| ARNT |
| ID: | 1490983780 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 367 (364) | ||
| Sequences: | 1050 (570.2) | ||
| Seq/Len: | 2.885 | ||
| Nf(neff/√len): | 29.9 |
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: 2.885).
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 |
| 330_F | 344_T | 2.712 | 1.00 |
| 2_R | 6_N | 2.587 | 1.00 |
| 2_R | 9_T | 2.267 | 1.00 |
| 1_E | 4_R | 2.139 | 1.00 |
| 303_C | 311_L | 2.105 | 1.00 |
| 300_V | 315_F | 2.055 | 1.00 |
| 6_N | 9_T | 2.016 | 1.00 |
| 33_T | 37_M | 1.972 | 1.00 |
| 164_R | 169_R | 1.967 | 1.00 |
| 117_H | 120_D | 1.926 | 0.99 |
| 293_E | 335_K | 1.826 | 0.99 |
| 116_V | 124_L | 1.751 | 0.99 |
| 1_E | 12_I | 1.751 | 0.99 |
| 5_R | 9_T | 1.740 | 0.99 |
| 270_H | 280_D | 1.717 | 0.98 |
| 32_L | 39_V | 1.687 | 0.98 |
| 304_H | 307_D | 1.671 | 0.98 |
| 141_D | 148_K | 1.661 | 0.98 |
| 166_F | 169_R | 1.647 | 0.98 |
| 30_D | 36_R | 1.647 | 0.98 |
| 4_R | 12_I | 1.635 | 0.98 |
| 33_T | 42_M | 1.618 | 0.97 |
| 35_L | 39_V | 1.586 | 0.97 |
| 31_K | 34_I | 1.575 | 0.97 |
| 351_N | 354_S | 1.548 | 0.96 |
| 138_R | 141_D | 1.535 | 0.96 |
| 4_R | 7_K | 1.529 | 0.96 |
| 189_R | 192_C | 1.525 | 0.96 |
| 1_E | 11_Y | 1.515 | 0.96 |
| 359_Y | 363_T | 1.505 | 0.95 |
| 210_H | 213_G | 1.503 | 0.95 |
| 68_K | 72_L | 1.496 | 0.95 |
| 25_L | 29_P | 1.488 | 0.95 |
| 96_V | 257_M | 1.485 | 0.95 |
| 30_D | 33_T | 1.474 | 0.95 |
| 2_R | 7_K | 1.473 | 0.95 |
| 141_D | 147_V | 1.468 | 0.95 |
| 97_T | 103_P | 1.463 | 0.94 |
| 2_R | 8_M | 1.451 | 0.94 |
| 72_L | 81_I | 1.448 | 0.94 |
| 2_R | 5_R | 1.447 | 0.94 |
| 4_R | 8_M | 1.443 | 0.94 |
| 17_D | 34_I | 1.418 | 0.93 |
| 31_K | 35_L | 1.412 | 0.93 |
| 16_S | 34_I | 1.405 | 0.93 |
| 37_M | 41_H | 1.404 | 0.93 |
| 20_P | 36_R | 1.402 | 0.93 |
| 20_P | 32_L | 1.402 | 0.93 |
| 141_D | 144_T | 1.400 | 0.93 |
| 138_R | 148_K | 1.382 | 0.92 |
| 72_L | 76_D | 1.380 | 0.92 |
| 143_K | 147_V | 1.377 | 0.92 |
| 31_K | 42_M | 1.376 | 0.92 |
| 34_I | 40_S | 1.370 | 0.91 |
| 140_L | 145_G | 1.368 | 0.91 |
| 144_T | 147_V | 1.367 | 0.91 |
| 209_V | 215_I | 1.353 | 0.91 |
| 270_H | 276_F | 1.337 | 0.90 |
| 269_R | 282_R | 1.337 | 0.90 |
| 124_L | 168_C | 1.333 | 0.90 |
| 209_V | 213_G | 1.314 | 0.89 |
| 5_R | 15_L | 1.313 | 0.89 |
| 332_F | 342_M | 1.310 | 0.89 |
| 1_E | 8_M | 1.308 | 0.89 |
| 107_W | 170_M | 1.306 | 0.89 |
| 92_V | 96_V | 1.305 | 0.89 |
| 33_T | 36_R | 1.303 | 0.89 |
| 8_M | 32_L | 1.299 | 0.88 |
| 31_K | 36_R | 1.298 | 0.88 |
| 270_H | 288_G | 1.291 | 0.88 |
| 7_K | 12_I | 1.285 | 0.88 |
| 213_G | 216_K | 1.284 | 0.88 |
| 265_E | 274_G | 1.284 | 0.88 |
| 76_D | 100_L | 1.283 | 0.87 |
| 93_S | 100_L | 1.275 | 0.87 |
| 30_D | 39_V | 1.274 | 0.87 |
| 330_F | 364_N | 1.261 | 0.86 |
| 28_K | 35_L | 1.260 | 0.86 |
| 349_F | 352_P | 1.260 | 0.86 |
| 344_T | 362_C | 1.257 | 0.86 |
| 2_R | 12_I | 1.256 | 0.86 |
| 209_V | 244_G | 1.254 | 0.86 |
| 289_Y | 335_K | 1.254 | 0.86 |
| 297_K | 302_F | 1.253 | 0.86 |
| 16_S | 26_A | 1.253 | 0.86 |
| 208_V | 211_C | 1.247 | 0.85 |
| 307_D | 331_R | 1.246 | 0.85 |
| 140_L | 143_K | 1.239 | 0.85 |
| 78_F | 87_G | 1.232 | 0.84 |
| 1_E | 45_L | 1.232 | 0.84 |
| 182_M | 186_S | 1.225 | 0.84 |
| 304_H | 331_R | 1.223 | 0.84 |
| 190_N | 193_R | 1.214 | 0.83 |
| 288_G | 293_E | 1.206 | 0.83 |
| 268_S | 276_F | 1.198 | 0.82 |
| 350_Q | 357_I | 1.197 | 0.82 |
| 1_E | 14_E | 1.189 | 0.81 |
| 1_E | 28_K | 1.188 | 0.81 |
| 74_A | 77_G | 1.185 | 0.81 |
| 7_K | 33_T | 1.177 | 0.81 |
| 198_S | 201_E | 1.176 | 0.81 |
| 28_K | 125_R | 1.174 | 0.80 |
| 323_G | 344_T | 1.171 | 0.80 |
| 177_V | 180_V | 1.166 | 0.80 |
| 276_F | 332_F | 1.166 | 0.80 |
| 304_H | 339_W | 1.165 | 0.80 |
| 76_D | 93_S | 1.162 | 0.79 |
| 112_L | 116_V | 1.162 | 0.79 |
| 78_F | 94_D | 1.159 | 0.79 |
| 36_R | 42_M | 1.159 | 0.79 |
| 3_R | 39_V | 1.145 | 0.78 |
| 4_R | 9_T | 1.140 | 0.78 |
| 58_K | 62_L | 1.140 | 0.78 |
| 327_S | 330_F | 1.132 | 0.77 |
| 96_V | 107_W | 1.131 | 0.77 |
| 68_K | 71_I | 1.128 | 0.77 |
| 269_R | 278_F | 1.127 | 0.76 |
| 177_V | 182_M | 1.125 | 0.76 |
| 30_D | 34_I | 1.124 | 0.76 |
| 2_R | 324_Q | 1.120 | 0.76 |
| 312_R | 315_F | 1.117 | 0.76 |
| 349_F | 358_E | 1.115 | 0.75 |
| 190_N | 194_N | 1.113 | 0.75 |
| 32_L | 35_L | 1.112 | 0.75 |
| 20_P | 37_M | 1.111 | 0.75 |
| 20_P | 38_A | 1.111 | 0.75 |
| 36_R | 117_H | 1.111 | 0.75 |
| 6_N | 29_P | 1.108 | 0.75 |
| 139_V | 142_L | 1.095 | 0.73 |
| 268_S | 344_T | 1.094 | 0.73 |
| 1_E | 5_R | 1.090 | 0.73 |
| 8_M | 12_I | 1.088 | 0.73 |
| 8_M | 28_K | 1.088 | 0.73 |
| 181_S | 186_S | 1.086 | 0.73 |
| 178_D | 181_S | 1.086 | 0.73 |
| 141_D | 145_G | 1.084 | 0.72 |
| 78_F | 91_Y | 1.082 | 0.72 |
| 123_K | 126_E | 1.075 | 0.72 |
| 270_H | 273_E | 1.072 | 0.71 |
| 325_V | 364_N | 1.071 | 0.71 |
| 287_V | 294_L | 1.066 | 0.71 |
| 12_I | 15_L | 1.066 | 0.71 |
| 180_V | 186_S | 1.064 | 0.70 |
| 16_S | 31_K | 1.063 | 0.70 |
| 140_L | 147_V | 1.062 | 0.70 |
| 36_R | 104_Q | 1.061 | 0.70 |
| 353_Y | 359_Y | 1.060 | 0.70 |
| 11_Y | 19_V | 1.060 | 0.70 |
| 88_R | 91_Y | 1.059 | 0.70 |
| 29_P | 37_M | 1.055 | 0.69 |
| 194_N | 197_G | 1.055 | 0.69 |
| 6_N | 27_R | 1.055 | 0.69 |
| 299_I | 303_C | 1.053 | 0.69 |
| 7_K | 20_P | 1.052 | 0.69 |
| 75_A | 101_N | 1.050 | 0.69 |
| 31_K | 39_V | 1.046 | 0.69 |
| 31_K | 38_A | 1.045 | 0.68 |
| 244_G | 266_F | 1.045 | 0.68 |
| 358_E | 362_C | 1.043 | 0.68 |
| 19_V | 25_L | 1.041 | 0.68 |
| 36_R | 44_S | 1.038 | 0.68 |
| 189_R | 194_N | 1.037 | 0.68 |
| 19_V | 22_C | 1.036 | 0.67 |
| 3_R | 28_K | 1.034 | 0.67 |
| 21_T | 25_L | 1.034 | 0.67 |
| 140_L | 144_T | 1.034 | 0.67 |
| 214_Y | 244_G | 1.032 | 0.67 |
| 330_F | 342_M | 1.029 | 0.67 |
| 4_R | 14_E | 1.027 | 0.66 |
| 20_P | 41_H | 1.024 | 0.66 |
| 210_H | 214_Y | 1.021 | 0.66 |
| 109_G | 364_N | 1.021 | 0.66 |
| 13_T | 34_I | 1.020 | 0.66 |
| 116_V | 121_V | 1.020 | 0.66 |
| 8_M | 33_T | 1.019 | 0.66 |
| 179_P | 186_S | 1.018 | 0.65 |
| 269_R | 280_D | 1.017 | 0.65 |
| 35_L | 274_G | 1.017 | 0.65 |
| 206_F | 280_D | 1.016 | 0.65 |
| 59_P | 62_L | 1.014 | 0.65 |
| 148_K | 151_G | 1.014 | 0.65 |
| 289_Y | 293_E | 1.012 | 0.65 |
| 30_D | 330_F | 1.010 | 0.65 |
| 12_I | 28_K | 1.008 | 0.64 |
| 94_D | 111_T | 1.008 | 0.64 |
| 102_Q | 110_S | 1.006 | 0.64 |
| 72_L | 89_V | 1.003 | 0.64 |
| 87_G | 100_L | 1.002 | 0.64 |
| 58_K | 61_F | 1.002 | 0.64 |
| 106_E | 270_H | 1.000 | 0.63 |
| 3_R | 35_L | 1.000 | 0.63 |
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 | |
| 4f3lB | 1 | 0.7875 | 100 | 0.369 | Contact Map |
| 4f3lA | 1 | 0.8311 | 100 | 0.422 | Contact Map |
| 1oj5A | 1 | 0.267 | 100 | 0.695 | Contact Map |
| 3gdiA | 2 | 0.6403 | 100 | 0.712 | Contact Map |
| 4m4xA | 2 | 0.3433 | 99.9 | 0.729 | Contact Map |
| 3rtyA | 8 | 0.6267 | 99.9 | 0.737 | Contact Map |
| 4dj3A | 2 | 0.6948 | 99.9 | 0.77 | Contact Map |
| 4dj2A | 4 | 0.6649 | 99.9 | 0.779 | Contact Map |
| 2kdkA | 1 | 0.3079 | 99.8 | 0.805 | Contact Map |
| 3f1pA | 1 | 0.297 | 99.6 | 0.832 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)