| OYE1 |
| ID: | 1503997874 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 421 (354) | ||
| Sequences: | 3130 (1798.6) | ||
| Seq/Len: | 8.842 | ||
| Nf(neff/√len): | 95.6 |
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: 8.842).
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 |
| 207_E | 256_Q | 4.253 | 1.00 |
| 260_S | 263_N | 3.650 | 1.00 |
| 218_A | 274_A | 3.616 | 1.00 |
| 189_V | 205_M | 3.320 | 1.00 |
| 205_M | 213_V | 3.275 | 1.00 |
| 133_D | 223_R | 3.204 | 1.00 |
| 118_V | 216_A | 3.160 | 1.00 |
| 146_I | 153_P | 3.143 | 1.00 |
| 273_E | 318_L | 3.130 | 1.00 |
| 154_S | 231_V | 2.986 | 1.00 |
| 205_M | 209_D | 2.940 | 1.00 |
| 222_E | 226_K | 2.867 | 1.00 |
| 77_W | 381_V | 2.821 | 1.00 |
| 93_T | 141_P | 2.699 | 1.00 |
| 140_R | 144_D | 2.617 | 1.00 |
| 265_M | 314_A | 2.570 | 1.00 |
| 207_E | 210_I | 2.553 | 1.00 |
| 193_A | 204_E | 2.495 | 1.00 |
| 65_I | 381_V | 2.471 | 1.00 |
| 66_T | 71_T | 2.471 | 1.00 |
| 286_A | 322_L | 2.466 | 1.00 |
| 263_N | 266_R | 2.319 | 1.00 |
| 101_A | 393_N | 2.305 | 1.00 |
| 279_I | 285_L | 2.268 | 1.00 |
| 242_L | 267_L | 2.254 | 1.00 |
| 203_R | 209_D | 2.247 | 1.00 |
| 236_M | 287_V | 2.230 | 1.00 |
| 62_F | 399_A | 2.213 | 1.00 |
| 344_V | 373_I | 2.174 | 1.00 |
| 215_D | 219_A | 2.149 | 1.00 |
| 222_E | 278_V | 2.132 | 1.00 |
| 147_R | 230_Q | 2.102 | 1.00 |
| 268_P | 287_V | 2.084 | 1.00 |
| 212_E | 216_A | 2.054 | 1.00 |
| 372_K | 376_E | 2.043 | 1.00 |
| 348_E | 378_K | 2.019 | 1.00 |
| 157_L | 220_A | 1.960 | 1.00 |
| 100_G | 149_H | 1.958 | 1.00 |
| 219_A | 223_R | 1.947 | 1.00 |
| 225_I | 283_L | 1.919 | 1.00 |
| 391_D | 397_R | 1.867 | 1.00 |
| 139_W | 229_F | 1.853 | 1.00 |
| 257_Y | 270_A | 1.841 | 1.00 |
| 242_L | 268_P | 1.823 | 1.00 |
| 207_E | 257_Y | 1.811 | 1.00 |
| 215_D | 274_A | 1.796 | 1.00 |
| 76_I | 395_P | 1.790 | 1.00 |
| 211_R | 256_Q | 1.786 | 1.00 |
| 72_I | 381_V | 1.754 | 1.00 |
| 364_I | 370_A | 1.729 | 1.00 |
| 72_I | 108_G | 1.726 | 1.00 |
| 373_I | 379_A | 1.699 | 1.00 |
| 77_W | 359_G | 1.698 | 1.00 |
| 314_A | 317_D | 1.681 | 1.00 |
| 130_M | 220_A | 1.678 | 1.00 |
| 242_L | 271_V | 1.661 | 1.00 |
| 396_L | 400_A | 1.661 | 1.00 |
| 60_L | 63_E | 1.659 | 1.00 |
| 107_C | 388_M | 1.629 | 1.00 |
| 274_A | 278_V | 1.617 | 1.00 |
| 348_E | 352_R | 1.611 | 1.00 |
| 266_R | 270_A | 1.604 | 1.00 |
| 211_R | 274_A | 1.589 | 1.00 |
| 136_V | 226_K | 1.587 | 1.00 |
| 225_I | 280_P | 1.569 | 1.00 |
| 206_T | 209_D | 1.569 | 1.00 |
| 78_L | 102_R | 1.567 | 1.00 |
| 204_E | 254_K | 1.558 | 1.00 |
| 60_L | 371_E | 1.539 | 1.00 |
| 143_A | 229_F | 1.538 | 1.00 |
| 78_L | 81_M | 1.533 | 1.00 |
| 261_L | 265_M | 1.532 | 1.00 |
| 274_A | 277_A | 1.524 | 1.00 |
| 115_C | 155_V | 1.517 | 1.00 |
| 351_R | 380_D | 1.515 | 1.00 |
| 221_A | 275_V | 1.511 | 1.00 |
| 96_L | 145_F | 1.504 | 1.00 |
| 189_V | 203_R | 1.498 | 1.00 |
| 60_L | 375_Q | 1.496 | 1.00 |
| 209_D | 212_E | 1.493 | 1.00 |
| 371_E | 374_L | 1.484 | 1.00 |
| 83_Q | 94_W | 1.476 | 1.00 |
| 207_E | 211_R | 1.448 | 0.99 |
| 93_T | 97_V | 1.445 | 0.99 |
| 241_L | 267_L | 1.445 | 0.99 |
| 236_M | 242_L | 1.440 | 0.99 |
| 371_E | 375_Q | 1.439 | 0.99 |
| 66_T | 69_Q | 1.437 | 0.99 |
| 100_G | 145_F | 1.432 | 0.99 |
| 211_R | 257_Y | 1.420 | 0.99 |
| 96_L | 142_I | 1.415 | 0.99 |
| 132_N | 135_Q | 1.400 | 0.99 |
| 388_M | 395_P | 1.393 | 0.99 |
| 69_Q | 282_E | 1.393 | 0.99 |
| 236_M | 268_P | 1.393 | 0.99 |
| 359_G | 383_L | 1.366 | 0.99 |
| 394_W | 398_A | 1.352 | 0.99 |
| 130_M | 135_Q | 1.351 | 0.99 |
| 214_I | 257_Y | 1.337 | 0.99 |
| 91_P | 138_A | 1.335 | 0.99 |
| 189_V | 209_D | 1.320 | 0.99 |
| 366_T | 394_W | 1.319 | 0.99 |
| 211_R | 270_A | 1.307 | 0.99 |
| 152_V | 230_Q | 1.302 | 0.99 |
| 73_P | 151_A | 1.297 | 0.99 |
| 279_I | 283_L | 1.295 | 0.99 |
| 97_V | 100_G | 1.289 | 0.99 |
| 218_A | 278_V | 1.289 | 0.99 |
| 100_G | 148_S | 1.288 | 0.98 |
| 81_M | 385_G | 1.276 | 0.98 |
| 136_V | 227_A | 1.266 | 0.98 |
| 131_W | 135_Q | 1.264 | 0.98 |
| 143_A | 153_P | 1.263 | 0.98 |
| 231_V | 286_A | 1.261 | 0.98 |
| 72_I | 77_W | 1.247 | 0.98 |
| 225_I | 279_I | 1.244 | 0.98 |
| 234_I | 275_V | 1.239 | 0.98 |
| 364_I | 373_I | 1.237 | 0.98 |
| 384_I | 387_E | 1.226 | 0.98 |
| 310_V | 313_G | 1.225 | 0.98 |
| 78_L | 110_V | 1.224 | 0.98 |
| 249_Q | 295_A | 1.224 | 0.98 |
| 147_R | 152_V | 1.222 | 0.98 |
| 90_A | 134_A | 1.221 | 0.98 |
| 70_L | 152_V | 1.218 | 0.98 |
| 91_P | 128_A | 1.215 | 0.98 |
| 310_V | 314_A | 1.208 | 0.97 |
| 73_P | 150_G | 1.208 | 0.97 |
| 218_A | 277_A | 1.206 | 0.97 |
| 238_H | 326_S | 1.205 | 0.97 |
| 154_S | 286_A | 1.204 | 0.97 |
| 104_A | 149_H | 1.200 | 0.97 |
| 349_R | 352_R | 1.200 | 0.97 |
| 361_V | 383_L | 1.194 | 0.97 |
| 144_D | 148_S | 1.191 | 0.97 |
| 316_R | 356_V | 1.184 | 0.97 |
| 273_E | 277_A | 1.182 | 0.97 |
| 190_A | 193_A | 1.176 | 0.97 |
| 272_A | 315_L | 1.173 | 0.97 |
| 246_L | 268_P | 1.166 | 0.97 |
| 130_M | 155_V | 1.165 | 0.97 |
| 304_D | 307_Q | 1.147 | 0.96 |
| 309_V | 313_G | 1.145 | 0.96 |
| 129_G | 135_Q | 1.143 | 0.96 |
| 235_H | 240_Y | 1.141 | 0.96 |
| 269_L | 318_L | 1.139 | 0.96 |
| 133_D | 136_V | 1.136 | 0.96 |
| 313_G | 353_E | 1.121 | 0.96 |
| 194_V | 202_P | 1.121 | 0.96 |
| 216_A | 219_A | 1.121 | 0.96 |
| 261_L | 310_V | 1.120 | 0.96 |
| 155_V | 224_S | 1.118 | 0.95 |
| 268_P | 311_L | 1.118 | 0.95 |
| 136_V | 223_R | 1.113 | 0.95 |
| 162_R | 250_A | 1.112 | 0.95 |
| 323_I | 356_V | 1.111 | 0.95 |
| 162_R | 202_P | 1.102 | 0.95 |
| 111_M | 154_S | 1.098 | 0.95 |
| 91_P | 139_W | 1.095 | 0.95 |
| 144_D | 147_R | 1.094 | 0.95 |
| 287_V | 315_L | 1.091 | 0.95 |
| 219_A | 222_E | 1.091 | 0.95 |
| 322_L | 359_G | 1.083 | 0.94 |
| 235_H | 238_H | 1.081 | 0.94 |
| 140_R | 226_K | 1.077 | 0.94 |
| 225_I | 282_E | 1.072 | 0.94 |
| 393_N | 396_L | 1.051 | 0.93 |
| 68_R | 321_D | 1.041 | 0.93 |
| 322_L | 381_V | 1.029 | 0.92 |
| 189_V | 213_V | 1.026 | 0.92 |
| 305_V | 349_R | 1.024 | 0.92 |
| 70_L | 231_V | 1.023 | 0.92 |
| 60_L | 374_L | 1.020 | 0.92 |
| 109_L | 154_S | 1.002 | 0.91 |
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 | |
| 2hsaB | 2 | 0.8219 | 100 | 0.385 | Contact Map |
| 4e2bA | 1 | 0.8314 | 100 | 0.395 | Contact Map |
| 3tjlA | 1 | 0.8504 | 100 | 0.398 | Contact Map |
| 4tmbA | 4 | 0.8575 | 100 | 0.399 | Contact Map |
| 3l5lA | 1 | 0.8409 | 100 | 0.4 | Contact Map |
| 4qnwA | 1 | 0.8076 | 100 | 0.401 | Contact Map |
| 4gbuA | 1 | 0.8527 | 100 | 0.402 | Contact Map |
| 4jicA | 3 | 0.8147 | 100 | 0.407 | Contact Map |
| 1o94A | 2 | 0.8219 | 100 | 0.411 | Contact Map |
| 3k30A | 2 | 0.8171 | 100 | 0.411 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)