| gremlin_3nmz_chainA |
| ID: | 1517448877 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 458 (398) | ||
| Sequences: | 3427 (2151.7) | ||
| Seq/Len: | 8.611 | ||
| Nf(neff/√len): | 107.9 |
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: 8.611).
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 |
| 75_L | 105_A | 2.869 | 1.00 |
| 130_E | 133_R | 2.863 | 1.00 |
| 269_N | 313_N | 2.861 | 1.00 |
| 185_M | 190_G | 2.763 | 1.00 |
| 57_S | 108_N | 2.611 | 1.00 |
| 66_M | 71_C | 2.610 | 1.00 |
| 264_A | 310_A | 2.544 | 1.00 |
| 118_R | 122_E | 2.535 | 1.00 |
| 271_S | 313_N | 2.465 | 1.00 |
| 311_L | 357_I | 2.462 | 1.00 |
| 407_S | 447_N | 2.394 | 1.00 |
| 57_S | 66_M | 2.372 | 1.00 |
| 176_S | 185_M | 2.195 | 1.00 |
| 375_L | 380_C | 2.190 | 1.00 |
| 176_S | 226_N | 2.175 | 1.00 |
| 267_L | 310_A | 2.136 | 1.00 |
| 271_S | 282_L | 2.042 | 1.00 |
| 312_W | 356_G | 2.034 | 1.00 |
| 221_G | 266_V | 2.020 | 1.00 |
| 360_N | 405_N | 1.989 | 1.00 |
| 128_L | 133_R | 1.976 | 1.00 |
| 128_L | 131_Q | 1.975 | 1.00 |
| 417_L | 422_A | 1.950 | 1.00 |
| 362_S | 375_L | 1.948 | 1.00 |
| 282_L | 287_S | 1.939 | 1.00 |
| 362_S | 405_N | 1.931 | 1.00 |
| 280_K | 284_E | 1.880 | 1.00 |
| 336_V | 380_C | 1.869 | 1.00 |
| 373_Q | 377_E | 1.868 | 1.00 |
| 313_N | 360_N | 1.804 | 1.00 |
| 106_L | 171_V | 1.795 | 1.00 |
| 172_L | 223_A | 1.790 | 1.00 |
| 228_T | 269_N | 1.779 | 1.00 |
| 415_E | 419_D | 1.768 | 1.00 |
| 385_L | 422_A | 1.761 | 1.00 |
| 325_I | 331_A | 1.744 | 1.00 |
| 72_L | 106_L | 1.739 | 1.00 |
| 183_H | 187_E | 1.705 | 1.00 |
| 76_I | 123_I | 1.659 | 1.00 |
| 77_Q | 80_H | 1.580 | 1.00 |
| 400_C | 426_L | 1.578 | 1.00 |
| 335_L | 357_I | 1.573 | 1.00 |
| 39_S | 42_G | 1.545 | 1.00 |
| 76_I | 125_V | 1.539 | 1.00 |
| 426_L | 444_A | 1.529 | 1.00 |
| 53_L | 105_A | 1.525 | 1.00 |
| 53_L | 56_M | 1.518 | 1.00 |
| 226_N | 269_N | 1.504 | 1.00 |
| 397_S | 436_M | 1.502 | 1.00 |
| 416_A | 420_M | 1.501 | 1.00 |
| 304_L | 350_I | 1.491 | 1.00 |
| 421_G | 424_S | 1.483 | 1.00 |
| 315_S | 325_I | 1.465 | 0.99 |
| 304_L | 307_V | 1.457 | 0.99 |
| 103_S | 171_V | 1.447 | 0.99 |
| 393_L | 396_V | 1.446 | 0.99 |
| 46_K | 49_M | 1.421 | 0.99 |
| 356_G | 398_N | 1.414 | 0.99 |
| 265_S | 306_S | 1.413 | 0.99 |
| 271_S | 310_A | 1.409 | 0.99 |
| 309_S | 353_S | 1.382 | 0.99 |
| 430_I | 442_A | 1.364 | 0.99 |
| 184_A | 188_L | 1.353 | 0.99 |
| 169_V | 223_A | 1.353 | 0.99 |
| 257_E | 300_K | 1.341 | 0.99 |
| 78_L | 98_A | 1.340 | 0.99 |
| 418_W | 423_V | 1.335 | 0.99 |
| 384_L | 399_A | 1.335 | 0.99 |
| 101_R | 104_A | 1.331 | 0.99 |
| 405_N | 447_N | 1.329 | 0.99 |
| 224_L | 270_L | 1.323 | 0.99 |
| 416_A | 419_D | 1.319 | 0.99 |
| 216_L | 259_L | 1.317 | 0.99 |
| 429_L | 437_I | 1.315 | 0.99 |
| 323_A | 326_C | 1.314 | 0.99 |
| 260_Q | 298_V | 1.308 | 0.99 |
| 304_L | 341_Y | 1.305 | 0.99 |
| 308_L | 357_I | 1.303 | 0.99 |
| 323_A | 327_A | 1.300 | 0.99 |
| 37_L | 40_M | 1.293 | 0.98 |
| 121_R | 181_H | 1.281 | 0.98 |
| 374_I | 378_N | 1.281 | 0.98 |
| 424_S | 428_N | 1.273 | 0.98 |
| 355_G | 387_H | 1.269 | 0.98 |
| 385_L | 426_L | 1.266 | 0.98 |
| 32_E | 35_Y | 1.265 | 0.98 |
| 50_S | 75_L | 1.256 | 0.98 |
| 217_R | 254_S | 1.247 | 0.98 |
| 311_L | 361_V | 1.245 | 0.98 |
| 107_H | 167_P | 1.240 | 0.98 |
| 48_D | 51_R | 1.228 | 0.98 |
| 38_L | 74_L | 1.220 | 0.98 |
| 351_I | 354_G | 1.219 | 0.98 |
| 379_N | 382_Q | 1.211 | 0.97 |
| 376_R | 381_L | 1.210 | 0.97 |
| 106_L | 175_L | 1.209 | 0.97 |
| 312_W | 353_S | 1.204 | 0.97 |
| 110_I | 174_K | 1.202 | 0.97 |
| 315_S | 360_N | 1.201 | 0.97 |
| 310_A | 314_L | 1.199 | 0.97 |
| 248_L | 266_V | 1.188 | 0.97 |
| 249_V | 285_V | 1.186 | 0.97 |
| 174_K | 360_N | 1.185 | 0.97 |
| 67_R | 116_D | 1.181 | 0.97 |
| 359_R | 401_G | 1.179 | 0.97 |
| 257_E | 302_S | 1.166 | 0.97 |
| 355_G | 402_T | 1.166 | 0.97 |
| 316_A | 360_N | 1.160 | 0.96 |
| 107_H | 170_C | 1.156 | 0.96 |
| 36_S | 40_M | 1.150 | 0.96 |
| 267_L | 282_L | 1.144 | 0.96 |
| 104_A | 170_C | 1.136 | 0.96 |
| 116_D | 120_R | 1.134 | 0.96 |
| 400_C | 429_L | 1.133 | 0.96 |
| 29_T | 32_E | 1.130 | 0.96 |
| 353_S | 356_G | 1.127 | 0.96 |
| 176_S | 182_R | 1.126 | 0.95 |
| 306_S | 353_S | 1.125 | 0.95 |
| 195_A | 249_V | 1.124 | 0.95 |
| 358_L | 402_T | 1.124 | 0.95 |
| 42_G | 74_L | 1.121 | 0.95 |
| 50_S | 57_S | 1.121 | 0.95 |
| 384_L | 402_T | 1.119 | 0.95 |
| 400_C | 444_A | 1.118 | 0.95 |
| 169_V | 384_L | 1.118 | 0.95 |
| 291_L | 310_A | 1.116 | 0.95 |
| 40_M | 52_T | 1.108 | 0.95 |
| 400_C | 441_S | 1.107 | 0.95 |
| 288_V | 326_C | 1.102 | 0.95 |
| 309_S | 352_E | 1.102 | 0.95 |
| 125_V | 171_V | 1.101 | 0.95 |
| 404_W | 430_I | 1.096 | 0.95 |
| 194_I | 220_A | 1.094 | 0.94 |
| 111_H | 174_K | 1.093 | 0.94 |
| 173_M | 222_M | 1.087 | 0.94 |
| 55_A | 58_S | 1.087 | 0.94 |
| 268_R | 313_N | 1.087 | 0.94 |
| 35_Y | 39_S | 1.086 | 0.94 |
| 358_L | 428_N | 1.082 | 0.94 |
| 403_L | 444_A | 1.081 | 0.94 |
| 222_M | 226_N | 1.080 | 0.94 |
| 175_L | 178_D | 1.077 | 0.94 |
| 222_M | 262_V | 1.076 | 0.94 |
| 287_S | 315_S | 1.075 | 0.94 |
| 27_L | 30_K | 1.072 | 0.94 |
| 390_S | 432_S | 1.072 | 0.94 |
| 76_I | 79_L | 1.068 | 0.94 |
| 315_S | 357_I | 1.066 | 0.93 |
| 387_H | 395_I | 1.065 | 0.93 |
| 110_I | 120_R | 1.064 | 0.93 |
| 268_R | 309_S | 1.062 | 0.93 |
| 120_R | 125_V | 1.058 | 0.93 |
| 268_R | 306_S | 1.057 | 0.93 |
| 238_L | 244_C | 1.056 | 0.93 |
| 38_L | 49_M | 1.053 | 0.93 |
| 172_L | 271_S | 1.052 | 0.93 |
| 240_S | 243_G | 1.046 | 0.93 |
| 173_M | 176_S | 1.046 | 0.93 |
| 227_L | 311_L | 1.042 | 0.92 |
| 80_H | 131_Q | 1.041 | 0.92 |
| 262_V | 265_S | 1.041 | 0.92 |
| 322_K | 330_G | 1.041 | 0.92 |
| 225_T | 262_V | 1.037 | 0.92 |
| 352_E | 395_I | 1.036 | 0.92 |
| 277_N | 412_K | 1.032 | 0.92 |
| 110_I | 309_S | 1.032 | 0.92 |
| 78_L | 102_A | 1.032 | 0.92 |
| 194_I | 198_L | 1.030 | 0.92 |
| 400_C | 427_K | 1.029 | 0.92 |
| 385_L | 421_G | 1.029 | 0.92 |
| 77_Q | 224_L | 1.029 | 0.92 |
| 351_I | 358_L | 1.027 | 0.92 |
| 115_D | 119_G | 1.026 | 0.92 |
| 378_N | 382_Q | 1.026 | 0.92 |
| 376_R | 406_L | 1.026 | 0.92 |
| 281_T | 285_V | 1.025 | 0.92 |
| 116_D | 119_G | 1.024 | 0.92 |
| 54_L | 101_R | 1.021 | 0.91 |
| 102_A | 425_M | 1.019 | 0.91 |
| 355_G | 448_L | 1.019 | 0.91 |
| 398_N | 401_G | 1.017 | 0.91 |
| 296_L | 308_L | 1.017 | 0.91 |
| 260_Q | 351_I | 1.014 | 0.91 |
| 305_K | 350_I | 1.011 | 0.91 |
| 393_L | 434_H | 1.009 | 0.91 |
| 327_A | 377_E | 1.004 | 0.90 |
| 360_N | 401_G | 1.004 | 0.90 |
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 | |
| 3nmzA | 2 | 0.8865 | 100 | 0.303 | Contact Map |
| 4rxhB | 1 | 0 | 100 | 0.396 | Contact Map |
| 4uaeA | 1 | 0.8079 | 100 | 0.401 | Contact Map |
| 4uafB | 1 | 0.8275 | 100 | 0.404 | Contact Map |
| 4uadA | 1 | 0.81 | 100 | 0.406 | Contact Map |
| 4rv1A | 6 | 0.869 | 100 | 0.408 | Contact Map |
| 3l6xA | 1 | 0.8362 | 100 | 0.414 | Contact Map |
| 2jdqA | 2 | 0.8668 | 100 | 0.417 | Contact Map |
| 3opbA | 2 | 0.8952 | 100 | 0.424 | Contact Map |
| 1xm9A | 1 | 0.8144 | 100 | 0.43 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)