| Srb T-TE |
| ID: | 1698789138 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 422 (395) | ||
| Sequences: | 1242 (987.1) | ||
| Seq/Len: | 3.144 | ||
| Nf(neff/√len): | 49.7 |
HHblits Results: (2016_02)
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 |
| 2_D | 77_R | 4.625 | 1.00 |
| 190_Q | 216_R | 3.685 | 1.00 |
| 182_V | 213_L | 3.560 | 1.00 |
| 186_F | 213_L | 3.346 | 1.00 |
| 126_H | 177_Y | 3.220 | 1.00 |
| 27_F | 32_A | 3.219 | 1.00 |
| 175_D | 207_R | 3.218 | 1.00 |
| 209_L | 352_V | 3.212 | 1.00 |
| 26_N | 29_Q | 3.204 | 1.00 |
| 125_F | 204_V | 3.190 | 1.00 |
| 196_L | 200_L | 2.837 | 1.00 |
| 22_G | 25_D | 2.836 | 1.00 |
| 124_M | 192_I | 2.800 | 1.00 |
| 203_E | 207_R | 2.776 | 1.00 |
| 135_F | 194_Y | 2.716 | 1.00 |
| 184_E | 189_F | 2.700 | 1.00 |
| 8_L | 44_L | 2.573 | 1.00 |
| 198_G | 223_S | 2.561 | 1.00 |
| 122_R | 192_I | 2.529 | 1.00 |
| 178_A | 204_V | 2.519 | 1.00 |
| 181_L | 204_V | 2.474 | 1.00 |
| 33_D | 36_I | 2.411 | 1.00 |
| 121_V | 149_P | 2.399 | 1.00 |
| 182_V | 211_R | 2.369 | 1.00 |
| 132_M | 152_G | 2.295 | 1.00 |
| 13_A | 20_K | 2.286 | 1.00 |
| 148_G | 190_Q | 2.267 | 1.00 |
| 189_F | 213_L | 2.201 | 1.00 |
| 12_W | 69_V | 2.144 | 1.00 |
| 182_V | 189_F | 2.141 | 1.00 |
| 24_D | 70_Q | 2.135 | 1.00 |
| 127_A | 134_Y | 2.114 | 1.00 |
| 4_L | 77_R | 2.052 | 1.00 |
| 184_E | 187_E | 2.037 | 1.00 |
| 203_E | 206_R | 2.032 | 1.00 |
| 124_M | 150_V | 2.011 | 1.00 |
| 395_G | 399_S | 1.981 | 1.00 |
| 117_G | 149_P | 1.893 | 0.99 |
| 2_D | 6_G | 1.889 | 0.99 |
| 28_Y | 32_A | 1.881 | 0.99 |
| 12_W | 32_A | 1.878 | 0.99 |
| 26_N | 67_P | 1.854 | 0.99 |
| 127_A | 194_Y | 1.848 | 0.99 |
| 12_W | 27_F | 1.798 | 0.99 |
| 178_A | 207_R | 1.798 | 0.99 |
| 156_A | 176_D | 1.769 | 0.99 |
| 3_E | 6_G | 1.755 | 0.99 |
| 126_H | 194_Y | 1.743 | 0.99 |
| 185_G | 189_F | 1.738 | 0.99 |
| 184_E | 188_E | 1.732 | 0.99 |
| 127_A | 135_F | 1.725 | 0.99 |
| 184_E | 213_L | 1.693 | 0.98 |
| 14_H | 43_R | 1.661 | 0.98 |
| 174_A | 207_R | 1.656 | 0.98 |
| 122_R | 150_V | 1.630 | 0.98 |
| 203_E | 346_F | 1.629 | 0.98 |
| 355_M | 388_F | 1.611 | 0.98 |
| 219_T | 358_L | 1.586 | 0.97 |
| 8_L | 73_G | 1.577 | 0.97 |
| 5_D | 23_R | 1.565 | 0.97 |
| 8_L | 40_V | 1.559 | 0.97 |
| 359_R | 392_D | 1.559 | 0.97 |
| 217_D | 413_L | 1.549 | 0.97 |
| 143_A | 414_A | 1.543 | 0.97 |
| 339_H | 343_A | 1.520 | 0.96 |
| 121_V | 151_V | 1.519 | 0.96 |
| 192_I | 219_T | 1.519 | 0.96 |
| 123_V | 151_V | 1.515 | 0.96 |
| 16_L | 27_F | 1.504 | 0.96 |
| 123_V | 184_E | 1.501 | 0.96 |
| 126_H | 135_F | 1.499 | 0.96 |
| 126_H | 173_L | 1.489 | 0.96 |
| 9_C | 23_R | 1.487 | 0.96 |
| 11_L | 44_L | 1.481 | 0.96 |
| 4_L | 7_R | 1.475 | 0.96 |
| 123_V | 181_L | 1.474 | 0.96 |
| 2_D | 23_R | 1.472 | 0.95 |
| 169_L | 172_R | 1.455 | 0.95 |
| 134_Y | 194_Y | 1.453 | 0.95 |
| 358_L | 409_V | 1.439 | 0.95 |
| 119_R | 148_G | 1.438 | 0.95 |
| 59_L | 62_Q | 1.437 | 0.95 |
| 171_D | 346_F | 1.429 | 0.94 |
| 195_C | 222_D | 1.417 | 0.94 |
| 196_L | 340_S | 1.401 | 0.94 |
| 396_N | 399_S | 1.400 | 0.94 |
| 114_G | 143_A | 1.398 | 0.94 |
| 354_D | 386_G | 1.369 | 0.93 |
| 384_C | 387_Q | 1.369 | 0.93 |
| 178_A | 181_L | 1.367 | 0.93 |
| 120_P | 190_Q | 1.360 | 0.92 |
| 123_V | 189_F | 1.358 | 0.92 |
| 210_E | 349_P | 1.348 | 0.92 |
| 31_G | 34_S | 1.343 | 0.92 |
| 125_F | 177_Y | 1.342 | 0.92 |
| 153_V | 181_L | 1.342 | 0.92 |
| 193_G | 197_G | 1.340 | 0.92 |
| 66_E | 75_M | 1.334 | 0.91 |
| 28_Y | 37_L | 1.331 | 0.91 |
| 45_R | 57_D | 1.327 | 0.91 |
| 23_R | 69_V | 1.322 | 0.91 |
| 123_V | 187_E | 1.322 | 0.91 |
| 119_R | 145_Q | 1.322 | 0.91 |
| 127_A | 130_G | 1.317 | 0.91 |
| 157_D | 336_V | 1.309 | 0.90 |
| 156_A | 173_L | 1.308 | 0.90 |
| 9_C | 69_V | 1.301 | 0.90 |
| 355_M | 384_C | 1.288 | 0.89 |
| 202_I | 346_F | 1.280 | 0.89 |
| 126_H | 130_G | 1.277 | 0.89 |
| 21_L | 30_R | 1.275 | 0.89 |
| 191_L | 208_L | 1.259 | 0.88 |
| 354_D | 387_Q | 1.257 | 0.88 |
| 9_C | 21_L | 1.257 | 0.88 |
| 336_V | 340_S | 1.254 | 0.88 |
| 5_D | 73_G | 1.235 | 0.86 |
| 356_N | 416_S | 1.205 | 0.85 |
| 220_L | 355_M | 1.204 | 0.84 |
| 138_L | 413_L | 1.201 | 0.84 |
| 157_D | 173_L | 1.201 | 0.84 |
| 394_P | 408_H | 1.197 | 0.84 |
| 32_A | 37_L | 1.197 | 0.84 |
| 206_R | 210_E | 1.187 | 0.83 |
| 108_F | 111_G | 1.181 | 0.83 |
| 4_L | 48_I | 1.178 | 0.83 |
| 206_R | 351_Y | 1.177 | 0.83 |
| 5_D | 22_G | 1.176 | 0.83 |
| 354_D | 389_R | 1.171 | 0.82 |
| 117_G | 121_V | 1.165 | 0.82 |
| 33_D | 37_L | 1.164 | 0.82 |
| 195_C | 397_H | 1.163 | 0.82 |
| 16_L | 32_A | 1.163 | 0.82 |
| 13_A | 19_A | 1.160 | 0.81 |
| 120_P | 216_R | 1.156 | 0.81 |
| 7_R | 47_E | 1.153 | 0.81 |
| 128_A | 195_C | 1.151 | 0.81 |
| 170_I | 200_L | 1.146 | 0.80 |
| 125_F | 200_L | 1.143 | 0.80 |
| 200_L | 204_V | 1.132 | 0.79 |
| 222_D | 397_H | 1.131 | 0.79 |
| 8_L | 11_L | 1.129 | 0.79 |
| 141_A | 410_A | 1.127 | 0.79 |
| 12_W | 21_L | 1.126 | 0.79 |
| 13_A | 18_I | 1.104 | 0.77 |
| 332_S | 336_V | 1.101 | 0.76 |
| 132_M | 139_G | 1.097 | 0.76 |
| 26_N | 32_A | 1.094 | 0.76 |
| 121_V | 148_G | 1.093 | 0.76 |
| 178_A | 182_V | 1.093 | 0.76 |
| 221_V | 400_V | 1.086 | 0.75 |
| 8_L | 20_K | 1.086 | 0.75 |
| 41_A | 58_T | 1.084 | 0.75 |
| 28_Y | 64_L | 1.078 | 0.74 |
| 354_D | 384_C | 1.076 | 0.74 |
| 62_Q | 75_M | 1.076 | 0.74 |
| 393_V | 400_V | 1.075 | 0.74 |
| 23_R | 70_Q | 1.073 | 0.74 |
| 198_G | 380_W | 1.072 | 0.74 |
| 61_R | 133_D | 1.070 | 0.73 |
| 191_L | 204_V | 1.068 | 0.73 |
| 43_R | 46_E | 1.064 | 0.73 |
| 15_A | 40_V | 1.063 | 0.73 |
| 185_G | 188_E | 1.061 | 0.73 |
| 125_F | 174_A | 1.060 | 0.72 |
| 125_F | 191_L | 1.058 | 0.72 |
| 130_G | 197_G | 1.055 | 0.72 |
| 206_R | 209_L | 1.053 | 0.72 |
| 343_A | 346_F | 1.053 | 0.72 |
| 207_R | 211_R | 1.051 | 0.72 |
| 173_L | 177_Y | 1.049 | 0.71 |
| 222_D | 360_C | 1.045 | 0.71 |
| 391_I | 412_H | 1.045 | 0.71 |
| 7_R | 48_I | 1.043 | 0.71 |
| 362_E | 396_N | 1.041 | 0.71 |
| 125_F | 153_V | 1.039 | 0.70 |
| 395_G | 409_V | 1.039 | 0.70 |
| 206_R | 349_P | 1.036 | 0.70 |
| 220_L | 223_S | 1.036 | 0.70 |
| 82_A | 218_L | 1.032 | 0.70 |
| 9_C | 13_A | 1.020 | 0.68 |
| 157_D | 166_P | 1.019 | 0.68 |
| 43_R | 47_E | 1.017 | 0.68 |
| 41_A | 63_M | 1.012 | 0.67 |
| 143_A | 148_G | 1.010 | 0.67 |
| 403_P | 406_V | 1.008 | 0.67 |
| 209_L | 351_Y | 1.006 | 0.67 |
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 | |
| 2vz8A | 2 | 0 | 100 | 0.323 | Contact Map |
| 3tejA | 2 | 0.7417 | 100 | 0.454 | Contact Map |
| 2vsqA | 1 | 0.6754 | 100 | 0.492 | Contact Map |
| 2px6A | 2 | 0.609 | 100 | 0.672 | Contact Map |
| 2cb9A | 1 | 0.4976 | 100 | 0.674 | Contact Map |
| 1jmkC | 2 | 0.5403 | 99.9 | 0.681 | Contact Map |
| 1kezA | 3 | 0.6256 | 99.9 | 0.706 | Contact Map |
| 3ilsA | 1 | 0.5853 | 99.9 | 0.726 | Contact Map |
| 2k2qB | 1 | 0.5592 | 99.9 | 0.728 | Contact Map |
| 4r0mB | 2 | 0.1682 | 99.9 | 0.737 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)