| yi3lianjiemei -force run |
| ID: | 1455687600 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 487 (461) | ||
| Sequences: | 59 (47.2) | ||
| Seq/Len: | 0.128 | ||
| Nf(neff/√len): | 2.2 |
HHblits Results: (2015_06)
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: 0.128).
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 |
| 254_R | 409_L | 1.942 | 0.45 |
| 36_V | 483_K | 1.869 | 0.41 |
| 449_V | 482_I | 1.863 | 0.41 |
| 410_V | 414_S | 1.829 | 0.39 |
| 444_V | 454_M | 1.815 | 0.38 |
| 112_A | 406_D | 1.629 | 0.29 |
| 223_L | 249_K | 1.620 | 0.29 |
| 109_C | 119_A | 1.619 | 0.29 |
| 22_G | 214_V | 1.569 | 0.27 |
| 363_S | 430_S | 1.550 | 0.26 |
| 156_L | 482_I | 1.542 | 0.26 |
| 131_H | 157_S | 1.538 | 0.25 |
| 182_V | 253_L | 1.500 | 0.24 |
| 46_V | 359_V | 1.486 | 0.23 |
| 441_D | 470_G | 1.455 | 0.22 |
| 11_V | 481_V | 1.444 | 0.22 |
| 124_V | 163_V | 1.439 | 0.22 |
| 14_R | 57_A | 1.431 | 0.21 |
| 122_K | 130_N | 1.416 | 0.21 |
| 194_V | 217_V | 1.416 | 0.21 |
| 48_C | 79_P | 1.413 | 0.21 |
| 100_A | 113_L | 1.408 | 0.20 |
| 21_E | 57_A | 1.405 | 0.20 |
| 59_T | 473_V | 1.400 | 0.20 |
| 178_L | 468_N | 1.391 | 0.20 |
| 45_I | 86_R | 1.386 | 0.20 |
| 214_V | 440_L | 1.384 | 0.20 |
| 167_C | 200_S | 1.376 | 0.19 |
| 173_M | 194_V | 1.376 | 0.19 |
| 190_Q | 341_S | 1.371 | 0.19 |
| 446_G | 454_M | 1.347 | 0.18 |
| 171_N | 482_I | 1.345 | 0.18 |
| 441_D | 469_W | 1.334 | 0.18 |
| 36_V | 255_L | 1.330 | 0.18 |
| 51_P | 181_A | 1.330 | 0.18 |
| 151_L | 361_E | 1.321 | 0.18 |
| 7_K | 473_V | 1.316 | 0.17 |
| 136_S | 163_V | 1.313 | 0.17 |
| 41_K | 49_T | 1.311 | 0.17 |
| 41_K | 158_R | 1.310 | 0.17 |
| 438_I | 445_E | 1.308 | 0.17 |
| 434_S | 447_A | 1.307 | 0.17 |
| 76_G | 406_D | 1.304 | 0.17 |
| 189_A | 210_S | 1.290 | 0.17 |
| 93_K | 115_V | 1.287 | 0.17 |
| 252_R | 260_E | 1.284 | 0.16 |
| 411_D | 414_S | 1.282 | 0.16 |
| 226_R | 248_S | 1.281 | 0.16 |
| 214_V | 269_F | 1.280 | 0.16 |
| 17_N | 404_T | 1.279 | 0.16 |
| 364_H | 430_S | 1.274 | 0.16 |
| 78_T | 156_L | 1.270 | 0.16 |
| 19_D | 449_V | 1.260 | 0.16 |
| 102_T | 151_L | 1.258 | 0.16 |
| 171_N | 421_S | 1.250 | 0.15 |
| 160_V | 269_F | 1.245 | 0.15 |
| 13_Q | 484_L | 1.244 | 0.15 |
| 10_L | 61_L | 1.238 | 0.15 |
| 121_H | 149_E | 1.232 | 0.15 |
| 115_V | 256_A | 1.232 | 0.15 |
| 61_L | 483_K | 1.229 | 0.15 |
| 420_S | 468_N | 1.228 | 0.15 |
| 292_P | 404_T | 1.225 | 0.15 |
| 454_M | 486_V | 1.223 | 0.15 |
| 170_R | 269_F | 1.221 | 0.15 |
| 36_V | 51_P | 1.220 | 0.15 |
| 39_E | 149_E | 1.217 | 0.15 |
| 158_R | 252_R | 1.217 | 0.15 |
| 436_C | 439_C | 1.216 | 0.15 |
| 436_C | 448_C | 1.216 | 0.15 |
| 436_C | 450_P | 1.216 | 0.15 |
| 436_C | 451_C | 1.216 | 0.15 |
| 436_C | 457_C | 1.216 | 0.15 |
| 439_C | 448_C | 1.216 | 0.15 |
| 439_C | 450_P | 1.216 | 0.15 |
| 439_C | 451_C | 1.216 | 0.15 |
| 439_C | 457_C | 1.216 | 0.15 |
| 448_C | 451_C | 1.216 | 0.15 |
| 448_C | 457_C | 1.216 | 0.15 |
| 450_P | 457_C | 1.216 | 0.15 |
| 451_C | 457_C | 1.216 | 0.15 |
| 61_L | 138_W | 1.214 | 0.15 |
| 55_N | 413_D | 1.210 | 0.14 |
| 22_G | 440_L | 1.205 | 0.14 |
| 28_A | 473_V | 1.202 | 0.14 |
| 268_W | 484_L | 1.202 | 0.14 |
| 50_K | 256_A | 1.202 | 0.14 |
| 165_L | 385_N | 1.200 | 0.14 |
| 295_I | 299_S | 1.198 | 0.14 |
| 127_A | 412_S | 1.197 | 0.14 |
| 52_E | 164_V | 1.196 | 0.14 |
| 169_S | 274_K | 1.193 | 0.14 |
| 178_L | 255_L | 1.193 | 0.14 |
| 202_L | 385_N | 1.191 | 0.14 |
| 190_Q | 481_V | 1.189 | 0.14 |
| 115_V | 131_H | 1.189 | 0.14 |
| 222_N | 227_G | 1.187 | 0.14 |
| 224_T | 229_R | 1.187 | 0.14 |
| 146_E | 410_V | 1.185 | 0.14 |
| 165_L | 469_W | 1.185 | 0.14 |
| 170_R | 470_G | 1.183 | 0.14 |
| 115_V | 188_D | 1.181 | 0.14 |
| 27_A | 259_N | 1.180 | 0.14 |
| 112_A | 418_I | 1.180 | 0.14 |
| 243_C | 247_K | 1.180 | 0.14 |
| 351_K | 412_S | 1.180 | 0.14 |
| 223_L | 246_R | 1.179 | 0.14 |
| 435_T | 447_A | 1.179 | 0.14 |
| 437_V | 441_D | 1.177 | 0.14 |
| 25_A | 75_N | 1.173 | 0.13 |
| 102_T | 466_T | 1.165 | 0.13 |
| 206_R | 262_D | 1.162 | 0.13 |
| 131_H | 256_A | 1.159 | 0.13 |
| 242_R | 250_T | 1.158 | 0.13 |
| 125_V | 128_I | 1.153 | 0.13 |
| 483_K | 486_V | 1.152 | 0.13 |
| 298_I | 301_G | 1.146 | 0.13 |
| 88_L | 91_T | 1.143 | 0.13 |
| 366_A | 483_K | 1.140 | 0.13 |
| 224_T | 227_G | 1.140 | 0.13 |
| 182_V | 207_L | 1.140 | 0.13 |
| 123_N | 127_A | 1.134 | 0.13 |
| 347_P | 353_S | 1.133 | 0.12 |
| 115_V | 157_S | 1.133 | 0.12 |
| 114_E | 302_A | 1.133 | 0.12 |
| 338_A | 341_S | 1.132 | 0.12 |
| 295_I | 302_A | 1.131 | 0.12 |
| 447_A | 454_M | 1.130 | 0.12 |
| 162_I | 189_A | 1.129 | 0.12 |
| 269_F | 441_D | 1.127 | 0.12 |
| 132_I | 221_P | 1.126 | 0.12 |
| 202_L | 257_P | 1.123 | 0.12 |
| 246_R | 249_K | 1.122 | 0.12 |
| 188_D | 256_A | 1.119 | 0.12 |
| 57_A | 104_I | 1.117 | 0.12 |
| 65_A | 182_V | 1.117 | 0.12 |
| 62_E | 101_N | 1.115 | 0.12 |
| 245_F | 248_S | 1.113 | 0.12 |
| 5_P | 119_A | 1.112 | 0.12 |
| 298_I | 331_S | 1.112 | 0.12 |
| 193_L | 413_D | 1.111 | 0.12 |
| 170_R | 440_L | 1.110 | 0.12 |
| 412_S | 425_N | 1.107 | 0.12 |
| 160_V | 277_P | 1.107 | 0.12 |
| 2_G | 470_G | 1.105 | 0.12 |
| 160_V | 270_C | 1.103 | 0.12 |
| 79_P | 200_S | 1.103 | 0.12 |
| 363_S | 464_I | 1.102 | 0.12 |
| 222_N | 225_P | 1.101 | 0.12 |
| 133_S | 438_I | 1.099 | 0.12 |
| 142_F | 268_W | 1.098 | 0.12 |
| 115_V | 168_G | 1.097 | 0.12 |
| 106_N | 137_G | 1.097 | 0.12 |
| 220_T | 355_S | 1.095 | 0.12 |
| 17_N | 269_F | 1.091 | 0.12 |
| 100_A | 120_G | 1.088 | 0.11 |
| 134_L | 441_D | 1.084 | 0.11 |
| 341_S | 428_K | 1.082 | 0.11 |
| 331_S | 371_P | 1.082 | 0.11 |
| 41_K | 143_Y | 1.079 | 0.11 |
| 292_P | 468_N | 1.079 | 0.11 |
| 268_W | 477_K | 1.075 | 0.11 |
| 333_S | 421_S | 1.075 | 0.11 |
| 93_K | 156_L | 1.073 | 0.11 |
| 230_R | 246_R | 1.073 | 0.11 |
| 256_A | 351_K | 1.069 | 0.11 |
| 275_G | 443_P | 1.069 | 0.11 |
| 14_R | 17_N | 1.068 | 0.11 |
| 79_P | 463_E | 1.068 | 0.11 |
| 147_F | 254_R | 1.068 | 0.11 |
| 102_T | 483_K | 1.067 | 0.11 |
| 162_I | 209_E | 1.066 | 0.11 |
| 97_S | 151_L | 1.066 | 0.11 |
| 168_G | 174_K | 1.066 | 0.11 |
| 96_L | 99_R | 1.065 | 0.11 |
| 139_M | 151_L | 1.064 | 0.11 |
| 4_Q | 469_W | 1.063 | 0.11 |
| 163_V | 477_K | 1.060 | 0.11 |
| 297_T | 344_L | 1.059 | 0.11 |
| 269_F | 440_L | 1.058 | 0.11 |
| 107_D | 135_F | 1.056 | 0.11 |
| 268_W | 431_N | 1.056 | 0.11 |
| 202_L | 322_R | 1.055 | 0.11 |
| 386_A | 481_V | 1.055 | 0.11 |
| 195_I | 381_M | 1.054 | 0.11 |
| 162_I | 201_Y | 1.054 | 0.11 |
| 208_Q | 362_A | 1.053 | 0.11 |
| 140_R | 153_P | 1.053 | 0.11 |
| 133_S | 435_T | 1.053 | 0.11 |
| 331_S | 382_H | 1.053 | 0.11 |
| 356_K | 464_I | 1.052 | 0.11 |
| 226_R | 242_R | 1.049 | 0.11 |
| 436_C | 455_A | 1.049 | 0.11 |
| 439_C | 455_A | 1.049 | 0.11 |
| 448_C | 455_A | 1.049 | 0.11 |
| 450_P | 455_A | 1.049 | 0.11 |
| 451_C | 455_A | 1.049 | 0.11 |
| 12_Y | 152_A | 1.048 | 0.11 |
| 165_L | 440_L | 1.048 | 0.11 |
| 257_P | 402_T | 1.047 | 0.11 |
| 98_Y | 363_S | 1.046 | 0.11 |
| 79_P | 179_E | 1.044 | 0.11 |
| 143_Y | 351_K | 1.043 | 0.11 |
| 213_S | 417_V | 1.043 | 0.11 |
| 114_E | 455_A | 1.041 | 0.10 |
| 39_E | 87_G | 1.041 | 0.10 |
| 193_L | 406_D | 1.041 | 0.10 |
| 127_A | 339_S | 1.040 | 0.10 |
| 3_Q | 168_G | 1.039 | 0.10 |
| 76_G | 164_V | 1.039 | 0.10 |
| 113_L | 144_G | 1.038 | 0.10 |
| 21_E | 136_S | 1.037 | 0.10 |
| 350_P | 406_D | 1.036 | 0.10 |
| 56_V | 198_W | 1.033 | 0.10 |
| 219_N | 256_A | 1.033 | 0.10 |
| 8_D | 364_H | 1.030 | 0.10 |
| 9_E | 94_L | 1.030 | 0.10 |
| 261_H | 385_N | 1.027 | 0.10 |
| 141_E | 152_A | 1.026 | 0.10 |
| 368_A | 371_P | 1.026 | 0.10 |
| 296_A | 302_A | 1.024 | 0.10 |
| 45_I | 79_P | 1.022 | 0.10 |
| 168_G | 188_D | 1.022 | 0.10 |
| 53_P | 108_A | 1.022 | 0.10 |
| 257_P | 344_L | 1.022 | 0.10 |
| 128_I | 135_F | 1.020 | 0.10 |
| 257_P | 440_L | 1.019 | 0.10 |
| 87_G | 126_R | 1.018 | 0.10 |
| 300_P | 331_S | 1.018 | 0.10 |
| 2_G | 170_R | 1.017 | 0.10 |
| 258_A | 447_A | 1.016 | 0.10 |
| 126_R | 180_L | 1.015 | 0.10 |
| 335_E | 466_T | 1.015 | 0.10 |
| 380_I | 417_V | 1.013 | 0.10 |
| 139_M | 413_D | 1.012 | 0.10 |
| 109_C | 390_A | 1.012 | 0.10 |
| 444_V | 483_K | 1.011 | 0.10 |
| 99_R | 113_L | 1.011 | 0.10 |
| 113_L | 137_G | 1.010 | 0.10 |
| 56_V | 438_I | 1.009 | 0.10 |
| 56_V | 216_I | 1.007 | 0.10 |
| 369_E | 372_N | 1.007 | 0.10 |
| 114_E | 426_E | 1.005 | 0.10 |
| 131_H | 434_S | 1.005 | 0.10 |
| 186_L | 412_S | 1.005 | 0.10 |
| 394_V | 440_L | 1.005 | 0.10 |
| 349_P | 353_S | 1.005 | 0.10 |
| 78_T | 174_K | 1.000 | 0.10 |
| 362_A | 365_D | 1.000 | 0.10 |
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 | |
| 4xczA | 1 | 0.2649 | 99.9 | 0.894 | Contact Map |
| 1dcqA | 1 | 0.3018 | 99.9 | 0.898 | Contact Map |
| 3lvqE | 1 | 0.4867 | 99.9 | 0.899 | Contact Map |
| 2b0oE | 4 | 0.306 | 99.9 | 0.899 | Contact Map |
| 4rlvA | 1 | 0.2628 | 99.9 | 0.9 | Contact Map |
| 3jueA | 2 | 0.2649 | 99.9 | 0.9 | Contact Map |
| 1yyhA | 2 | 0.2608 | 99.9 | 0.901 | Contact Map |
| 4tumA | 5 | 0.2505 | 99.9 | 0.903 | Contact Map |
| 3aaaC | 1 | 0.2402 | 99.9 | 0.904 | Contact Map |
| 3v31A | 1 | 0.2813 | 99.9 | 0.904 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)