| diana |
| ID: | 1485272350 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 419 (388) | ||
| Sequences: | 1238 (804.9) | ||
| Seq/Len: | 3.191 | ||
| Nf(neff/√len): | 40.9 |
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: 3.191).
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 |
| 43_A | 387_G | 2.886 | 1.00 |
| 37_F | 395_Y | 2.827 | 1.00 |
| 34_F | 38_G | 2.357 | 1.00 |
| 56_G | 382_N | 2.246 | 1.00 |
| 47_V | 66_W | 2.116 | 1.00 |
| 241_V | 347_A | 2.035 | 1.00 |
| 245_L | 344_Y | 2.028 | 1.00 |
| 69_F | 355_T | 1.999 | 1.00 |
| 46_R | 50_E | 1.985 | 1.00 |
| 42_Y | 46_R | 1.980 | 1.00 |
| 37_F | 398_L | 1.976 | 1.00 |
| 31_A | 35_V | 1.935 | 1.00 |
| 118_V | 127_A | 1.923 | 1.00 |
| 33_V | 394_A | 1.918 | 1.00 |
| 313_K | 317_W | 1.875 | 0.99 |
| 379_Y | 385_E | 1.866 | 0.99 |
| 38_G | 42_Y | 1.862 | 0.99 |
| 268_G | 343_F | 1.850 | 0.99 |
| 41_L | 45_Y | 1.763 | 0.99 |
| 30_M | 398_L | 1.756 | 0.99 |
| 64_G | 362_T | 1.726 | 0.99 |
| 244_V | 347_A | 1.716 | 0.99 |
| 36_F | 394_A | 1.694 | 0.99 |
| 29_W | 401_S | 1.665 | 0.98 |
| 54_V | 384_A | 1.662 | 0.98 |
| 75_A | 235_A | 1.629 | 0.98 |
| 128_W | 132_W | 1.629 | 0.98 |
| 129_F | 132_W | 1.600 | 0.98 |
| 108_L | 399_V | 1.594 | 0.98 |
| 101_L | 247_C | 1.581 | 0.97 |
| 327_P | 353_G | 1.552 | 0.97 |
| 45_Y | 49_A | 1.534 | 0.97 |
| 323_C | 327_P | 1.515 | 0.96 |
| 55_T | 66_W | 1.510 | 0.96 |
| 386_W | 390_V | 1.487 | 0.96 |
| 39_W | 387_G | 1.469 | 0.96 |
| 114_M | 118_V | 1.449 | 0.95 |
| 46_R | 384_A | 1.448 | 0.95 |
| 326_V | 349_L | 1.433 | 0.95 |
| 42_Y | 390_V | 1.432 | 0.95 |
| 115_L | 395_Y | 1.430 | 0.95 |
| 129_F | 133_H | 1.418 | 0.94 |
| 197_T | 235_A | 1.404 | 0.94 |
| 67_I | 70_D | 1.399 | 0.94 |
| 279_L | 324_G | 1.392 | 0.94 |
| 28_M | 31_A | 1.388 | 0.93 |
| 150_Y | 197_T | 1.386 | 0.93 |
| 245_L | 347_A | 1.379 | 0.93 |
| 70_D | 199_H | 1.378 | 0.93 |
| 43_A | 384_A | 1.364 | 0.93 |
| 111_S | 399_V | 1.361 | 0.93 |
| 47_V | 52_L | 1.347 | 0.92 |
| 25_K | 28_M | 1.344 | 0.92 |
| 47_V | 54_V | 1.339 | 0.92 |
| 19_E | 418_R | 1.337 | 0.92 |
| 144_I | 148_T | 1.332 | 0.91 |
| 70_D | 117_L | 1.331 | 0.91 |
| 38_G | 41_L | 1.319 | 0.91 |
| 106_G | 154_L | 1.316 | 0.91 |
| 312_G | 353_G | 1.315 | 0.91 |
| 112_G | 396_A | 1.309 | 0.90 |
| 104_I | 403_S | 1.302 | 0.90 |
| 143_V | 199_H | 1.302 | 0.90 |
| 205_G | 228_F | 1.301 | 0.90 |
| 75_A | 78_A | 1.295 | 0.90 |
| 42_Y | 45_Y | 1.280 | 0.89 |
| 77_G | 150_Y | 1.280 | 0.89 |
| 341_V | 345_S | 1.271 | 0.89 |
| 70_D | 143_V | 1.268 | 0.89 |
| 115_L | 277_V | 1.267 | 0.88 |
| 248_T | 344_Y | 1.264 | 0.88 |
| 143_V | 200_Q | 1.264 | 0.88 |
| 32_F | 36_F | 1.261 | 0.88 |
| 81_F | 235_A | 1.241 | 0.87 |
| 269_K | 339_N | 1.238 | 0.87 |
| 52_L | 66_W | 1.238 | 0.87 |
| 336_L | 342_L | 1.236 | 0.87 |
| 271_A | 350_D | 1.230 | 0.86 |
| 237_G | 275_L | 1.230 | 0.86 |
| 44_A | 47_V | 1.227 | 0.86 |
| 235_A | 358_R | 1.226 | 0.86 |
| 28_M | 32_F | 1.226 | 0.86 |
| 24_S | 34_F | 1.225 | 0.86 |
| 102_A | 150_Y | 1.223 | 0.86 |
| 120_D | 200_Q | 1.220 | 0.86 |
| 269_K | 273_T | 1.214 | 0.85 |
| 325_L | 338_N | 1.212 | 0.85 |
| 121_I | 127_A | 1.204 | 0.85 |
| 272_G | 332_I | 1.200 | 0.85 |
| 105_I | 246_V | 1.197 | 0.84 |
| 268_G | 331_L | 1.194 | 0.84 |
| 23_L | 245_L | 1.193 | 0.84 |
| 32_F | 35_V | 1.192 | 0.84 |
| 61_F | 363_V | 1.190 | 0.84 |
| 143_V | 147_I | 1.189 | 0.84 |
| 57_L | 66_W | 1.189 | 0.84 |
| 154_L | 195_L | 1.183 | 0.83 |
| 244_V | 268_G | 1.182 | 0.83 |
| 348_I | 352_I | 1.182 | 0.83 |
| 84_G | 150_Y | 1.180 | 0.83 |
| 66_W | 70_D | 1.178 | 0.83 |
| 31_A | 41_L | 1.177 | 0.83 |
| 47_V | 55_T | 1.177 | 0.83 |
| 234_S | 358_R | 1.175 | 0.83 |
| 169_N | 172_K | 1.167 | 0.82 |
| 333_V | 336_L | 1.163 | 0.82 |
| 27_M | 30_M | 1.160 | 0.82 |
| 123_Q | 126_R | 1.149 | 0.81 |
| 52_L | 57_L | 1.143 | 0.80 |
| 72_A | 393_V | 1.140 | 0.80 |
| 52_L | 55_T | 1.137 | 0.80 |
| 402_L | 406_Y | 1.137 | 0.80 |
| 100_N | 408_P | 1.136 | 0.80 |
| 249_L | 253_M | 1.130 | 0.79 |
| 131_Y | 148_T | 1.129 | 0.79 |
| 323_C | 353_G | 1.127 | 0.79 |
| 31_A | 48_L | 1.124 | 0.79 |
| 95_L | 266_L | 1.122 | 0.79 |
| 140_L | 353_G | 1.119 | 0.78 |
| 400_L | 410_F | 1.118 | 0.78 |
| 399_V | 402_L | 1.117 | 0.78 |
| 36_F | 42_Y | 1.115 | 0.78 |
| 31_A | 38_G | 1.111 | 0.78 |
| 86_L | 236_V | 1.110 | 0.78 |
| 383_W | 387_G | 1.109 | 0.78 |
| 33_V | 37_F | 1.106 | 0.77 |
| 138_S | 379_Y | 1.105 | 0.77 |
| 94_P | 262_E | 1.105 | 0.77 |
| 218_R | 364_Q | 1.103 | 0.77 |
| 299_L | 303_Q | 1.099 | 0.77 |
| 322_Y | 349_L | 1.098 | 0.77 |
| 54_V | 387_G | 1.098 | 0.77 |
| 57_L | 389_S | 1.098 | 0.77 |
| 196_S | 200_Q | 1.096 | 0.76 |
| 35_V | 39_W | 1.096 | 0.76 |
| 348_I | 386_W | 1.096 | 0.76 |
| 46_R | 49_A | 1.094 | 0.76 |
| 106_G | 196_S | 1.087 | 0.76 |
| 33_V | 43_A | 1.087 | 0.76 |
| 31_A | 387_G | 1.087 | 0.76 |
| 34_F | 398_L | 1.085 | 0.75 |
| 35_V | 265_S | 1.081 | 0.75 |
| 21_C | 417_N | 1.081 | 0.75 |
| 330_I | 336_L | 1.077 | 0.75 |
| 193_A | 197_T | 1.076 | 0.74 |
| 36_F | 41_L | 1.076 | 0.74 |
| 34_F | 41_L | 1.073 | 0.74 |
| 47_V | 384_A | 1.072 | 0.74 |
| 101_L | 400_L | 1.070 | 0.74 |
| 198_F | 205_G | 1.070 | 0.74 |
| 152_L | 348_I | 1.068 | 0.74 |
| 197_T | 200_Q | 1.066 | 0.73 |
| 330_I | 342_L | 1.065 | 0.73 |
| 212_G | 369_P | 1.064 | 0.73 |
| 36_F | 390_V | 1.062 | 0.73 |
| 402_L | 407_L | 1.060 | 0.73 |
| 95_L | 270_I | 1.059 | 0.73 |
| 233_L | 400_L | 1.058 | 0.73 |
| 213_R | 370_V | 1.056 | 0.72 |
| 35_V | 38_G | 1.055 | 0.72 |
| 278_Y | 357_N | 1.053 | 0.72 |
| 347_A | 351_C | 1.052 | 0.72 |
| 24_S | 38_G | 1.048 | 0.72 |
| 81_F | 196_S | 1.047 | 0.72 |
| 219_E | 288_A | 1.045 | 0.71 |
| 94_P | 266_L | 1.044 | 0.71 |
| 42_Y | 54_V | 1.043 | 0.71 |
| 35_V | 390_V | 1.040 | 0.71 |
| 39_W | 46_R | 1.038 | 0.71 |
| 142_E | 146_C | 1.037 | 0.71 |
| 78_A | 193_A | 1.036 | 0.70 |
| 354_I | 357_N | 1.033 | 0.70 |
| 339_N | 343_F | 1.032 | 0.70 |
| 266_L | 269_K | 1.031 | 0.70 |
| 25_K | 45_Y | 1.027 | 0.69 |
| 321_F | 326_V | 1.027 | 0.69 |
| 84_G | 102_A | 1.026 | 0.69 |
| 35_V | 42_Y | 1.025 | 0.69 |
| 293_L | 298_G | 1.019 | 0.69 |
| 42_Y | 49_A | 1.018 | 0.69 |
| 70_D | 204_G | 1.018 | 0.69 |
| 143_V | 285_D | 1.016 | 0.68 |
| 237_G | 350_D | 1.015 | 0.68 |
| 30_M | 34_F | 1.015 | 0.68 |
| 315_M | 356_I | 1.014 | 0.68 |
| 403_S | 407_L | 1.011 | 0.68 |
| 69_F | 389_S | 1.010 | 0.68 |
| 50_E | 53_G | 1.010 | 0.68 |
| 103_V | 154_L | 1.007 | 0.67 |
| 44_A | 119_L | 1.007 | 0.67 |
| 34_F | 390_V | 1.004 | 0.67 |
| 71_L | 83_S | 1.002 | 0.67 |
| 77_G | 196_S | 1.001 | 0.67 |
| 20_R | 418_R | 1.000 | 0.67 |
| 23_L | 41_L | 1.000 | 0.67 |
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 | |
| 2vpzC | 2 | 0.5871 | 100 | 0.646 | Contact Map |
| 4o6yA | 2 | 0.4869 | 60.2 | 0.958 | Contact Map |
| 3s8fA | 1 | 0.5012 | 17.1 | 0.969 | Contact Map |
| 3l1lA | 1 | 0.8115 | 17 | 0.969 | Contact Map |
| 4ev6A | 5 | 0.2029 | 11 | 0.971 | Contact Map |
| 2m7gA | 1 | 0.0883 | 7.6 | 0.973 | Contact Map |
| 4wgvA | 2 | 0.7589 | 7.2 | 0.974 | Contact Map |
| 4i0uA | 10 | 0.1909 | 5.9 | 0.975 | Contact Map |
| 2kogA | 1 | 0.1169 | 4.4 | 0.976 | Contact Map |
| 2k1eA | 4 | 0.2434 | 4.3 | 0.976 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)