| EcIDH |
| ID: | 1412716622 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 416 (373) | ||
| Sequences: | 3698 (1781.8) | ||
| Seq/Len: | 9.914 | ||
| Nf(neff/√len): | 92.3 |
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: 9.914).
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 |
| 211_R | 252_E | 4.544 | 1.00 |
| 284_A | 288_Q | 3.554 | 1.00 |
| 210_V | 245_G | 3.460 | 1.00 |
| 44_A | 409_G | 3.290 | 1.00 |
| 47_K | 410_D | 3.203 | 1.00 |
| 211_R | 215_E | 3.134 | 1.00 |
| 218_I | 255_G | 2.852 | 1.00 |
| 86_A | 90_D | 2.837 | 1.00 |
| 203_E | 207_K | 2.828 | 1.00 |
| 369_W | 372_A | 2.795 | 1.00 |
| 93_R | 122_L | 2.746 | 1.00 |
| 365_R | 377_V | 2.588 | 1.00 |
| 50_D | 65_W | 2.574 | 1.00 |
| 42_T | 356_I | 2.558 | 1.00 |
| 386_A | 415_N | 2.528 | 1.00 |
| 354_G | 412_I | 2.492 | 1.00 |
| 74_S | 85_P | 2.422 | 1.00 |
| 218_I | 274_E | 2.410 | 1.00 |
| 44_A | 47_K | 2.408 | 1.00 |
| 365_R | 374_D | 2.390 | 1.00 |
| 382_G | 415_N | 2.375 | 1.00 |
| 210_V | 300_A | 2.360 | 1.00 |
| 30_P | 91_L | 2.359 | 1.00 |
| 31_Y | 46_L | 2.226 | 1.00 |
| 207_K | 247_Q | 2.224 | 1.00 |
| 150_V | 216_Y | 2.211 | 1.00 |
| 226_T | 278_K | 2.189 | 1.00 |
| 411_A | 414_E | 2.173 | 1.00 |
| 39_V | 43_P | 2.170 | 1.00 |
| 383_A | 415_N | 2.149 | 1.00 |
| 357_I | 412_I | 2.113 | 1.00 |
| 349_D | 406_S | 2.108 | 1.00 |
| 207_K | 244_W | 2.091 | 1.00 |
| 349_D | 404_K | 2.091 | 1.00 |
| 358_L | 380_M | 2.038 | 1.00 |
| 37_I | 351_V | 1.999 | 1.00 |
| 228_V | 285_F | 1.987 | 1.00 |
| 207_K | 211_R | 1.969 | 1.00 |
| 409_G | 413_I | 1.968 | 1.00 |
| 93_R | 121_E | 1.957 | 1.00 |
| 49_V | 63_I | 1.956 | 1.00 |
| 245_G | 277_I | 1.912 | 1.00 |
| 82_V | 86_A | 1.905 | 1.00 |
| 32_I | 70_T | 1.899 | 1.00 |
| 215_E | 253_F | 1.894 | 1.00 |
| 28_I | 64_S | 1.888 | 1.00 |
| 211_R | 253_F | 1.874 | 1.00 |
| 224_S | 278_K | 1.832 | 1.00 |
| 90_D | 94_E | 1.826 | 1.00 |
| 388_T | 411_A | 1.821 | 1.00 |
| 128_L | 150_V | 1.821 | 1.00 |
| 69_Y | 77_V | 1.816 | 1.00 |
| 225_V | 277_I | 1.783 | 1.00 |
| 292_R | 295_E | 1.782 | 1.00 |
| 290_L | 312_A | 1.767 | 1.00 |
| 410_D | 414_E | 1.760 | 1.00 |
| 57_Y | 375_L | 1.753 | 1.00 |
| 68_I | 91_L | 1.748 | 1.00 |
| 394_E | 402_L | 1.723 | 1.00 |
| 361_E | 377_V | 1.718 | 1.00 |
| 349_D | 405_C | 1.685 | 1.00 |
| 365_R | 373_A | 1.676 | 1.00 |
| 151_I | 310_S | 1.675 | 1.00 |
| 244_W | 247_Q | 1.675 | 1.00 |
| 46_L | 67_E | 1.670 | 1.00 |
| 240_A | 244_W | 1.658 | 1.00 |
| 30_P | 95_Y | 1.626 | 1.00 |
| 248_L | 252_E | 1.623 | 1.00 |
| 413_I | 416_M | 1.607 | 1.00 |
| 45_M | 360_A | 1.576 | 1.00 |
| 374_D | 378_K | 1.573 | 1.00 |
| 345_Y | 351_V | 1.568 | 1.00 |
| 70_T | 118_L | 1.561 | 1.00 |
| 227_L | 245_G | 1.552 | 1.00 |
| 203_E | 247_Q | 1.531 | 1.00 |
| 65_W | 360_A | 1.522 | 1.00 |
| 84_L | 89_L | 1.515 | 1.00 |
| 52_A | 376_I | 1.490 | 1.00 |
| 30_P | 92_I | 1.485 | 1.00 |
| 45_M | 356_I | 1.476 | 1.00 |
| 246_Y | 279_D | 1.466 | 1.00 |
| 47_K | 413_I | 1.464 | 1.00 |
| 383_A | 411_A | 1.445 | 1.00 |
| 404_K | 407_E | 1.444 | 1.00 |
| 388_T | 403_L | 1.436 | 1.00 |
| 286_L | 309_I | 1.430 | 1.00 |
| 117_A | 121_E | 1.423 | 1.00 |
| 378_K | 382_G | 1.410 | 0.99 |
| 152_F | 212_A | 1.410 | 0.99 |
| 227_L | 279_D | 1.403 | 0.99 |
| 69_Y | 78_Y | 1.401 | 0.99 |
| 89_L | 121_E | 1.400 | 0.99 |
| 48_V | 376_I | 1.388 | 0.99 |
| 222_R | 297_D | 1.384 | 0.99 |
| 370_T | 374_D | 1.365 | 0.99 |
| 90_D | 93_R | 1.360 | 0.99 |
| 210_V | 248_L | 1.356 | 0.99 |
| 408_F | 412_I | 1.343 | 0.99 |
| 159_I | 302_M | 1.341 | 0.99 |
| 128_L | 152_F | 1.335 | 0.99 |
| 247_Q | 251_E | 1.329 | 0.99 |
| 152_F | 216_Y | 1.324 | 0.99 |
| 51_A | 413_I | 1.322 | 0.99 |
| 73_K | 77_V | 1.318 | 0.99 |
| 151_I | 313_L | 1.313 | 0.99 |
| 100_K | 115_N | 1.309 | 0.99 |
| 85_P | 88_T | 1.309 | 0.99 |
| 69_Y | 74_S | 1.306 | 0.99 |
| 155_N | 327_N | 1.300 | 0.99 |
| 345_Y | 391_Y | 1.298 | 0.99 |
| 132_R | 381_E | 1.294 | 0.99 |
| 344_K | 391_Y | 1.291 | 0.99 |
| 47_K | 409_G | 1.290 | 0.99 |
| 78_Y | 82_V | 1.290 | 0.99 |
| 211_R | 248_L | 1.289 | 0.99 |
| 354_G | 408_F | 1.287 | 0.99 |
| 216_Y | 220_N | 1.281 | 0.99 |
| 74_S | 78_Y | 1.268 | 0.99 |
| 228_V | 282_A | 1.266 | 0.99 |
| 215_E | 218_I | 1.265 | 0.99 |
| 45_M | 99_I | 1.264 | 0.99 |
| 66_M | 95_Y | 1.257 | 0.99 |
| 92_I | 98_A | 1.255 | 0.99 |
| 214_I | 253_F | 1.250 | 0.99 |
| 30_P | 68_I | 1.250 | 0.99 |
| 350_K | 391_Y | 1.245 | 0.98 |
| 215_E | 219_A | 1.244 | 0.98 |
| 46_L | 50_D | 1.240 | 0.98 |
| 44_A | 349_D | 1.238 | 0.98 |
| 364_L | 372_A | 1.227 | 0.98 |
| 213_A | 225_V | 1.227 | 0.98 |
| 149_M | 289_I | 1.226 | 0.98 |
| 74_S | 88_T | 1.221 | 0.98 |
| 135_Q | 385_N | 1.221 | 0.98 |
| 280_V | 284_A | 1.212 | 0.98 |
| 125_Y | 330_D | 1.209 | 0.98 |
| 214_I | 249_A | 1.208 | 0.98 |
| 288_Q | 295_E | 1.208 | 0.98 |
| 243_D | 247_Q | 1.196 | 0.98 |
| 285_F | 296_Y | 1.190 | 0.98 |
| 199_K | 302_M | 1.184 | 0.98 |
| 204_E | 207_K | 1.181 | 0.98 |
| 66_M | 94_E | 1.179 | 0.98 |
| 45_M | 357_I | 1.169 | 0.97 |
| 214_I | 275_I | 1.168 | 0.97 |
| 280_V | 296_Y | 1.167 | 0.97 |
| 245_G | 300_A | 1.158 | 0.97 |
| 280_V | 288_Q | 1.158 | 0.97 |
| 344_K | 351_V | 1.154 | 0.97 |
| 357_I | 376_I | 1.151 | 0.97 |
| 286_L | 312_A | 1.145 | 0.97 |
| 41_V | 356_I | 1.141 | 0.97 |
| 280_V | 285_F | 1.135 | 0.97 |
| 61_R | 369_W | 1.134 | 0.97 |
| 201_C | 206_T | 1.132 | 0.97 |
| 231_G | 242_K | 1.130 | 0.97 |
| 49_V | 360_A | 1.127 | 0.97 |
| 136_G | 385_N | 1.114 | 0.96 |
| 223_D | 297_D | 1.111 | 0.96 |
| 102_P | 339_H | 1.096 | 0.96 |
| 238_E | 305_N | 1.094 | 0.96 |
| 33_E | 67_E | 1.078 | 0.95 |
| 203_E | 244_W | 1.077 | 0.95 |
| 354_G | 384_I | 1.077 | 0.95 |
| 132_R | 148_D | 1.076 | 0.95 |
| 360_A | 363_M | 1.072 | 0.95 |
| 407_E | 410_D | 1.065 | 0.95 |
| 225_V | 248_L | 1.062 | 0.95 |
| 337_A | 356_I | 1.061 | 0.95 |
| 229_H | 242_K | 1.059 | 0.95 |
| 357_I | 380_M | 1.059 | 0.95 |
| 127_C | 338_T | 1.056 | 0.95 |
| 206_T | 210_V | 1.056 | 0.95 |
| 224_S | 276_V | 1.056 | 0.95 |
| 291_L | 315_A | 1.049 | 0.94 |
| 354_G | 380_M | 1.048 | 0.94 |
| 44_A | 410_D | 1.042 | 0.94 |
| 384_I | 389_V | 1.039 | 0.94 |
| 278_K | 295_E | 1.036 | 0.94 |
| 218_I | 225_V | 1.035 | 0.94 |
| 225_V | 275_I | 1.033 | 0.94 |
| 123_D | 208_R | 1.027 | 0.93 |
| 365_R | 370_T | 1.027 | 0.93 |
| 345_Y | 350_K | 1.018 | 0.93 |
| 403_L | 411_A | 1.010 | 0.93 |
| 41_V | 101_G | 1.009 | 0.93 |
| 225_V | 298_V | 1.006 | 0.93 |
| 411_A | 415_N | 1.005 | 0.92 |
| 228_V | 309_I | 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 | |
| 2d4vA | 4 | 0.9952 | 100 | 0.077 | Contact Map |
| 3dmsA | 1 | 0.988 | 100 | 0.082 | Contact Map |
| 2iv0A | 2 | 0.9784 | 100 | 0.09 | Contact Map |
| 1hqsA | 2 | 0.976 | 100 | 0.095 | Contact Map |
| 1tyoA | 2 | 0.9856 | 100 | 0.095 | Contact Map |
| 2e0cA | 2 | 0.9567 | 100 | 0.099 | Contact Map |
| 3flkA | 4 | 0.8197 | 100 | 0.173 | Contact Map |
| 1x0lA | 2 | 0.7885 | 100 | 0.18 | Contact Map |
| 2d1cA | 2 | 0.8462 | 100 | 0.181 | Contact Map |
| 3ty4A | 2 | 0.8125 | 100 | 0.182 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)