| secy |
| ID: | 1403392981 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 443 (429) | ||
| Sequences: | 1699 (1012.3) | ||
| Seq/Len: | 3.960 | ||
| Nf(neff/√len): | 48.9 |
HHblits Results: (2013_03)
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: 3.960).
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 |
| 36_G | 78_F | 3.875 | 1.00 |
| 322_A | 382_T | 3.598 | 1.00 |
| 360_E | 364_K | 3.539 | 1.00 |
| 92_I | 116_I | 3.452 | 1.00 |
| 29_A | 174_L | 3.351 | 1.00 |
| 330_F | 375_L | 3.261 | 1.00 |
| 343_A | 363_A | 2.694 | 1.00 |
| 24_L | 28_G | 2.560 | 1.00 |
| 105_I | 119_Y | 2.484 | 1.00 |
| 39_I | 77_I | 2.478 | 1.00 |
| 326_I | 382_T | 2.460 | 1.00 |
| 25_F | 29_A | 2.413 | 1.00 |
| 102_L | 116_I | 2.292 | 1.00 |
| 140_P | 157_Y | 2.179 | 1.00 |
| 277_A | 385_C | 2.137 | 1.00 |
| 92_I | 102_L | 2.125 | 1.00 |
| 32_V | 170_F | 2.113 | 1.00 |
| 267_L | 370_M | 2.100 | 1.00 |
| 110_E | 113_R | 2.042 | 1.00 |
| 322_A | 326_I | 2.018 | 1.00 |
| 132_S | 165_V | 2.016 | 1.00 |
| 170_F | 174_L | 2.008 | 1.00 |
| 367_D | 371_T | 2.004 | 1.00 |
| 329_C | 381_I | 1.920 | 1.00 |
| 65_N | 73_S | 1.876 | 1.00 |
| 248_Y | 351_A | 1.855 | 1.00 |
| 240_G | 269_V | 1.823 | 1.00 |
| 23_L | 27_I | 1.787 | 0.99 |
| 125_L | 169_M | 1.759 | 0.99 |
| 124_T | 168_T | 1.758 | 0.99 |
| 246_V | 265_L | 1.747 | 0.99 |
| 437_N | 440_G | 1.701 | 0.99 |
| 169_M | 172_M | 1.701 | 0.99 |
| 101_T | 104_E | 1.694 | 0.99 |
| 238_E | 380_Y | 1.688 | 0.99 |
| 239_R | 414_M | 1.676 | 0.99 |
| 18_E | 21_R | 1.651 | 0.99 |
| 344_D | 347_K | 1.643 | 0.99 |
| 129_I | 165_V | 1.639 | 0.99 |
| 26_V | 189_I | 1.625 | 0.99 |
| 92_I | 123_G | 1.624 | 0.99 |
| 115_K | 118_Q | 1.617 | 0.99 |
| 33_F | 194_G | 1.576 | 0.98 |
| 168_T | 171_L | 1.557 | 0.98 |
| 30_L | 189_I | 1.551 | 0.98 |
| 253_Q | 260_A | 1.508 | 0.98 |
| 421_Q | 432_A | 1.505 | 0.98 |
| 316_L | 319_L | 1.504 | 0.98 |
| 341_E | 345_N | 1.491 | 0.97 |
| 283_I | 324_A | 1.490 | 0.97 |
| 32_V | 174_L | 1.485 | 0.97 |
| 154_F | 158_F | 1.477 | 0.97 |
| 30_L | 193_A | 1.472 | 0.97 |
| 233_F | 383_F | 1.462 | 0.97 |
| 379_L | 383_F | 1.462 | 0.97 |
| 87_S | 277_A | 1.444 | 0.97 |
| 305_T | 309_Y | 1.443 | 0.97 |
| 315_P | 319_L | 1.434 | 0.96 |
| 238_E | 268_K | 1.425 | 0.96 |
| 83_M | 87_S | 1.410 | 0.96 |
| 88_A | 123_G | 1.406 | 0.96 |
| 103_A | 107_K | 1.405 | 0.96 |
| 221_L | 225_V | 1.383 | 0.95 |
| 127_L | 432_A | 1.380 | 0.95 |
| 359_G | 362_T | 1.364 | 0.95 |
| 368_K | 372_R | 1.356 | 0.95 |
| 237_V | 265_L | 1.321 | 0.94 |
| 250_K | 259_A | 1.320 | 0.94 |
| 29_A | 170_F | 1.316 | 0.94 |
| 286_F | 405_S | 1.314 | 0.94 |
| 22_R | 158_F | 1.313 | 0.93 |
| 156_F | 160_A | 1.300 | 0.93 |
| 110_E | 114_R | 1.300 | 0.93 |
| 10_Q | 13_K | 1.295 | 0.93 |
| 339_P | 367_D | 1.289 | 0.93 |
| 237_V | 380_Y | 1.289 | 0.93 |
| 129_I | 161_V | 1.273 | 0.92 |
| 344_D | 348_K | 1.273 | 0.92 |
| 73_S | 76_S | 1.272 | 0.92 |
| 415_D | 419_Q | 1.272 | 0.92 |
| 208_E | 211_R | 1.268 | 0.92 |
| 19_L | 183_I | 1.266 | 0.92 |
| 271_M | 370_M | 1.263 | 0.92 |
| 315_P | 318_V | 1.257 | 0.91 |
| 121_R | 176_E | 1.252 | 0.91 |
| 189_I | 416_F | 1.251 | 0.91 |
| 233_F | 237_V | 1.249 | 0.91 |
| 267_L | 373_L | 1.245 | 0.91 |
| 96_T | 106_K | 1.244 | 0.91 |
| 80_L | 87_S | 1.243 | 0.91 |
| 253_Q | 256_R | 1.240 | 0.91 |
| 32_V | 37_S | 1.236 | 0.90 |
| 323_S | 327_F | 1.235 | 0.90 |
| 256_R | 260_A | 1.224 | 0.90 |
| 288_A | 291_A | 1.222 | 0.90 |
| 358_P | 362_T | 1.216 | 0.90 |
| 265_L | 428_Q | 1.214 | 0.89 |
| 98_V | 119_Y | 1.208 | 0.89 |
| 121_R | 172_M | 1.208 | 0.89 |
| 26_V | 182_G | 1.204 | 0.89 |
| 210_A | 220_L | 1.201 | 0.89 |
| 183_I | 416_F | 1.199 | 0.89 |
| 96_T | 116_I | 1.199 | 0.89 |
| 326_I | 378_A | 1.198 | 0.89 |
| 104_E | 108_E | 1.197 | 0.89 |
| 408_I | 412_V | 1.186 | 0.88 |
| 289_T | 293_W | 1.183 | 0.88 |
| 128_A | 168_T | 1.177 | 0.87 |
| 209_Q | 214_D | 1.176 | 0.87 |
| 345_N | 349_S | 1.176 | 0.87 |
| 22_R | 269_V | 1.174 | 0.87 |
| 102_L | 105_I | 1.170 | 0.87 |
| 434_K | 437_N | 1.159 | 0.86 |
| 269_V | 343_A | 1.156 | 0.86 |
| 334_A | 367_D | 1.155 | 0.86 |
| 424_M | 427_S | 1.150 | 0.86 |
| 172_M | 176_E | 1.150 | 0.86 |
| 230_V | 234_V | 1.145 | 0.85 |
| 306_I | 310_L | 1.140 | 0.85 |
| 361_Q | 364_K | 1.139 | 0.85 |
| 33_F | 37_S | 1.137 | 0.85 |
| 118_Q | 122_Y | 1.137 | 0.85 |
| 124_T | 230_V | 1.137 | 0.85 |
| 37_S | 71_A | 1.130 | 0.84 |
| 255_R | 260_A | 1.124 | 0.84 |
| 421_Q | 431_S | 1.122 | 0.84 |
| 274_V | 403_G | 1.121 | 0.84 |
| 235_V | 349_S | 1.118 | 0.83 |
| 17_G | 21_R | 1.118 | 0.83 |
| 16_L | 424_M | 1.113 | 0.83 |
| 39_I | 390_F | 1.110 | 0.83 |
| 75_A | 275_I | 1.099 | 0.82 |
| 51_K | 54_E | 1.095 | 0.82 |
| 243_R | 264_H | 1.094 | 0.82 |
| 329_C | 378_A | 1.094 | 0.82 |
| 31_I | 35_I | 1.093 | 0.82 |
| 101_T | 105_I | 1.092 | 0.81 |
| 45_D | 48_V | 1.091 | 0.81 |
| 286_F | 290_I | 1.090 | 0.81 |
| 161_V | 165_V | 1.089 | 0.81 |
| 291_A | 306_I | 1.089 | 0.81 |
| 102_L | 250_K | 1.083 | 0.81 |
| 324_A | 335_L | 1.079 | 0.80 |
| 253_Q | 257_V | 1.078 | 0.80 |
| 235_V | 271_M | 1.077 | 0.80 |
| 22_R | 228_F | 1.063 | 0.79 |
| 188_S | 412_V | 1.053 | 0.78 |
| 119_Y | 337_F | 1.051 | 0.78 |
| 159_T | 326_I | 1.048 | 0.78 |
| 335_L | 351_A | 1.048 | 0.78 |
| 252_Q | 257_V | 1.047 | 0.78 |
| 272_A | 378_A | 1.046 | 0.77 |
| 337_F | 342_T | 1.044 | 0.77 |
| 183_I | 375_L | 1.038 | 0.77 |
| 252_Q | 428_Q | 1.036 | 0.76 |
| 92_I | 119_Y | 1.036 | 0.76 |
| 76_S | 135_I | 1.036 | 0.76 |
| 233_F | 330_F | 1.035 | 0.76 |
| 72_L | 284_I | 1.034 | 0.76 |
| 239_R | 418_A | 1.028 | 0.76 |
| 416_F | 419_Q | 1.027 | 0.76 |
| 247_N | 422_T | 1.023 | 0.75 |
| 382_T | 386_L | 1.023 | 0.75 |
| 82_I | 172_M | 1.021 | 0.75 |
| 253_Q | 259_A | 1.021 | 0.75 |
| 340_R | 363_A | 1.020 | 0.75 |
| 128_A | 165_V | 1.017 | 0.75 |
| 41_I | 104_E | 1.016 | 0.75 |
| 121_R | 274_V | 1.016 | 0.75 |
| 22_R | 423_L | 1.016 | 0.75 |
| 33_F | 76_S | 1.015 | 0.74 |
| 24_L | 221_L | 1.015 | 0.74 |
| 80_L | 342_T | 1.014 | 0.74 |
| 395_M | 398_P | 1.013 | 0.74 |
| 312_P | 317_Y | 1.011 | 0.74 |
| 379_L | 385_C | 1.011 | 0.74 |
| 124_T | 172_M | 1.009 | 0.74 |
| 92_I | 275_I | 1.008 | 0.74 |
| 63_M | 67_F | 1.006 | 0.73 |
| 380_Y | 407_L | 1.006 | 0.73 |
| 108_E | 249_A | 1.005 | 0.73 |
| 83_M | 333_T | 1.004 | 0.73 |
| 41_I | 160_A | 1.001 | 0.73 |
| 19_L | 62_E | 1.000 | 0.73 |
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 | |
| 3j01A | 1 | 0.9819 | 100 | 0.067 | Contact Map |
| 3dinC | 2 | 0.8894 | 100 | 0.107 | Contact Map |
| 3dl8G | 2 | 0.9097 | 100 | 0.109 | Contact Map |
| 2zjsY | 1 | 0.9233 | 100 | 0.115 | Contact Map |
| 3mp7A | 1 | 0.7494 | 100 | 0.204 | Contact Map |
| 1rh5A | 1 | 0.8465 | 100 | 0.208 | Contact Map |
| 2ww9A | 1 | 0.9165 | 100 | 0.229 | Contact Map |
| 2wwbA | 1 | 0.8984 | 100 | 0.254 | Contact Map |
| 3oaaA | 12 | 0.1558 | 5.9 | 0.981 | Contact Map |
| 3ar4A | 1 | 0.2867 | 3.2 | 0.983 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)