| 1f88 |
| ID: | 1398568075 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 348 (289) | ||
| Sequences: | 10355 (6843.9) | ||
| Seq/Len: | 35.830 | ||
| Nf(neff/√len): | 402.6 |
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: 35.830).
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 |
| 51_G | 87_V | 5.609 | 1.00 |
| 78_N | 161_W | 3.704 | 1.00 |
| 136_Y | 141_K | 3.102 | 1.00 |
| 221_F | 225_Q | 3.005 | 1.00 |
| 130_V | 160_T | 2.788 | 1.00 |
| 110_C | 187_C | 2.770 | 1.00 |
| 78_N | 127_S | 2.750 | 1.00 |
| 108_T | 112_L | 2.531 | 1.00 |
| 68_L | 73_N | 2.529 | 1.00 |
| 115_F | 119_L | 2.398 | 1.00 |
| 103_F | 106_G | 2.383 | 1.00 |
| 107_P | 111_N | 2.309 | 1.00 |
| 130_V | 156_G | 2.139 | 1.00 |
| 91_F | 94_T | 2.135 | 1.00 |
| 265_W | 295_A | 2.091 | 1.00 |
| 59_L | 77_L | 2.067 | 1.00 |
| 224_G | 228_F | 2.013 | 1.00 |
| 225_Q | 228_F | 1.950 | 1.00 |
| 218_V | 222_C | 1.937 | 1.00 |
| 136_Y | 140_C | 1.902 | 1.00 |
| 260_A | 305_I | 1.765 | 1.00 |
| 136_Y | 225_Q | 1.764 | 1.00 |
| 62_T | 77_L | 1.759 | 1.00 |
| 74_Y | 157_V | 1.751 | 1.00 |
| 149_G | 152_H | 1.692 | 1.00 |
| 151_N | 155_M | 1.689 | 1.00 |
| 156_G | 160_T | 1.648 | 1.00 |
| 83_D | 302_N | 1.647 | 1.00 |
| 155_M | 159_F | 1.630 | 1.00 |
| 255_I | 259_I | 1.597 | 1.00 |
| 75_I | 153_A | 1.588 | 1.00 |
| 270_G | 274_Y | 1.587 | 1.00 |
| 77_L | 81_V | 1.583 | 1.00 |
| 128_L | 219_I | 1.582 | 1.00 |
| 51_G | 300_V | 1.580 | 1.00 |
| 144_S | 147_R | 1.565 | 1.00 |
| 253_M | 309_M | 1.563 | 1.00 |
| 216_L | 262_L | 1.560 | 1.00 |
| 225_Q | 229_T | 1.558 | 1.00 |
| 136_Y | 222_C | 1.549 | 1.00 |
| 161_W | 303_P | 1.545 | 1.00 |
| 138_V | 142_P | 1.520 | 1.00 |
| 56_F | 60_Y | 1.519 | 1.00 |
| 119_L | 165_L | 1.513 | 1.00 |
| 140_C | 229_T | 1.484 | 1.00 |
| 65_H | 316_C | 1.482 | 1.00 |
| 129_V | 222_C | 1.479 | 1.00 |
| 82_A | 123_I | 1.478 | 1.00 |
| 127_S | 157_V | 1.474 | 1.00 |
| 70_T | 73_N | 1.464 | 1.00 |
| 206_Y | 210_V | 1.457 | 1.00 |
| 262_L | 266_L | 1.455 | 1.00 |
| 56_F | 84_L | 1.433 | 1.00 |
| 228_F | 232_E | 1.429 | 1.00 |
| 54_I | 300_V | 1.408 | 1.00 |
| 248_K | 252_R | 1.405 | 0.99 |
| 127_S | 161_W | 1.399 | 0.99 |
| 90_G | 94_T | 1.393 | 0.99 |
| 78_N | 157_V | 1.384 | 0.99 |
| 230_V | 250_V | 1.373 | 0.99 |
| 134_E | 138_V | 1.368 | 0.99 |
| 133_I | 222_C | 1.364 | 0.99 |
| 227_V | 231_K | 1.363 | 0.99 |
| 129_V | 218_V | 1.357 | 0.99 |
| 123_I | 164_A | 1.352 | 0.99 |
| 83_D | 298_S | 1.346 | 0.99 |
| 54_I | 304_V | 1.343 | 0.99 |
| 74_Y | 154_I | 1.338 | 0.99 |
| 141_K | 144_S | 1.333 | 0.99 |
| 223_Y | 226_L | 1.332 | 0.99 |
| 59_L | 81_V | 1.329 | 0.99 |
| 227_V | 230_V | 1.324 | 0.99 |
| 38_S | 42_A | 1.324 | 0.99 |
| 220_F | 224_G | 1.317 | 0.99 |
| 82_A | 124_A | 1.310 | 0.99 |
| 266_L | 270_G | 1.305 | 0.99 |
| 219_I | 223_Y | 1.291 | 0.99 |
| 154_I | 158_A | 1.290 | 0.99 |
| 150_E | 154_I | 1.288 | 0.99 |
| 85_F | 120_G | 1.281 | 0.99 |
| 256_I | 309_M | 1.269 | 0.99 |
| 171_P | 174_G | 1.268 | 0.99 |
| 59_L | 80_A | 1.267 | 0.99 |
| 75_I | 131_L | 1.264 | 0.99 |
| 268_Y | 272_A | 1.263 | 0.99 |
| 125_L | 261_F | 1.259 | 0.99 |
| 58_T | 307_I | 1.257 | 0.99 |
| 126_W | 163_M | 1.254 | 0.99 |
| 52_F | 87_V | 1.249 | 0.99 |
| 83_D | 124_A | 1.243 | 0.98 |
| 92_T | 95_L | 1.238 | 0.98 |
| 253_M | 256_I | 1.225 | 0.98 |
| 302_N | 306_Y | 1.217 | 0.98 |
| 212_F | 216_L | 1.217 | 0.98 |
| 123_I | 127_S | 1.217 | 0.98 |
| 227_V | 251_T | 1.216 | 0.98 |
| 62_T | 69_R | 1.203 | 0.98 |
| 115_F | 165_L | 1.202 | 0.98 |
| 208_F | 213_I | 1.193 | 0.98 |
| 89_G | 92_T | 1.173 | 0.98 |
| 212_F | 266_L | 1.171 | 0.98 |
| 230_V | 233_A | 1.156 | 0.97 |
| 59_L | 62_T | 1.155 | 0.97 |
| 115_F | 172_L | 1.155 | 0.97 |
| 297_T | 301_Y | 1.149 | 0.97 |
| 151_N | 154_I | 1.139 | 0.97 |
| 169_A | 173_V | 1.134 | 0.97 |
| 66_K | 69_R | 1.129 | 0.97 |
| 53_P | 56_F | 1.128 | 0.97 |
| 86_M | 299_A | 1.126 | 0.97 |
| 136_Y | 221_F | 1.121 | 0.97 |
| 125_L | 129_V | 1.118 | 0.96 |
| 124_A | 298_S | 1.116 | 0.96 |
| 202_S | 206_Y | 1.116 | 0.96 |
| 52_F | 84_L | 1.115 | 0.96 |
| 90_G | 93_T | 1.107 | 0.96 |
| 226_L | 254_V | 1.106 | 0.96 |
| 256_I | 305_I | 1.101 | 0.96 |
| 139_V | 143_M | 1.093 | 0.96 |
| 169_A | 172_L | 1.091 | 0.96 |
| 122_E | 211_H | 1.087 | 0.96 |
| 92_T | 96_Y | 1.085 | 0.96 |
| 284_G | 287_F | 1.077 | 0.95 |
| 58_T | 302_N | 1.074 | 0.95 |
| 74_Y | 150_E | 1.074 | 0.95 |
| 159_F | 163_M | 1.066 | 0.95 |
| 80_A | 302_N | 1.058 | 0.95 |
| 137_V | 141_K | 1.054 | 0.95 |
| 80_A | 83_D | 1.053 | 0.95 |
| 82_A | 161_W | 1.052 | 0.95 |
| 126_W | 215_P | 1.051 | 0.94 |
| 250_V | 253_M | 1.049 | 0.94 |
| 315_N | 318_V | 1.046 | 0.94 |
| 60_Y | 320_T | 1.041 | 0.94 |
| 65_H | 319_T | 1.039 | 0.94 |
| 316_C | 319_T | 1.038 | 0.94 |
| 126_W | 164_A | 1.033 | 0.94 |
| 63_V | 77_L | 1.030 | 0.94 |
| 106_G | 109_G | 1.027 | 0.94 |
| 59_L | 84_L | 1.027 | 0.94 |
| 129_V | 219_I | 1.027 | 0.94 |
| 305_I | 309_M | 1.025 | 0.93 |
| 229_T | 232_E | 1.020 | 0.93 |
| 73_N | 76_L | 1.013 | 0.93 |
| 187_C | 192_Y | 1.006 | 0.93 |
| 292_A | 296_K | 1.001 | 0.92 |
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 | |
| 1u19A | 2 | 1 | 100 | 0.247 | Contact Map |
| 2r4rA | 1 | 0.6034 | 100 | 0.371 | Contact Map |
| 4iarA | 1 | 0.8075 | 100 | 0.372 | Contact Map |
| 2rh1A | 1 | 0.8247 | 100 | 0.376 | Contact Map |
| 4grvA | 1 | 0.8218 | 100 | 0.377 | Contact Map |
| 4ntjA | 1 | 0.7615 | 100 | 0.377 | Contact Map |
| 3uonA | 1 | 0.8103 | 100 | 0.388 | Contact Map |
| 3vw7A | 1 | 0.8132 | 100 | 0.393 | Contact Map |
| 4eiyA | 1 | 0.8448 | 100 | 0.395 | Contact Map |
| 3rzeA | 1 | 0.7845 | 100 | 0.398 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)