| GREMLIN 1000 PP-PYR mg fasta 0 Iterations 75 coverage |
| ID: | 1435928180 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 306 (305) | ||
| Sequences: | 496 (323.4) | ||
| Seq/Len: | 1.626 | ||
| Nf(neff/√len): | 18.5 |
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: 1.626).
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 |
| 286_K | 289_E | 3.764 | 1.00 |
| 49_A | 79_G | 3.610 | 1.00 |
| 53_A | 82_D | 3.325 | 1.00 |
| 176_D | 228_S | 3.242 | 1.00 |
| 234_A | 291_L | 3.106 | 1.00 |
| 91_V | 140_I | 2.767 | 1.00 |
| 162_E | 305_T | 2.635 | 1.00 |
| 67_G | 76_L | 2.624 | 1.00 |
| 62_V | 144_Y | 2.611 | 1.00 |
| 93_L | 154_I | 2.480 | 1.00 |
| 172_I | 215_A | 2.474 | 1.00 |
| 231_G | 260_F | 2.261 | 0.99 |
| 233_F | 237_M | 2.255 | 0.99 |
| 213_I | 243_Q | 2.238 | 0.99 |
| 62_V | 91_V | 2.187 | 0.99 |
| 216_Q | 248_L | 2.148 | 0.99 |
| 162_E | 165_R | 2.060 | 0.99 |
| 1_V | 29_A | 2.056 | 0.99 |
| 58_L | 219_F | 2.034 | 0.99 |
| 126_V | 132_L | 1.946 | 0.98 |
| 175_S | 198_T | 1.923 | 0.98 |
| 76_L | 92_A | 1.881 | 0.97 |
| 244_V | 293_A | 1.850 | 0.97 |
| 5_K | 9_A | 1.845 | 0.97 |
| 243_Q | 293_A | 1.796 | 0.96 |
| 176_D | 226_T | 1.795 | 0.96 |
| 158_P | 304_L | 1.793 | 0.96 |
| 136_V | 152_V | 1.734 | 0.95 |
| 299_T | 303_D | 1.679 | 0.94 |
| 67_G | 92_A | 1.664 | 0.93 |
| 216_Q | 249_P | 1.653 | 0.93 |
| 23_F | 26_T | 1.651 | 0.93 |
| 74_T | 78_N | 1.621 | 0.92 |
| 300_R | 303_D | 1.581 | 0.91 |
| 169_P | 188_L | 1.579 | 0.91 |
| 53_A | 57_K | 1.556 | 0.90 |
| 124_R | 138_E | 1.546 | 0.90 |
| 49_A | 90_V | 1.531 | 0.89 |
| 163_I | 227_L | 1.511 | 0.88 |
| 10_W | 137_D | 1.483 | 0.87 |
| 62_V | 140_I | 1.449 | 0.85 |
| 65_V | 76_L | 1.435 | 0.84 |
| 128_S | 131_S | 1.434 | 0.84 |
| 176_D | 232_G | 1.424 | 0.84 |
| 3_M | 26_T | 1.408 | 0.83 |
| 240_I | 293_A | 1.396 | 0.82 |
| 205_M | 235_M | 1.394 | 0.82 |
| 283_D | 286_K | 1.389 | 0.82 |
| 59_T | 218_S | 1.374 | 0.81 |
| 54_A | 58_L | 1.370 | 0.80 |
| 58_L | 197_T | 1.368 | 0.80 |
| 80_L | 119_V | 1.359 | 0.80 |
| 135_V | 152_V | 1.358 | 0.80 |
| 207_N | 211_G | 1.357 | 0.80 |
| 287_V | 290_A | 1.356 | 0.80 |
| 197_T | 215_A | 1.356 | 0.80 |
| 65_V | 92_A | 1.350 | 0.79 |
| 226_T | 232_G | 1.348 | 0.79 |
| 158_P | 162_E | 1.347 | 0.79 |
| 131_S | 134_H | 1.344 | 0.79 |
| 80_L | 92_A | 1.336 | 0.78 |
| 91_V | 152_V | 1.308 | 0.76 |
| 43_R | 234_A | 1.279 | 0.74 |
| 49_A | 65_V | 1.263 | 0.72 |
| 40_I | 216_Q | 1.256 | 0.72 |
| 8_E | 33_E | 1.249 | 0.71 |
| 288_G | 295_G | 1.246 | 0.71 |
| 59_T | 295_G | 1.226 | 0.69 |
| 8_E | 34_R | 1.225 | 0.69 |
| 46_E | 75_H | 1.201 | 0.67 |
| 216_Q | 223_Q | 1.201 | 0.67 |
| 17_G | 267_Q | 1.199 | 0.67 |
| 134_H | 138_E | 1.192 | 0.66 |
| 3_M | 136_V | 1.185 | 0.65 |
| 78_N | 204_T | 1.183 | 0.65 |
| 171_A | 223_Q | 1.182 | 0.65 |
| 80_L | 120_S | 1.180 | 0.65 |
| 47_A | 236_Q | 1.177 | 0.65 |
| 40_I | 99_S | 1.174 | 0.64 |
| 120_S | 151_V | 1.174 | 0.64 |
| 6_V | 10_W | 1.162 | 0.63 |
| 167_A | 188_L | 1.162 | 0.63 |
| 77_I | 112_E | 1.155 | 0.62 |
| 49_A | 76_L | 1.149 | 0.62 |
| 47_A | 54_A | 1.148 | 0.62 |
| 158_P | 301_Y | 1.142 | 0.61 |
| 285_G | 297_T | 1.142 | 0.61 |
| 86_D | 199_S | 1.122 | 0.59 |
| 16_Y | 218_S | 1.121 | 0.59 |
| 228_S | 236_Q | 1.119 | 0.59 |
| 77_I | 115_M | 1.117 | 0.59 |
| 3_M | 245_K | 1.113 | 0.58 |
| 99_S | 155_P | 1.103 | 0.57 |
| 47_A | 93_L | 1.103 | 0.57 |
| 144_Y | 147_R | 1.100 | 0.57 |
| 50_L | 204_T | 1.098 | 0.57 |
| 27_M | 39_Y | 1.093 | 0.56 |
| 115_M | 268_E | 1.092 | 0.56 |
| 152_V | 294_K | 1.092 | 0.56 |
| 57_K | 82_D | 1.091 | 0.56 |
| 93_L | 126_V | 1.091 | 0.56 |
| 209_V | 250_I | 1.087 | 0.55 |
| 212_G | 226_T | 1.084 | 0.55 |
| 40_I | 217_L | 1.077 | 0.54 |
| 4_V | 11_G | 1.071 | 0.54 |
| 60_G | 73_A | 1.071 | 0.54 |
| 165_R | 302_E | 1.069 | 0.54 |
| 129_P | 132_L | 1.067 | 0.53 |
| 208_G | 225_F | 1.061 | 0.53 |
| 94_L | 116_F | 1.060 | 0.53 |
| 173_F | 225_F | 1.056 | 0.52 |
| 6_V | 137_D | 1.053 | 0.52 |
| 5_K | 8_E | 1.053 | 0.52 |
| 192_G | 195_R | 1.053 | 0.52 |
| 175_S | 196_F | 1.052 | 0.52 |
| 292_G | 295_G | 1.052 | 0.52 |
| 1_V | 32_Q | 1.052 | 0.52 |
| 31_Y | 230_D | 1.044 | 0.51 |
| 5_K | 173_F | 1.041 | 0.51 |
| 128_S | 221_D | 1.039 | 0.50 |
| 172_I | 219_F | 1.038 | 0.50 |
| 55_D | 61_K | 1.037 | 0.50 |
| 298_I | 304_L | 1.036 | 0.50 |
| 209_V | 233_F | 1.036 | 0.50 |
| 111_N | 114_P | 1.035 | 0.50 |
| 184_S | 196_F | 1.034 | 0.50 |
| 164_N | 189_D | 1.033 | 0.50 |
| 184_S | 227_L | 1.033 | 0.50 |
| 184_S | 190_M | 1.031 | 0.50 |
| 58_L | 88_V | 1.028 | 0.49 |
| 303_D | 306_P | 1.028 | 0.49 |
| 138_E | 227_L | 1.026 | 0.49 |
| 228_S | 232_G | 1.019 | 0.48 |
| 76_L | 94_L | 1.012 | 0.48 |
| 81_Y | 202_F | 1.011 | 0.47 |
| 151_V | 304_L | 1.006 | 0.47 |
| 13_D | 61_K | 1.006 | 0.47 |
| 47_A | 239_D | 1.003 | 0.47 |
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 | |
| 1t9bA | 2 | 0.9967 | 100 | 0.347 | Contact Map |
| 1ybhA | 1 | 0.9967 | 100 | 0.357 | Contact Map |
| 1ozhA | 4 | 0.9804 | 100 | 0.359 | Contact Map |
| 3eyaA | 12 | 0.9608 | 100 | 0.36 | Contact Map |
| 1v5eA | 1 | 1 | 100 | 0.362 | Contact Map |
| 2panA | 6 | 0.9967 | 100 | 0.365 | Contact Map |
| 4rjjA | 8 | 0.9902 | 100 | 0.366 | Contact Map |
| 4kgdA | 2 | 1 | 100 | 0.368 | Contact Map |
| 1q6zA | 1 | 0.9869 | 100 | 0.374 | Contact Map |
| 2ihtA | 4 | 0.9869 | 100 | 0.376 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)