| secY |
| ID: | 1408421202 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 441 (429) | ||
| Sequences: | 1666 (987.2) | ||
| Seq/Len: | 3.883 | ||
| Nf(neff/√len): | 47.7 |
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: 3.883).
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 |
| 34_M | 76_M | 3.824 | 1.00 |
| 316_A | 376_A | 3.628 | 1.00 |
| 90_V | 114_I | 3.530 | 1.00 |
| 354_K | 358_E | 3.449 | 1.00 |
| 27_L | 173_L | 3.402 | 1.00 |
| 324_F | 369_F | 3.185 | 1.00 |
| 337_A | 357_A | 2.665 | 1.00 |
| 320_I | 376_A | 2.532 | 1.00 |
| 37_V | 75_V | 2.505 | 1.00 |
| 103_L | 117_I | 2.503 | 1.00 |
| 22_L | 26_G | 2.502 | 1.00 |
| 23_L | 27_L | 2.494 | 1.00 |
| 90_V | 100_L | 2.229 | 1.00 |
| 100_L | 114_I | 2.220 | 1.00 |
| 270_L | 364_L | 2.137 | 1.00 |
| 108_E | 111_R | 2.092 | 1.00 |
| 138_K | 156_W | 2.089 | 1.00 |
| 316_A | 320_I | 2.050 | 1.00 |
| 361_D | 365_S | 2.018 | 1.00 |
| 169_F | 173_L | 1.981 | 1.00 |
| 130_A | 164_T | 1.952 | 1.00 |
| 257_N | 261_V | 1.947 | 1.00 |
| 280_I | 379_S | 1.911 | 1.00 |
| 123_I | 168_I | 1.910 | 1.00 |
| 30_V | 169_F | 1.899 | 1.00 |
| 323_S | 375_L | 1.852 | 1.00 |
| 249_Y | 345_G | 1.849 | 1.00 |
| 153_A | 157_V | 1.812 | 0.99 |
| 99_Y | 102_K | 1.790 | 0.99 |
| 122_T | 167_T | 1.756 | 0.99 |
| 241_A | 272_L | 1.740 | 0.99 |
| 247_V | 268_I | 1.727 | 0.99 |
| 63_N | 71_A | 1.722 | 0.99 |
| 168_I | 171_M | 1.708 | 0.99 |
| 90_V | 121_L | 1.649 | 0.99 |
| 21_I | 25_I | 1.641 | 0.99 |
| 310_G | 313_V | 1.620 | 0.99 |
| 113_K | 116_Q | 1.599 | 0.98 |
| 24_T | 188_L | 1.586 | 0.98 |
| 257_N | 260_N | 1.581 | 0.98 |
| 240_T | 411_I | 1.563 | 0.98 |
| 239_V | 271_K | 1.550 | 0.98 |
| 16_E | 19_N | 1.544 | 0.98 |
| 28_I | 188_L | 1.540 | 0.98 |
| 31_Y | 193_G | 1.525 | 0.98 |
| 338_E | 341_K | 1.504 | 0.97 |
| 30_V | 173_L | 1.504 | 0.97 |
| 254_V | 263_G | 1.496 | 0.97 |
| 207_V | 211_T | 1.487 | 0.97 |
| 127_L | 164_T | 1.483 | 0.97 |
| 81_M | 85_S | 1.476 | 0.97 |
| 309_L | 313_V | 1.470 | 0.97 |
| 239_V | 374_F | 1.467 | 0.97 |
| 418_N | 429_L | 1.464 | 0.97 |
| 27_L | 169_F | 1.443 | 0.97 |
| 286_I | 318_L | 1.441 | 0.96 |
| 335_K | 339_D | 1.401 | 0.96 |
| 362_S | 366_R | 1.379 | 0.95 |
| 353_G | 356_T | 1.371 | 0.95 |
| 234_L | 377_A | 1.365 | 0.95 |
| 373_L | 377_A | 1.363 | 0.95 |
| 17_L | 182_V | 1.355 | 0.95 |
| 317_L | 321_I | 1.355 | 0.95 |
| 28_I | 192_V | 1.353 | 0.94 |
| 125_I | 429_L | 1.348 | 0.94 |
| 309_L | 312_N | 1.346 | 0.94 |
| 167_T | 170_A | 1.345 | 0.94 |
| 270_L | 367_I | 1.336 | 0.94 |
| 85_S | 280_I | 1.335 | 0.94 |
| 274_A | 364_L | 1.333 | 0.94 |
| 78_L | 85_S | 1.325 | 0.94 |
| 238_L | 374_F | 1.308 | 0.93 |
| 238_L | 268_I | 1.306 | 0.93 |
| 338_E | 342_R | 1.293 | 0.93 |
| 127_L | 160_I | 1.290 | 0.92 |
| 251_R | 262_A | 1.287 | 0.92 |
| 101_Q | 105_K | 1.280 | 0.92 |
| 328_A | 361_D | 1.277 | 0.92 |
| 412_D | 416_Q | 1.273 | 0.92 |
| 299_F | 303_L | 1.272 | 0.92 |
| 431_K | 434_N | 1.268 | 0.92 |
| 188_L | 413_T | 1.262 | 0.91 |
| 108_E | 112_K | 1.257 | 0.91 |
| 49_A | 52_E | 1.235 | 0.90 |
| 119_R | 171_M | 1.229 | 0.90 |
| 289_I | 402_S | 1.222 | 0.89 |
| 86_A | 121_L | 1.219 | 0.89 |
| 24_T | 181_G | 1.208 | 0.89 |
| 126_T | 167_T | 1.203 | 0.89 |
| 155_F | 159_S | 1.202 | 0.88 |
| 94_G | 114_I | 1.202 | 0.88 |
| 100_L | 103_L | 1.195 | 0.88 |
| 306_I | 311_Y | 1.194 | 0.88 |
| 333_T | 361_D | 1.188 | 0.88 |
| 231_V | 235_T | 1.188 | 0.88 |
| 9_K | 13_S | 1.187 | 0.88 |
| 160_I | 164_T | 1.187 | 0.88 |
| 355_D | 358_E | 1.185 | 0.87 |
| 352_P | 356_T | 1.184 | 0.87 |
| 119_R | 175_E | 1.184 | 0.87 |
| 102_K | 106_D | 1.176 | 0.87 |
| 323_S | 372_S | 1.170 | 0.87 |
| 291_M | 294_A | 1.167 | 0.86 |
| 376_A | 380_I | 1.164 | 0.86 |
| 222_L | 226_I | 1.160 | 0.86 |
| 35_A | 69_A | 1.156 | 0.86 |
| 257_N | 263_G | 1.152 | 0.85 |
| 182_V | 413_T | 1.151 | 0.85 |
| 236_V | 274_A | 1.143 | 0.85 |
| 289_I | 293_L | 1.142 | 0.85 |
| 71_A | 74_S | 1.140 | 0.85 |
| 14_I | 421_L | 1.140 | 0.85 |
| 116_Q | 120_W | 1.139 | 0.85 |
| 7_R | 96_A | 1.136 | 0.84 |
| 94_G | 104_Q | 1.136 | 0.84 |
| 99_Y | 103_L | 1.133 | 0.84 |
| 171_M | 175_E | 1.131 | 0.84 |
| 234_L | 238_L | 1.131 | 0.84 |
| 260_N | 264_S | 1.129 | 0.84 |
| 339_D | 343_S | 1.118 | 0.83 |
| 268_I | 425_H | 1.116 | 0.83 |
| 405_I | 409_V | 1.116 | 0.83 |
| 30_V | 35_A | 1.113 | 0.83 |
| 6_N | 9_K | 1.100 | 0.82 |
| 256_G | 261_V | 1.097 | 0.81 |
| 320_I | 372_S | 1.097 | 0.81 |
| 94_G | 268_I | 1.097 | 0.81 |
| 148_F | 435_S | 1.092 | 0.81 |
| 31_Y | 35_A | 1.090 | 0.81 |
| 15_E | 19_N | 1.088 | 0.81 |
| 11_I | 417_I | 1.087 | 0.81 |
| 61_L | 65_F | 1.083 | 0.80 |
| 234_L | 324_F | 1.082 | 0.80 |
| 277_V | 400_G | 1.082 | 0.80 |
| 244_K | 267_Y | 1.080 | 0.80 |
| 56_G | 60_G | 1.079 | 0.80 |
| 367_I | 372_S | 1.078 | 0.80 |
| 29_A | 33_F | 1.077 | 0.80 |
| 292_A | 296_R | 1.076 | 0.80 |
| 256_G | 260_N | 1.075 | 0.80 |
| 43_D | 46_Q | 1.069 | 0.79 |
| 215_A | 225_I | 1.067 | 0.79 |
| 255_A | 349_G | 1.067 | 0.79 |
| 31_Y | 217_G | 1.066 | 0.79 |
| 31_Y | 74_S | 1.065 | 0.79 |
| 106_D | 250_A | 1.061 | 0.78 |
| 16_E | 230_V | 1.061 | 0.78 |
| 318_L | 329_I | 1.060 | 0.78 |
| 329_I | 345_G | 1.057 | 0.78 |
| 59_L | 72_R | 1.055 | 0.78 |
| 175_E | 251_R | 1.052 | 0.77 |
| 26_G | 29_A | 1.051 | 0.77 |
| 187_S | 409_V | 1.050 | 0.77 |
| 331_I | 360_L | 1.049 | 0.77 |
| 256_G | 263_G | 1.047 | 0.77 |
| 331_I | 336_M | 1.044 | 0.77 |
| 188_L | 378_L | 1.042 | 0.77 |
| 90_V | 117_I | 1.042 | 0.77 |
| 96_A | 117_I | 1.040 | 0.76 |
| 421_L | 424_R | 1.039 | 0.76 |
| 236_V | 343_S | 1.036 | 0.76 |
| 22_L | 222_L | 1.033 | 0.76 |
| 127_L | 192_V | 1.033 | 0.76 |
| 10_D | 424_R | 1.033 | 0.76 |
| 44_P | 48_A | 1.033 | 0.76 |
| 52_E | 431_K | 1.030 | 0.75 |
| 251_R | 256_G | 1.029 | 0.75 |
| 202_F | 206_F | 1.029 | 0.75 |
| 248_Q | 419_S | 1.025 | 0.75 |
| 70_F | 287_M | 1.025 | 0.75 |
| 81_M | 327_T | 1.021 | 0.74 |
| 122_T | 231_V | 1.019 | 0.74 |
| 275_A | 372_S | 1.017 | 0.74 |
| 418_N | 428_G | 1.016 | 0.74 |
| 75_V | 324_F | 1.016 | 0.74 |
| 20_K | 420_Y | 1.013 | 0.74 |
| 255_A | 261_V | 1.013 | 0.74 |
| 373_L | 379_S | 1.012 | 0.74 |
| 240_T | 415_Q | 1.012 | 0.74 |
| 198_F | 369_F | 1.011 | 0.73 |
| 122_T | 171_M | 1.010 | 0.73 |
| 39_L | 102_K | 1.009 | 0.73 |
| 36_A | 63_N | 1.005 | 0.73 |
| 277_V | 281_I | 1.004 | 0.73 |
| 73_A | 278_M | 1.003 | 0.73 |
| 255_A | 263_G | 1.000 | 0.72 |
| 74_S | 326_Y | 1.000 | 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 | |
| 3dinC | 2 | 0.8844 | 100 | 0.064 | Contact Map |
| 3j01A | 1 | 0.9637 | 100 | 0.079 | Contact Map |
| 3dl8G | 2 | 0.9002 | 100 | 0.082 | Contact Map |
| 2zjsY | 1 | 0.9206 | 100 | 0.083 | Contact Map |
| 3mp7A | 1 | 0.7347 | 100 | 0.183 | Contact Map |
| 1rh5A | 1 | 0.8322 | 100 | 0.184 | Contact Map |
| 2ww9A | 1 | 0.9093 | 100 | 0.201 | Contact Map |
| 2wwbA | 1 | 0.8889 | 100 | 0.235 | Contact Map |
| 1vwz1 | 1 | 0.7778 | 100 | 0.316 | Contact Map |
| 1xg7A | 2 | 0.2426 | 14.4 | 0.976 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)