| VV_TRAP_LARGE |
| ID: | 1515979586 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 429 (414) | ||
| Sequences: | 20978 (11466.3) | ||
| Seq/Len: | 50.671 | ||
| Nf(neff/√len): | 563.5 |
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: 50.671).
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 |
| 102_L | 182_C | 3.636 | 1.00 |
| 127_R | 133_D | 3.536 | 1.00 |
| 388_P | 391_T | 3.419 | 1.00 |
| 320_N | 364_N | 3.344 | 1.00 |
| 299_Q | 303_D | 3.068 | 1.00 |
| 311_N | 314_V | 3.056 | 1.00 |
| 71_S | 263_G | 2.908 | 1.00 |
| 81_F | 85_M | 2.562 | 1.00 |
| 300_M | 304_Y | 2.442 | 1.00 |
| 391_T | 394_R | 2.427 | 1.00 |
| 101_S | 118_L | 2.415 | 1.00 |
| 229_G | 235_F | 2.395 | 1.00 |
| 290_W | 294_R | 2.374 | 1.00 |
| 184_A | 406_V | 2.364 | 1.00 |
| 95_H | 186_M | 2.338 | 1.00 |
| 76_E | 80_N | 2.291 | 1.00 |
| 89_I | 92_S | 2.270 | 1.00 |
| 390_H | 394_R | 2.269 | 1.00 |
| 214_K | 218_L | 2.261 | 1.00 |
| 269_R | 273_N | 2.252 | 1.00 |
| 81_F | 84_S | 2.217 | 1.00 |
| 270_E | 273_N | 2.214 | 1.00 |
| 347_A | 357_F | 2.189 | 1.00 |
| 67_H | 270_E | 2.182 | 1.00 |
| 188_M | 402_P | 2.167 | 1.00 |
| 300_M | 303_D | 2.124 | 1.00 |
| 260_T | 263_G | 2.099 | 1.00 |
| 166_S | 169_A | 2.095 | 1.00 |
| 401_V | 405_I | 2.079 | 1.00 |
| 397_L | 401_V | 2.077 | 1.00 |
| 134_D | 391_T | 2.063 | 1.00 |
| 95_H | 190_Y | 2.015 | 1.00 |
| 71_S | 266_E | 2.014 | 1.00 |
| 71_S | 270_E | 2.007 | 1.00 |
| 348_S | 354_P | 2.005 | 1.00 |
| 415_Q | 422_E | 1.991 | 1.00 |
| 262_T | 266_E | 1.990 | 1.00 |
| 25_I | 284_G | 1.989 | 1.00 |
| 67_H | 70_N | 1.972 | 1.00 |
| 46_Q | 294_R | 1.884 | 1.00 |
| 415_Q | 419_L | 1.881 | 1.00 |
| 296_Q | 299_Q | 1.878 | 1.00 |
| 320_N | 411_A | 1.876 | 1.00 |
| 71_S | 267_I | 1.868 | 1.00 |
| 325_F | 329_F | 1.863 | 1.00 |
| 323_L | 339_L | 1.854 | 1.00 |
| 326_L | 335_L | 1.828 | 1.00 |
| 179_I | 183_V | 1.826 | 1.00 |
| 303_D | 306_L | 1.802 | 1.00 |
| 156_L | 359_V | 1.751 | 1.00 |
| 187_V | 191_F | 1.708 | 1.00 |
| 303_D | 307_S | 1.704 | 1.00 |
| 67_H | 71_S | 1.699 | 1.00 |
| 415_Q | 418_L | 1.693 | 1.00 |
| 68_L | 252_G | 1.689 | 1.00 |
| 67_H | 271_T | 1.663 | 1.00 |
| 97_N | 140_T | 1.663 | 1.00 |
| 315_L | 350_V | 1.651 | 1.00 |
| 304_Y | 307_S | 1.629 | 1.00 |
| 169_A | 422_E | 1.626 | 1.00 |
| 408_A | 412_V | 1.603 | 1.00 |
| 181_C | 403_L | 1.576 | 1.00 |
| 115_A | 381_V | 1.568 | 1.00 |
| 169_A | 172_L | 1.558 | 1.00 |
| 160_G | 167_I | 1.546 | 1.00 |
| 290_W | 293_A | 1.540 | 1.00 |
| 310_E | 314_V | 1.533 | 1.00 |
| 321_L | 325_F | 1.523 | 1.00 |
| 191_F | 194_K | 1.509 | 1.00 |
| 262_T | 265_V | 1.508 | 1.00 |
| 188_M | 192_I | 1.503 | 1.00 |
| 217_F | 221_M | 1.489 | 1.00 |
| 418_L | 422_E | 1.480 | 1.00 |
| 250_F | 254_V | 1.464 | 1.00 |
| 116_G | 380_V | 1.461 | 1.00 |
| 335_L | 365_L | 1.459 | 1.00 |
| 98_I | 189_S | 1.434 | 1.00 |
| 46_Q | 290_W | 1.432 | 1.00 |
| 64_L | 268_L | 1.424 | 1.00 |
| 77_R | 81_F | 1.422 | 1.00 |
| 169_A | 355_V | 1.422 | 1.00 |
| 168_G | 172_L | 1.404 | 0.99 |
| 163_S | 344_V | 1.395 | 0.99 |
| 159_Y | 358_G | 1.388 | 0.99 |
| 304_Y | 308_I | 1.383 | 0.99 |
| 173_A | 417_T | 1.382 | 0.99 |
| 111_A | 377_A | 1.378 | 0.99 |
| 419_L | 422_E | 1.374 | 0.99 |
| 51_I | 283_M | 1.369 | 0.99 |
| 183_V | 187_V | 1.364 | 0.99 |
| 73_G | 76_E | 1.361 | 0.99 |
| 317_L | 408_A | 1.356 | 0.99 |
| 9_G | 12_G | 1.355 | 0.99 |
| 190_Y | 194_K | 1.351 | 0.99 |
| 331_E | 334_A | 1.345 | 0.99 |
| 266_E | 270_E | 1.329 | 0.99 |
| 405_I | 409_L | 1.329 | 0.99 |
| 205_S | 208_E | 1.324 | 0.99 |
| 409_L | 413_F | 1.324 | 0.99 |
| 316_L | 411_A | 1.317 | 0.99 |
| 211_T | 214_K | 1.313 | 0.99 |
| 138_G | 395_G | 1.310 | 0.99 |
| 28_A | 291_I | 1.307 | 0.99 |
| 389_F | 393_T | 1.305 | 0.99 |
| 18_M | 23_S | 1.304 | 0.99 |
| 413_F | 416_I | 1.303 | 0.99 |
| 222_T | 247_Y | 1.296 | 0.99 |
| 266_E | 269_R | 1.283 | 0.99 |
| 340_V | 361_A | 1.279 | 0.99 |
| 184_A | 402_P | 1.276 | 0.99 |
| 28_A | 287_V | 1.265 | 0.99 |
| 47_M | 287_V | 1.262 | 0.99 |
| 186_M | 190_Y | 1.251 | 0.99 |
| 112_L | 380_V | 1.248 | 0.99 |
| 315_L | 347_A | 1.245 | 0.98 |
| 185_L | 403_L | 1.244 | 0.98 |
| 123_I | 385_G | 1.242 | 0.98 |
| 102_L | 178_G | 1.242 | 0.98 |
| 70_N | 76_E | 1.242 | 0.98 |
| 315_L | 319_I | 1.235 | 0.98 |
| 410_V | 417_T | 1.230 | 0.98 |
| 409_L | 416_I | 1.230 | 0.98 |
| 103_L | 107_M | 1.229 | 0.98 |
| 46_Q | 49_G | 1.228 | 0.98 |
| 319_I | 343_L | 1.223 | 0.98 |
| 382_S | 389_F | 1.222 | 0.98 |
| 150_V | 178_G | 1.215 | 0.98 |
| 137_G | 392_L | 1.213 | 0.98 |
| 101_S | 114_D | 1.211 | 0.98 |
| 344_V | 348_S | 1.204 | 0.98 |
| 169_A | 421_P | 1.200 | 0.98 |
| 80_N | 215_E | 1.197 | 0.98 |
| 133_D | 391_T | 1.190 | 0.98 |
| 320_N | 360_M | 1.189 | 0.98 |
| 176_I | 416_I | 1.188 | 0.98 |
| 125_S | 128_D | 1.181 | 0.98 |
| 81_F | 213_F | 1.178 | 0.98 |
| 412_V | 415_Q | 1.178 | 0.98 |
| 138_G | 142_A | 1.177 | 0.98 |
| 292_V | 297_L | 1.172 | 0.98 |
| 171_F | 175_A | 1.171 | 0.98 |
| 302_A | 306_L | 1.170 | 0.97 |
| 317_L | 321_L | 1.170 | 0.97 |
| 387_I | 392_L | 1.166 | 0.97 |
| 176_I | 180_L | 1.160 | 0.97 |
| 23_S | 27_V | 1.154 | 0.97 |
| 370_L | 400_L | 1.154 | 0.97 |
| 137_G | 385_G | 1.152 | 0.97 |
| 172_L | 420_L | 1.147 | 0.97 |
| 227_I | 231_F | 1.141 | 0.97 |
| 90_T | 194_K | 1.141 | 0.97 |
| 263_G | 266_E | 1.137 | 0.97 |
| 42_F | 45_Q | 1.128 | 0.97 |
| 151_P | 160_G | 1.126 | 0.97 |
| 148_P | 366_M | 1.126 | 0.97 |
| 41_N | 45_Q | 1.122 | 0.97 |
| 61_F | 241_A | 1.119 | 0.96 |
| 21_G | 284_G | 1.111 | 0.96 |
| 210_F | 213_F | 1.103 | 0.96 |
| 158_I | 333_L | 1.103 | 0.96 |
| 298_P | 302_A | 1.099 | 0.96 |
| 319_I | 347_A | 1.092 | 0.96 |
| 124_K | 128_D | 1.090 | 0.96 |
| 113_A | 116_G | 1.088 | 0.96 |
| 68_L | 245_S | 1.082 | 0.96 |
| 67_H | 267_I | 1.081 | 0.95 |
| 395_G | 398_P | 1.080 | 0.95 |
| 175_A | 179_I | 1.079 | 0.95 |
| 221_M | 225_I | 1.076 | 0.95 |
| 137_G | 381_V | 1.073 | 0.95 |
| 187_V | 190_Y | 1.070 | 0.95 |
| 353_D | 356_H | 1.063 | 0.95 |
| 289_G | 338_L | 1.062 | 0.95 |
| 115_A | 377_A | 1.061 | 0.95 |
| 106_G | 114_D | 1.059 | 0.95 |
| 65_T | 244_S | 1.059 | 0.95 |
| 104_F | 114_D | 1.057 | 0.95 |
| 26_F | 30_V | 1.055 | 0.95 |
| 31_F | 291_I | 1.055 | 0.95 |
| 251_L | 255_V | 1.054 | 0.95 |
| 398_P | 402_P | 1.046 | 0.94 |
| 72_A | 252_G | 1.044 | 0.94 |
| 77_R | 80_N | 1.044 | 0.94 |
| 77_R | 216_A | 1.043 | 0.94 |
| 336_L | 365_L | 1.041 | 0.94 |
| 211_T | 215_E | 1.034 | 0.94 |
| 120_Q | 124_K | 1.033 | 0.94 |
| 281_M | 285_V | 1.030 | 0.94 |
| 364_N | 411_A | 1.030 | 0.94 |
| 119_G | 384_V | 1.028 | 0.94 |
| 360_M | 411_A | 1.028 | 0.94 |
| 328_T | 400_L | 1.028 | 0.94 |
| 135_F | 195_K | 1.026 | 0.94 |
| 210_F | 214_K | 1.024 | 0.93 |
| 322_L | 326_L | 1.020 | 0.93 |
| 98_I | 185_L | 1.013 | 0.93 |
| 176_I | 419_L | 1.012 | 0.93 |
| 222_T | 248_A | 1.011 | 0.93 |
| 98_I | 143_S | 1.011 | 0.93 |
| 378_L | 393_T | 1.007 | 0.93 |
| 160_G | 170_L | 1.004 | 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 | |
| 4f35D | 4 | 0.9114 | 100 | 0.411 | Contact Map |
| 4r1iA | 2 | 0.9697 | 100 | 0.593 | Contact Map |
| 4r0cA | 4 | 0 | 99.9 | 0.615 | Contact Map |
| 4pd6A | 1 | 0.7902 | 17.1 | 0.956 | Contact Map |
| 3qe7A | 1 | 0.4476 | 12.6 | 0.959 | Contact Map |
| 2kncA | 1 | 0.1212 | 10.8 | 0.96 | Contact Map |
| 3giaA | 1 | 0.4522 | 6.5 | 0.964 | Contact Map |
| 2nq2A | 2 | 0.4126 | 5.4 | 0.965 | Contact Map |
| 2m67A | 1 | 0.1865 | 4.6 | 0.966 | Contact Map |
| 4g1uA | 2 | 0.4103 | 3.9 | 0.968 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)