| 1ade |
| ID: | 1411585474 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 431 (428) | ||
| Sequences: | 1652 (907.8) | ||
| Seq/Len: | 3.860 | ||
| Nf(neff/√len): | 43.9 |
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: 3.860).
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 |
| 340_E | 374_T | 6.515 | 1.00 |
| 348_R | 369_E | 6.179 | 1.00 |
| 53_H | 300_T | 5.980 | 1.00 |
| 84_K | 196_I | 3.899 | 1.00 |
| 51_V | 299_A | 3.823 | 1.00 |
| 339_K | 379_S | 3.690 | 1.00 |
| 329_L | 399_I | 3.614 | 1.00 |
| 373_E | 401_R | 3.493 | 1.00 |
| 393_Q | 397_N | 3.240 | 1.00 |
| 387_D | 390_G | 3.170 | 1.00 |
| 388_R | 396_L | 3.144 | 1.00 |
| 351_D | 367_G | 3.124 | 1.00 |
| 401_R | 405_L | 3.067 | 1.00 |
| 291_C | 304_R | 3.010 | 1.00 |
| 343_L | 401_R | 2.899 | 1.00 |
| 310_L | 315_V | 2.847 | 1.00 |
| 48_E | 89_R | 2.666 | 1.00 |
| 336_D | 382_T | 2.603 | 1.00 |
| 312_T | 405_L | 2.570 | 1.00 |
| 75_S | 111_V | 2.556 | 1.00 |
| 288_E | 292_K | 2.551 | 1.00 |
| 343_L | 375_M | 2.499 | 1.00 |
| 337_G | 380_E | 2.445 | 1.00 |
| 289_F | 293_Q | 2.372 | 1.00 |
| 92_P | 95_E | 2.369 | 1.00 |
| 340_E | 376_P | 2.363 | 1.00 |
| 289_F | 338_L | 2.356 | 1.00 |
| 184_Q | 188_D | 2.323 | 1.00 |
| 388_R | 400_K | 2.278 | 1.00 |
| 105_L | 148_V | 2.274 | 1.00 |
| 115_N | 130_G | 2.272 | 1.00 |
| 29_Y | 211_A | 2.266 | 1.00 |
| 394_A | 397_N | 2.233 | 1.00 |
| 343_L | 405_L | 2.228 | 1.00 |
| 342_K | 374_T | 2.214 | 1.00 |
| 31_V | 252_S | 2.205 | 1.00 |
| 77_A | 189_D | 2.146 | 1.00 |
| 152_F | 201_V | 2.146 | 1.00 |
| 348_R | 354_E | 2.136 | 1.00 |
| 349_M | 368_V | 2.081 | 1.00 |
| 182_D | 185_K | 2.032 | 1.00 |
| 28_K | 216_D | 2.022 | 1.00 |
| 327_F | 406_T | 1.979 | 1.00 |
| 227_L | 314_A | 1.951 | 1.00 |
| 380_E | 394_A | 1.923 | 1.00 |
| 292_K | 297_F | 1.922 | 1.00 |
| 125_A | 275_A | 1.906 | 1.00 |
| 109_Y | 164_V | 1.899 | 1.00 |
| 349_M | 367_G | 1.896 | 1.00 |
| 326_G | 411_D | 1.868 | 1.00 |
| 158_A | 162_K | 1.862 | 1.00 |
| 68_I | 72_V | 1.846 | 1.00 |
| 84_K | 88_D | 1.841 | 1.00 |
| 261_Y | 326_G | 1.825 | 1.00 |
| 400_K | 425_L | 1.794 | 0.99 |
| 74_L | 103_C | 1.794 | 0.99 |
| 195_D | 198_T | 1.775 | 0.99 |
| 157_F | 190_T | 1.748 | 0.99 |
| 396_L | 400_K | 1.738 | 0.99 |
| 37_H | 106_I | 1.738 | 0.99 |
| 210_Q | 214_R | 1.735 | 0.99 |
| 336_D | 381_S | 1.719 | 0.99 |
| 344_C | 370_P | 1.715 | 0.99 |
| 402_I | 410_I | 1.701 | 0.99 |
| 148_V | 201_V | 1.699 | 0.99 |
| 161_L | 183_Y | 1.695 | 0.99 |
| 291_C | 297_F | 1.695 | 0.99 |
| 9_T | 324_L | 1.687 | 0.99 |
| 375_M | 401_R | 1.685 | 0.99 |
| 401_R | 404_E | 1.643 | 0.99 |
| 284_D | 287_G | 1.625 | 0.99 |
| 67_I | 204_V | 1.606 | 0.98 |
| 287_G | 307_T | 1.589 | 0.98 |
| 345_V | 354_E | 1.574 | 0.98 |
| 376_P | 397_N | 1.565 | 0.98 |
| 393_Q | 396_L | 1.563 | 0.98 |
| 68_I | 74_L | 1.554 | 0.98 |
| 45_I | 60_L | 1.550 | 0.98 |
| 103_C | 148_V | 1.548 | 0.98 |
| 47_G | 418_D | 1.538 | 0.98 |
| 349_M | 355_V | 1.527 | 0.98 |
| 385_V | 390_G | 1.525 | 0.98 |
| 376_P | 394_A | 1.519 | 0.98 |
| 310_L | 402_I | 1.505 | 0.97 |
| 226_T | 322_N | 1.495 | 0.97 |
| 173_V | 180_A | 1.492 | 0.97 |
| 386_K | 390_G | 1.488 | 0.97 |
| 319_V | 324_L | 1.483 | 0.97 |
| 79_L | 97_L | 1.466 | 0.97 |
| 337_G | 379_S | 1.465 | 0.97 |
| 413_I | 423_M | 1.461 | 0.97 |
| 312_T | 401_R | 1.460 | 0.97 |
| 98_L | 207_L | 1.450 | 0.97 |
| 104_P | 145_G | 1.444 | 0.96 |
| 209_D | 258_Y | 1.434 | 0.96 |
| 213_Q | 407_G | 1.432 | 0.96 |
| 209_D | 213_Q | 1.414 | 0.96 |
| 399_I | 410_I | 1.409 | 0.96 |
| 346_A | 354_E | 1.409 | 0.96 |
| 74_L | 79_L | 1.407 | 0.96 |
| 70_N | 232_H | 1.395 | 0.95 |
| 212_R | 218_V | 1.384 | 0.95 |
| 8_G | 14_E | 1.382 | 0.95 |
| 185_K | 189_D | 1.371 | 0.95 |
| 293_Q | 337_G | 1.370 | 0.95 |
| 386_K | 420_T | 1.366 | 0.95 |
| 397_N | 400_K | 1.357 | 0.95 |
| 37_H | 78_A | 1.355 | 0.94 |
| 415_T | 421_E | 1.350 | 0.94 |
| 257_R | 323_S | 1.344 | 0.94 |
| 194_A | 198_T | 1.333 | 0.94 |
| 76_P | 197_L | 1.323 | 0.94 |
| 354_E | 369_E | 1.321 | 0.93 |
| 403_E | 425_L | 1.315 | 0.93 |
| 183_Y | 187_L | 1.313 | 0.93 |
| 154_K | 191_M | 1.307 | 0.93 |
| 138_E | 142_A | 1.293 | 0.92 |
| 162_K | 183_Y | 1.289 | 0.92 |
| 386_K | 421_E | 1.289 | 0.92 |
| 187_L | 191_M | 1.284 | 0.92 |
| 361_A | 364_D | 1.284 | 0.92 |
| 266_L | 315_V | 1.283 | 0.92 |
| 220_F | 254_L | 1.278 | 0.92 |
| 80_M | 196_I | 1.277 | 0.92 |
| 162_K | 166_E | 1.277 | 0.92 |
| 157_F | 161_L | 1.274 | 0.92 |
| 79_L | 83_M | 1.266 | 0.91 |
| 313_V | 346_A | 1.262 | 0.91 |
| 257_R | 325_S | 1.251 | 0.91 |
| 349_M | 364_D | 1.247 | 0.91 |
| 74_L | 148_V | 1.244 | 0.90 |
| 158_A | 187_L | 1.242 | 0.90 |
| 312_T | 315_V | 1.242 | 0.90 |
| 336_D | 380_E | 1.228 | 0.90 |
| 345_V | 373_E | 1.217 | 0.89 |
| 290_L | 341_V | 1.216 | 0.89 |
| 98_L | 202_V | 1.212 | 0.89 |
| 37_H | 75_S | 1.202 | 0.88 |
| 290_L | 330_T | 1.193 | 0.88 |
| 282_L | 287_G | 1.191 | 0.88 |
| 213_Q | 258_Y | 1.190 | 0.88 |
| 87_E | 94_R | 1.176 | 0.87 |
| 385_V | 396_L | 1.174 | 0.87 |
| 283_F | 286_T | 1.165 | 0.86 |
| 373_E | 405_L | 1.165 | 0.86 |
| 5_V | 248_V | 1.155 | 0.86 |
| 65_T | 98_L | 1.155 | 0.86 |
| 152_F | 198_T | 1.153 | 0.85 |
| 21_D | 419_R | 1.145 | 0.85 |
| 319_V | 408_V | 1.141 | 0.85 |
| 384_G | 415_T | 1.135 | 0.84 |
| 208_L | 218_V | 1.135 | 0.84 |
| 146_L | 157_F | 1.134 | 0.84 |
| 271_T | 331_K | 1.130 | 0.84 |
| 101_E | 360_L | 1.122 | 0.83 |
| 228_L | 272_R | 1.122 | 0.83 |
| 265_I | 422_T | 1.120 | 0.83 |
| 33_Y | 243_T | 1.114 | 0.83 |
| 116_A | 172_L | 1.113 | 0.83 |
| 153_D | 363_D | 1.111 | 0.82 |
| 226_T | 318_A | 1.103 | 0.82 |
| 358_T | 365_W | 1.096 | 0.81 |
| 336_D | 379_S | 1.091 | 0.81 |
| 190_T | 193_V | 1.091 | 0.81 |
| 29_Y | 65_T | 1.086 | 0.80 |
| 26_R | 427_D | 1.079 | 0.80 |
| 383_F | 415_T | 1.078 | 0.80 |
| 209_D | 320_Q | 1.072 | 0.79 |
| 102_A | 360_L | 1.072 | 0.79 |
| 158_A | 183_Y | 1.070 | 0.79 |
| 140_K | 231_D | 1.065 | 0.79 |
| 399_I | 403_E | 1.064 | 0.78 |
| 84_K | 87_E | 1.063 | 0.78 |
| 208_L | 252_S | 1.063 | 0.78 |
| 244_T | 247_G | 1.060 | 0.78 |
| 141_V | 230_I | 1.053 | 0.77 |
| 389_S | 396_L | 1.053 | 0.77 |
| 263_L | 326_G | 1.039 | 0.76 |
| 77_A | 193_V | 1.038 | 0.76 |
| 224_Q | 228_L | 1.037 | 0.76 |
| 189_D | 192_A | 1.031 | 0.75 |
| 77_A | 81_K | 1.029 | 0.75 |
| 3_N | 220_F | 1.029 | 0.75 |
| 409_P | 426_R | 1.029 | 0.75 |
| 100_S | 204_V | 1.016 | 0.74 |
| 349_M | 353_R | 1.015 | 0.74 |
| 403_E | 410_I | 1.014 | 0.74 |
| 122_G | 275_A | 1.010 | 0.73 |
| 30_V | 64_V | 1.007 | 0.73 |
| 165_M | 169_N | 1.006 | 0.73 |
| 342_K | 372_Y | 1.004 | 0.73 |
| 25_E | 61_R | 1.002 | 0.72 |
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 | |
| 3hidA | 1 | 0.9814 | 100 | 0.007 | Contact Map |
| 4m9dA | 2 | 0.993 | 100 | 0.01 | Contact Map |
| 3ue9A | 4 | 0.9722 | 100 | 0.011 | Contact Map |
| 1dj2A | 2 | 0.9768 | 100 | 0.028 | Contact Map |
| 1p9bA | 1 | 0.9722 | 100 | 0.03 | Contact Map |
| 3r7tA | 1 | 0.9443 | 100 | 0.034 | Contact Map |
| 2v40A | 1 | 0.9536 | 100 | 0.035 | Contact Map |
| 2d7uA | 1 | 0.7401 | 100 | 0.199 | Contact Map |
| 3dfzA | 2 | 0.4037 | 14.2 | 0.984 | Contact Map |
| 2pnwA | 1 | 0.1346 | 10.3 | 0.985 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)