| TEST |
| ID: | 1503390291 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 454 (421) | ||
| Sequences: | 18540 (12333.1) | ||
| Seq/Len: | 44.038 | ||
| Nf(neff/√len): | 601.1 |
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: 44.038).
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 |
| 41_E | 73_N | 4.234 | 1.00 |
| 116_L | 336_P | 3.904 | 1.00 |
| 425_S | 428_E | 3.639 | 1.00 |
| 170_T | 304_E | 3.571 | 1.00 |
| 248_I | 427_E | 3.558 | 1.00 |
| 255_A | 259_N | 3.410 | 1.00 |
| 169_K | 306_D | 3.181 | 1.00 |
| 252_Q | 256_D | 3.170 | 1.00 |
| 41_E | 71_K | 3.149 | 1.00 |
| 67_H | 341_E | 2.972 | 1.00 |
| 117_D | 152_N | 2.902 | 1.00 |
| 57_K | 61_K | 2.864 | 1.00 |
| 43_T | 73_N | 2.777 | 1.00 |
| 70_V | 338_E | 2.706 | 1.00 |
| 427_E | 431_K | 2.692 | 1.00 |
| 63_F | 341_E | 2.671 | 1.00 |
| 187_T | 190_E | 2.632 | 1.00 |
| 167_Y | 306_D | 2.584 | 1.00 |
| 256_D | 260_K | 2.569 | 1.00 |
| 170_T | 174_K | 2.564 | 1.00 |
| 431_K | 435_P | 2.538 | 1.00 |
| 64_E | 71_K | 2.529 | 1.00 |
| 62_K | 345_Y | 2.502 | 1.00 |
| 341_E | 344_L | 2.422 | 1.00 |
| 192_I | 256_D | 2.404 | 1.00 |
| 62_K | 65_E | 2.398 | 1.00 |
| 434_K | 438_Q | 2.388 | 1.00 |
| 172_F | 286_F | 2.333 | 1.00 |
| 193_D | 197_K | 2.328 | 1.00 |
| 245_P | 249_E | 2.304 | 1.00 |
| 142_R | 153_L | 2.241 | 1.00 |
| 418_P | 423_K | 2.241 | 1.00 |
| 177_I | 194_V | 2.240 | 1.00 |
| 132_D | 368_K | 2.232 | 1.00 |
| 169_K | 173_E | 2.227 | 1.00 |
| 252_Q | 426_A | 2.217 | 1.00 |
| 348_A | 352_G | 2.217 | 1.00 |
| 58_N | 61_K | 2.194 | 1.00 |
| 243_D | 431_K | 2.180 | 1.00 |
| 61_K | 65_E | 2.164 | 1.00 |
| 335_H | 338_E | 2.152 | 1.00 |
| 190_E | 193_D | 2.149 | 1.00 |
| 39_K | 71_K | 2.144 | 1.00 |
| 424_M | 432_K | 2.136 | 1.00 |
| 99_F | 330_S | 2.121 | 1.00 |
| 135_E | 139_N | 2.114 | 1.00 |
| 97_D | 335_H | 2.100 | 1.00 |
| 43_T | 75_V | 2.036 | 1.00 |
| 196_K | 260_K | 2.032 | 1.00 |
| 60_V | 342_L | 2.015 | 1.00 |
| 60_V | 64_E | 2.013 | 1.00 |
| 196_K | 200_K | 1.999 | 1.00 |
| 81_Q | 84_T | 1.982 | 1.00 |
| 249_E | 252_Q | 1.927 | 1.00 |
| 193_D | 196_K | 1.904 | 1.00 |
| 418_P | 424_M | 1.877 | 1.00 |
| 62_K | 355_A | 1.869 | 1.00 |
| 119_T | 152_N | 1.847 | 1.00 |
| 121_Y | 340_V | 1.826 | 1.00 |
| 438_Q | 442_D | 1.815 | 1.00 |
| 435_P | 439_K | 1.814 | 1.00 |
| 337_K | 341_E | 1.803 | 1.00 |
| 248_I | 426_A | 1.801 | 1.00 |
| 428_E | 432_K | 1.799 | 1.00 |
| 329_V | 343_A | 1.792 | 1.00 |
| 167_Y | 308_I | 1.768 | 1.00 |
| 189_Q | 192_I | 1.759 | 1.00 |
| 171_M | 285_G | 1.729 | 1.00 |
| 385_Q | 389_D | 1.712 | 1.00 |
| 271_Q | 274_D | 1.707 | 1.00 |
| 141_Y | 326_G | 1.706 | 1.00 |
| 40_I | 338_E | 1.703 | 1.00 |
| 115_L | 328_G | 1.698 | 1.00 |
| 419_V | 429_Y | 1.693 | 1.00 |
| 428_E | 431_K | 1.693 | 1.00 |
| 415_N | 432_K | 1.690 | 1.00 |
| 60_V | 74_I | 1.683 | 1.00 |
| 432_K | 435_P | 1.676 | 1.00 |
| 197_K | 201_D | 1.658 | 1.00 |
| 63_F | 342_L | 1.652 | 1.00 |
| 411_E | 436_K | 1.651 | 1.00 |
| 186_Y | 190_E | 1.647 | 1.00 |
| 255_A | 419_V | 1.644 | 1.00 |
| 61_K | 64_E | 1.639 | 1.00 |
| 90_I | 95_I | 1.633 | 1.00 |
| 139_N | 142_R | 1.631 | 1.00 |
| 58_N | 62_K | 1.620 | 1.00 |
| 189_Q | 193_D | 1.619 | 1.00 |
| 165_L | 308_I | 1.604 | 1.00 |
| 63_F | 70_V | 1.601 | 1.00 |
| 172_F | 177_I | 1.600 | 1.00 |
| 252_Q | 427_E | 1.598 | 1.00 |
| 278_R | 283_Q | 1.588 | 1.00 |
| 333_T | 336_P | 1.585 | 1.00 |
| 116_L | 331_S | 1.582 | 1.00 |
| 165_L | 286_F | 1.573 | 1.00 |
| 354_K | 358_D | 1.573 | 1.00 |
| 424_M | 429_Y | 1.572 | 1.00 |
| 432_K | 436_K | 1.567 | 1.00 |
| 53_Q | 57_K | 1.551 | 1.00 |
| 40_I | 335_H | 1.549 | 1.00 |
| 198_L | 285_G | 1.549 | 1.00 |
| 63_F | 345_Y | 1.547 | 1.00 |
| 62_K | 66_K | 1.546 | 1.00 |
| 101_F | 328_G | 1.543 | 1.00 |
| 192_I | 196_K | 1.540 | 1.00 |
| 39_K | 69_N | 1.521 | 1.00 |
| 169_K | 304_E | 1.516 | 1.00 |
| 248_I | 252_Q | 1.505 | 1.00 |
| 331_S | 336_P | 1.479 | 1.00 |
| 78_S | 81_Q | 1.473 | 1.00 |
| 410_D | 414_R | 1.465 | 1.00 |
| 98_V | 343_A | 1.464 | 1.00 |
| 329_V | 339_A | 1.458 | 1.00 |
| 155_G | 326_G | 1.421 | 1.00 |
| 110_V | 154_Y | 1.419 | 1.00 |
| 171_M | 198_L | 1.415 | 1.00 |
| 173_E | 179_L | 1.403 | 0.99 |
| 279_W | 305_Y | 1.402 | 0.99 |
| 192_I | 257_M | 1.392 | 0.99 |
| 253_F | 256_D | 1.391 | 0.99 |
| 415_N | 424_M | 1.388 | 0.99 |
| 355_A | 359_Q | 1.384 | 0.99 |
| 64_E | 68_P | 1.383 | 0.99 |
| 431_K | 434_K | 1.372 | 0.99 |
| 60_V | 72_V | 1.370 | 0.99 |
| 436_K | 439_K | 1.364 | 0.99 |
| 415_N | 418_P | 1.357 | 0.99 |
| 350_P | 354_K | 1.348 | 0.99 |
| 419_V | 426_A | 1.346 | 0.99 |
| 117_D | 120_K | 1.345 | 0.99 |
| 70_V | 341_E | 1.339 | 0.99 |
| 63_F | 67_H | 1.324 | 0.99 |
| 175_A | 198_L | 1.322 | 0.99 |
| 63_F | 338_E | 1.321 | 0.99 |
| 86_L | 99_F | 1.316 | 0.99 |
| 54_T | 57_K | 1.301 | 0.99 |
| 234_D | 238_T | 1.298 | 0.99 |
| 98_V | 339_A | 1.294 | 0.99 |
| 164_A | 387_F | 1.290 | 0.99 |
| 246_K | 249_E | 1.287 | 0.99 |
| 177_I | 197_K | 1.286 | 0.99 |
| 195_C | 286_F | 1.281 | 0.99 |
| 64_E | 67_H | 1.270 | 0.99 |
| 342_L | 346_L | 1.264 | 0.99 |
| 54_T | 58_N | 1.261 | 0.99 |
| 340_V | 344_L | 1.256 | 0.99 |
| 389_D | 393_D | 1.255 | 0.99 |
| 132_D | 366_S | 1.252 | 0.99 |
| 350_P | 368_K | 1.247 | 0.99 |
| 352_G | 355_A | 1.243 | 0.98 |
| 192_I | 260_K | 1.242 | 0.98 |
| 225_V | 230_A | 1.239 | 0.98 |
| 191_F | 213_T | 1.238 | 0.98 |
| 164_A | 307_L | 1.236 | 0.98 |
| 251_L | 419_V | 1.232 | 0.98 |
| 418_P | 432_K | 1.229 | 0.98 |
| 256_D | 259_N | 1.225 | 0.98 |
| 415_N | 433_A | 1.222 | 0.98 |
| 228_N | 249_E | 1.220 | 0.98 |
| 158_K | 327_I | 1.220 | 0.98 |
| 45_M | 89_A | 1.215 | 0.98 |
| 225_V | 247_F | 1.202 | 0.98 |
| 58_N | 355_A | 1.194 | 0.98 |
| 192_I | 253_F | 1.193 | 0.98 |
| 18_V | 21_A | 1.192 | 0.98 |
| 342_L | 345_Y | 1.191 | 0.98 |
| 243_D | 434_K | 1.190 | 0.98 |
| 345_Y | 352_G | 1.190 | 0.98 |
| 234_D | 239_K | 1.187 | 0.98 |
| 424_M | 428_E | 1.186 | 0.98 |
| 141_Y | 153_L | 1.183 | 0.98 |
| 171_M | 174_K | 1.174 | 0.98 |
| 252_Q | 255_A | 1.173 | 0.98 |
| 338_E | 341_E | 1.172 | 0.98 |
| 98_V | 342_L | 1.168 | 0.97 |
| 336_P | 340_V | 1.166 | 0.97 |
| 172_F | 194_V | 1.160 | 0.97 |
| 214_G | 284_L | 1.154 | 0.97 |
| 348_A | 351_E | 1.152 | 0.97 |
| 194_V | 197_K | 1.147 | 0.97 |
| 72_V | 342_L | 1.142 | 0.97 |
| 155_G | 328_G | 1.136 | 0.97 |
| 116_L | 333_T | 1.134 | 0.97 |
| 435_P | 438_Q | 1.133 | 0.97 |
| 278_R | 284_L | 1.132 | 0.97 |
| 134_W | 367_V | 1.129 | 0.97 |
| 180_P | 185_P | 1.129 | 0.97 |
| 255_A | 426_A | 1.129 | 0.97 |
| 135_E | 367_V | 1.127 | 0.97 |
| 408_W | 437_M | 1.116 | 0.96 |
| 42_L | 342_L | 1.113 | 0.96 |
| 194_V | 286_F | 1.112 | 0.96 |
| 113_N | 331_S | 1.112 | 0.96 |
| 248_I | 430_V | 1.109 | 0.96 |
| 277_Q | 281_R | 1.108 | 0.96 |
| 171_M | 175_A | 1.106 | 0.96 |
| 59_V | 62_K | 1.104 | 0.96 |
| 231_D | 235_E | 1.101 | 0.96 |
| 351_E | 354_K | 1.097 | 0.96 |
| 110_V | 149_G | 1.087 | 0.96 |
| 355_A | 358_D | 1.086 | 0.96 |
| 64_E | 69_N | 1.086 | 0.96 |
| 58_N | 359_Q | 1.073 | 0.95 |
| 95_I | 330_S | 1.071 | 0.95 |
| 168_N | 171_M | 1.069 | 0.95 |
| 17_A | 20_S | 1.065 | 0.95 |
| 90_I | 114_V | 1.063 | 0.95 |
| 185_P | 190_E | 1.053 | 0.95 |
| 85_K | 89_A | 1.052 | 0.95 |
| 40_I | 69_N | 1.049 | 0.94 |
| 329_V | 340_V | 1.048 | 0.94 |
| 191_F | 195_C | 1.047 | 0.94 |
| 414_R | 436_K | 1.045 | 0.94 |
| 22_L | 25_C | 1.044 | 0.94 |
| 199_T | 212_G | 1.038 | 0.94 |
| 415_N | 429_Y | 1.034 | 0.94 |
| 253_F | 257_M | 1.034 | 0.94 |
| 62_K | 351_E | 1.027 | 0.94 |
| 166_G | 289_V | 1.023 | 0.93 |
| 119_T | 153_L | 1.022 | 0.93 |
| 172_F | 198_L | 1.019 | 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 | |
| 3uorA | 2 | 0.8612 | 100 | 0.156 | Contact Map |
| 4r9fA | 1 | 0.837 | 100 | 0.157 | Contact Map |
| 4r6kA | 1 | 0.859 | 100 | 0.168 | Contact Map |
| 4r2fA | 1 | 0.8238 | 100 | 0.169 | Contact Map |
| 4mfiA | 1 | 0.859 | 100 | 0.169 | Contact Map |
| 4ovjA | 1 | 0.8392 | 100 | 0.207 | Contact Map |
| 3vxbA | 1 | 0.8194 | 100 | 0.213 | Contact Map |
| 2w7yA | 2 | 0.8194 | 100 | 0.216 | Contact Map |
| 3k01A | 1 | 0.8436 | 100 | 0.234 | Contact Map |
| 4r6hA | 1 | 0.8304 | 100 | 0.235 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)