| sub4 |
| ID: | 1404136527 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 409 (388) | ||
| Sequences: | 1987 (1137.6) | ||
| Seq/Len: | 5.121 | ||
| Nf(neff/√len): | 57.8 |
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: 5.121).
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 |
| 198_P | 291_K | 4.602 | 1.00 |
| 285_E | 288_K | 3.909 | 1.00 |
| 195_E | 291_K | 3.290 | 1.00 |
| 225_P | 228_V | 3.220 | 1.00 |
| 269_R | 274_D | 3.144 | 1.00 |
| 119_I | 293_A | 2.729 | 1.00 |
| 68_K | 71_E | 2.713 | 1.00 |
| 191_K | 295_E | 2.653 | 1.00 |
| 224_I | 234_L | 2.642 | 1.00 |
| 267_G | 281_R | 2.613 | 1.00 |
| 111_P | 259_T | 2.591 | 1.00 |
| 123_L | 156_I | 2.584 | 1.00 |
| 202_D | 284_R | 2.580 | 1.00 |
| 267_G | 274_D | 2.555 | 1.00 |
| 281_R | 285_E | 2.420 | 1.00 |
| 118_V | 256_G | 2.379 | 1.00 |
| 263_D | 285_E | 2.313 | 1.00 |
| 162_W | 189_E | 2.294 | 1.00 |
| 104_L | 342_V | 2.257 | 1.00 |
| 45_V | 55_V | 2.138 | 1.00 |
| 341_E | 356_Y | 2.123 | 1.00 |
| 86_D | 403_V | 2.090 | 1.00 |
| 119_I | 290_I | 2.075 | 1.00 |
| 98_A | 173_I | 2.058 | 1.00 |
| 187_V | 294_L | 2.033 | 1.00 |
| 341_E | 358_V | 2.025 | 1.00 |
| 215_Y | 219_R | 1.986 | 1.00 |
| 96_A | 346_T | 1.976 | 1.00 |
| 110_P | 113_A | 1.865 | 1.00 |
| 259_T | 296_R | 1.849 | 1.00 |
| 85_M | 370_V | 1.847 | 1.00 |
| 70_M | 368_V | 1.844 | 1.00 |
| 52_V | 393_M | 1.770 | 1.00 |
| 95_L | 121_N | 1.761 | 1.00 |
| 191_K | 291_K | 1.704 | 1.00 |
| 45_V | 393_M | 1.701 | 1.00 |
| 222_G | 396_I | 1.691 | 1.00 |
| 112_R | 181_D | 1.691 | 1.00 |
| 126_L | 283_M | 1.688 | 1.00 |
| 260_Y | 293_A | 1.686 | 1.00 |
| 116_I | 178_V | 1.685 | 1.00 |
| 70_M | 78_N | 1.684 | 1.00 |
| 384_A | 400_L | 1.671 | 0.99 |
| 403_V | 406_D | 1.621 | 0.99 |
| 115_T | 260_Y | 1.618 | 0.99 |
| 100_A | 357_I | 1.585 | 0.99 |
| 234_L | 380_S | 1.576 | 0.99 |
| 115_T | 256_G | 1.572 | 0.99 |
| 118_V | 293_A | 1.543 | 0.99 |
| 215_Y | 273_F | 1.536 | 0.99 |
| 102_E | 117_R | 1.535 | 0.99 |
| 205_E | 284_R | 1.523 | 0.99 |
| 357_I | 368_V | 1.521 | 0.99 |
| 228_V | 383_Y | 1.520 | 0.99 |
| 155_T | 196_V | 1.518 | 0.99 |
| 159_L | 190_L | 1.517 | 0.99 |
| 54_E | 386_K | 1.509 | 0.99 |
| 114_E | 255_S | 1.502 | 0.99 |
| 166_Q | 169_H | 1.502 | 0.99 |
| 261_T | 292_Q | 1.501 | 0.99 |
| 343_Y | 354_G | 1.492 | 0.99 |
| 191_K | 294_L | 1.489 | 0.98 |
| 96_A | 355_Y | 1.480 | 0.98 |
| 39_G | 42_R | 1.467 | 0.98 |
| 118_V | 260_Y | 1.457 | 0.98 |
| 358_V | 366_Y | 1.455 | 0.98 |
| 129_H | 282_E | 1.449 | 0.98 |
| 388_E | 396_I | 1.427 | 0.98 |
| 342_V | 357_I | 1.425 | 0.98 |
| 256_G | 260_Y | 1.401 | 0.98 |
| 38_H | 41_L | 1.399 | 0.97 |
| 198_P | 287_V | 1.384 | 0.97 |
| 186_F | 190_L | 1.381 | 0.97 |
| 82_T | 94_D | 1.378 | 0.97 |
| 194_L | 291_K | 1.377 | 0.97 |
| 71_E | 367_R | 1.377 | 0.97 |
| 46_T | 54_E | 1.372 | 0.97 |
| 48_S | 53_L | 1.372 | 0.97 |
| 329_K | 333_E | 1.370 | 0.97 |
| 209_A | 276_M | 1.369 | 0.97 |
| 314_R | 317_L | 1.367 | 0.97 |
| 255_S | 260_Y | 1.366 | 0.97 |
| 201_I | 283_M | 1.342 | 0.97 |
| 93_H | 355_Y | 1.325 | 0.96 |
| 355_Y | 370_V | 1.322 | 0.96 |
| 43_L | 55_V | 1.317 | 0.96 |
| 113_A | 178_V | 1.312 | 0.96 |
| 246_Y | 251_A | 1.303 | 0.96 |
| 109_V | 114_E | 1.298 | 0.96 |
| 263_D | 288_K | 1.298 | 0.96 |
| 89_H | 403_V | 1.294 | 0.96 |
| 245_N | 250_K | 1.291 | 0.95 |
| 229_A | 270_G | 1.290 | 0.95 |
| 92_A | 349_A | 1.284 | 0.95 |
| 115_T | 298_E | 1.283 | 0.95 |
| 359_S | 365_P | 1.283 | 0.95 |
| 89_H | 92_A | 1.280 | 0.95 |
| 270_G | 274_D | 1.265 | 0.95 |
| 226_P | 244_V | 1.262 | 0.95 |
| 187_V | 191_K | 1.249 | 0.94 |
| 152_E | 204_Y | 1.246 | 0.94 |
| 198_P | 284_R | 1.235 | 0.94 |
| 86_D | 350_R | 1.233 | 0.94 |
| 103_K | 342_V | 1.231 | 0.94 |
| 322_E | 325_I | 1.231 | 0.94 |
| 86_D | 89_H | 1.228 | 0.94 |
| 383_Y | 386_K | 1.226 | 0.93 |
| 345_P | 352_E | 1.214 | 0.93 |
| 188_P | 192_K | 1.212 | 0.93 |
| 128_S | 401_D | 1.206 | 0.93 |
| 262_F | 292_Q | 1.194 | 0.92 |
| 205_E | 280_I | 1.182 | 0.92 |
| 398_A | 402_P | 1.175 | 0.91 |
| 214_F | 218_A | 1.174 | 0.91 |
| 372_A | 406_D | 1.173 | 0.91 |
| 289_I | 292_Q | 1.171 | 0.91 |
| 100_A | 342_V | 1.169 | 0.91 |
| 30_V | 45_V | 1.163 | 0.91 |
| 159_L | 186_F | 1.148 | 0.90 |
| 229_A | 239_L | 1.145 | 0.90 |
| 306_N | 312_P | 1.145 | 0.90 |
| 88_L | 401_D | 1.140 | 0.90 |
| 241_A | 278_V | 1.137 | 0.90 |
| 115_T | 296_R | 1.137 | 0.90 |
| 360_D | 366_Y | 1.135 | 0.90 |
| 321_M | 325_I | 1.131 | 0.89 |
| 92_A | 124_S | 1.131 | 0.89 |
| 134_G | 149_A | 1.129 | 0.89 |
| 183_P | 186_F | 1.120 | 0.89 |
| 127_A | 156_I | 1.118 | 0.89 |
| 195_E | 198_P | 1.116 | 0.88 |
| 96_A | 344_V | 1.108 | 0.88 |
| 260_Y | 289_I | 1.108 | 0.88 |
| 111_P | 114_E | 1.106 | 0.88 |
| 118_V | 255_S | 1.106 | 0.88 |
| 279_R | 282_E | 1.103 | 0.88 |
| 127_A | 160_F | 1.096 | 0.87 |
| 30_V | 393_M | 1.095 | 0.87 |
| 355_Y | 368_V | 1.095 | 0.87 |
| 304_D | 307_P | 1.095 | 0.87 |
| 111_P | 115_T | 1.093 | 0.87 |
| 122_E | 125_R | 1.091 | 0.87 |
| 108_V | 114_E | 1.089 | 0.87 |
| 128_S | 131_V | 1.087 | 0.87 |
| 86_D | 401_D | 1.085 | 0.86 |
| 120_L | 172_Y | 1.085 | 0.86 |
| 245_N | 251_A | 1.085 | 0.86 |
| 228_V | 231_D | 1.085 | 0.86 |
| 30_V | 37_T | 1.084 | 0.86 |
| 85_M | 355_Y | 1.081 | 0.86 |
| 30_V | 394_V | 1.081 | 0.86 |
| 239_L | 244_V | 1.078 | 0.86 |
| 187_V | 297_L | 1.074 | 0.86 |
| 78_N | 365_P | 1.073 | 0.86 |
| 132_F | 401_D | 1.070 | 0.85 |
| 89_H | 406_D | 1.063 | 0.85 |
| 238_S | 400_L | 1.061 | 0.85 |
| 127_A | 131_V | 1.056 | 0.84 |
| 86_D | 406_D | 1.056 | 0.84 |
| 104_L | 359_S | 1.050 | 0.84 |
| 55_V | 393_M | 1.050 | 0.84 |
| 272_V | 396_I | 1.046 | 0.84 |
| 43_L | 393_M | 1.045 | 0.84 |
| 100_A | 344_V | 1.044 | 0.83 |
| 198_P | 202_D | 1.042 | 0.83 |
| 219_R | 273_F | 1.042 | 0.83 |
| 234_L | 238_S | 1.041 | 0.83 |
| 92_A | 121_N | 1.037 | 0.83 |
| 89_H | 93_H | 1.034 | 0.83 |
| 273_F | 277_L | 1.032 | 0.83 |
| 83_P | 171_N | 1.030 | 0.82 |
| 217_R | 249_R | 1.027 | 0.82 |
| 272_V | 395_A | 1.027 | 0.82 |
| 184_E | 187_V | 1.024 | 0.82 |
| 70_M | 82_T | 1.023 | 0.82 |
| 348_S | 353_L | 1.021 | 0.82 |
| 320_S | 323_A | 1.018 | 0.81 |
| 245_N | 264_V | 1.018 | 0.81 |
| 125_R | 286_S | 1.016 | 0.81 |
| 125_R | 249_R | 1.015 | 0.81 |
| 382_P | 386_K | 1.015 | 0.81 |
| 197_L | 283_M | 1.013 | 0.81 |
| 350_R | 402_P | 1.012 | 0.81 |
| 44_M | 56_V | 1.012 | 0.81 |
| 320_S | 330_H | 1.009 | 0.81 |
| 25_V | 46_T | 1.002 | 0.80 |
| 128_S | 350_R | 1.001 | 0.80 |
| 89_H | 401_D | 1.000 | 0.80 |
| 194_L | 287_V | 1.000 | 0.80 |
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 | |
| 3i9v4 | 2 | 0.9218 | 100 | 0.055 | Contact Map |
| 4kn9L | 2 | 0.8606 | 100 | 0.283 | Contact Map |
| 4omfA | 1 | 0.8557 | 100 | 0.289 | Contact Map |
| 3ze9B | 1 | 0.8631 | 100 | 0.291 | Contact Map |
| 1yqwQ | 3 | 0.89 | 100 | 0.329 | Contact Map |
| 1wuiL | 1 | 0.8729 | 100 | 0.338 | Contact Map |
| 1yq9H | 2 | 0.868 | 100 | 0.345 | Contact Map |
| 1e3dB | 2 | 0.8826 | 100 | 0.345 | Contact Map |
| 3myrB | 4 | 0.8802 | 100 | 0.402 | Contact Map |
| 3uqyL | 2 | 0.9095 | 100 | 0.406 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)