| TRPV1 -force run |
| ID: | 1494154571 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 434 (431) | ||
| Sequences: | 75 (34.9) | ||
| Seq/Len: | 0.174 | ||
| Nf(neff/√len): | 1.7 |
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: 0.174).
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 |
| 164_N | 177_L | 1.857 | 0.49 |
| 192_A | 200_K | 1.762 | 0.43 |
| 153_T | 157_C | 1.623 | 0.35 |
| 130_E | 230_A | 1.604 | 0.34 |
| 263_I | 389_T | 1.592 | 0.34 |
| 192_A | 195_T | 1.590 | 0.34 |
| 173_I | 196_D | 1.526 | 0.30 |
| 63_C | 399_I | 1.484 | 0.28 |
| 65_Y | 78_V | 1.464 | 0.27 |
| 353_L | 387_I | 1.463 | 0.27 |
| 180_A | 186_L | 1.460 | 0.27 |
| 255_A | 258_T | 1.441 | 0.26 |
| 260_Q | 289_H | 1.425 | 0.26 |
| 289_H | 292_V | 1.413 | 0.25 |
| 256_A | 289_H | 1.405 | 0.25 |
| 289_H | 309_Y | 1.403 | 0.25 |
| 258_T | 289_H | 1.402 | 0.25 |
| 255_A | 289_H | 1.398 | 0.25 |
| 259_N | 304_F | 1.397 | 0.25 |
| 260_Q | 292_V | 1.395 | 0.24 |
| 256_A | 260_Q | 1.387 | 0.24 |
| 260_Q | 309_Y | 1.385 | 0.24 |
| 256_A | 292_V | 1.384 | 0.24 |
| 255_A | 260_Q | 1.382 | 0.24 |
| 292_V | 309_Y | 1.375 | 0.24 |
| 258_T | 292_V | 1.374 | 0.24 |
| 256_A | 309_Y | 1.373 | 0.23 |
| 255_A | 292_V | 1.371 | 0.23 |
| 149_K | 159_L | 1.367 | 0.23 |
| 258_T | 309_Y | 1.363 | 0.23 |
| 62_D | 211_R | 1.361 | 0.23 |
| 255_A | 309_Y | 1.360 | 0.23 |
| 409_R | 416_E | 1.347 | 0.22 |
| 216_L | 240_K | 1.341 | 0.22 |
| 237_K | 357_I | 1.340 | 0.22 |
| 49_L | 57_E | 1.334 | 0.22 |
| 260_Q | 290_A | 1.321 | 0.21 |
| 385_S | 389_T | 1.317 | 0.21 |
| 163_L | 176_L | 1.315 | 0.21 |
| 256_A | 290_A | 1.308 | 0.21 |
| 304_F | 401_Y | 1.306 | 0.21 |
| 153_T | 164_N | 1.302 | 0.21 |
| 190_V | 219_L | 1.302 | 0.21 |
| 290_A | 309_Y | 1.300 | 0.21 |
| 258_T | 290_A | 1.300 | 0.21 |
| 312_I | 324_K | 1.298 | 0.20 |
| 255_A | 290_A | 1.297 | 0.20 |
| 121_V | 176_L | 1.277 | 0.20 |
| 144_T | 305_V | 1.274 | 0.20 |
| 113_D | 238_K | 1.272 | 0.20 |
| 289_H | 295_A | 1.268 | 0.19 |
| 194_Y | 244_G | 1.259 | 0.19 |
| 275_A | 301_N | 1.255 | 0.19 |
| 250_L | 301_N | 1.253 | 0.19 |
| 62_D | 413_L | 1.252 | 0.19 |
| 335_T | 339_L | 1.250 | 0.19 |
| 285_N | 340_A | 1.250 | 0.19 |
| 260_Q | 295_A | 1.249 | 0.19 |
| 285_N | 334_L | 1.247 | 0.19 |
| 155_K | 158_L | 1.241 | 0.18 |
| 155_K | 160_K | 1.241 | 0.18 |
| 251_P | 255_A | 1.241 | 0.18 |
| 292_V | 295_A | 1.241 | 0.18 |
| 256_A | 295_A | 1.235 | 0.18 |
| 249_E | 254_L | 1.232 | 0.18 |
| 251_P | 258_T | 1.232 | 0.18 |
| 295_A | 309_Y | 1.228 | 0.18 |
| 251_P | 309_Y | 1.228 | 0.18 |
| 258_T | 295_A | 1.228 | 0.18 |
| 255_A | 295_A | 1.225 | 0.18 |
| 408_N | 416_E | 1.220 | 0.18 |
| 145_D | 221_V | 1.216 | 0.18 |
| 105_G | 121_V | 1.209 | 0.17 |
| 202_Q | 429_F | 1.208 | 0.17 |
| 157_C | 164_N | 1.207 | 0.17 |
| 312_I | 335_T | 1.205 | 0.17 |
| 251_P | 289_H | 1.204 | 0.17 |
| 333_G | 340_A | 1.203 | 0.17 |
| 251_P | 260_Q | 1.193 | 0.17 |
| 286_T | 296_D | 1.193 | 0.17 |
| 111_L | 244_G | 1.188 | 0.17 |
| 25_P | 193_S | 1.186 | 0.17 |
| 74_P | 113_D | 1.183 | 0.16 |
| 285_N | 333_G | 1.182 | 0.16 |
| 251_P | 292_V | 1.182 | 0.16 |
| 251_P | 256_A | 1.174 | 0.16 |
| 172_T | 202_Q | 1.170 | 0.16 |
| 211_R | 413_L | 1.170 | 0.16 |
| 286_T | 290_A | 1.169 | 0.16 |
| 211_R | 411_D | 1.165 | 0.16 |
| 147_E | 164_N | 1.164 | 0.16 |
| 285_N | 326_E | 1.162 | 0.16 |
| 290_A | 295_A | 1.159 | 0.16 |
| 326_E | 340_A | 1.156 | 0.16 |
| 140_K | 222_E | 1.151 | 0.15 |
| 407_P | 418_L | 1.146 | 0.15 |
| 281_D | 289_H | 1.144 | 0.15 |
| 161_A | 203_T | 1.140 | 0.15 |
| 401_Y | 429_F | 1.136 | 0.15 |
| 172_T | 302_T | 1.135 | 0.15 |
| 340_A | 345_K | 1.133 | 0.15 |
| 147_E | 173_I | 1.132 | 0.15 |
| 326_E | 333_G | 1.132 | 0.15 |
| 207_I | 395_V | 1.131 | 0.15 |
| 270_N | 295_A | 1.126 | 0.15 |
| 167_N | 218_T | 1.125 | 0.15 |
| 155_K | 161_A | 1.118 | 0.14 |
| 158_L | 161_A | 1.118 | 0.14 |
| 189_F | 194_Y | 1.116 | 0.14 |
| 256_A | 281_D | 1.116 | 0.14 |
| 289_H | 308_M | 1.116 | 0.14 |
| 378_H | 392_K | 1.113 | 0.14 |
| 260_Q | 308_M | 1.109 | 0.14 |
| 281_D | 292_V | 1.106 | 0.14 |
| 159_L | 171_D | 1.105 | 0.14 |
| 130_E | 346_I | 1.105 | 0.14 |
| 251_P | 290_A | 1.102 | 0.14 |
| 224_G | 231_A | 1.100 | 0.14 |
| 292_V | 308_M | 1.099 | 0.14 |
| 181_R | 223_N | 1.098 | 0.14 |
| 281_D | 309_Y | 1.098 | 0.14 |
| 258_T | 281_D | 1.098 | 0.14 |
| 195_T | 200_K | 1.096 | 0.14 |
| 164_N | 363_R | 1.095 | 0.14 |
| 61_L | 377_V | 1.094 | 0.14 |
| 255_A | 281_D | 1.094 | 0.14 |
| 256_A | 308_M | 1.094 | 0.14 |
| 162_M | 203_T | 1.094 | 0.14 |
| 260_Q | 340_A | 1.093 | 0.14 |
| 334_L | 340_A | 1.090 | 0.14 |
| 295_A | 304_F | 1.090 | 0.14 |
| 256_A | 288_L | 1.088 | 0.14 |
| 292_V | 340_A | 1.088 | 0.14 |
| 318_K | 357_I | 1.087 | 0.14 |
| 260_Q | 285_N | 1.086 | 0.14 |
| 285_N | 292_V | 1.082 | 0.13 |
| 260_Q | 288_L | 1.081 | 0.13 |
| 258_T | 308_M | 1.081 | 0.13 |
| 316_G | 400_A | 1.080 | 0.13 |
| 163_L | 179_V | 1.080 | 0.13 |
| 309_Y | 340_A | 1.079 | 0.13 |
| 258_T | 340_A | 1.079 | 0.13 |
| 255_A | 308_M | 1.077 | 0.13 |
| 254_L | 281_D | 1.077 | 0.13 |
| 260_Q | 281_D | 1.076 | 0.13 |
| 66_E | 81_V | 1.075 | 0.13 |
| 66_E | 218_T | 1.075 | 0.13 |
| 189_F | 211_R | 1.075 | 0.13 |
| 63_C | 124_S | 1.074 | 0.13 |
| 255_A | 340_A | 1.073 | 0.13 |
| 256_A | 259_N | 1.073 | 0.13 |
| 285_N | 309_Y | 1.073 | 0.13 |
| 258_T | 285_N | 1.072 | 0.13 |
| 348_V | 390_C | 1.071 | 0.13 |
| 133_L | 183_T | 1.070 | 0.13 |
| 255_A | 259_N | 1.069 | 0.13 |
| 303_K | 314_I | 1.068 | 0.13 |
| 417_P | 426_W | 1.067 | 0.13 |
| 288_L | 292_V | 1.067 | 0.13 |
| 250_L | 275_A | 1.066 | 0.13 |
| 255_A | 288_L | 1.066 | 0.13 |
| 255_A | 285_N | 1.065 | 0.13 |
| 326_E | 334_L | 1.065 | 0.13 |
| 336_P | 345_K | 1.062 | 0.13 |
| 287_V | 297_N | 1.062 | 0.13 |
| 250_L | 296_D | 1.062 | 0.13 |
| 231_A | 421_L | 1.061 | 0.13 |
| 190_V | 357_I | 1.060 | 0.13 |
| 303_K | 404_S | 1.059 | 0.13 |
| 288_L | 309_Y | 1.058 | 0.13 |
| 249_E | 281_D | 1.058 | 0.13 |
| 258_T | 288_L | 1.058 | 0.13 |
| 1_M | 6_S | 1.057 | 0.13 |
| 114_R | 157_C | 1.055 | 0.13 |
| 153_T | 177_L | 1.051 | 0.13 |
| 168_G | 253_S | 1.050 | 0.13 |
| 416_E | 421_L | 1.048 | 0.13 |
| 159_L | 194_Y | 1.048 | 0.13 |
| 194_Y | 379_S | 1.048 | 0.13 |
| 401_Y | 406_T | 1.046 | 0.13 |
| 267_L | 288_L | 1.046 | 0.13 |
| 412_M | 416_E | 1.045 | 0.13 |
| 172_T | 203_T | 1.045 | 0.13 |
| 260_Q | 333_G | 1.045 | 0.13 |
| 148_F | 329_T | 1.044 | 0.12 |
| 289_H | 340_A | 1.044 | 0.12 |
| 180_A | 373_A | 1.043 | 0.12 |
| 259_N | 289_H | 1.040 | 0.12 |
| 281_D | 290_A | 1.039 | 0.12 |
| 29_P | 411_D | 1.038 | 0.12 |
| 285_N | 289_H | 1.037 | 0.12 |
| 157_C | 177_L | 1.036 | 0.12 |
| 155_K | 176_L | 1.035 | 0.12 |
| 158_L | 176_L | 1.035 | 0.12 |
| 160_K | 176_L | 1.035 | 0.12 |
| 409_R | 421_L | 1.035 | 0.12 |
| 203_T | 429_F | 1.034 | 0.12 |
| 256_A | 340_A | 1.033 | 0.12 |
| 162_M | 202_Q | 1.031 | 0.12 |
| 124_S | 342_S | 1.031 | 0.12 |
| 409_R | 412_M | 1.030 | 0.12 |
| 211_R | 373_A | 1.030 | 0.12 |
| 143_L | 253_S | 1.030 | 0.12 |
| 143_L | 168_G | 1.029 | 0.12 |
| 80_S | 117_I | 1.029 | 0.12 |
| 256_A | 285_N | 1.029 | 0.12 |
| 156_T | 380_S | 1.027 | 0.12 |
| 349_L | 386_C | 1.027 | 0.12 |
| 115_R | 221_V | 1.025 | 0.12 |
| 190_V | 243_P | 1.025 | 0.12 |
| 251_P | 295_A | 1.025 | 0.12 |
| 290_A | 340_A | 1.023 | 0.12 |
| 260_Q | 326_E | 1.023 | 0.12 |
| 119_D | 319_L | 1.019 | 0.12 |
| 194_Y | 266_F | 1.018 | 0.12 |
| 254_L | 258_T | 1.017 | 0.12 |
| 285_N | 290_A | 1.017 | 0.12 |
| 292_V | 333_G | 1.015 | 0.12 |
| 371_E | 407_P | 1.015 | 0.12 |
| 192_A | 380_S | 1.014 | 0.12 |
| 404_S | 429_F | 1.014 | 0.12 |
| 259_N | 292_V | 1.010 | 0.12 |
| 149_K | 180_A | 1.010 | 0.12 |
| 238_K | 413_L | 1.008 | 0.12 |
| 308_M | 344_G | 1.008 | 0.12 |
| 127_Q | 347_G | 1.008 | 0.12 |
| 155_K | 163_L | 1.007 | 0.12 |
| 158_L | 163_L | 1.007 | 0.12 |
| 160_K | 163_L | 1.007 | 0.12 |
| 287_V | 296_D | 1.006 | 0.12 |
| 214_M | 389_T | 1.006 | 0.12 |
| 309_Y | 333_G | 1.005 | 0.12 |
| 258_T | 333_G | 1.004 | 0.12 |
| 308_M | 345_K | 1.004 | 0.12 |
| 290_A | 308_M | 1.001 | 0.11 |
| 379_S | 413_L | 1.001 | 0.11 |
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 | |
| 3j5pB | 4 | 0.7465 | 100 | 0.71 | Contact Map |
| 2pnnA | 1 | 0.5714 | 100 | 0.822 | Contact Map |
| 2etbA | 1 | 0.5806 | 100 | 0.823 | Contact Map |
| 3w9fA | 4 | 0.5945 | 100 | 0.834 | Contact Map |
| 4n5qA | 2 | 0.5668 | 100 | 0.842 | Contact Map |
| 2rfaA | 1 | 0.5115 | 99.9 | 0.876 | Contact Map |
| 3j9pD | 4 | 0.5046 | 99.9 | 0.885 | Contact Map |
| 1k1aA | 1 | 0.4654 | 99.8 | 0.898 | Contact Map |
| 3hraA | 1 | 0.4562 | 99.8 | 0.899 | Contact Map |
| 1iknD | 1 | 0.4931 | 99.8 | 0.901 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)