| 154 |
| ID: | 1380437168 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 401 (372) | ||
| Sequences: | 1339 (1116.3) | ||
| Seq/Len: | 3.599 | ||
| Nf(neff/√len): | 57.9 |
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: 3.599).
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 |
| 212_H | 229_I | 3.656 | 1.00 |
| 216_V | 240_D | 3.613 | 1.00 |
| 123_T | 127_E | 3.367 | 1.00 |
| 94_L | 158_A | 3.358 | 1.00 |
| 171_V | 174_D | 3.305 | 1.00 |
| 234_P | 246_K | 3.294 | 1.00 |
| 218_V | 240_D | 3.294 | 1.00 |
| 197_D | 213_D | 3.012 | 1.00 |
| 156_G | 160_V | 2.904 | 1.00 |
| 280_E | 294_A | 2.835 | 1.00 |
| 167_M | 179_G | 2.794 | 1.00 |
| 29_L | 37_L | 2.777 | 1.00 |
| 94_L | 159_I | 2.763 | 1.00 |
| 214_M | 223_D | 2.545 | 1.00 |
| 215_Q | 219_E | 2.543 | 1.00 |
| 106_A | 124_L | 2.515 | 1.00 |
| 133_I | 168_G | 2.422 | 1.00 |
| 45_E | 49_E | 2.323 | 1.00 |
| 190_N | 220_P | 2.323 | 1.00 |
| 129_D | 132_G | 2.316 | 1.00 |
| 197_D | 215_Q | 2.313 | 1.00 |
| 242_M | 245_G | 2.277 | 1.00 |
| 60_P | 86_T | 2.218 | 1.00 |
| 186_S | 212_H | 2.205 | 1.00 |
| 159_I | 180_G | 2.204 | 1.00 |
| 247_D | 278_A | 2.134 | 1.00 |
| 234_P | 260_S | 2.107 | 1.00 |
| 26_R | 41_I | 2.105 | 1.00 |
| 241_I | 245_G | 2.085 | 1.00 |
| 186_S | 210_A | 2.060 | 1.00 |
| 155_L | 166_A | 2.045 | 1.00 |
| 217_T | 241_I | 2.031 | 1.00 |
| 191_T | 238_L | 1.990 | 1.00 |
| 234_P | 247_D | 1.972 | 1.00 |
| 260_S | 278_A | 1.966 | 1.00 |
| 170_T | 176_S | 1.966 | 1.00 |
| 247_D | 258_K | 1.937 | 1.00 |
| 24_R | 28_R | 1.881 | 1.00 |
| 90_L | 93_R | 1.879 | 1.00 |
| 122_A | 177_E | 1.875 | 1.00 |
| 191_T | 197_D | 1.861 | 1.00 |
| 224_R | 250_T | 1.856 | 1.00 |
| 273_M | 281_M | 1.853 | 1.00 |
| 224_R | 232_E | 1.826 | 0.99 |
| 220_P | 224_R | 1.822 | 0.99 |
| 168_G | 178_L | 1.816 | 0.99 |
| 160_V | 165_L | 1.811 | 0.99 |
| 123_T | 175_T | 1.806 | 0.99 |
| 28_R | 199_A | 1.790 | 0.99 |
| 133_I | 170_T | 1.756 | 0.99 |
| 221_R | 246_K | 1.695 | 0.99 |
| 130_G | 171_V | 1.680 | 0.99 |
| 61_D | 64_L | 1.663 | 0.99 |
| 236_L | 260_S | 1.641 | 0.99 |
| 119_L | 180_G | 1.635 | 0.98 |
| 118_L | 181_A | 1.632 | 0.98 |
| 106_A | 109_Y | 1.581 | 0.98 |
| 105_N | 142_F | 1.569 | 0.98 |
| 129_D | 172_N | 1.561 | 0.98 |
| 94_L | 155_L | 1.559 | 0.98 |
| 118_L | 179_G | 1.558 | 0.98 |
| 232_E | 258_K | 1.542 | 0.98 |
| 56_R | 148_L | 1.538 | 0.97 |
| 190_N | 214_M | 1.534 | 0.97 |
| 30_E | 287_I | 1.532 | 0.97 |
| 237_V | 264_V | 1.532 | 0.97 |
| 224_R | 229_I | 1.530 | 0.97 |
| 130_G | 133_I | 1.527 | 0.97 |
| 90_L | 158_A | 1.525 | 0.97 |
| 216_V | 219_E | 1.504 | 0.97 |
| 107_L | 110_C | 1.481 | 0.97 |
| 50_E | 90_L | 1.465 | 0.96 |
| 241_I | 249_M | 1.451 | 0.96 |
| 238_L | 246_K | 1.450 | 0.96 |
| 170_T | 173_C | 1.446 | 0.96 |
| 232_E | 250_T | 1.442 | 0.96 |
| 217_T | 246_K | 1.441 | 0.96 |
| 189_M | 200_E | 1.431 | 0.96 |
| 220_P | 246_K | 1.425 | 0.96 |
| 251_I | 256_R | 1.416 | 0.95 |
| 194_F | 197_D | 1.410 | 0.95 |
| 238_L | 241_I | 1.395 | 0.95 |
| 128_D | 132_G | 1.383 | 0.95 |
| 170_T | 174_D | 1.383 | 0.95 |
| 203_A | 288_L | 1.379 | 0.94 |
| 77_T | 108_R | 1.378 | 0.94 |
| 249_M | 252_C | 1.378 | 0.94 |
| 81_T | 103_L | 1.374 | 0.94 |
| 273_M | 278_A | 1.330 | 0.93 |
| 218_V | 241_I | 1.319 | 0.93 |
| 189_M | 197_D | 1.301 | 0.92 |
| 245_G | 249_M | 1.285 | 0.91 |
| 201_V | 213_D | 1.280 | 0.91 |
| 212_H | 223_D | 1.272 | 0.91 |
| 233_N | 295_V | 1.272 | 0.91 |
| 159_I | 164_A | 1.271 | 0.91 |
| 94_L | 180_G | 1.271 | 0.91 |
| 189_M | 211_K | 1.270 | 0.91 |
| 159_I | 166_A | 1.266 | 0.90 |
| 251_I | 279_L | 1.260 | 0.90 |
| 216_V | 238_L | 1.256 | 0.90 |
| 135_P | 141_I | 1.247 | 0.89 |
| 5_A | 9_Q | 1.239 | 0.89 |
| 201_V | 205_I | 1.237 | 0.89 |
| 25_L | 37_L | 1.213 | 0.88 |
| 363_Y | 366_L | 1.213 | 0.88 |
| 290_T | 294_A | 1.209 | 0.87 |
| 231_R | 295_V | 1.207 | 0.87 |
| 18_L | 22_L | 1.202 | 0.87 |
| 221_R | 241_I | 1.201 | 0.87 |
| 23_V | 196_E | 1.199 | 0.87 |
| 123_T | 176_S | 1.193 | 0.87 |
| 167_M | 180_G | 1.187 | 0.86 |
| 132_G | 135_P | 1.186 | 0.86 |
| 270_D | 290_T | 1.183 | 0.86 |
| 204_L | 295_V | 1.177 | 0.86 |
| 197_D | 238_L | 1.177 | 0.86 |
| 251_I | 258_K | 1.173 | 0.85 |
| 24_R | 196_E | 1.171 | 0.85 |
| 191_T | 216_V | 1.163 | 0.85 |
| 128_D | 136_E | 1.162 | 0.85 |
| 233_N | 261_G | 1.158 | 0.84 |
| 186_S | 229_I | 1.149 | 0.84 |
| 280_E | 298_A | 1.146 | 0.83 |
| 74_Q | 103_L | 1.146 | 0.83 |
| 120_L | 177_E | 1.140 | 0.83 |
| 17_E | 93_R | 1.134 | 0.83 |
| 259_W | 295_V | 1.134 | 0.83 |
| 218_V | 222_G | 1.131 | 0.82 |
| 190_N | 246_K | 1.128 | 0.82 |
| 10_L | 17_E | 1.123 | 0.82 |
| 217_T | 238_L | 1.123 | 0.82 |
| 214_M | 220_P | 1.122 | 0.82 |
| 236_L | 273_M | 1.110 | 0.81 |
| 43_Q | 96_E | 1.104 | 0.80 |
| 207_A | 292_P | 1.101 | 0.80 |
| 236_L | 244_P | 1.095 | 0.79 |
| 14_I | 51_L | 1.093 | 0.79 |
| 118_L | 167_M | 1.089 | 0.79 |
| 11_I | 93_R | 1.078 | 0.78 |
| 270_D | 283_A | 1.076 | 0.78 |
| 137_N | 178_L | 1.073 | 0.77 |
| 192_I | 235_D | 1.063 | 0.77 |
| 56_R | 142_F | 1.055 | 0.76 |
| 19_R | 52_L | 1.052 | 0.75 |
| 225_A | 253_R | 1.051 | 0.75 |
| 192_I | 238_L | 1.046 | 0.75 |
| 190_N | 234_P | 1.040 | 0.74 |
| 166_A | 180_G | 1.031 | 0.73 |
| 30_E | 38_N | 1.027 | 0.73 |
| 70_L | 81_T | 1.027 | 0.73 |
| 238_L | 243_L | 1.022 | 0.72 |
| 214_M | 219_E | 1.022 | 0.72 |
| 24_R | 40_D | 1.019 | 0.72 |
| 150_T | 247_D | 1.018 | 0.72 |
| 212_H | 227_E | 1.014 | 0.72 |
| 269_L | 272_D | 1.010 | 0.71 |
| 50_E | 93_R | 1.009 | 0.71 |
| 127_E | 175_T | 1.008 | 0.71 |
| 196_E | 199_A | 1.008 | 0.71 |
| 223_D | 229_I | 1.005 | 0.71 |
| 24_R | 195_V | 1.005 | 0.71 |
| 187_W | 204_L | 1.004 | 0.71 |
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 | |
| 2c2aA | 1 | 0.4564 | 100 | 0.658 | Contact Map |
| 4i5sA | 2 | 0.4439 | 100 | 0.664 | Contact Map |
| 3r0jA | 2 | 0.5187 | 100 | 0.665 | Contact Map |
| 1y8oA | 1 | 0.5436 | 100 | 0.674 | Contact Map |
| 2gwrA | 1 | 0.5337 | 100 | 0.674 | Contact Map |
| 4mpcA | 1 | 0.5237 | 100 | 0.676 | Contact Map |
| 2oqrA | 1 | 0.5312 | 100 | 0.677 | Contact Map |
| 2e0aA | 2 | 0.5037 | 100 | 0.679 | Contact Map |
| 4gczA | 2 | 0.4813 | 100 | 0.68 | Contact Map |
| 1ys7A | 2 | 0.5262 | 100 | 0.683 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)