| T0835 21-424 -force run |
| ID: | 1406431991 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 404 (352) | ||
| Sequences: | 267 (233.1) | ||
| Seq/Len: | 0.759 | ||
| Nf(neff/√len): | 12.4 |
Jackhmmer Results: (2014_04_16)
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: 0.759).
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 |
| 353_I | 368_S | 2.431 | 0.98 |
| 48_I | 81_I | 2.176 | 0.96 |
| 310_V | 379_T | 2.156 | 0.96 |
| 124_T | 188_A | 2.152 | 0.95 |
| 51_V | 54_A | 2.007 | 0.93 |
| 267_D | 325_Y | 1.929 | 0.91 |
| 266_L | 316_A | 1.921 | 0.90 |
| 262_A | 325_Y | 1.886 | 0.89 |
| 8_L | 377_L | 1.854 | 0.88 |
| 359_D | 363_T | 1.804 | 0.86 |
| 250_G | 262_A | 1.737 | 0.83 |
| 15_V | 99_H | 1.663 | 0.80 |
| 334_L | 339_N | 1.656 | 0.79 |
| 91_F | 99_H | 1.643 | 0.78 |
| 14_K | 99_H | 1.616 | 0.77 |
| 103_K | 106_K | 1.604 | 0.76 |
| 84_Q | 95_I | 1.551 | 0.73 |
| 280_N | 341_P | 1.537 | 0.72 |
| 192_A | 199_P | 1.533 | 0.71 |
| 121_W | 124_T | 1.532 | 0.71 |
| 86_A | 103_K | 1.518 | 0.70 |
| 101_I | 268_H | 1.503 | 0.69 |
| 279_L | 305_I | 1.483 | 0.68 |
| 209_A | 258_M | 1.474 | 0.67 |
| 244_Y | 332_L | 1.467 | 0.66 |
| 220_T | 223_P | 1.461 | 0.66 |
| 217_V | 257_D | 1.458 | 0.66 |
| 247_L | 262_A | 1.455 | 0.66 |
| 43_E | 47_A | 1.454 | 0.65 |
| 54_A | 77_L | 1.443 | 0.65 |
| 226_G | 233_N | 1.418 | 0.63 |
| 19_N | 40_D | 1.415 | 0.62 |
| 314_I | 329_A | 1.405 | 0.62 |
| 232_Q | 304_Y | 1.393 | 0.61 |
| 20_K | 305_I | 1.387 | 0.60 |
| 40_D | 43_E | 1.378 | 0.59 |
| 250_G | 253_L | 1.368 | 0.58 |
| 346_M | 354_A | 1.367 | 0.58 |
| 280_N | 301_Q | 1.367 | 0.58 |
| 80_F | 300_S | 1.362 | 0.58 |
| 78_V | 140_R | 1.352 | 0.57 |
| 73_K | 269_F | 1.349 | 0.57 |
| 342_A | 358_I | 1.345 | 0.57 |
| 39_K | 226_G | 1.335 | 0.56 |
| 10_A | 368_S | 1.334 | 0.56 |
| 122_A | 210_A | 1.315 | 0.54 |
| 193_Q | 375_E | 1.314 | 0.54 |
| 250_G | 259_I | 1.311 | 0.54 |
| 247_L | 319_I | 1.309 | 0.53 |
| 274_I | 341_P | 1.308 | 0.53 |
| 21_T | 34_D | 1.305 | 0.53 |
| 20_K | 43_E | 1.297 | 0.52 |
| 77_L | 368_S | 1.295 | 0.52 |
| 12_Y | 77_L | 1.294 | 0.52 |
| 308_P | 375_E | 1.292 | 0.52 |
| 99_H | 273_L | 1.290 | 0.52 |
| 11_L | 321_R | 1.287 | 0.52 |
| 94_F | 106_K | 1.279 | 0.51 |
| 281_E | 300_S | 1.279 | 0.51 |
| 243_A | 262_A | 1.276 | 0.51 |
| 47_A | 274_I | 1.275 | 0.51 |
| 20_K | 106_K | 1.270 | 0.50 |
| 210_A | 258_M | 1.266 | 0.50 |
| 178_A | 230_S | 1.265 | 0.50 |
| 47_A | 57_F | 1.262 | 0.49 |
| 180_D | 183_S | 1.262 | 0.49 |
| 7_H | 373_T | 1.250 | 0.48 |
| 248_V | 315_K | 1.245 | 0.48 |
| 96_Y | 102_N | 1.240 | 0.47 |
| 20_K | 99_H | 1.239 | 0.47 |
| 213_M | 261_A | 1.238 | 0.47 |
| 288_G | 297_K | 1.226 | 0.46 |
| 355_F | 366_K | 1.222 | 0.46 |
| 48_I | 119_A | 1.215 | 0.45 |
| 106_K | 124_T | 1.212 | 0.45 |
| 309_M | 332_L | 1.212 | 0.45 |
| 47_A | 232_Q | 1.211 | 0.45 |
| 275_S | 278_L | 1.210 | 0.45 |
| 45_V | 302_I | 1.204 | 0.44 |
| 95_I | 106_K | 1.201 | 0.44 |
| 73_K | 281_E | 1.197 | 0.44 |
| 92_Y | 103_K | 1.195 | 0.44 |
| 337_F | 343_Q | 1.191 | 0.43 |
| 15_V | 20_K | 1.189 | 0.43 |
| 145_I | 358_I | 1.188 | 0.43 |
| 300_S | 316_A | 1.183 | 0.43 |
| 216_Q | 265_E | 1.181 | 0.42 |
| 244_Y | 315_K | 1.176 | 0.42 |
| 348_Y | 351_T | 1.175 | 0.42 |
| 55_A | 77_L | 1.173 | 0.42 |
| 51_V | 354_A | 1.172 | 0.42 |
| 117_W | 188_A | 1.166 | 0.41 |
| 268_H | 273_L | 1.164 | 0.41 |
| 306_I | 345_Q | 1.160 | 0.41 |
| 135_N | 150_D | 1.158 | 0.41 |
| 83_Y | 99_H | 1.156 | 0.40 |
| 306_I | 329_A | 1.155 | 0.40 |
| 225_N | 253_L | 1.154 | 0.40 |
| 281_E | 305_I | 1.153 | 0.40 |
| 20_K | 94_F | 1.148 | 0.40 |
| 120_L | 145_I | 1.145 | 0.39 |
| 99_H | 106_K | 1.141 | 0.39 |
| 129_T | 189_L | 1.141 | 0.39 |
| 47_A | 268_H | 1.133 | 0.38 |
| 180_D | 188_A | 1.133 | 0.38 |
| 310_V | 375_E | 1.130 | 0.38 |
| 266_L | 312_A | 1.130 | 0.38 |
| 54_A | 208_L | 1.130 | 0.38 |
| 56_I | 122_A | 1.129 | 0.38 |
| 47_A | 101_I | 1.128 | 0.38 |
| 56_I | 299_F | 1.125 | 0.38 |
| 13_Q | 300_S | 1.125 | 0.38 |
| 95_I | 306_I | 1.118 | 0.37 |
| 224_V | 242_Q | 1.107 | 0.36 |
| 265_E | 375_E | 1.105 | 0.36 |
| 13_Q | 16_T | 1.104 | 0.36 |
| 255_D | 258_M | 1.101 | 0.36 |
| 336_F | 377_L | 1.100 | 0.36 |
| 11_L | 205_M | 1.098 | 0.36 |
| 147_A | 154_K | 1.097 | 0.36 |
| 231_W | 302_I | 1.095 | 0.35 |
| 189_L | 208_L | 1.091 | 0.35 |
| 13_Q | 20_K | 1.090 | 0.35 |
| 15_V | 107_T | 1.089 | 0.35 |
| 186_L | 208_L | 1.089 | 0.35 |
| 19_N | 94_F | 1.088 | 0.35 |
| 94_F | 103_K | 1.084 | 0.35 |
| 98_D | 327_E | 1.080 | 0.34 |
| 180_D | 226_G | 1.076 | 0.34 |
| 19_N | 102_N | 1.073 | 0.34 |
| 121_W | 188_A | 1.067 | 0.33 |
| 39_K | 45_V | 1.066 | 0.33 |
| 315_K | 318_E | 1.063 | 0.33 |
| 306_I | 346_M | 1.063 | 0.33 |
| 278_L | 341_P | 1.058 | 0.33 |
| 243_A | 265_E | 1.058 | 0.33 |
| 125_Q | 191_D | 1.058 | 0.33 |
| 333_S | 337_F | 1.058 | 0.33 |
| 102_N | 106_K | 1.055 | 0.32 |
| 266_L | 300_S | 1.051 | 0.32 |
| 95_I | 101_I | 1.050 | 0.32 |
| 213_M | 258_M | 1.048 | 0.32 |
| 7_H | 377_L | 1.046 | 0.32 |
| 8_L | 57_F | 1.046 | 0.32 |
| 268_H | 274_I | 1.044 | 0.32 |
| 47_A | 51_V | 1.043 | 0.31 |
| 110_A | 347_Y | 1.041 | 0.31 |
| 119_A | 140_R | 1.041 | 0.31 |
| 41_P | 83_Y | 1.040 | 0.31 |
| 300_S | 359_D | 1.038 | 0.31 |
| 301_Q | 360_S | 1.037 | 0.31 |
| 54_A | 122_A | 1.034 | 0.31 |
| 186_L | 249_A | 1.032 | 0.31 |
| 84_Q | 316_A | 1.032 | 0.31 |
| 181_Q | 184_V | 1.031 | 0.31 |
| 288_G | 300_S | 1.031 | 0.31 |
| 294_I | 297_K | 1.029 | 0.30 |
| 184_V | 193_Q | 1.028 | 0.30 |
| 43_E | 101_I | 1.028 | 0.30 |
| 87_D | 254_G | 1.027 | 0.30 |
| 16_T | 231_W | 1.026 | 0.30 |
| 293_L | 353_I | 1.026 | 0.30 |
| 12_Y | 353_I | 1.025 | 0.30 |
| 127_Y | 376_A | 1.023 | 0.30 |
| 101_I | 273_L | 1.023 | 0.30 |
| 76_S | 214_L | 1.023 | 0.30 |
| 39_K | 180_D | 1.021 | 0.30 |
| 19_N | 379_T | 1.021 | 0.30 |
| 344_A | 364_V | 1.020 | 0.30 |
| 301_Q | 341_P | 1.020 | 0.30 |
| 262_A | 301_Q | 1.018 | 0.30 |
| 107_T | 283_T | 1.017 | 0.30 |
| 13_Q | 283_T | 1.016 | 0.29 |
| 45_V | 231_W | 1.015 | 0.29 |
| 179_G | 184_V | 1.015 | 0.29 |
| 244_Y | 355_F | 1.014 | 0.29 |
| 16_T | 45_V | 1.014 | 0.29 |
| 333_S | 379_T | 1.013 | 0.29 |
| 336_F | 364_V | 1.009 | 0.29 |
| 366_K | 375_E | 1.008 | 0.29 |
| 8_L | 17_V | 1.008 | 0.29 |
| 101_I | 311_F | 1.007 | 0.29 |
| 189_L | 249_A | 1.007 | 0.29 |
| 98_D | 194_A | 1.005 | 0.29 |
| 281_E | 359_D | 1.004 | 0.29 |
| 103_K | 107_T | 1.003 | 0.29 |
| 57_F | 81_I | 1.001 | 0.28 |
| 80_F | 352_G | 1.000 | 0.28 |
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 | |
| 3vw5A | 3 | 0.8639 | 99.9 | 0.839 | Contact Map |
| 3wkgA | 1 | 0.8886 | 99.9 | 0.84 | Contact Map |
| 3gt5A | 1 | 0.8639 | 99.9 | 0.845 | Contact Map |
| 1fp3A | 2 | 0.8787 | 99.9 | 0.845 | Contact Map |
| 2gz6A | 2 | 0.8218 | 99.9 | 0.847 | Contact Map |
| 2zblA | 6 | 0.8812 | 99.8 | 0.863 | Contact Map |
| 4c1sA | 2 | 0.755 | 99.3 | 0.909 | Contact Map |
| 3wkxA | 1 | 0.75 | 99.2 | 0.912 | Contact Map |
| 3k7xA | 1 | 0.5866 | 99.2 | 0.913 | Contact Map |
| 2ahfA | 2 | 0.7302 | 99.1 | 0.914 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)