| DHQS |
| ID: | 1497378661 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 362 (352) | ||
| Sequences: | 8586 (5094.7) | ||
| Seq/Len: | 24.392 | ||
| Nf(neff/√len): | 271.5 |
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: 24.392).
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 |
| 102_L | 114_T | 3.272 | 1.00 |
| 179_R | 269_E | 3.194 | 1.00 |
| 87_L | 120_I | 3.020 | 1.00 |
| 203_D | 295_D | 3.012 | 1.00 |
| 339_E | 343_S | 2.976 | 1.00 |
| 126_D | 164_K | 2.728 | 1.00 |
| 178_Q | 182_I | 2.451 | 1.00 |
| 86_I | 117_A | 2.387 | 1.00 |
| 49_A | 53_L | 2.311 | 1.00 |
| 88_S | 92_E | 2.249 | 1.00 |
| 25_V | 171_E | 2.220 | 1.00 |
| 104_A | 114_T | 2.209 | 1.00 |
| 54_T | 58_A | 2.187 | 1.00 |
| 248_F | 275_M | 2.183 | 1.00 |
| 280_D | 297_N | 2.183 | 1.00 |
| 82_S | 85_K | 2.171 | 1.00 |
| 81_Q | 84_D | 2.165 | 1.00 |
| 89_T | 93_N | 2.160 | 1.00 |
| 339_E | 345_S | 2.143 | 1.00 |
| 119_A | 159_A | 2.126 | 1.00 |
| 24_S | 171_E | 2.112 | 1.00 |
| 259_C | 321_A | 2.111 | 1.00 |
| 234_M | 242_A | 2.089 | 1.00 |
| 31_I | 59_A | 1.980 | 1.00 |
| 230_Q | 234_M | 1.970 | 1.00 |
| 177_P | 180_E | 1.962 | 1.00 |
| 90_L | 95_F | 1.955 | 1.00 |
| 28_F | 55_K | 1.944 | 1.00 |
| 111_G | 129_Q | 1.935 | 1.00 |
| 43_V | 114_T | 1.871 | 1.00 |
| 317_E | 320_E | 1.852 | 1.00 |
| 29_S | 32_L | 1.821 | 1.00 |
| 83_L | 113_I | 1.795 | 1.00 |
| 83_L | 117_A | 1.787 | 1.00 |
| 81_Q | 151_Q | 1.781 | 1.00 |
| 40_V | 100_T | 1.771 | 1.00 |
| 282_S | 338_I | 1.754 | 1.00 |
| 279_I | 296_F | 1.728 | 1.00 |
| 183_A | 266_K | 1.688 | 1.00 |
| 57_L | 61_V | 1.680 | 1.00 |
| 223_R | 226_Q | 1.678 | 1.00 |
| 193_F | 338_I | 1.675 | 1.00 |
| 41_L | 90_L | 1.667 | 1.00 |
| 191_Y | 224_S | 1.663 | 1.00 |
| 45_N | 48_V | 1.662 | 1.00 |
| 283_H | 293_A | 1.657 | 1.00 |
| 45_N | 73_D | 1.655 | 1.00 |
| 41_L | 95_F | 1.655 | 1.00 |
| 111_G | 140_S | 1.650 | 1.00 |
| 338_I | 344_L | 1.644 | 1.00 |
| 316_K | 355_E | 1.635 | 1.00 |
| 90_L | 102_L | 1.631 | 1.00 |
| 116_F | 120_I | 1.630 | 1.00 |
| 284_Y | 356_Q | 1.623 | 1.00 |
| 188_V | 224_S | 1.622 | 1.00 |
| 69_C | 89_T | 1.621 | 1.00 |
| 40_V | 103_V | 1.610 | 1.00 |
| 265_L | 273_V | 1.597 | 1.00 |
| 80_Q | 148_I | 1.592 | 1.00 |
| 294_K | 298_D | 1.583 | 1.00 |
| 227_I | 239_L | 1.578 | 1.00 |
| 80_Q | 84_D | 1.576 | 1.00 |
| 245_I | 344_L | 1.574 | 1.00 |
| 83_L | 148_I | 1.535 | 1.00 |
| 226_Q | 230_Q | 1.534 | 1.00 |
| 257_E | 270_A | 1.523 | 1.00 |
| 47_T | 51_L | 1.510 | 1.00 |
| 193_F | 296_F | 1.507 | 1.00 |
| 46_T | 72_E | 1.495 | 1.00 |
| 98_N | 329_S | 1.494 | 1.00 |
| 222_K | 226_Q | 1.491 | 1.00 |
| 47_T | 73_D | 1.480 | 1.00 |
| 195_S | 227_I | 1.466 | 1.00 |
| 128_I | 165_V | 1.460 | 1.00 |
| 100_T | 128_I | 1.458 | 1.00 |
| 229_A | 233_A | 1.453 | 1.00 |
| 43_V | 117_A | 1.453 | 1.00 |
| 289_S | 292_Q | 1.441 | 1.00 |
| 242_A | 245_I | 1.428 | 1.00 |
| 95_F | 99_S | 1.423 | 1.00 |
| 153_G | 156_M | 1.411 | 1.00 |
| 83_L | 87_L | 1.411 | 1.00 |
| 67_R | 93_N | 1.406 | 0.99 |
| 71_L | 77_Y | 1.394 | 0.99 |
| 56_F | 105_L | 1.392 | 0.99 |
| 118_A | 124_G | 1.392 | 0.99 |
| 252_F | 277_Q | 1.392 | 0.99 |
| 253_G | 270_A | 1.379 | 0.99 |
| 9_S | 19_N | 1.377 | 0.99 |
| 49_A | 70_I | 1.375 | 0.99 |
| 205_N | 208_K | 1.365 | 0.99 |
| 58_A | 62_D | 1.350 | 0.99 |
| 43_V | 86_I | 1.344 | 0.99 |
| 189_V | 221_V | 1.344 | 0.99 |
| 285_L | 353_E | 1.343 | 0.99 |
| 6_S | 222_K | 1.343 | 0.99 |
| 54_T | 57_L | 1.343 | 0.99 |
| 89_T | 92_E | 1.331 | 0.99 |
| 44_T | 49_A | 1.327 | 0.99 |
| 83_L | 120_I | 1.317 | 0.99 |
| 192_A | 220_M | 1.316 | 0.99 |
| 298_D | 302_S | 1.315 | 0.99 |
| 150_H | 157_I | 1.304 | 0.99 |
| 195_S | 230_Q | 1.301 | 0.99 |
| 111_G | 131_P | 1.299 | 0.99 |
| 183_A | 269_E | 1.283 | 0.99 |
| 104_A | 129_Q | 1.277 | 0.99 |
| 219_E | 223_R | 1.275 | 0.99 |
| 142_V | 225_C | 1.274 | 0.99 |
| 186_A | 305_I | 1.263 | 0.99 |
| 41_L | 89_T | 1.257 | 0.99 |
| 314_C | 317_E | 1.250 | 0.99 |
| 42_V | 53_L | 1.247 | 0.99 |
| 290_Q | 294_K | 1.236 | 0.98 |
| 276_A | 297_N | 1.236 | 0.98 |
| 162_Q | 236_E | 1.235 | 0.98 |
| 85_K | 88_S | 1.232 | 0.98 |
| 26_L | 29_S | 1.232 | 0.98 |
| 301_V | 307_I | 1.226 | 0.98 |
| 230_Q | 235_D | 1.224 | 0.98 |
| 258_K | 321_A | 1.219 | 0.98 |
| 25_V | 169_S | 1.211 | 0.98 |
| 340_N | 343_S | 1.211 | 0.98 |
| 178_Q | 212_K | 1.206 | 0.98 |
| 69_C | 95_F | 1.202 | 0.98 |
| 138_V | 188_V | 1.202 | 0.98 |
| 336_I | 346_L | 1.198 | 0.98 |
| 25_V | 28_F | 1.198 | 0.98 |
| 83_L | 147_A | 1.196 | 0.98 |
| 47_T | 50_K | 1.192 | 0.98 |
| 265_L | 270_A | 1.190 | 0.98 |
| 26_L | 167_Y | 1.188 | 0.98 |
| 69_C | 93_N | 1.186 | 0.98 |
| 281_F | 335_F | 1.184 | 0.98 |
| 185_M | 188_V | 1.181 | 0.98 |
| 58_A | 61_V | 1.180 | 0.98 |
| 189_V | 303_F | 1.175 | 0.98 |
| 53_L | 57_L | 1.174 | 0.98 |
| 231_V | 245_I | 1.173 | 0.98 |
| 182_I | 304_G | 1.173 | 0.98 |
| 75_E | 82_S | 1.167 | 0.97 |
| 219_E | 222_K | 1.165 | 0.97 |
| 41_L | 69_C | 1.155 | 0.97 |
| 19_N | 33_E | 1.153 | 0.97 |
| 199_Y | 341_I | 1.150 | 0.97 |
| 46_T | 73_D | 1.146 | 0.97 |
| 84_D | 88_S | 1.146 | 0.97 |
| 30_H | 56_F | 1.145 | 0.97 |
| 38_K | 99_S | 1.143 | 0.97 |
| 185_M | 228_K | 1.137 | 0.97 |
| 23_D | 29_S | 1.131 | 0.97 |
| 71_L | 82_S | 1.129 | 0.97 |
| 272_G | 300_I | 1.119 | 0.96 |
| 308_D | 311_N | 1.115 | 0.96 |
| 102_L | 118_A | 1.111 | 0.96 |
| 145_K | 158_G | 1.110 | 0.96 |
| 37_N | 100_T | 1.105 | 0.96 |
| 230_Q | 233_A | 1.091 | 0.96 |
| 100_T | 126_D | 1.084 | 0.96 |
| 21_I | 165_V | 1.082 | 0.96 |
| 102_L | 125_I | 1.081 | 0.95 |
| 104_A | 111_G | 1.079 | 0.95 |
| 319_L | 355_E | 1.075 | 0.95 |
| 207_D | 302_S | 1.069 | 0.95 |
| 57_L | 68_T | 1.068 | 0.95 |
| 71_L | 110_I | 1.061 | 0.95 |
| 334_K | 348_K | 1.060 | 0.95 |
| 201_W | 205_N | 1.056 | 0.95 |
| 43_V | 74_G | 1.053 | 0.95 |
| 179_R | 266_K | 1.052 | 0.95 |
| 352_N | 355_E | 1.049 | 0.94 |
| 39_Q | 99_S | 1.049 | 0.94 |
| 88_S | 152_L | 1.049 | 0.94 |
| 44_T | 110_I | 1.046 | 0.94 |
| 171_E | 174_K | 1.043 | 0.94 |
| 196_K | 200_L | 1.030 | 0.94 |
| 266_K | 269_E | 1.029 | 0.94 |
| 27_D | 169_S | 1.029 | 0.94 |
| 299_F | 302_S | 1.028 | 0.94 |
| 297_N | 301_V | 1.027 | 0.94 |
| 129_Q | 166_V | 1.026 | 0.94 |
| 319_L | 323_L | 1.025 | 0.93 |
| 30_H | 130_I | 1.022 | 0.93 |
| 30_H | 167_Y | 1.018 | 0.93 |
| 48_V | 52_Y | 1.018 | 0.93 |
| 39_Q | 65_D | 1.011 | 0.93 |
| 140_S | 166_V | 1.011 | 0.93 |
| 23_D | 170_I | 1.010 | 0.93 |
| 337_L | 347_Q | 1.010 | 0.93 |
| 355_E | 359_D | 1.006 | 0.93 |
| 27_D | 172_F | 1.005 | 0.93 |
| 215_V | 219_E | 1.002 | 0.92 |
| 20_I | 225_C | 1.000 | 0.92 |
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 | |
| 3okfA | 2 | 0.9779 | 100 | 0.126 | Contact Map |
| 2gruA | 2 | 0.9751 | 100 | 0.131 | Contact Map |
| 3zokA | 4 | 0.9751 | 100 | 0.14 | Contact Map |
| 3qbeA | 1 | 0.9586 | 100 | 0.153 | Contact Map |
| 1xahA | 2 | 0.9006 | 100 | 0.154 | Contact Map |
| 1ujnA | 2 | 0.9061 | 100 | 0.156 | Contact Map |
| 4p53A | 1 | 0.953 | 100 | 0.166 | Contact Map |
| 1sg6A | 2 | 0.9392 | 100 | 0.176 | Contact Map |
| 3clhA | 2 | 0.8453 | 100 | 0.185 | Contact Map |
| 1rrmA | 2 | 0.8978 | 100 | 0.336 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)