| TREK1 |
| ID: | 1425404865 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 411 (369) | ||
| Sequences: | 4898 (2963.9) | ||
| Seq/Len: | 13.274 | ||
| Nf(neff/√len): | 154.3 |
Jackhmmer Results: (2015_01_07)
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: 13.274).
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 |
| 222_F | 226_P | 4.116 | 1.00 |
| 222_F | 225_L | 2.919 | 1.00 |
| 224_A | 228_V | 2.768 | 1.00 |
| 162_Y | 165_L | 2.576 | 1.00 |
| 222_F | 228_V | 2.360 | 1.00 |
| 220_V | 224_A | 2.297 | 1.00 |
| 223_V | 226_P | 2.188 | 1.00 |
| 159_C | 162_Y | 2.132 | 1.00 |
| 141_T | 144_G | 2.108 | 1.00 |
| 390_I | 396_T | 2.035 | 1.00 |
| 225_L | 228_V | 2.020 | 1.00 |
| 226_P | 230_F | 1.945 | 1.00 |
| 316_E | 326_K | 1.934 | 1.00 |
| 367_R | 370_S | 1.821 | 1.00 |
| 251_T | 255_G | 1.788 | 1.00 |
| 313_H | 330_R | 1.784 | 1.00 |
| 343_A | 346_V | 1.780 | 1.00 |
| 223_V | 227_A | 1.763 | 1.00 |
| 231_K | 234_E | 1.759 | 1.00 |
| 222_F | 227_A | 1.756 | 1.00 |
| 243_Y | 256_D | 1.748 | 1.00 |
| 224_A | 227_A | 1.739 | 1.00 |
| 220_V | 223_V | 1.724 | 1.00 |
| 342_R | 346_V | 1.715 | 1.00 |
| 316_E | 321_V | 1.696 | 1.00 |
| 351_S | 355_A | 1.652 | 1.00 |
| 337_Y | 342_R | 1.597 | 1.00 |
| 395_L | 398_H | 1.559 | 1.00 |
| 252_I | 255_G | 1.553 | 1.00 |
| 221_L | 225_L | 1.551 | 1.00 |
| 220_V | 226_P | 1.526 | 1.00 |
| 248_T | 256_D | 1.504 | 1.00 |
| 342_R | 347_K | 1.503 | 1.00 |
| 255_G | 259_A | 1.494 | 1.00 |
| 224_A | 230_F | 1.493 | 1.00 |
| 366_R | 370_S | 1.476 | 1.00 |
| 251_T | 254_F | 1.463 | 1.00 |
| 157_I | 162_Y | 1.444 | 1.00 |
| 248_T | 254_F | 1.437 | 1.00 |
| 194_D | 198_K | 1.424 | 1.00 |
| 152_T | 155_G | 1.411 | 1.00 |
| 344_T | 347_K | 1.398 | 0.99 |
| 134_F | 144_G | 1.394 | 0.99 |
| 154_G | 158_F | 1.392 | 0.99 |
| 351_S | 354_L | 1.385 | 0.99 |
| 221_L | 224_A | 1.384 | 0.99 |
| 240_D | 271_K | 1.373 | 0.99 |
| 162_Y | 166_G | 1.366 | 0.99 |
| 224_A | 234_E | 1.357 | 0.99 |
| 230_F | 234_E | 1.354 | 0.99 |
| 248_T | 252_I | 1.333 | 0.99 |
| 343_A | 347_K | 1.330 | 0.99 |
| 243_Y | 247_I | 1.304 | 0.99 |
| 403_D | 406_V | 1.298 | 0.99 |
| 351_S | 356_G | 1.297 | 0.99 |
| 360_Q | 363_T | 1.294 | 0.99 |
| 373_H | 377_E | 1.293 | 0.99 |
| 286_A | 290_S | 1.279 | 0.99 |
| 243_Y | 253_G | 1.278 | 0.99 |
| 158_F | 162_Y | 1.276 | 0.99 |
| 228_V | 234_E | 1.272 | 0.99 |
| 138_T | 142_T | 1.271 | 0.99 |
| 137_G | 144_G | 1.264 | 0.99 |
| 337_Y | 341_Q | 1.258 | 0.99 |
| 134_F | 141_T | 1.253 | 0.99 |
| 226_P | 229_I | 1.252 | 0.99 |
| 406_V | 409_N | 1.248 | 0.99 |
| 254_F | 258_V | 1.241 | 0.98 |
| 340_F | 343_A | 1.240 | 0.98 |
| 154_G | 157_I | 1.233 | 0.98 |
| 62_A | 133_F | 1.226 | 0.98 |
| 223_V | 228_V | 1.222 | 0.98 |
| 359_N | 362_L | 1.218 | 0.98 |
| 134_F | 137_G | 1.199 | 0.98 |
| 290_S | 293_G | 1.199 | 0.98 |
| 113_G | 116_P | 1.198 | 0.98 |
| 109_A | 113_G | 1.198 | 0.98 |
| 363_T | 367_R | 1.175 | 0.98 |
| 243_Y | 255_G | 1.174 | 0.98 |
| 137_G | 141_T | 1.173 | 0.98 |
| 376_S | 379_E | 1.172 | 0.98 |
| 138_T | 141_T | 1.171 | 0.98 |
| 328_T | 357_N | 1.170 | 0.97 |
| 153_E | 156_K | 1.170 | 0.97 |
| 359_N | 363_T | 1.168 | 0.97 |
| 342_R | 345_S | 1.162 | 0.97 |
| 248_T | 251_T | 1.158 | 0.97 |
| 255_G | 258_V | 1.158 | 0.97 |
| 286_A | 289_L | 1.155 | 0.97 |
| 248_T | 255_G | 1.147 | 0.97 |
| 222_F | 229_I | 1.146 | 0.97 |
| 159_C | 165_L | 1.145 | 0.97 |
| 244_F | 248_T | 1.143 | 0.97 |
| 74_I | 77_R | 1.137 | 0.97 |
| 58_L | 140_I | 1.137 | 0.97 |
| 367_R | 371_V | 1.135 | 0.97 |
| 150_P | 154_G | 1.135 | 0.97 |
| 247_I | 251_T | 1.131 | 0.97 |
| 214_F | 227_A | 1.126 | 0.97 |
| 364_P | 378_R | 1.123 | 0.97 |
| 381_L | 384_L | 1.121 | 0.97 |
| 110_I | 115_I | 1.115 | 0.96 |
| 72_Q | 76_Q | 1.113 | 0.96 |
| 212_I | 222_F | 1.112 | 0.96 |
| 355_A | 359_N | 1.110 | 0.96 |
| 388_E | 405_A | 1.107 | 0.96 |
| 135_F | 159_C | 1.107 | 0.96 |
| 194_D | 197_I | 1.103 | 0.96 |
| 397_P | 401_G | 1.102 | 0.96 |
| 107_V | 110_I | 1.100 | 0.96 |
| 110_I | 114_I | 1.084 | 0.96 |
| 391_Y | 394_G | 1.084 | 0.96 |
| 248_T | 253_G | 1.080 | 0.95 |
| 225_L | 229_I | 1.073 | 0.95 |
| 214_F | 222_F | 1.071 | 0.95 |
| 256_D | 271_K | 1.059 | 0.95 |
| 332_L | 336_I | 1.058 | 0.95 |
| 227_A | 230_F | 1.058 | 0.95 |
| 56_L | 60_I | 1.057 | 0.95 |
| 99_L | 103_I | 1.057 | 0.95 |
| 214_F | 224_A | 1.052 | 0.95 |
| 277_W | 281_G | 1.052 | 0.95 |
| 193_E | 198_K | 1.047 | 0.94 |
| 108_A | 111_N | 1.046 | 0.94 |
| 77_R | 81_V | 1.044 | 0.94 |
| 111_N | 114_I | 1.044 | 0.94 |
| 135_F | 141_T | 1.042 | 0.94 |
| 315_A | 319_A | 1.040 | 0.94 |
| 261_G | 270_Y | 1.037 | 0.94 |
| 63_T | 67_A | 1.028 | 0.94 |
| 243_Y | 254_F | 1.027 | 0.94 |
| 259_A | 274_V | 1.027 | 0.94 |
| 220_V | 227_A | 1.025 | 0.93 |
| 387_A | 394_G | 1.023 | 0.93 |
| 351_S | 363_T | 1.020 | 0.93 |
| 79_T | 82_I | 1.016 | 0.93 |
| 100_D | 104_Q | 1.016 | 0.93 |
| 211_T | 222_F | 1.014 | 0.93 |
| 381_L | 385_L | 1.013 | 0.93 |
| 105_Q | 110_I | 1.012 | 0.93 |
| 348_R | 351_S | 1.011 | 0.93 |
| 398_H | 401_G | 1.007 | 0.93 |
| 47_V | 50_I | 1.005 | 0.93 |
| 180_Q | 183_T | 1.005 | 0.93 |
| 223_V | 229_I | 1.004 | 0.93 |
| 395_L | 405_A | 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 | |
| 4twkA | 2 | 0.6399 | 100 | 0.468 | Contact Map |
| 4bw5A | 4 | 0.6253 | 100 | 0.469 | Contact Map |
| 4wfeA | 2 | 0.6204 | 100 | 0.472 | Contact Map |
| 3ukmA | 4 | 0.6083 | 100 | 0.493 | Contact Map |
| 3behA | 4 | 0.5109 | 100 | 0.653 | Contact Map |
| 2r9rB | 2 | 0.6472 | 99.9 | 0.707 | Contact Map |
| 4bgnA | 2 | 0.4842 | 99.8 | 0.741 | Contact Map |
| 2a9hA | 4 | 0.219 | 99.8 | 0.755 | Contact Map |
| 3pjsK | 4 | 0.3187 | 99.8 | 0.757 | Contact Map |
| 3rvyA | 2 | 0.4964 | 99.8 | 0.765 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)