| ToMV_full_aln |
| ID: | 1500292846 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 441 (401) | ||
| Sequences: | 1519 (1422.9) | ||
| Seq/Len: | 3.788 | ||
| Nf(neff/√len): | 71.1 |
Jackhmmer Results: (2016_04)
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: 3.788).
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 |
| 307_L | 405_S | 3.336 | 1.00 |
| 296_T | 299_C | 3.140 | 1.00 |
| 378_A | 409_K | 3.026 | 1.00 |
| 370_H | 399_H | 2.894 | 1.00 |
| 379_D | 410_S | 2.695 | 1.00 |
| 326_S | 329_M | 2.587 | 1.00 |
| 239_L | 373_Q | 2.406 | 1.00 |
| 344_K | 378_A | 2.394 | 1.00 |
| 230_F | 233_L | 2.380 | 1.00 |
| 173_I | 261_Y | 2.355 | 1.00 |
| 240_M | 373_Q | 2.234 | 1.00 |
| 231_K | 256_D | 2.134 | 1.00 |
| 329_M | 332_G | 2.088 | 1.00 |
| 382_L | 403_S | 2.081 | 1.00 |
| 186_V | 191_A | 2.076 | 1.00 |
| 323_K | 326_S | 1.997 | 1.00 |
| 268_P | 373_Q | 1.972 | 1.00 |
| 239_L | 268_P | 1.963 | 1.00 |
| 378_A | 408_T | 1.942 | 1.00 |
| 279_P | 282_F | 1.937 | 1.00 |
| 143_R | 146_L | 1.932 | 1.00 |
| 377_Y | 380_V | 1.881 | 1.00 |
| 146_L | 149_G | 1.878 | 1.00 |
| 346_K | 380_V | 1.848 | 1.00 |
| 194_M | 198_R | 1.813 | 0.99 |
| 240_M | 268_P | 1.788 | 0.99 |
| 346_K | 350_F | 1.786 | 0.99 |
| 267_I | 373_Q | 1.774 | 0.99 |
| 185_L | 218_F | 1.757 | 0.99 |
| 270_I | 373_Q | 1.725 | 0.99 |
| 184_I | 195_I | 1.720 | 0.99 |
| 211_N | 214_T | 1.707 | 0.99 |
| 372_V | 377_Y | 1.671 | 0.99 |
| 159_V | 291_E | 1.659 | 0.99 |
| 166_G | 169_K | 1.651 | 0.99 |
| 142_L | 146_L | 1.636 | 0.99 |
| 303_V | 307_L | 1.606 | 0.98 |
| 293_R | 298_R | 1.593 | 0.98 |
| 328_E | 331_S | 1.555 | 0.98 |
| 323_K | 327_Q | 1.528 | 0.98 |
| 327_Q | 331_S | 1.524 | 0.98 |
| 303_V | 411_L | 1.490 | 0.97 |
| 346_K | 377_Y | 1.478 | 0.97 |
| 189_R | 192_A | 1.471 | 0.97 |
| 379_D | 412_K | 1.438 | 0.96 |
| 240_M | 401_L | 1.423 | 0.96 |
| 240_M | 270_I | 1.423 | 0.96 |
| 157_K | 257_I | 1.417 | 0.96 |
| 372_V | 380_V | 1.412 | 0.96 |
| 270_I | 370_H | 1.405 | 0.96 |
| 240_M | 307_L | 1.401 | 0.95 |
| 240_M | 375_E | 1.400 | 0.95 |
| 296_T | 370_H | 1.388 | 0.95 |
| 349_T | 355_K | 1.385 | 0.95 |
| 239_L | 401_L | 1.368 | 0.95 |
| 239_L | 267_I | 1.364 | 0.95 |
| 381_S | 414_Y | 1.362 | 0.94 |
| 186_V | 192_A | 1.362 | 0.94 |
| 422_V | 425_I | 1.353 | 0.94 |
| 329_M | 333_A | 1.343 | 0.94 |
| 212_V | 216_D | 1.342 | 0.94 |
| 183_L | 230_F | 1.333 | 0.94 |
| 167_C | 176_R | 1.325 | 0.93 |
| 351_T | 354_D | 1.321 | 0.93 |
| 352_Q | 368_T | 1.317 | 0.93 |
| 326_S | 331_S | 1.317 | 0.93 |
| 311_Y | 401_L | 1.308 | 0.93 |
| 238_G | 241_L | 1.306 | 0.93 |
| 240_M | 267_I | 1.305 | 0.93 |
| 98_T | 336_I | 1.300 | 0.93 |
| 299_C | 370_H | 1.298 | 0.92 |
| 382_L | 413_Y | 1.298 | 0.92 |
| 347_I | 358_L | 1.297 | 0.92 |
| 213_R | 217_S | 1.292 | 0.92 |
| 354_D | 383_V | 1.290 | 0.92 |
| 188_G | 191_A | 1.286 | 0.92 |
| 299_C | 304_T | 1.284 | 0.92 |
| 252_M | 402_V | 1.282 | 0.92 |
| 190_Q | 194_M | 1.279 | 0.92 |
| 214_T | 217_S | 1.274 | 0.91 |
| 186_V | 195_I | 1.269 | 0.91 |
| 296_T | 304_T | 1.262 | 0.91 |
| 189_R | 240_M | 1.261 | 0.91 |
| 376_T | 407_H | 1.242 | 0.90 |
| 299_C | 307_L | 1.240 | 0.90 |
| 164_V | 167_C | 1.238 | 0.90 |
| 240_M | 245_C | 1.232 | 0.90 |
| 190_Q | 375_E | 1.231 | 0.90 |
| 84_V | 87_S | 1.229 | 0.89 |
| 98_T | 102_K | 1.222 | 0.89 |
| 165_P | 265_Q | 1.215 | 0.89 |
| 242_H | 245_C | 1.214 | 0.89 |
| 234_F | 239_L | 1.212 | 0.89 |
| 367_H | 401_L | 1.210 | 0.88 |
| 367_H | 372_V | 1.207 | 0.88 |
| 240_M | 296_T | 1.200 | 0.88 |
| 323_K | 329_M | 1.199 | 0.88 |
| 173_I | 195_I | 1.191 | 0.87 |
| 280_A | 283_A | 1.185 | 0.87 |
| 211_N | 215_V | 1.185 | 0.87 |
| 239_L | 270_I | 1.176 | 0.86 |
| 379_D | 415_T | 1.169 | 0.86 |
| 163_G | 166_G | 1.169 | 0.86 |
| 367_H | 371_E | 1.168 | 0.86 |
| 345_G | 350_F | 1.167 | 0.86 |
| 143_R | 149_G | 1.166 | 0.86 |
| 375_E | 402_V | 1.166 | 0.86 |
| 265_Q | 397_S | 1.165 | 0.86 |
| 268_P | 375_E | 1.165 | 0.86 |
| 150_E | 153_V | 1.165 | 0.86 |
| 346_K | 351_T | 1.163 | 0.86 |
| 345_G | 379_D | 1.163 | 0.86 |
| 92_A | 95_V | 1.162 | 0.86 |
| 242_H | 261_Y | 1.157 | 0.85 |
| 382_L | 411_L | 1.147 | 0.85 |
| 303_V | 310_R | 1.147 | 0.85 |
| 239_L | 269_Y | 1.147 | 0.85 |
| 350_F | 354_D | 1.141 | 0.84 |
| 342_P | 346_K | 1.139 | 0.84 |
| 269_Y | 373_Q | 1.135 | 0.84 |
| 328_E | 332_G | 1.134 | 0.84 |
| 212_V | 215_V | 1.133 | 0.84 |
| 303_V | 407_H | 1.131 | 0.83 |
| 76_D | 79_S | 1.130 | 0.83 |
| 373_Q | 401_L | 1.122 | 0.83 |
| 293_R | 303_V | 1.119 | 0.83 |
| 240_M | 271_N | 1.113 | 0.82 |
| 262_G | 373_Q | 1.113 | 0.82 |
| 173_I | 234_F | 1.111 | 0.82 |
| 171_K | 306_F | 1.111 | 0.82 |
| 54_L | 57_I | 1.107 | 0.82 |
| 188_G | 239_L | 1.107 | 0.82 |
| 266_Q | 374_G | 1.100 | 0.81 |
| 143_R | 297_L | 1.099 | 0.81 |
| 327_Q | 330_V | 1.099 | 0.81 |
| 104_H | 108_L | 1.098 | 0.81 |
| 273_V | 276_F | 1.095 | 0.81 |
| 232_R | 257_I | 1.094 | 0.81 |
| 270_I | 371_E | 1.093 | 0.80 |
| 163_G | 169_K | 1.091 | 0.80 |
| 262_G | 402_V | 1.091 | 0.80 |
| 212_V | 218_F | 1.090 | 0.80 |
| 97_E | 101_R | 1.089 | 0.80 |
| 164_V | 265_Q | 1.087 | 0.80 |
| 163_G | 168_G | 1.074 | 0.79 |
| 158_V | 258_A | 1.069 | 0.78 |
| 304_T | 307_L | 1.064 | 0.78 |
| 278_Y | 282_F | 1.063 | 0.78 |
| 303_V | 399_H | 1.062 | 0.78 |
| 205_I | 208_T | 1.060 | 0.78 |
| 150_E | 154_S | 1.056 | 0.77 |
| 211_N | 217_S | 1.056 | 0.77 |
| 278_Y | 281_H | 1.053 | 0.77 |
| 186_V | 299_C | 1.053 | 0.77 |
| 234_F | 267_I | 1.052 | 0.77 |
| 187_P | 240_M | 1.050 | 0.77 |
| 176_R | 259_Y | 1.048 | 0.76 |
| 369_V | 403_S | 1.046 | 0.76 |
| 305_H | 309_Q | 1.043 | 0.76 |
| 306_F | 310_R | 1.034 | 0.75 |
| 368_T | 371_E | 1.033 | 0.75 |
| 176_R | 373_Q | 1.031 | 0.75 |
| 214_T | 218_F | 1.028 | 0.74 |
| 263_D | 266_Q | 1.025 | 0.74 |
| 422_V | 426_R | 1.025 | 0.74 |
| 296_T | 415_T | 1.025 | 0.74 |
| 267_I | 399_H | 1.022 | 0.74 |
| 193_E | 199_A | 1.021 | 0.74 |
| 240_M | 366_V | 1.020 | 0.74 |
| 291_E | 295_T | 1.019 | 0.74 |
| 164_V | 401_L | 1.018 | 0.73 |
| 61_T | 403_S | 1.018 | 0.73 |
| 97_E | 100_A | 1.017 | 0.73 |
| 33_V | 37_K | 1.016 | 0.73 |
| 240_M | 299_C | 1.015 | 0.73 |
| 187_P | 405_S | 1.014 | 0.73 |
| 346_K | 354_D | 1.014 | 0.73 |
| 138_K | 141_T | 1.012 | 0.73 |
| 240_M | 399_H | 1.005 | 0.72 |
| 262_G | 368_T | 1.005 | 0.72 |
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 | |
| 3vkwA | 1 | 0.9977 | 100 | 0.274 | Contact Map |
| 2xzlA | 1 | 0.9365 | 100 | 0.485 | Contact Map |
| 2wjyA | 1 | 0.9002 | 100 | 0.494 | Contact Map |
| 2gk6A | 2 | 0.8753 | 100 | 0.496 | Contact Map |
| 4b3fX | 1 | 0.9501 | 100 | 0.499 | Contact Map |
| 4pj3A | 1 | 0.9569 | 100 | 0.499 | Contact Map |
| 3upuA | 3 | 0.6077 | 100 | 0.526 | Contact Map |
| 3e1sA | 1 | 0.8844 | 100 | 0.542 | Contact Map |
| 1w36D | 2 | 0.8503 | 100 | 0.547 | Contact Map |
| 4n0nA | 1 | 0.7642 | 100 | 0.57 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)