 | 0.99 |
| 136_D | 224_M | 1.378 | 0.99 |
| 47_F | 60_I | 1.374 | 0.99 |
| 8_V | 38_E | 1.363 | 0.99 |
| 275_L | 278_E | 1.358 | 0.99 |
| 137_K | 203_H | 1.354 | 0.99 |
| 59_I | 280_L | 1.352 | 0.99 |
| 17_Y | 21_A | 1.340 | 0.99 |
| 122_L | 135_L | 1.336 | 0.99 |
| 135_L | 138_E | 1.334 | 0.99 |
| 215_A | 219_K | 1.331 | 0.99 |
| 355_Q | 359_E | 1.330 | 0.99 |
| 59_I | 276_A | 1.328 | 0.99 |
| 24_G | 35_V | 1.320 | 0.99 |
| 118_N | 121_L | 1.320 | 0.99 |
| 189_K | 361_L | 1.316 | 0.99 |
| 27_F | 283_Y | 1.316 | 0.99 |
| 292_A | 296_D | 1.313 | 0.99 |
| 10_W | 50_V | 1.296 | 0.99 |
| 346_A | 349_N | 1.292 | 0.99 |
| 342_A | 367_R | 1.274 | 0.99 |
| 289_G | 292_A | 1.273 | 0.99 |
| 318_A | 322_E | 1.272 | 0.99 |
| 192_L | 350_A | 1.269 | 0.99 |
| 349_N | 363_D | 1.259 | 0.99 |
| 59_I | 279_F | 1.257 | 0.99 |
| 197_D | 200_K | 1.249 | 0.99 |
| 135_L | 224_M | 1.244 | 0.98 |
| 22_E | 292_A | 1.237 | 0.98 |
| 46_K | 50_V | 1.234 | 0.98 |
| 193_T | 196_V | 1.229 | 0.98 |
| 122_L | 139_L | 1.227 | 0.98 |
| 105_A | 263_S | 1.218 | 0.98 |
| 266_I | 276_A | 1.200 | 0.98 |
| 26_K | 288_E | 1.197 | 0.98 |
| 88_K | 306_S | 1.185 | 0.98 |
| 216_A | 222_T | 1.180 | 0.98 |
| 273_K | 277_K | 1.179 | 0.98 |
| 62_W | 265_G | 1.171 | 0.98 |
| 164_D | 190_A | 1.170 | 0.97 |
| 114_S | 244_V | 1.166 | 0.97 |
| 28_E | 32_G | 1.164 | 0.97 |
| 288_E | 291_E | 1.155 | 0.97 |
| 140_K | 203_H | 1.152 | 0.97 |
| 196_V | 357_V | 1.146 | 0.97 |
| 138_E | 141_A | 1.143 | 0.97 |
| 58_D | 270_S | 1.143 | 0.97 |
| 18_N | 21_A | 1.135 | 0.97 |
| 130_E | 251_K | 1.123 | 0.97 |
| 71_A | 99_Y | 1.119 | 0.96 |
| 105_A | 265_G | 1.114 | 0.96 |
| 35_V | 279_F | 1.112 | 0.96 |
| 277_K | 281_E | 1.109 | 0.96 |
| 136_D | 203_H | 1.105 | 0.96 |
| 5_G | 272_N | 1.097 | 0.96 |
| 77_A | 270_S | 1.093 | 0.96 |
| 184_D | 365_Q | 1.092 | 0.96 |
| 366_T | 369_T | 1.086 | 0.96 |
| 97_V | 103_L | 1.078 | 0.95 |
| 194_F | 198_L | 1.068 | 0.95 |
| 279_F | 284_L | 1.061 | 0.95 |
| 170_K | 175_K | 1.061 | 0.95 |
| 30_D | 278_E | 1.057 | 0.95 |
| 132_I | 136_D | 1.056 | 0.95 |
| 346_A | 364_A | 1.055 | 0.95 |
| 140_K | 146_A | 1.054 | 0.95 |
| 227_N | 231_A | 1.046 | 0.94 |
| 161_I | 188_A | 1.046 | 0.94 |
| 274_E | 277_K | 1.040 | 0.94 |
| 108_I | 264_A | 1.031 | 0.94 |
| 116_I | 227_N | 1.024 | 0.93 |
| 279_F | 283_Y | 1.021 | 0.93 |
| 190_A | 194_F | 1.021 | 0.93 |
| 283_Y | 289_G | 1.018 | 0.93 |
| 322_E | 325_Q | 1.018 | 0.93 |
| 44_E | 66_R | 1.017 | 0.93 |
| 74_G | 268_A | 1.009 | 0.93 |
| 94_W | 103_L | 1.002 | 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 | |
| 3oaiA | 2 | 0.9919 | 100 | 0.025 | Contact Map |
| 3dm0A | 1 | 1 | 100 | 0.028 | Contact Map |
| 2nvuB | 1 | 0.9676 | 100 | 0.031 | Contact Map |
| 3csgA | 1 | 0.9865 | 100 | 0.034 | Contact Map |
| 4kegA | 1 | 1 | 100 | 0.034 | Contact Map |
| 3f5fA | 1 | 1 | 100 | 0.035 | Contact Map |
| 3py7A | 1 | 0.9973 | 100 | 0.036 | Contact Map |
| 3o3uN | 1 | 0.9973 | 100 | 0.037 | Contact Map |
| 1hsjA | 2 | 1 | 100 | 0.037 | Contact Map |
| 3waiA | 1 | 0.9757 | 100 | 0.038 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)