| 1gy7AB |
| ID: | 1456186045 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 243 (243) | ||
| Sequences: | 4835 (4835) | ||
| Seq/Len: | 19.897 | ||
| Nf(neff/√len): | 310.2 |
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: 19.897).
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 |
| 180_W | 211_Y | 3.364 | 1.00 |
| 73_P | 153_D | 3.301 | 1.00 |
| 31_K | 195_D | 3.200 | 1.00 |
| 129_E | 133_R | 3.139 | 1.00 |
| 7_K | 11_T | 2.889 | 1.00 |
| 16_M | 27_L | 2.620 | 1.00 |
| 184_V | 208_I | 2.492 | 1.00 |
| 121_S | 243_S | 2.469 | 1.00 |
| 138_E | 149_L | 2.284 | 1.00 |
| 139_A | 183_Y | 2.283 | 1.00 |
| 151_R | 227_D | 2.280 | 1.00 |
| 159_N | 240_I | 2.272 | 1.00 |
| 62_V | 86_F | 2.267 | 1.00 |
| 76_T | 104_P | 2.265 | 1.00 |
| 29_T | 110_R | 2.214 | 1.00 |
| 33_M | 42_F | 2.197 | 1.00 |
| 206_F | 217_M | 2.173 | 1.00 |
| 80_L | 221_A | 2.165 | 1.00 |
| 155_L | 164_K | 2.105 | 1.00 |
| 41_Y | 50_A | 2.067 | 1.00 |
| 10_A | 81_V | 2.015 | 1.00 |
| 85_L | 96_V | 2.008 | 1.00 |
| 220_Q | 236_L | 1.973 | 1.00 |
| 207_M | 218_F | 1.947 | 1.00 |
| 163_T | 172_T | 1.923 | 1.00 |
| 28_Y | 114_D | 1.921 | 1.00 |
| 9_F | 102_L | 1.920 | 1.00 |
| 181_V | 207_M | 1.912 | 1.00 |
| 117_Q | 187_R | 1.910 | 1.00 |
| 17_A | 61_Y | 1.908 | 1.00 |
| 80_L | 237_I | 1.884 | 1.00 |
| 94_I | 118_C | 1.882 | 1.00 |
| 103_V | 112_F | 1.881 | 1.00 |
| 99_V | 202_L | 1.865 | 1.00 |
| 186_M | 206_F | 1.841 | 1.00 |
| 78_L | 200_L | 1.815 | 1.00 |
| 56_V | 87_L | 1.779 | 1.00 |
| 29_T | 105_D | 1.766 | 1.00 |
| 151_R | 232_F | 1.762 | 1.00 |
| 59_Q | 85_L | 1.751 | 1.00 |
| 134_Q | 149_L | 1.744 | 1.00 |
| 39_N | 50_A | 1.744 | 1.00 |
| 105_D | 110_R | 1.736 | 1.00 |
| 123_K | 127_Y | 1.726 | 1.00 |
| 161_K | 172_T | 1.726 | 1.00 |
| 222_L | 236_L | 1.657 | 1.00 |
| 78_L | 235_N | 1.637 | 1.00 |
| 25_Y | 45_E | 1.634 | 1.00 |
| 97_V | 219_V | 1.623 | 1.00 |
| 209_I | 216_I | 1.614 | 1.00 |
| 98_Q | 114_D | 1.583 | 1.00 |
| 71_A | 78_L | 1.582 | 1.00 |
| 67_L | 239_Y | 1.582 | 1.00 |
| 156_A | 172_T | 1.579 | 1.00 |
| 72_G | 198_P | 1.574 | 1.00 |
| 119_L | 204_A | 1.568 | 1.00 |
| 18_A | 61_Y | 1.564 | 1.00 |
| 147_A | 167_K | 1.536 | 1.00 |
| 150_F | 236_L | 1.534 | 1.00 |
| 158_I | 238_F | 1.519 | 1.00 |
| 113_C | 200_L | 1.511 | 1.00 |
| 15_K | 19_T | 1.508 | 1.00 |
| 124_Y | 192_P | 1.508 | 1.00 |
| 122_G | 125_E | 1.507 | 1.00 |
| 36_W | 116_F | 1.503 | 1.00 |
| 138_E | 148_K | 1.469 | 1.00 |
| 38_H | 189_L | 1.468 | 1.00 |
| 69_A | 157_I | 1.464 | 1.00 |
| 90_T | 94_I | 1.464 | 1.00 |
| 34_M | 50_A | 1.463 | 1.00 |
| 136_Y | 220_Q | 1.460 | 1.00 |
| 34_M | 47_I | 1.460 | 1.00 |
| 65_C | 239_Y | 1.454 | 1.00 |
| 14_F | 98_Q | 1.452 | 1.00 |
| 17_A | 54_I | 1.450 | 1.00 |
| 100_L | 114_D | 1.444 | 1.00 |
| 119_L | 241_A | 1.443 | 1.00 |
| 198_P | 226_P | 1.430 | 1.00 |
| 179_D | 210_D | 1.429 | 1.00 |
| 131_F | 224_L | 1.426 | 1.00 |
| 217_M | 243_S | 1.422 | 1.00 |
| 156_A | 169_I | 1.417 | 1.00 |
| 144_S | 174_I | 1.410 | 1.00 |
| 84_L | 95_I | 1.408 | 1.00 |
| 126_S | 130_K | 1.392 | 0.99 |
| 137_A | 141_T | 1.384 | 0.99 |
| 138_E | 146_L | 1.380 | 0.99 |
| 61_Y | 96_V | 1.373 | 0.99 |
| 64_Q | 84_L | 1.361 | 0.99 |
| 134_Q | 138_E | 1.359 | 0.99 |
| 28_Y | 32_S | 1.347 | 0.99 |
| 40_H | 122_G | 1.341 | 0.99 |
| 12_K | 27_L | 1.330 | 0.99 |
| 5_W | 77_T | 1.325 | 0.99 |
| 219_V | 241_A | 1.318 | 0.99 |
| 132_T | 203_V | 1.308 | 0.99 |
| 36_W | 54_I | 1.305 | 0.99 |
| 135_F | 150_F | 1.291 | 0.99 |
| 16_M | 26_N | 1.287 | 0.99 |
| 124_Y | 199_V | 1.286 | 0.99 |
| 132_T | 222_L | 1.285 | 0.99 |
| 17_A | 59_Q | 1.282 | 0.99 |
| 58_S | 89_N | 1.276 | 0.99 |
| 117_Q | 189_L | 1.260 | 0.99 |
| 69_A | 235_N | 1.260 | 0.99 |
| 87_L | 94_I | 1.252 | 0.99 |
| 153_D | 164_K | 1.250 | 0.99 |
| 225_V | 234_L | 1.236 | 0.98 |
| 178_A | 181_V | 1.230 | 0.98 |
| 2_I | 70_P | 1.217 | 0.98 |
| 31_K | 42_F | 1.209 | 0.98 |
| 56_V | 59_Q | 1.205 | 0.98 |
| 193_A | 200_L | 1.191 | 0.98 |
| 67_L | 160_G | 1.182 | 0.98 |
| 139_A | 181_V | 1.180 | 0.98 |
| 95_I | 217_M | 1.180 | 0.98 |
| 136_Y | 183_Y | 1.177 | 0.98 |
| 135_F | 236_L | 1.167 | 0.97 |
| 186_M | 217_M | 1.167 | 0.97 |
| 22_R | 52_A | 1.165 | 0.97 |
| 5_W | 109_A | 1.162 | 0.97 |
| 65_C | 160_G | 1.162 | 0.97 |
| 3_M | 162_V | 1.149 | 0.97 |
| 124_Y | 127_Y | 1.148 | 0.97 |
| 14_F | 81_V | 1.146 | 0.97 |
| 63_I | 81_V | 1.142 | 0.97 |
| 13_F | 114_D | 1.142 | 0.97 |
| 140_A | 182_Q | 1.137 | 0.97 |
| 127_Y | 199_V | 1.126 | 0.97 |
| 2_I | 77_T | 1.125 | 0.97 |
| 17_A | 24_L | 1.118 | 0.96 |
| 14_F | 61_Y | 1.116 | 0.96 |
| 158_I | 176_Y | 1.115 | 0.96 |
| 11_T | 15_K | 1.109 | 0.96 |
| 156_A | 236_L | 1.101 | 0.96 |
| 82_A | 241_A | 1.089 | 0.96 |
| 134_Q | 230_S | 1.088 | 0.96 |
| 121_S | 217_M | 1.080 | 0.95 |
| 10_A | 66_L | 1.068 | 0.95 |
| 178_A | 209_I | 1.063 | 0.95 |
| 61_Y | 85_L | 1.063 | 0.95 |
| 198_P | 225_V | 1.059 | 0.95 |
| 140_A | 183_Y | 1.047 | 0.94 |
| 171_D | 175_S | 1.045 | 0.94 |
| 139_A | 176_Y | 1.041 | 0.94 |
| 16_M | 24_L | 1.041 | 0.94 |
| 96_V | 118_C | 1.022 | 0.93 |
| 12_K | 16_M | 1.020 | 0.93 |
| 117_Q | 202_L | 1.018 | 0.93 |
| 46_K | 49_S | 1.015 | 0.93 |
| 87_L | 118_C | 1.010 | 0.93 |
| 99_V | 221_A | 1.004 | 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 | |
| 1gy7A | 4 | 0.5021 | 99.7 | 0.836 | Contact Map |
| 1gy6A | 2 | 0.5021 | 99.6 | 0.846 | Contact Map |
| 1zo2A | 2 | 0.5062 | 99.6 | 0.849 | Contact Map |
| 3ujmA | 2 | 0.4733 | 99.5 | 0.85 | Contact Map |
| 4fcjA | 2 | 0.5185 | 99.5 | 0.851 | Contact Map |
| 4x2hB | 1 | 0 | 99.5 | 0.852 | Contact Map |
| 1jkgA | 1 | 0.5267 | 99.5 | 0.859 | Contact Map |
| 3nv0B | 1 | 0.4815 | 99.4 | 0.86 | Contact Map |
| 2qiyA | 2 | 0.4897 | 99.4 | 0.863 | Contact Map |
| 1of5B | 1 | 0.3951 | 99.3 | 0.868 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)