| CHT |
| ID: | 1512945846 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 352 (326) | ||
| Sequences: | 11886 (9115.2) | ||
| Seq/Len: | 36.460 | ||
| Nf(neff/√len): | 504.8 |
HHblits Results: (2016_02)
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: 36.460).
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 |
| 52_A | 165_T | 5.228 | 1.00 |
| 52_A | 116_L | 4.018 | 1.00 |
| 199_F | 212_F | 3.263 | 1.00 |
| 39_V | 166_T | 2.832 | 1.00 |
| 54_K | 58_D | 2.566 | 1.00 |
| 42_G | 46_I | 2.381 | 1.00 |
| 195_K | 199_F | 2.347 | 1.00 |
| 75_I | 87_S | 2.326 | 1.00 |
| 259_Y | 340_T | 2.310 | 1.00 |
| 40_F | 163_L | 2.285 | 1.00 |
| 209_R | 213_R | 2.186 | 1.00 |
| 52_A | 163_L | 2.186 | 1.00 |
| 232_W | 236_T | 2.105 | 1.00 |
| 87_S | 90_D | 2.079 | 1.00 |
| 116_L | 163_L | 2.056 | 1.00 |
| 119_G | 165_T | 2.052 | 1.00 |
| 43_A | 46_I | 2.036 | 1.00 |
| 201_Y | 204_N | 2.012 | 1.00 |
| 115_F | 162_L | 1.991 | 1.00 |
| 231_C | 235_C | 1.958 | 1.00 |
| 90_D | 94_S | 1.954 | 1.00 |
| 119_G | 122_E | 1.945 | 1.00 |
| 69_F | 72_L | 1.910 | 1.00 |
| 55_I | 163_L | 1.894 | 1.00 |
| 44_A | 167_R | 1.879 | 1.00 |
| 59_W | 114_L | 1.859 | 1.00 |
| 339_M | 343_E | 1.846 | 1.00 |
| 24_L | 28_E | 1.830 | 1.00 |
| 254_T | 257_A | 1.793 | 1.00 |
| 260_V | 264_S | 1.778 | 1.00 |
| 122_E | 167_R | 1.762 | 1.00 |
| 213_R | 217_E | 1.762 | 1.00 |
| 298_I | 304_D | 1.743 | 1.00 |
| 89_A | 93_V | 1.737 | 1.00 |
| 260_V | 344_F | 1.716 | 1.00 |
| 72_L | 75_I | 1.713 | 1.00 |
| 45_G | 48_K | 1.710 | 1.00 |
| 234_V | 238_L | 1.687 | 1.00 |
| 339_M | 342_Q | 1.643 | 1.00 |
| 191_E | 195_K | 1.640 | 1.00 |
| 195_K | 216_Q | 1.630 | 1.00 |
| 112_R | 161_S | 1.623 | 1.00 |
| 196_E | 200_K | 1.586 | 1.00 |
| 49_T | 53_R | 1.578 | 1.00 |
| 56_M | 116_L | 1.565 | 1.00 |
| 87_S | 94_S | 1.553 | 1.00 |
| 223_T | 228_P | 1.550 | 1.00 |
| 261_F | 264_S | 1.546 | 1.00 |
| 87_S | 95_C | 1.530 | 1.00 |
| 230_V | 233_I | 1.507 | 1.00 |
| 121_D | 167_R | 1.500 | 1.00 |
| 18_S | 21_L | 1.496 | 1.00 |
| 340_T | 343_E | 1.495 | 1.00 |
| 41_Q | 183_H | 1.488 | 1.00 |
| 40_F | 51_L | 1.470 | 1.00 |
| 214_L | 249_A | 1.457 | 1.00 |
| 59_W | 116_L | 1.451 | 1.00 |
| 76_H | 79_E | 1.438 | 1.00 |
| 56_M | 72_L | 1.427 | 1.00 |
| 58_D | 61_L | 1.426 | 1.00 |
| 336_F | 342_Q | 1.424 | 1.00 |
| 214_L | 218_N | 1.422 | 1.00 |
| 79_E | 82_L | 1.419 | 1.00 |
| 195_K | 212_F | 1.407 | 0.99 |
| 25_F | 28_E | 1.406 | 0.99 |
| 212_F | 216_Q | 1.385 | 0.99 |
| 24_L | 27_P | 1.363 | 0.99 |
| 197_Y | 201_Y | 1.358 | 0.99 |
| 338_H | 343_E | 1.352 | 0.99 |
| 91_L | 95_C | 1.343 | 0.99 |
| 87_S | 91_L | 1.341 | 0.99 |
| 23_L | 26_E | 1.341 | 0.99 |
| 119_G | 123_L | 1.339 | 0.99 |
| 301_E | 304_D | 1.335 | 0.99 |
| 323_V | 327_E | 1.332 | 0.99 |
| 208_A | 211_A | 1.331 | 0.99 |
| 201_Y | 238_L | 1.330 | 0.99 |
| 289_A | 336_F | 1.330 | 0.99 |
| 86_R | 89_A | 1.329 | 0.99 |
| 342_Q | 346_A | 1.321 | 0.99 |
| 55_I | 116_L | 1.313 | 0.99 |
| 190_S | 193_K | 1.301 | 0.99 |
| 87_S | 117_M | 1.293 | 0.99 |
| 112_R | 159_K | 1.291 | 0.99 |
| 210_E | 214_L | 1.291 | 0.99 |
| 41_Q | 185_E | 1.288 | 0.99 |
| 92_I | 96_W | 1.277 | 0.99 |
| 58_D | 62_G | 1.274 | 0.99 |
| 337_S | 341_F | 1.269 | 0.99 |
| 257_A | 260_V | 1.265 | 0.99 |
| 286_C | 348_M | 1.261 | 0.99 |
| 300_F | 304_D | 1.258 | 0.99 |
| 198_F | 235_C | 1.256 | 0.99 |
| 53_R | 56_M | 1.252 | 0.99 |
| 221_L | 226_F | 1.250 | 0.99 |
| 291_D | 295_N | 1.250 | 0.99 |
| 287_S | 291_D | 1.249 | 0.99 |
| 86_R | 90_D | 1.248 | 0.99 |
| 22_E | 26_E | 1.240 | 0.98 |
| 81_S | 84_T | 1.233 | 0.98 |
| 72_L | 76_H | 1.228 | 0.98 |
| 72_L | 77_C | 1.228 | 0.98 |
| 192_A | 196_E | 1.228 | 0.98 |
| 57_L | 61_L | 1.226 | 0.98 |
| 77_C | 117_M | 1.225 | 0.98 |
| 41_Q | 166_T | 1.219 | 0.98 |
| 230_V | 234_V | 1.217 | 0.98 |
| 91_L | 94_S | 1.213 | 0.98 |
| 114_L | 161_S | 1.212 | 0.98 |
| 195_K | 213_R | 1.205 | 0.98 |
| 22_E | 28_E | 1.200 | 0.98 |
| 90_D | 95_C | 1.196 | 0.98 |
| 21_L | 27_P | 1.191 | 0.98 |
| 37_T | 162_L | 1.169 | 0.97 |
| 21_L | 28_E | 1.165 | 0.97 |
| 167_R | 343_E | 1.157 | 0.97 |
| 73_F | 76_H | 1.155 | 0.97 |
| 232_W | 235_C | 1.152 | 0.97 |
| 168_P | 173_K | 1.146 | 0.97 |
| 210_E | 245_G | 1.146 | 0.97 |
| 302_E | 306_R | 1.144 | 0.97 |
| 21_L | 25_F | 1.138 | 0.97 |
| 118_D | 121_D | 1.136 | 0.97 |
| 214_L | 245_G | 1.136 | 0.97 |
| 214_L | 217_E | 1.134 | 0.97 |
| 80_V | 83_R | 1.127 | 0.97 |
| 78_R | 122_E | 1.127 | 0.97 |
| 323_V | 326_K | 1.127 | 0.97 |
| 255_T | 259_Y | 1.126 | 0.97 |
| 209_R | 212_F | 1.121 | 0.97 |
| 22_E | 27_P | 1.117 | 0.96 |
| 321_M | 324_F | 1.111 | 0.96 |
| 208_A | 212_F | 1.111 | 0.96 |
| 102_P | 106_I | 1.109 | 0.96 |
| 115_F | 160_A | 1.105 | 0.96 |
| 340_T | 344_F | 1.103 | 0.96 |
| 166_T | 170_A | 1.103 | 0.96 |
| 36_H | 161_S | 1.097 | 0.96 |
| 146_I | 150_S | 1.088 | 0.96 |
| 119_G | 167_R | 1.081 | 0.95 |
| 18_S | 28_E | 1.066 | 0.95 |
| 73_F | 77_C | 1.066 | 0.95 |
| 92_I | 106_I | 1.062 | 0.95 |
| 38_V | 184_V | 1.055 | 0.95 |
| 287_S | 290_A | 1.052 | 0.95 |
| 207_Q | 211_A | 1.051 | 0.94 |
| 199_F | 216_Q | 1.051 | 0.94 |
| 41_Q | 168_P | 1.035 | 0.94 |
| 201_Y | 239_K | 1.034 | 0.94 |
| 102_P | 107_L | 1.032 | 0.94 |
| 103_V | 106_I | 1.031 | 0.94 |
| 322_N | 325_Q | 1.029 | 0.94 |
| 228_P | 232_W | 1.022 | 0.93 |
| 85_P | 89_A | 1.018 | 0.93 |
| 280_D | 284_G | 1.017 | 0.93 |
| 89_A | 95_C | 1.008 | 0.93 |
| 196_E | 199_F | 1.005 | 0.93 |
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 | |
| 4kxfK | 8 | 0.8864 | 100 | 0.438 | Contact Map |
| 1z6tA | 4 | 0.858 | 99.3 | 0.731 | Contact Map |
| 2a5yB | 2 | 0.875 | 99.1 | 0.755 | Contact Map |
| 2qenA | 1 | 0.8324 | 99 | 0.771 | Contact Map |
| 1vt4I | 8 | 0.8267 | 98.9 | 0.777 | Contact Map |
| 3sfzA | 1 | 0.858 | 98.9 | 0.778 | Contact Map |
| 2fnaA | 2 | 0.7955 | 98.8 | 0.783 | Contact Map |
| 2qbyA | 1 | 0.8949 | 98.6 | 0.8 | Contact Map |
| 4xgcA | 1 | 0.7784 | 98.5 | 0.807 | Contact Map |
| 4xgcE | 1 | 0.75 | 98.5 | 0.807 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)