| dbpa2 |
| ID: | 1502215302 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 457 (454) | ||
| Sequences: | 1649 (997.2) | ||
| Seq/Len: | 3.632 | ||
| Nf(neff/√len): | 46.8 |
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: 3.632).
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 |
| 58_G | 91_L | 3.875 | 1.00 |
| 136_H | 141_T | 3.835 | 1.00 |
| 128_A | 142_V | 3.587 | 1.00 |
| 11_P | 63_Q | 3.545 | 1.00 |
| 20_E | 97_F | 2.907 | 1.00 |
| 134_L | 138_Q | 2.906 | 1.00 |
| 128_A | 133_L | 2.899 | 1.00 |
| 41_K | 203_L | 2.795 | 1.00 |
| 29_V | 45_V | 2.764 | 1.00 |
| 150_L | 171_I | 2.560 | 1.00 |
| 75_L | 147_L | 2.538 | 1.00 |
| 61_L | 74_A | 2.463 | 1.00 |
| 134_L | 169_D | 2.378 | 1.00 |
| 104_L | 123_P | 2.350 | 1.00 |
| 309_S | 337_N | 2.293 | 1.00 |
| 251_K | 274_D | 2.242 | 1.00 |
| 14_Q | 63_Q | 2.228 | 1.00 |
| 36_A | 205_I | 2.123 | 1.00 |
| 138_Q | 169_D | 2.102 | 1.00 |
| 10_L | 59_L | 2.052 | 1.00 |
| 217_E | 340_L | 2.026 | 1.00 |
| 12_P | 16_T | 1.992 | 1.00 |
| 254_C | 272_H | 1.980 | 1.00 |
| 37_I | 181_L | 1.955 | 1.00 |
| 71_Q | 146_A | 1.952 | 1.00 |
| 126_I | 142_V | 1.943 | 1.00 |
| 169_D | 173_F | 1.933 | 1.00 |
| 386_C | 390_G | 1.931 | 1.00 |
| 40_G | 179_Q | 1.918 | 1.00 |
| 134_L | 137_L | 1.909 | 1.00 |
| 318_L | 343_S | 1.901 | 1.00 |
| 67_A | 124_H | 1.886 | 1.00 |
| 257_V | 296_V | 1.872 | 1.00 |
| 399_D | 447_K | 1.858 | 1.00 |
| 390_G | 397_P | 1.853 | 1.00 |
| 390_G | 395_M | 1.836 | 0.99 |
| 77_L | 133_L | 1.792 | 0.99 |
| 387_I | 390_G | 1.767 | 0.99 |
| 446_I | 451_C | 1.748 | 0.99 |
| 385_L | 389_G | 1.743 | 0.99 |
| 2_T | 6_T | 1.732 | 0.99 |
| 381_E | 390_G | 1.718 | 0.99 |
| 285_V | 289_N | 1.716 | 0.99 |
| 217_E | 365_N | 1.660 | 0.99 |
| 315_N | 329_I | 1.649 | 0.99 |
| 16_T | 97_F | 1.646 | 0.99 |
| 386_C | 389_G | 1.642 | 0.99 |
| 218_Q | 329_I | 1.638 | 0.99 |
| 112_F | 141_T | 1.636 | 0.99 |
| 381_E | 386_C | 1.629 | 0.98 |
| 215_P | 338_S | 1.622 | 0.98 |
| 23_Y | 94_L | 1.621 | 0.98 |
| 233_Q | 264_V | 1.603 | 0.98 |
| 231_L | 344_F | 1.595 | 0.98 |
| 390_G | 394_K | 1.595 | 0.98 |
| 20_E | 96_R | 1.594 | 0.98 |
| 258_C | 270_S | 1.579 | 0.98 |
| 42_D | 178_R | 1.569 | 0.98 |
| 382_M | 390_G | 1.532 | 0.97 |
| 381_E | 384_T | 1.527 | 0.97 |
| 73_Q | 124_H | 1.517 | 0.97 |
| 315_N | 343_S | 1.513 | 0.97 |
| 192_A | 204_A | 1.512 | 0.97 |
| 242_S | 311_E | 1.509 | 0.97 |
| 254_C | 270_S | 1.501 | 0.97 |
| 66_D | 124_H | 1.475 | 0.97 |
| 219_Q | 340_L | 1.471 | 0.97 |
| 137_L | 147_L | 1.469 | 0.97 |
| 236_L | 294_V | 1.466 | 0.96 |
| 390_G | 393_A | 1.464 | 0.96 |
| 91_L | 125_I | 1.455 | 0.96 |
| 235_L | 342_I | 1.453 | 0.96 |
| 61_L | 149_T | 1.444 | 0.96 |
| 189_E | 193_A | 1.435 | 0.96 |
| 427_V | 446_I | 1.414 | 0.95 |
| 116_R | 141_T | 1.409 | 0.95 |
| 384_T | 390_G | 1.407 | 0.95 |
| 228_K | 317_E | 1.404 | 0.95 |
| 248_C | 254_C | 1.402 | 0.95 |
| 251_K | 272_H | 1.395 | 0.95 |
| 381_E | 389_G | 1.385 | 0.95 |
| 133_L | 142_V | 1.384 | 0.95 |
| 221_Y | 367_Q | 1.381 | 0.95 |
| 391_K | 397_P | 1.380 | 0.95 |
| 357_S | 363_K | 1.380 | 0.95 |
| 402_G | 406_G | 1.362 | 0.94 |
| 168_D | 197_R | 1.362 | 0.94 |
| 389_G | 395_M | 1.357 | 0.94 |
| 72_T | 142_V | 1.356 | 0.94 |
| 36_A | 203_L | 1.351 | 0.94 |
| 42_D | 180_T | 1.346 | 0.94 |
| 382_M | 385_L | 1.344 | 0.94 |
| 237_S | 266_Q | 1.342 | 0.93 |
| 229_I | 257_V | 1.328 | 0.93 |
| 370_P | 400_V | 1.317 | 0.93 |
| 401_L | 415_I | 1.316 | 0.93 |
| 73_Q | 148_N | 1.316 | 0.93 |
| 315_N | 341_A | 1.315 | 0.93 |
| 110_Q | 136_H | 1.308 | 0.92 |
| 381_E | 387_I | 1.303 | 0.92 |
| 137_L | 144_L | 1.302 | 0.92 |
| 383_A | 390_G | 1.297 | 0.92 |
| 383_A | 386_C | 1.286 | 0.91 |
| 32_A | 203_L | 1.285 | 0.91 |
| 5_S | 19_N | 1.272 | 0.91 |
| 269_L | 286_R | 1.270 | 0.91 |
| 88_A | 105_T | 1.268 | 0.91 |
| 382_M | 386_C | 1.263 | 0.90 |
| 220_F | 366_W | 1.263 | 0.90 |
| 23_Y | 55_A | 1.261 | 0.90 |
| 147_L | 174_A | 1.260 | 0.90 |
| 396_R | 399_D | 1.257 | 0.90 |
| 116_R | 139_K | 1.249 | 0.90 |
| 137_L | 173_F | 1.246 | 0.90 |
| 361_Q | 370_P | 1.243 | 0.89 |
| 66_D | 73_Q | 1.241 | 0.89 |
| 235_L | 314_V | 1.237 | 0.89 |
| 112_F | 116_R | 1.235 | 0.89 |
| 389_G | 397_P | 1.226 | 0.89 |
| 123_P | 126_I | 1.220 | 0.88 |
| 219_Q | 367_Q | 1.219 | 0.88 |
| 382_M | 387_I | 1.218 | 0.88 |
| 78_C | 87_V | 1.212 | 0.88 |
| 36_A | 39_A | 1.210 | 0.88 |
| 61_L | 151_V | 1.209 | 0.88 |
| 74_A | 149_T | 1.209 | 0.88 |
| 4_F | 26_M | 1.209 | 0.88 |
| 383_A | 388_D | 1.204 | 0.87 |
| 382_M | 395_M | 1.204 | 0.87 |
| 249_N | 312_L | 1.199 | 0.87 |
| 287_F | 295_L | 1.198 | 0.87 |
| 323_E | 326_V | 1.198 | 0.87 |
| 381_E | 395_M | 1.196 | 0.87 |
| 44_R | 195_S | 1.193 | 0.87 |
| 243_S | 310_L | 1.185 | 0.86 |
| 157_R | 160_D | 1.170 | 0.85 |
| 18_L | 424_H | 1.169 | 0.85 |
| 76_V | 91_L | 1.167 | 0.85 |
| 42_D | 202_P | 1.160 | 0.85 |
| 135_D | 139_K | 1.160 | 0.85 |
| 218_Q | 315_N | 1.156 | 0.84 |
| 386_C | 392_K | 1.152 | 0.84 |
| 384_T | 387_I | 1.151 | 0.84 |
| 383_A | 455_L | 1.148 | 0.84 |
| 290_G | 337_N | 1.145 | 0.84 |
| 239_H | 311_E | 1.143 | 0.83 |
| 213_L | 216_I | 1.137 | 0.83 |
| 382_M | 388_D | 1.137 | 0.83 |
| 16_T | 20_E | 1.129 | 0.82 |
| 296_V | 317_E | 1.127 | 0.82 |
| 286_R | 291_S | 1.124 | 0.82 |
| 400_V | 425_V | 1.123 | 0.82 |
| 169_D | 172_R | 1.123 | 0.82 |
| 387_I | 400_V | 1.117 | 0.81 |
| 23_Y | 58_G | 1.117 | 0.81 |
| 399_D | 402_G | 1.112 | 0.81 |
| 269_L | 292_A | 1.110 | 0.81 |
| 91_L | 103_I | 1.110 | 0.81 |
| 418_I | 427_V | 1.109 | 0.81 |
| 51_S | 106_L | 1.104 | 0.80 |
| 387_I | 394_K | 1.101 | 0.80 |
| 394_K | 397_P | 1.100 | 0.80 |
| 266_Q | 294_V | 1.100 | 0.80 |
| 146_A | 439_K | 1.099 | 0.80 |
| 231_L | 369_P | 1.097 | 0.80 |
| 223_T | 231_L | 1.092 | 0.79 |
| 419_A | 448_G | 1.089 | 0.79 |
| 395_M | 400_V | 1.088 | 0.79 |
| 414_D | 433_V | 1.087 | 0.79 |
| 244_C | 314_V | 1.076 | 0.78 |
| 393_A | 449_K | 1.076 | 0.78 |
| 235_L | 239_H | 1.075 | 0.78 |
| 244_C | 294_V | 1.072 | 0.78 |
| 387_I | 395_M | 1.070 | 0.77 |
| 255_Q | 272_H | 1.069 | 0.77 |
| 445_K | 450_T | 1.067 | 0.77 |
| 416_G | 428_A | 1.067 | 0.77 |
| 357_S | 360_L | 1.065 | 0.77 |
| 439_K | 442_Q | 1.064 | 0.77 |
| 382_M | 389_G | 1.063 | 0.77 |
| 281_D | 284_L | 1.060 | 0.76 |
| 32_A | 205_I | 1.050 | 0.76 |
| 412_G | 415_I | 1.050 | 0.76 |
| 351_Q | 354_N | 1.049 | 0.75 |
| 385_L | 393_A | 1.049 | 0.75 |
| 106_L | 141_T | 1.048 | 0.75 |
| 69_L | 124_H | 1.048 | 0.75 |
| 385_L | 388_D | 1.046 | 0.75 |
| 403_A | 407_D | 1.045 | 0.75 |
| 261_L | 294_V | 1.043 | 0.75 |
| 391_K | 395_M | 1.040 | 0.75 |
| 114_M | 117_D | 1.040 | 0.75 |
| 107_C | 281_D | 1.038 | 0.74 |
| 385_L | 395_M | 1.034 | 0.74 |
| 77_L | 170_V | 1.034 | 0.74 |
| 243_S | 287_F | 1.034 | 0.74 |
| 143_S | 146_A | 1.034 | 0.74 |
| 253_D | 317_E | 1.031 | 0.74 |
| 1_M | 6_T | 1.031 | 0.74 |
| 65_I | 124_H | 1.025 | 0.73 |
| 402_G | 407_D | 1.025 | 0.73 |
| 421_H | 426_Y | 1.019 | 0.72 |
| 106_L | 136_H | 1.017 | 0.72 |
| 311_E | 342_I | 1.015 | 0.72 |
| 3_A | 6_T | 1.014 | 0.72 |
| 176_A | 200_R | 1.014 | 0.72 |
| 193_A | 196_G | 1.013 | 0.72 |
| 24_L | 105_T | 1.012 | 0.72 |
| 134_L | 173_F | 1.010 | 0.71 |
| 234_R | 237_S | 1.008 | 0.71 |
| 90_E | 93_R | 1.005 | 0.71 |
| 159_L | 191_I | 1.000 | 0.70 |
| 63_Q | 76_V | 1.000 | 0.70 |
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 | |
| 3sqwA | 1 | 0.9606 | 100 | 0.465 | Contact Map |
| 3i5xA | 1 | 0.9716 | 100 | 0.471 | Contact Map |
| 4pxaA | 1 | 0.8184 | 100 | 0.482 | Contact Map |
| 2db3A | 4 | 0.8074 | 100 | 0.487 | Contact Map |
| 3fmpB | 2 | 0.4464 | 100 | 0.501 | Contact Map |
| 4ljyA | 1 | 0.8446 | 100 | 0.503 | Contact Map |
| 4nhoA | 1 | 0.8031 | 100 | 0.505 | Contact Map |
| 4d25A | 1 | 0.8096 | 100 | 0.508 | Contact Map |
| 4w7sA | 2 | 0.8512 | 100 | 0.508 | Contact Map |
| 4c9bA | 1 | 0.8118 | 100 | 0.519 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)