| IR8a-LBD |
| ID: | 1446804484 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 300 (289) | ||
| Sequences: | 2491 (1648) | ||
| Seq/Len: | 8.619 | ||
| Nf(neff/√len): | 96.9 |
HHblits Results: (2015_06)
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: 8.619).
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 |
| 81_G | 85_R | 3.598 | 1.00 |
| 105_I | 258_A | 3.462 | 1.00 |
| 5_F | 58_E | 3.387 | 1.00 |
| 9_G | 88_T | 3.070 | 1.00 |
| 5_F | 56_E | 2.729 | 1.00 |
| 52_K | 275_E | 2.643 | 1.00 |
| 281_F | 284_E | 2.631 | 1.00 |
| 97_M | 256_A | 2.537 | 1.00 |
| 80_V | 105_I | 2.493 | 1.00 |
| 91_A | 95_L | 2.435 | 1.00 |
| 48_R | 281_F | 2.419 | 1.00 |
| 208_D | 211_E | 2.390 | 1.00 |
| 82_D | 87_E | 2.370 | 1.00 |
| 108_L | 270_S | 2.331 | 1.00 |
| 228_H | 233_I | 2.305 | 1.00 |
| 260_Q | 263_S | 2.228 | 1.00 |
| 42_C | 111_Y | 2.216 | 1.00 |
| 283_E | 287_A | 2.186 | 1.00 |
| 266_G | 270_S | 2.133 | 1.00 |
| 128_V | 133_Q | 2.031 | 1.00 |
| 259_V | 263_S | 1.990 | 1.00 |
| 95_L | 258_A | 1.988 | 1.00 |
| 48_R | 51_Q | 1.919 | 1.00 |
| 49_L | 269_L | 1.914 | 1.00 |
| 108_L | 259_V | 1.897 | 1.00 |
| 7_R | 58_E | 1.890 | 1.00 |
| 83_L | 258_A | 1.869 | 1.00 |
| 259_V | 269_L | 1.835 | 1.00 |
| 130_S | 133_Q | 1.835 | 1.00 |
| 49_L | 55_F | 1.814 | 1.00 |
| 79_V | 91_A | 1.803 | 1.00 |
| 216_V | 222_A | 1.762 | 1.00 |
| 92_I | 257_V | 1.745 | 1.00 |
| 82_D | 88_T | 1.732 | 1.00 |
| 270_S | 273_I | 1.729 | 1.00 |
| 17_S | 43_I | 1.660 | 1.00 |
| 207_A | 211_E | 1.655 | 1.00 |
| 217_D | 242_N | 1.648 | 1.00 |
| 45_F | 282_F | 1.619 | 1.00 |
| 106_D | 262_G | 1.593 | 1.00 |
| 20_R | 39_E | 1.572 | 1.00 |
| 206_V | 212_G | 1.562 | 1.00 |
| 44_D | 288_K | 1.543 | 1.00 |
| 45_F | 276_L | 1.536 | 1.00 |
| 101_R | 107_F | 1.526 | 1.00 |
| 212_G | 226_F | 1.516 | 1.00 |
| 78_G | 81_G | 1.495 | 1.00 |
| 9_G | 79_V | 1.483 | 1.00 |
| 49_L | 272_A | 1.477 | 1.00 |
| 277_Q | 282_F | 1.476 | 1.00 |
| 274_L | 278_K | 1.417 | 0.99 |
| 44_D | 289_Y | 1.409 | 0.99 |
| 83_L | 91_A | 1.404 | 0.99 |
| 47_I | 59_I | 1.394 | 0.99 |
| 46_I | 59_I | 1.382 | 0.99 |
| 52_K | 276_L | 1.371 | 0.99 |
| 98_Y | 101_R | 1.371 | 0.99 |
| 119_I | 225_A | 1.355 | 0.99 |
| 9_G | 62_P | 1.354 | 0.99 |
| 129_Q | 133_Q | 1.329 | 0.99 |
| 68_G | 78_G | 1.314 | 0.99 |
| 280_R | 284_E | 1.309 | 0.99 |
| 96_K | 107_F | 1.308 | 0.99 |
| 48_R | 276_L | 1.304 | 0.99 |
| 10_T | 17_S | 1.303 | 0.99 |
| 185_W | 195_H | 1.294 | 0.98 |
| 229_D | 232_E | 1.291 | 0.98 |
| 15_P | 18_Y | 1.291 | 0.98 |
| 7_R | 60_V | 1.291 | 0.98 |
| 18_Y | 39_E | 1.288 | 0.98 |
| 237_I | 243_L | 1.277 | 0.98 |
| 19_L | 61_A | 1.271 | 0.98 |
| 50_S | 57_F | 1.268 | 0.98 |
| 50_S | 55_F | 1.266 | 0.98 |
| 7_R | 89_D | 1.264 | 0.98 |
| 213_F | 243_L | 1.262 | 0.98 |
| 282_F | 286_K | 1.257 | 0.98 |
| 134_L | 137_Q | 1.249 | 0.98 |
| 272_A | 275_E | 1.245 | 0.98 |
| 96_K | 101_R | 1.241 | 0.98 |
| 8_I | 46_I | 1.227 | 0.98 |
| 71_N | 75_E | 1.216 | 0.97 |
| 214_A | 218_A | 1.207 | 0.97 |
| 235_Y | 247_G | 1.205 | 0.97 |
| 169_K | 172_A | 1.204 | 0.97 |
| 22_E | 25_T | 1.202 | 0.97 |
| 108_L | 269_L | 1.197 | 0.97 |
| 91_A | 258_A | 1.195 | 0.97 |
| 120_A | 233_I | 1.185 | 0.97 |
| 197_L | 200_I | 1.159 | 0.96 |
| 86_G | 260_Q | 1.159 | 0.96 |
| 118_S | 245_E | 1.158 | 0.96 |
| 17_S | 42_C | 1.155 | 0.96 |
| 108_L | 257_V | 1.139 | 0.96 |
| 52_K | 272_A | 1.136 | 0.96 |
| 3_R | 7_R | 1.134 | 0.96 |
| 215_N | 222_A | 1.133 | 0.96 |
| 217_D | 240_N | 1.131 | 0.96 |
| 120_A | 213_F | 1.126 | 0.96 |
| 41_Y | 285_L | 1.119 | 0.95 |
| 34_G | 37_I | 1.118 | 0.95 |
| 259_V | 266_G | 1.112 | 0.95 |
| 46_I | 55_F | 1.106 | 0.95 |
| 276_L | 282_F | 1.103 | 0.95 |
| 46_I | 92_I | 1.092 | 0.94 |
| 222_A | 226_F | 1.092 | 0.94 |
| 179_F | 185_W | 1.090 | 0.94 |
| 124_P | 244_T | 1.089 | 0.94 |
| 241_C | 298_C | 1.087 | 0.94 |
| 206_V | 215_N | 1.087 | 0.94 |
| 50_S | 269_L | 1.081 | 0.94 |
| 47_I | 57_F | 1.077 | 0.94 |
| 53_L | 272_A | 1.070 | 0.94 |
| 68_G | 77_D | 1.067 | 0.94 |
| 276_L | 281_F | 1.061 | 0.93 |
| 234_K | 286_K | 1.056 | 0.93 |
| 282_F | 285_L | 1.055 | 0.93 |
| 41_Y | 282_F | 1.050 | 0.93 |
| 76_W | 81_G | 1.049 | 0.93 |
| 39_E | 44_D | 1.048 | 0.93 |
| 167_M | 171_L | 1.047 | 0.93 |
| 123_K | 244_T | 1.047 | 0.93 |
| 257_V | 269_L | 1.029 | 0.92 |
| 101_R | 106_D | 1.027 | 0.92 |
| 6_F | 53_L | 1.024 | 0.92 |
| 143_T | 224_Y | 1.022 | 0.91 |
| 191_E | 195_H | 1.017 | 0.91 |
| 96_K | 115_T | 1.016 | 0.91 |
| 64_V | 67_M | 1.014 | 0.91 |
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 | |
| 4uqqA | 4 | 0.8467 | 100 | 0.323 | Contact Map |
| 4u2pA | 4 | 0.8733 | 100 | 0.347 | Contact Map |
| 4tllA | 2 | 0.07 | 100 | 0.353 | Contact Map |
| 1yaeA | 6 | 0.8467 | 100 | 0.354 | Contact Map |
| 2rc8A | 2 | 0.8333 | 100 | 0.373 | Contact Map |
| 4tllB | 2 | 0.04 | 100 | 0.379 | Contact Map |
| 3g3kA | 2 | 0.8367 | 100 | 0.379 | Contact Map |
| 4wxjA | 2 | 0 | 100 | 0.38 | Contact Map |
| 2v3uA | 1 | 0.81 | 100 | 0.407 | Contact Map |
| 1pb7A | 1 | 0.7967 | 100 | 0.419 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)