| Mcd 160-548 |
| ID: | 1485516630 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 389 (380) | ||
| Sequences: | 19812 (10606.7) | ||
| Seq/Len: | 52.137 | ||
| Nf(neff/√len): | 544.1 |
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: 52.137).
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 |
| 147_E | 227_R | 4.065 | 1.00 |
| 151_H | 225_G | 3.683 | 1.00 |
| 23_R | 45_A | 3.677 | 1.00 |
| 301_E | 339_A | 3.514 | 1.00 |
| 104_D | 108_A | 3.015 | 1.00 |
| 113_K | 118_E | 2.873 | 1.00 |
| 17_R | 76_E | 2.856 | 1.00 |
| 203_M | 224_D | 2.856 | 1.00 |
| 273_Q | 277_E | 2.701 | 1.00 |
| 265_Q | 306_R | 2.611 | 1.00 |
| 183_S | 233_L | 2.585 | 1.00 |
| 294_K | 343_N | 2.507 | 1.00 |
| 153_N | 222_G | 2.498 | 1.00 |
| 30_G | 35_D | 2.445 | 1.00 |
| 66_S | 69_S | 2.327 | 1.00 |
| 275_A | 347_I | 2.222 | 1.00 |
| 44_E | 48_E | 2.175 | 1.00 |
| 143_K | 230_A | 2.172 | 1.00 |
| 18_R | 22_E | 2.154 | 1.00 |
| 355_L | 360_S | 2.142 | 1.00 |
| 79_R | 269_E | 2.098 | 1.00 |
| 284_A | 287_E | 2.083 | 1.00 |
| 203_M | 222_G | 2.062 | 1.00 |
| 104_D | 107_K | 2.057 | 1.00 |
| 166_M | 189_K | 2.052 | 1.00 |
| 267_A | 341_A | 2.048 | 1.00 |
| 268_L | 302_I | 2.019 | 1.00 |
| 75_E | 306_R | 1.995 | 1.00 |
| 170_A | 185_F | 1.993 | 1.00 |
| 45_A | 48_E | 1.953 | 1.00 |
| 265_Q | 269_E | 1.948 | 1.00 |
| 264_A | 302_I | 1.940 | 1.00 |
| 144_D | 227_R | 1.936 | 1.00 |
| 149_V | 225_G | 1.929 | 1.00 |
| 298_M | 340_A | 1.890 | 1.00 |
| 113_K | 119_I | 1.890 | 1.00 |
| 76_E | 79_R | 1.851 | 1.00 |
| 153_N | 220_E | 1.815 | 1.00 |
| 108_A | 112_P | 1.801 | 1.00 |
| 305_A | 333_G | 1.786 | 1.00 |
| 103_T | 106_Q | 1.730 | 1.00 |
| 283_K | 287_E | 1.727 | 1.00 |
| 148_W | 185_F | 1.726 | 1.00 |
| 160_A | 219_Y | 1.725 | 1.00 |
| 339_A | 343_N | 1.694 | 1.00 |
| 122_T | 166_M | 1.686 | 1.00 |
| 144_D | 149_V | 1.666 | 1.00 |
| 240_Q | 243_K | 1.653 | 1.00 |
| 266_N | 270_V | 1.646 | 1.00 |
| 205_G | 222_G | 1.641 | 1.00 |
| 360_S | 364_C | 1.633 | 1.00 |
| 279_K | 284_A | 1.618 | 1.00 |
| 229_K | 232_N | 1.613 | 1.00 |
| 149_V | 227_R | 1.607 | 1.00 |
| 291_V | 347_I | 1.601 | 1.00 |
| 127_E | 154_K | 1.590 | 1.00 |
| 144_D | 147_E | 1.587 | 1.00 |
| 68_A | 314_W | 1.586 | 1.00 |
| 58_E | 64_G | 1.582 | 1.00 |
| 351_N | 357_Y | 1.581 | 1.00 |
| 14_D | 18_R | 1.577 | 1.00 |
| 11_M | 14_D | 1.573 | 1.00 |
| 335_R | 376_A | 1.568 | 1.00 |
| 275_A | 291_V | 1.563 | 1.00 |
| 20_A | 80_G | 1.553 | 1.00 |
| 270_V | 273_Q | 1.547 | 1.00 |
| 57_P | 99_L | 1.517 | 1.00 |
| 311_H | 315_E | 1.517 | 1.00 |
| 112_P | 116_S | 1.510 | 1.00 |
| 6_D | 9_L | 1.506 | 1.00 |
| 151_H | 224_D | 1.505 | 1.00 |
| 75_E | 265_Q | 1.499 | 1.00 |
| 209_E | 355_L | 1.495 | 1.00 |
| 270_V | 358_Q | 1.475 | 1.00 |
| 271_G | 344_A | 1.473 | 1.00 |
| 338_W | 370_N | 1.466 | 1.00 |
| 236_G | 240_Q | 1.463 | 1.00 |
| 78_S | 85_G | 1.460 | 1.00 |
| 13_R | 76_E | 1.456 | 1.00 |
| 266_N | 362_I | 1.451 | 1.00 |
| 264_A | 340_A | 1.443 | 1.00 |
| 314_W | 318_H | 1.441 | 1.00 |
| 16_F | 51_V | 1.434 | 1.00 |
| 302_I | 340_A | 1.431 | 1.00 |
| 79_R | 265_Q | 1.427 | 1.00 |
| 261_I | 302_I | 1.418 | 1.00 |
| 60_F | 107_K | 1.416 | 1.00 |
| 11_M | 15_Q | 1.414 | 1.00 |
| 342_D | 367_R | 1.409 | 1.00 |
| 124_V | 157_I | 1.406 | 0.99 |
| 280_Q | 288_F | 1.404 | 0.99 |
| 75_E | 310_Y | 1.403 | 0.99 |
| 304_V | 332_L | 1.401 | 0.99 |
| 188_E | 232_N | 1.395 | 0.99 |
| 45_A | 49_M | 1.394 | 0.99 |
| 142_V | 151_H | 1.381 | 0.99 |
| 146_D | 230_A | 1.379 | 0.99 |
| 44_E | 47_A | 1.372 | 0.99 |
| 272_M | 276_E | 1.367 | 0.99 |
| 290_R | 293_G | 1.354 | 0.99 |
| 101_G | 247_Q | 1.340 | 0.99 |
| 228_V | 232_N | 1.333 | 0.99 |
| 344_A | 359_I | 1.333 | 0.99 |
| 105_A | 109_A | 1.328 | 0.99 |
| 161_A | 219_Y | 1.312 | 0.99 |
| 327_G | 379_Q | 1.311 | 0.99 |
| 315_E | 325_E | 1.306 | 0.99 |
| 198_F | 226_F | 1.304 | 0.99 |
| 298_M | 343_N | 1.301 | 0.99 |
| 114_L | 121_P | 1.298 | 0.99 |
| 113_K | 116_S | 1.291 | 0.99 |
| 338_W | 342_D | 1.286 | 0.99 |
| 147_E | 230_A | 1.276 | 0.99 |
| 337_A | 366_A | 1.271 | 0.99 |
| 148_W | 230_A | 1.266 | 0.99 |
| 19_F | 45_A | 1.257 | 0.99 |
| 31_W | 215_G | 1.252 | 0.99 |
| 81_Y | 84_V | 1.251 | 0.99 |
| 270_V | 348_H | 1.249 | 0.99 |
| 107_K | 111_L | 1.248 | 0.99 |
| 263_V | 337_A | 1.232 | 0.98 |
| 301_E | 336_V | 1.229 | 0.98 |
| 16_F | 20_A | 1.226 | 0.98 |
| 301_E | 343_N | 1.226 | 0.98 |
| 109_A | 113_K | 1.224 | 0.98 |
| 338_W | 363_L | 1.221 | 0.98 |
| 150_V | 170_A | 1.220 | 0.98 |
| 299_A | 303_M | 1.220 | 0.98 |
| 283_K | 288_F | 1.216 | 0.98 |
| 124_V | 223_F | 1.214 | 0.98 |
| 54_L | 73_V | 1.212 | 0.98 |
| 272_M | 295_L | 1.206 | 0.98 |
| 109_A | 231_E | 1.204 | 0.98 |
| 205_G | 220_E | 1.198 | 0.98 |
| 305_A | 336_V | 1.198 | 0.98 |
| 197_P | 226_F | 1.196 | 0.98 |
| 71_V | 313_A | 1.193 | 0.98 |
| 150_V | 185_F | 1.192 | 0.98 |
| 40_M | 44_E | 1.189 | 0.98 |
| 94_A | 121_P | 1.189 | 0.98 |
| 335_R | 380_A | 1.182 | 0.98 |
| 276_E | 286_I | 1.171 | 0.98 |
| 169_L | 184_M | 1.171 | 0.98 |
| 297_M | 343_N | 1.170 | 0.97 |
| 297_M | 380_A | 1.170 | 0.97 |
| 261_I | 309_T | 1.170 | 0.97 |
| 189_K | 198_F | 1.170 | 0.97 |
| 258_A | 309_T | 1.167 | 0.97 |
| 303_M | 311_H | 1.167 | 0.97 |
| 141_A | 185_F | 1.164 | 0.97 |
| 260_A | 369_L | 1.163 | 0.97 |
| 102_G | 106_Q | 1.162 | 0.97 |
| 71_V | 258_A | 1.158 | 0.97 |
| 335_R | 339_A | 1.155 | 0.97 |
| 172_T | 183_S | 1.153 | 0.97 |
| 56_I | 115_A | 1.151 | 0.97 |
| 17_R | 21_D | 1.150 | 0.97 |
| 47_A | 52_F | 1.149 | 0.97 |
| 146_D | 227_R | 1.147 | 0.97 |
| 168_L | 187_A | 1.143 | 0.97 |
| 143_K | 238_E | 1.142 | 0.97 |
| 27_H | 30_G | 1.135 | 0.97 |
| 13_R | 72_V | 1.134 | 0.97 |
| 342_D | 370_N | 1.134 | 0.97 |
| 312_S | 329_A | 1.131 | 0.97 |
| 227_R | 230_A | 1.122 | 0.97 |
| 341_A | 366_A | 1.122 | 0.97 |
| 168_L | 223_F | 1.121 | 0.97 |
| 16_F | 73_V | 1.121 | 0.97 |
| 268_L | 272_M | 1.120 | 0.96 |
| 10_E | 13_R | 1.114 | 0.96 |
| 10_E | 14_D | 1.107 | 0.96 |
| 142_V | 149_V | 1.105 | 0.96 |
| 230_A | 233_L | 1.103 | 0.96 |
| 41_E | 44_E | 1.099 | 0.96 |
| 193_T | 196_D | 1.099 | 0.96 |
| 140_R | 151_H | 1.092 | 0.96 |
| 275_A | 285_L | 1.091 | 0.96 |
| 126_T | 156_W | 1.090 | 0.96 |
| 271_G | 347_I | 1.090 | 0.96 |
| 9_L | 69_S | 1.089 | 0.96 |
| 331_L | 380_A | 1.084 | 0.96 |
| 65_L | 69_S | 1.080 | 0.95 |
| 148_W | 172_T | 1.076 | 0.95 |
| 67_K | 317_D | 1.075 | 0.95 |
| 105_A | 231_E | 1.070 | 0.95 |
| 129_N | 138_R | 1.067 | 0.95 |
| 263_V | 366_A | 1.063 | 0.95 |
| 193_T | 232_N | 1.061 | 0.95 |
| 267_A | 362_I | 1.055 | 0.95 |
| 15_Q | 49_M | 1.049 | 0.94 |
| 297_M | 301_E | 1.045 | 0.94 |
| 119_I | 165_V | 1.039 | 0.94 |
| 311_H | 314_W | 1.038 | 0.94 |
| 15_Q | 18_R | 1.030 | 0.94 |
| 20_A | 77_L | 1.028 | 0.94 |
| 30_G | 34_R | 1.027 | 0.94 |
| 105_A | 108_A | 1.026 | 0.94 |
| 9_L | 66_S | 1.023 | 0.93 |
| 100_C | 247_Q | 1.020 | 0.93 |
| 124_V | 166_M | 1.019 | 0.93 |
| 7_E | 11_M | 1.018 | 0.93 |
| 275_A | 295_L | 1.012 | 0.93 |
| 345_L | 359_I | 1.009 | 0.93 |
| 21_D | 79_R | 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 | |
| 2d29A | 2 | 0.9743 | 100 | 0.046 | Contact Map |
| 3owaA | 4 | 0.964 | 100 | 0.048 | Contact Map |
| 2jifA | 4 | 0.9692 | 100 | 0.051 | Contact Map |
| 2z1qA | 2 | 0.9614 | 100 | 0.052 | Contact Map |
| 1ivhA | 4 | 0.9743 | 100 | 0.053 | Contact Map |
| 4l1fA | 2 | 0.9717 | 100 | 0.054 | Contact Map |
| 3r7kA | 4 | 0.9666 | 100 | 0.055 | Contact Map |
| 4m9aA | 4 | 0.964 | 100 | 0.056 | Contact Map |
| 4u83A | 4 | 0.946 | 100 | 0.056 | Contact Map |
| 3pfdA | 4 | 0.9486 | 100 | 0.056 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)