| T-TE HHblits |
| ID: | 1507661485 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 424 (400) | ||
| Sequences: | 1404 (1115) | ||
| Seq/Len: | 3.510 | ||
| Nf(neff/√len): | 55.8 |
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: 3.510).
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 |
| 12_D | 90_R | 4.604 | 1.00 |
| 189_M | 220_V | 3.601 | 1.00 |
| 197_Q | 223_A | 3.558 | 1.00 |
| 37_F | 42_A | 3.526 | 1.00 |
| 216_M | 358_M | 3.289 | 1.00 |
| 182_D | 214_R | 3.184 | 1.00 |
| 193_H | 220_V | 3.092 | 1.00 |
| 36_S | 39_E | 2.975 | 1.00 |
| 133_H | 184_Y | 2.860 | 1.00 |
| 18_L | 54_L | 2.829 | 1.00 |
| 132_F | 211_V | 2.794 | 1.00 |
| 205_G | 230_I | 2.748 | 1.00 |
| 32_G | 35_Q | 2.743 | 1.00 |
| 131_V | 199_I | 2.739 | 1.00 |
| 43_D | 46_I | 2.674 | 1.00 |
| 203_L | 207_I | 2.669 | 1.00 |
| 129_R | 199_I | 2.663 | 1.00 |
| 139_M | 159_G | 2.614 | 1.00 |
| 210_E | 214_R | 2.589 | 1.00 |
| 189_M | 218_R | 2.491 | 1.00 |
| 142_F | 201_Y | 2.489 | 1.00 |
| 11_L | 33_R | 2.421 | 1.00 |
| 191_T | 196_L | 2.395 | 1.00 |
| 185_A | 211_V | 2.328 | 1.00 |
| 128_L | 156_S | 2.312 | 1.00 |
| 34_S | 83_A | 2.293 | 1.00 |
| 23_A | 30_S | 2.290 | 1.00 |
| 14_L | 90_R | 2.268 | 1.00 |
| 189_M | 196_L | 2.223 | 1.00 |
| 196_L | 220_V | 2.200 | 1.00 |
| 22_W | 82_V | 2.166 | 1.00 |
| 155_G | 197_Q | 2.152 | 1.00 |
| 188_L | 211_V | 2.126 | 1.00 |
| 399_G | 403_S | 2.070 | 1.00 |
| 134_A | 141_I | 2.000 | 1.00 |
| 163_A | 183_D | 1.998 | 1.00 |
| 210_E | 213_R | 1.992 | 1.00 |
| 134_A | 142_F | 1.982 | 1.00 |
| 124_Q | 156_S | 1.954 | 1.00 |
| 24_E | 53_R | 1.942 | 1.00 |
| 22_W | 37_F | 1.875 | 1.00 |
| 12_D | 16_S | 1.849 | 0.99 |
| 134_A | 201_Y | 1.840 | 0.99 |
| 129_R | 157_I | 1.824 | 0.99 |
| 11_L | 83_A | 1.808 | 0.99 |
| 36_S | 80_P | 1.787 | 0.99 |
| 8_E | 33_R | 1.767 | 0.99 |
| 191_T | 194_S | 1.745 | 0.99 |
| 22_W | 42_A | 1.744 | 0.99 |
| 38_Y | 42_A | 1.740 | 0.99 |
| 131_V | 157_I | 1.717 | 0.99 |
| 10_K | 15_E | 1.692 | 0.99 |
| 8_E | 34_S | 1.685 | 0.99 |
| 192_G | 196_L | 1.682 | 0.99 |
| 361_I | 388_C | 1.657 | 0.99 |
| 19_A | 33_R | 1.653 | 0.99 |
| 133_H | 142_F | 1.636 | 0.98 |
| 181_A | 214_R | 1.627 | 0.98 |
| 13_E | 16_S | 1.626 | 0.98 |
| 133_H | 201_Y | 1.619 | 0.98 |
| 176_L | 179_T | 1.597 | 0.98 |
| 79_Y | 88_F | 1.574 | 0.98 |
| 130_V | 196_L | 1.567 | 0.98 |
| 21_L | 54_L | 1.550 | 0.98 |
| 360_D | 390_G | 1.541 | 0.97 |
| 185_A | 214_R | 1.537 | 0.97 |
| 128_L | 158_V | 1.535 | 0.97 |
| 130_V | 158_V | 1.534 | 0.97 |
| 134_A | 137_G | 1.527 | 0.97 |
| 226_V | 364_L | 1.520 | 0.97 |
| 126_G | 155_G | 1.504 | 0.97 |
| 150_K | 418_E | 1.500 | 0.97 |
| 127_L | 197_Q | 1.493 | 0.97 |
| 38_Y | 47_M | 1.486 | 0.97 |
| 55_R | 61_D | 1.480 | 0.96 |
| 10_K | 33_R | 1.475 | 0.96 |
| 345_Q | 349_A | 1.459 | 0.96 |
| 12_D | 33_R | 1.458 | 0.96 |
| 365_L | 396_T | 1.455 | 0.96 |
| 15_E | 33_R | 1.440 | 0.96 |
| 130_V | 194_S | 1.438 | 0.96 |
| 133_H | 137_G | 1.436 | 0.96 |
| 163_A | 180_V | 1.434 | 0.96 |
| 191_T | 220_V | 1.433 | 0.96 |
| 26_L | 37_F | 1.425 | 0.95 |
| 18_L | 86_A | 1.420 | 0.95 |
| 124_Q | 128_L | 1.412 | 0.95 |
| 18_L | 50_V | 1.412 | 0.95 |
| 130_V | 191_T | 1.405 | 0.95 |
| 360_D | 391_E | 1.403 | 0.95 |
| 203_L | 346_S | 1.402 | 0.95 |
| 160_V | 188_L | 1.400 | 0.95 |
| 400_N | 403_S | 1.395 | 0.95 |
| 41_G | 44_S | 1.393 | 0.95 |
| 31_I | 40_H | 1.388 | 0.94 |
| 185_A | 189_M | 1.385 | 0.94 |
| 202_S | 229_D | 1.372 | 0.94 |
| 33_R | 82_V | 1.367 | 0.94 |
| 133_H | 180_V | 1.367 | 0.94 |
| 342_V | 346_S | 1.367 | 0.94 |
| 121_G | 150_K | 1.360 | 0.94 |
| 14_L | 17_I | 1.347 | 0.93 |
| 19_A | 31_I | 1.344 | 0.93 |
| 199_I | 226_V | 1.344 | 0.93 |
| 128_L | 155_G | 1.339 | 0.93 |
| 210_E | 352_Y | 1.330 | 0.93 |
| 130_V | 188_L | 1.325 | 0.92 |
| 43_D | 47_M | 1.323 | 0.92 |
| 132_F | 207_I | 1.317 | 0.92 |
| 141_I | 201_Y | 1.316 | 0.92 |
| 127_L | 223_A | 1.303 | 0.92 |
| 388_C | 391_E | 1.299 | 0.91 |
| 14_L | 58_L | 1.298 | 0.91 |
| 139_M | 146_L | 1.296 | 0.91 |
| 207_I | 211_V | 1.290 | 0.91 |
| 361_I | 392_L | 1.288 | 0.91 |
| 23_A | 29_V | 1.287 | 0.91 |
| 19_A | 82_V | 1.281 | 0.91 |
| 15_E | 86_A | 1.267 | 0.90 |
| 185_A | 188_L | 1.266 | 0.90 |
| 75_Q | 88_F | 1.260 | 0.90 |
| 72_L | 75_Q | 1.259 | 0.90 |
| 224_D | 417_L | 1.259 | 0.90 |
| 164_D | 342_V | 1.258 | 0.90 |
| 26_L | 42_A | 1.243 | 0.89 |
| 191_T | 195_E | 1.238 | 0.89 |
| 18_L | 21_L | 1.236 | 0.89 |
| 132_F | 160_V | 1.222 | 0.88 |
| 228_I | 404_C | 1.219 | 0.88 |
| 17_I | 57_K | 1.215 | 0.87 |
| 198_L | 215_L | 1.201 | 0.87 |
| 9_E | 32_G | 1.198 | 0.86 |
| 178_E | 352_Y | 1.189 | 0.86 |
| 132_F | 184_Y | 1.180 | 0.85 |
| 51_A | 76_M | 1.172 | 0.85 |
| 227_L | 361_I | 1.169 | 0.84 |
| 200_G | 204_G | 1.165 | 0.84 |
| 189_M | 194_S | 1.162 | 0.84 |
| 23_A | 28_L | 1.159 | 0.84 |
| 148_H | 414_A | 1.150 | 0.83 |
| 398_E | 412_R | 1.142 | 0.83 |
| 205_G | 384_W | 1.130 | 0.82 |
| 217_E | 355_L | 1.122 | 0.81 |
| 360_D | 393_G | 1.110 | 0.80 |
| 130_V | 195_E | 1.101 | 0.79 |
| 42_A | 47_M | 1.101 | 0.79 |
| 134_A | 184_Y | 1.092 | 0.78 |
| 25_A | 50_V | 1.088 | 0.78 |
| 26_L | 41_G | 1.085 | 0.78 |
| 395_I | 416_L | 1.083 | 0.78 |
| 213_R | 357_Y | 1.082 | 0.78 |
| 202_S | 401_H | 1.079 | 0.77 |
| 209_V | 352_Y | 1.077 | 0.77 |
| 17_I | 58_L | 1.074 | 0.77 |
| 79_Y | 84_D | 1.071 | 0.77 |
| 22_W | 36_S | 1.071 | 0.77 |
| 10_K | 32_G | 1.066 | 0.76 |
| 177_I | 181_A | 1.065 | 0.76 |
| 192_G | 195_E | 1.063 | 0.76 |
| 28_L | 31_I | 1.061 | 0.76 |
| 8_E | 22_W | 1.060 | 0.76 |
| 25_A | 46_I | 1.059 | 0.75 |
| 49_Q | 53_R | 1.058 | 0.75 |
| 47_M | 77_L | 1.054 | 0.75 |
| 19_A | 23_A | 1.053 | 0.75 |
| 216_M | 357_Y | 1.045 | 0.74 |
| 117_L | 160_V | 1.044 | 0.74 |
| 74_R | 140_D | 1.042 | 0.74 |
| 226_V | 362_R | 1.036 | 0.73 |
| 150_K | 155_G | 1.033 | 0.73 |
| 203_L | 350_A | 1.031 | 0.73 |
| 338_G | 342_V | 1.030 | 0.73 |
| 11_L | 15_E | 1.026 | 0.72 |
| 383_F | 399_G | 1.025 | 0.72 |
| 137_G | 204_G | 1.024 | 0.72 |
| 214_R | 218_R | 1.023 | 0.72 |
| 116_V | 187_C | 1.018 | 0.71 |
| 125_E | 154_I | 1.009 | 0.70 |
| 132_F | 198_L | 1.008 | 0.70 |
| 362_R | 420_P | 1.007 | 0.70 |
| 36_S | 42_A | 1.006 | 0.70 |
| 8_E | 11_L | 1.006 | 0.70 |
| 145_L | 417_L | 1.004 | 0.70 |
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 | 0.0071 | 100 | 0.413 | Contact Map |
| 3tejA | 2 | 0.75 | 100 | 0.501 | Contact Map |
| 2vsqA | 1 | 0.691 | 100 | 0.526 | Contact Map |
| 2px6A | 2 | 0.6014 | 99.9 | 0.703 | Contact Map |
| 2cb9A | 1 | 0.4929 | 99.9 | 0.715 | Contact Map |
| 1jmkC | 2 | 0.5354 | 99.9 | 0.717 | Contact Map |
| 1kezA | 3 | 0.6226 | 99.9 | 0.747 | Contact Map |
| 4r0mB | 2 | 0.191 | 99.9 | 0.748 | Contact Map |
| 3ilsA | 1 | 0.5778 | 99.8 | 0.757 | Contact Map |
| 2k2qB | 1 | 0.5519 | 99.8 | 0.76 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)