| T0814 -force run |
| ID: | 1404850175 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 424 (412) | ||
| Sequences: | 232 (210.3) | ||
| Seq/Len: | 0.563 | ||
| Nf(neff/√len): | 10.4 |
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: 0.563).
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 |
| 348_N | 355_E | 6.329 | 1.00 |
| 82_N | 86_T | 4.093 | 1.00 |
| 160_E | 410_R | 3.619 | 1.00 |
| 277_D | 369_Y | 3.013 | 0.99 |
| 402_R | 409_D | 2.718 | 0.99 |
| 167_A | 397_I | 2.656 | 0.98 |
| 186_F | 397_I | 2.492 | 0.97 |
| 134_S | 160_E | 2.466 | 0.97 |
| 290_D | 392_Q | 2.268 | 0.95 |
| 345_M | 356_K | 2.129 | 0.92 |
| 74_Y | 151_I | 2.067 | 0.90 |
| 327_S | 344_K | 1.948 | 0.86 |
| 195_I | 202_L | 1.942 | 0.86 |
| 396_S | 414_V | 1.913 | 0.85 |
| 157_S | 411_L | 1.908 | 0.85 |
| 82_N | 408_Y | 1.884 | 0.84 |
| 66_G | 74_Y | 1.883 | 0.83 |
| 141_V | 152_F | 1.781 | 0.79 |
| 211_R | 214_N | 1.777 | 0.78 |
| 271_N | 315_H | 1.773 | 0.78 |
| 244_E | 392_Q | 1.704 | 0.74 |
| 80_H | 88_S | 1.682 | 0.73 |
| 112_G | 345_M | 1.655 | 0.71 |
| 329_Y | 343_S | 1.651 | 0.71 |
| 398_Y | 411_L | 1.649 | 0.71 |
| 40_V | 154_A | 1.641 | 0.70 |
| 260_V | 274_L | 1.627 | 0.69 |
| 340_D | 343_S | 1.627 | 0.69 |
| 40_V | 62_I | 1.617 | 0.68 |
| 244_E | 292_D | 1.588 | 0.66 |
| 40_V | 60_I | 1.568 | 0.65 |
| 157_S | 398_Y | 1.556 | 0.64 |
| 203_K | 402_R | 1.553 | 0.64 |
| 151_I | 165_I | 1.553 | 0.64 |
| 202_L | 229_I | 1.534 | 0.62 |
| 88_S | 198_P | 1.517 | 0.61 |
| 163_V | 193_F | 1.517 | 0.61 |
| 403_P | 406_A | 1.516 | 0.61 |
| 245_Y | 344_K | 1.501 | 0.60 |
| 219_L | 237_L | 1.490 | 0.59 |
| 134_S | 184_V | 1.476 | 0.58 |
| 94_E | 407_R | 1.470 | 0.58 |
| 244_E | 290_D | 1.464 | 0.57 |
| 297_I | 326_G | 1.459 | 0.57 |
| 165_I | 399_V | 1.440 | 0.55 |
| 241_A | 389_Y | 1.413 | 0.53 |
| 202_L | 399_V | 1.406 | 0.53 |
| 92_P | 100_Q | 1.372 | 0.50 |
| 253_N | 312_Y | 1.371 | 0.50 |
| 62_I | 154_A | 1.356 | 0.49 |
| 63_N | 306_D | 1.340 | 0.47 |
| 133_V | 310_D | 1.337 | 0.47 |
| 207_Y | 212_R | 1.335 | 0.47 |
| 280_R | 385_E | 1.327 | 0.46 |
| 176_D | 181_H | 1.320 | 0.46 |
| 292_D | 392_Q | 1.317 | 0.45 |
| 276_T | 317_T | 1.307 | 0.45 |
| 122_L | 139_I | 1.295 | 0.44 |
| 335_F | 343_S | 1.286 | 0.43 |
| 11_M | 51_Y | 1.285 | 0.43 |
| 38_L | 62_I | 1.281 | 0.43 |
| 153_T | 236_N | 1.267 | 0.42 |
| 35_I | 344_K | 1.262 | 0.41 |
| 270_Y | 389_Y | 1.260 | 0.41 |
| 141_V | 309_A | 1.257 | 0.41 |
| 171_G | 178_N | 1.247 | 0.40 |
| 78_V | 180_S | 1.241 | 0.40 |
| 213_D | 399_V | 1.239 | 0.39 |
| 82_N | 409_D | 1.237 | 0.39 |
| 360_L | 365_Y | 1.235 | 0.39 |
| 79_V | 140_Q | 1.232 | 0.39 |
| 207_Y | 398_Y | 1.228 | 0.39 |
| 252_S | 310_D | 1.226 | 0.38 |
| 93_I | 287_Y | 1.219 | 0.38 |
| 95_Y | 158_V | 1.217 | 0.38 |
| 256_N | 260_V | 1.213 | 0.37 |
| 76_Y | 126_N | 1.208 | 0.37 |
| 329_Y | 344_K | 1.206 | 0.37 |
| 171_G | 251_L | 1.205 | 0.37 |
| 37_T | 195_I | 1.199 | 0.36 |
| 66_G | 139_I | 1.198 | 0.36 |
| 206_V | 347_Y | 1.196 | 0.36 |
| 182_Q | 393_N | 1.192 | 0.36 |
| 216_V | 260_V | 1.189 | 0.36 |
| 193_F | 401_Y | 1.187 | 0.36 |
| 195_I | 201_D | 1.184 | 0.35 |
| 52_I | 60_I | 1.179 | 0.35 |
| 204_I | 301_D | 1.177 | 0.35 |
| 250_F | 312_Y | 1.174 | 0.35 |
| 166_S | 360_L | 1.173 | 0.35 |
| 14_F | 19_G | 1.173 | 0.35 |
| 53_A | 330_L | 1.165 | 0.34 |
| 351_T | 355_E | 1.165 | 0.34 |
| 315_H | 365_Y | 1.164 | 0.34 |
| 94_E | 309_A | 1.163 | 0.34 |
| 106_D | 121_R | 1.163 | 0.34 |
| 330_L | 358_V | 1.161 | 0.34 |
| 23_Q | 330_L | 1.155 | 0.33 |
| 299_C | 302_C | 1.154 | 0.33 |
| 28_T | 31_N | 1.152 | 0.33 |
| 188_I | 399_V | 1.144 | 0.32 |
| 76_Y | 98_G | 1.142 | 0.32 |
| 51_Y | 132_K | 1.131 | 0.32 |
| 247_R | 364_S | 1.129 | 0.31 |
| 74_Y | 152_F | 1.128 | 0.31 |
| 318_L | 384_I | 1.120 | 0.31 |
| 207_Y | 396_S | 1.119 | 0.31 |
| 131_F | 284_T | 1.116 | 0.31 |
| 316_F | 360_L | 1.115 | 0.30 |
| 183_Q | 238_I | 1.114 | 0.30 |
| 283_G | 317_T | 1.113 | 0.30 |
| 66_G | 212_R | 1.113 | 0.30 |
| 97_N | 130_Q | 1.112 | 0.30 |
| 95_Y | 345_M | 1.109 | 0.30 |
| 101_G | 133_V | 1.108 | 0.30 |
| 188_I | 276_T | 1.108 | 0.30 |
| 162_V | 241_A | 1.106 | 0.30 |
| 38_L | 251_L | 1.103 | 0.30 |
| 176_D | 369_Y | 1.103 | 0.30 |
| 127_D | 188_I | 1.098 | 0.29 |
| 366_N | 403_P | 1.096 | 0.29 |
| 12_M | 373_P | 1.093 | 0.29 |
| 196_T | 245_Y | 1.092 | 0.29 |
| 28_T | 251_L | 1.091 | 0.29 |
| 160_E | 345_M | 1.090 | 0.29 |
| 77_N | 108_A | 1.090 | 0.29 |
| 165_I | 415_T | 1.087 | 0.29 |
| 343_S | 358_V | 1.080 | 0.28 |
| 246_R | 385_E | 1.079 | 0.28 |
| 328_V | 358_V | 1.078 | 0.28 |
| 206_V | 237_L | 1.076 | 0.28 |
| 213_D | 370_L | 1.074 | 0.28 |
| 215_A | 401_Y | 1.073 | 0.28 |
| 184_V | 356_K | 1.072 | 0.28 |
| 55_G | 166_S | 1.072 | 0.28 |
| 167_A | 186_F | 1.071 | 0.28 |
| 67_L | 160_E | 1.070 | 0.28 |
| 251_L | 364_S | 1.069 | 0.27 |
| 212_R | 215_A | 1.067 | 0.27 |
| 37_T | 376_S | 1.066 | 0.27 |
| 188_I | 413_G | 1.066 | 0.27 |
| 117_Y | 213_D | 1.065 | 0.27 |
| 84_D | 190_N | 1.065 | 0.27 |
| 245_Y | 337_N | 1.064 | 0.27 |
| 138_A | 206_V | 1.061 | 0.27 |
| 198_P | 203_K | 1.061 | 0.27 |
| 9_L | 16_L | 1.059 | 0.27 |
| 119_N | 341_E | 1.059 | 0.27 |
| 31_N | 152_F | 1.057 | 0.27 |
| 100_Q | 152_F | 1.056 | 0.27 |
| 215_A | 218_D | 1.056 | 0.27 |
| 249_E | 288_D | 1.055 | 0.27 |
| 107_F | 203_K | 1.054 | 0.27 |
| 38_L | 245_Y | 1.051 | 0.26 |
| 124_L | 131_F | 1.049 | 0.26 |
| 157_S | 407_R | 1.049 | 0.26 |
| 186_F | 204_I | 1.047 | 0.26 |
| 245_Y | 298_R | 1.044 | 0.26 |
| 98_G | 126_N | 1.043 | 0.26 |
| 90_L | 260_V | 1.042 | 0.26 |
| 165_I | 397_I | 1.040 | 0.26 |
| 131_F | 252_S | 1.035 | 0.25 |
| 21_N | 345_M | 1.032 | 0.25 |
| 292_D | 336_N | 1.032 | 0.25 |
| 280_R | 369_Y | 1.032 | 0.25 |
| 82_N | 234_N | 1.030 | 0.25 |
| 52_I | 365_Y | 1.028 | 0.25 |
| 214_N | 368_Q | 1.023 | 0.25 |
| 40_V | 249_E | 1.022 | 0.25 |
| 87_Q | 398_Y | 1.015 | 0.24 |
| 181_H | 387_N | 1.014 | 0.24 |
| 76_Y | 287_Y | 1.012 | 0.24 |
| 213_D | 375_G | 1.011 | 0.24 |
| 252_S | 255_Y | 1.009 | 0.24 |
| 82_N | 402_R | 1.005 | 0.24 |
| 403_P | 410_R | 1.004 | 0.24 |
| 215_A | 312_Y | 1.003 | 0.23 |
| 86_T | 346_G | 1.002 | 0.23 |
| 89_Q | 403_P | 1.001 | 0.23 |
| 197_Y | 200_T | 1.000 | 0.23 |
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 | |
| 2qlvB | 2 | 0.2028 | 96.9 | 0.954 | Contact Map |
| 4aefA | 2 | 0.2807 | 96.2 | 0.957 | Contact Map |
| 4aeeA | 2 | 0.2759 | 95.7 | 0.959 | Contact Map |
| 2lu3A | 1 | 0.2453 | 95.5 | 0.959 | Contact Map |
| 4cfeB | 2 | 0.2241 | 94.6 | 0.961 | Contact Map |
| 1ac0A | 1 | 0.2382 | 94.3 | 0.962 | Contact Map |
| 1z0nA | 3 | 0.2052 | 94 | 0.962 | Contact Map |
| 2z0bA | 6 | 0.2524 | 88.4 | 0.968 | Contact Map |
| 1m7xA | 4 | 0.2948 | 78.8 | 0.971 | Contact Map |
| 4pyhA | 1 | 0.5991 | 65.1 | 0.974 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)