| MdfA |
| ID: | 1516178710 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 391 (358) | ||
| Sequences: | 75775 (48036) | ||
| Seq/Len: | 211.662 | ||
| Nf(neff/√len): | 2538.8 |
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: 211.662).
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 |
| 94_Q | 98_Q | 3.898 | 1.00 |
| 89_A | 102_L | 3.738 | 1.00 |
| 82_W | 109_S | 3.421 | 1.00 |
| 91_L | 166_V | 3.392 | 1.00 |
| 72_R | 123_E | 3.034 | 1.00 |
| 55_G | 104_F | 2.912 | 1.00 |
| 84_I | 172_A | 2.902 | 1.00 |
| 79_G | 112_F | 2.787 | 1.00 |
| 86_T | 102_L | 2.787 | 1.00 |
| 97_E | 101_L | 2.771 | 1.00 |
| 95_N | 98_Q | 2.761 | 1.00 |
| 129_V | 132_K | 2.595 | 1.00 |
| 125_F | 133_I | 2.541 | 1.00 |
| 258_A | 312_S | 2.527 | 1.00 |
| 244_S | 247_E | 2.465 | 1.00 |
| 131_I | 271_S | 2.380 | 1.00 |
| 63_L | 112_F | 2.340 | 1.00 |
| 292_V | 310_G | 2.279 | 1.00 |
| 220_G | 351_I | 2.272 | 1.00 |
| 86_T | 109_S | 2.245 | 1.00 |
| 159_L | 163_G | 2.234 | 1.00 |
| 59_L | 108_I | 2.214 | 1.00 |
| 126_E | 129_V | 2.180 | 1.00 |
| 77_L | 180_Q | 2.139 | 1.00 |
| 86_T | 105_L | 2.125 | 1.00 |
| 40_A | 96_I | 2.115 | 1.00 |
| 262_G | 316_F | 2.102 | 1.00 |
| 93_A | 98_Q | 2.053 | 1.00 |
| 285_P | 317_G | 2.023 | 1.00 |
| 88_L | 169_A | 2.020 | 1.00 |
| 51_A | 104_F | 2.018 | 1.00 |
| 44_W | 96_I | 2.014 | 1.00 |
| 68_D | 338_G | 2.002 | 1.00 |
| 90_I | 102_L | 1.987 | 1.00 |
| 73_R | 77_L | 1.976 | 1.00 |
| 41_G | 44_W | 1.934 | 1.00 |
| 224_L | 355_G | 1.929 | 1.00 |
| 96_I | 100_T | 1.899 | 1.00 |
| 228_A | 359_S | 1.860 | 1.00 |
| 90_I | 99_F | 1.853 | 1.00 |
| 177_F | 181_R | 1.827 | 1.00 |
| 81_V | 176_F | 1.792 | 1.00 |
| 48_S | 99_F | 1.789 | 1.00 |
| 204_K | 208_K | 1.766 | 1.00 |
| 71_G | 74_P | 1.730 | 1.00 |
| 84_I | 169_A | 1.702 | 1.00 |
| 77_L | 176_F | 1.696 | 1.00 |
| 84_I | 176_F | 1.692 | 1.00 |
| 282_G | 320_L | 1.684 | 1.00 |
| 65_P | 69_R | 1.658 | 1.00 |
| 205_L | 336_S | 1.658 | 1.00 |
| 33_A | 36_E | 1.654 | 1.00 |
| 268_R | 272_R | 1.622 | 1.00 |
| 216_A | 347_L | 1.598 | 1.00 |
| 51_A | 100_T | 1.591 | 1.00 |
| 93_A | 102_L | 1.574 | 1.00 |
| 67_S | 116_V | 1.563 | 1.00 |
| 243_L | 247_E | 1.558 | 1.00 |
| 127_E | 130_C | 1.558 | 1.00 |
| 30_G | 156_I | 1.545 | 1.00 |
| 160_P | 163_G | 1.529 | 1.00 |
| 98_Q | 102_L | 1.520 | 1.00 |
| 59_L | 111_C | 1.512 | 1.00 |
| 157_H | 246_Y | 1.508 | 1.00 |
| 289_G | 310_G | 1.480 | 1.00 |
| 247_E | 250_L | 1.478 | 1.00 |
| 121_I | 137_M | 1.457 | 1.00 |
| 55_G | 59_L | 1.450 | 1.00 |
| 97_E | 100_T | 1.450 | 1.00 |
| 67_S | 72_R | 1.446 | 1.00 |
| 155_W | 163_G | 1.446 | 1.00 |
| 166_V | 170_A | 1.439 | 1.00 |
| 267_A | 271_S | 1.437 | 1.00 |
| 74_P | 78_A | 1.434 | 1.00 |
| 255_I | 315_A | 1.416 | 1.00 |
| 84_I | 173_A | 1.393 | 0.99 |
| 40_A | 44_W | 1.391 | 0.99 |
| 179_L | 183_M | 1.390 | 0.99 |
| 305_L | 309_A | 1.380 | 0.99 |
| 89_A | 98_Q | 1.378 | 0.99 |
| 66_L | 70_I | 1.351 | 0.99 |
| 275_V | 331_F | 1.348 | 0.99 |
| 86_T | 106_Q | 1.345 | 0.99 |
| 289_G | 317_G | 1.343 | 0.99 |
| 88_L | 92_L | 1.306 | 0.99 |
| 274_T | 277_S | 1.303 | 0.99 |
| 303_A | 306_W | 1.302 | 0.99 |
| 289_G | 314_Y | 1.295 | 0.99 |
| 238_I | 248_Y | 1.286 | 0.99 |
| 213_V | 217_L | 1.285 | 0.99 |
| 91_L | 169_A | 1.278 | 0.99 |
| 66_L | 75_V | 1.275 | 0.99 |
| 178_G | 182_A | 1.256 | 0.99 |
| 132_K | 268_R | 1.254 | 0.99 |
| 33_A | 37_Q | 1.247 | 0.99 |
| 78_A | 82_W | 1.245 | 0.98 |
| 55_G | 107_G | 1.235 | 0.98 |
| 305_L | 308_T | 1.234 | 0.98 |
| 154_A | 246_Y | 1.231 | 0.98 |
| 266_L | 320_L | 1.230 | 0.98 |
| 282_G | 321_A | 1.229 | 0.98 |
| 80_V | 176_F | 1.226 | 0.98 |
| 59_L | 62_L | 1.225 | 0.98 |
| 74_P | 185_E | 1.221 | 0.98 |
| 64_G | 68_D | 1.221 | 0.98 |
| 154_A | 158_V | 1.210 | 0.98 |
| 210_G | 214_A | 1.209 | 0.98 |
| 265_L | 268_R | 1.206 | 0.98 |
| 85_V | 89_A | 1.205 | 0.98 |
| 222_V | 321_A | 1.200 | 0.98 |
| 68_D | 339_T | 1.200 | 0.98 |
| 70_I | 75_V | 1.199 | 0.98 |
| 79_G | 109_S | 1.199 | 0.98 |
| 333_S | 336_S | 1.195 | 0.98 |
| 92_L | 166_V | 1.194 | 0.98 |
| 35_V | 40_A | 1.194 | 0.98 |
| 243_L | 251_L | 1.188 | 0.98 |
| 70_I | 74_P | 1.186 | 0.98 |
| 277_S | 280_I | 1.182 | 0.98 |
| 74_P | 77_L | 1.179 | 0.98 |
| 73_R | 185_E | 1.178 | 0.98 |
| 120_A | 183_M | 1.178 | 0.98 |
| 286_I | 317_G | 1.175 | 0.98 |
| 227_L | 352_F | 1.173 | 0.98 |
| 71_G | 75_V | 1.166 | 0.97 |
| 87_C | 168_F | 1.166 | 0.97 |
| 336_S | 339_T | 1.166 | 0.97 |
| 212_F | 216_A | 1.165 | 0.97 |
| 236_I | 241_E | 1.159 | 0.97 |
| 170_A | 174_I | 1.157 | 0.97 |
| 269_L | 273_R | 1.150 | 0.97 |
| 122_R | 130_C | 1.150 | 0.97 |
| 262_G | 265_L | 1.149 | 0.97 |
| 43_D | 364_L | 1.148 | 0.97 |
| 37_Q | 162_E | 1.146 | 0.97 |
| 205_L | 208_K | 1.145 | 0.97 |
| 21_Y | 141_A | 1.136 | 0.97 |
| 219_L | 344_M | 1.136 | 0.97 |
| 37_Q | 161_W | 1.134 | 0.97 |
| 207_L | 213_V | 1.132 | 0.97 |
| 250_L | 254_P | 1.130 | 0.97 |
| 251_L | 308_T | 1.121 | 0.97 |
| 329_T | 344_M | 1.121 | 0.97 |
| 68_D | 72_R | 1.119 | 0.96 |
| 82_W | 86_T | 1.117 | 0.96 |
| 35_V | 45_V | 1.115 | 0.96 |
| 330_L | 341_S | 1.113 | 0.96 |
| 54_A | 353_T | 1.106 | 0.96 |
| 209_N | 213_V | 1.099 | 0.96 |
| 163_G | 166_V | 1.096 | 0.96 |
| 281_M | 284_W | 1.091 | 0.96 |
| 361_H | 365_N | 1.079 | 0.95 |
| 30_G | 164_M | 1.078 | 0.95 |
| 77_L | 81_V | 1.076 | 0.95 |
| 78_A | 81_V | 1.074 | 0.95 |
| 72_R | 119_A | 1.073 | 0.95 |
| 89_A | 92_L | 1.071 | 0.95 |
| 52_Y | 110_L | 1.062 | 0.95 |
| 132_K | 271_S | 1.062 | 0.95 |
| 238_I | 245_S | 1.060 | 0.95 |
| 258_A | 262_G | 1.056 | 0.95 |
| 289_G | 313_I | 1.055 | 0.95 |
| 282_G | 317_G | 1.052 | 0.95 |
| 26_M | 152_G | 1.050 | 0.94 |
| 123_E | 337_K | 1.050 | 0.94 |
| 333_S | 340_V | 1.044 | 0.94 |
| 132_K | 136_L | 1.039 | 0.94 |
| 94_Q | 97_E | 1.035 | 0.94 |
| 274_T | 278_L | 1.032 | 0.94 |
| 287_M | 291_L | 1.025 | 0.93 |
| 130_C | 331_F | 1.024 | 0.93 |
| 177_F | 180_Q | 1.023 | 0.93 |
| 304_Y | 308_T | 1.022 | 0.93 |
| 101_L | 105_L | 1.022 | 0.93 |
| 277_S | 281_M | 1.020 | 0.93 |
| 237_I | 243_L | 1.015 | 0.93 |
| 76_M | 179_L | 1.014 | 0.93 |
| 75_V | 78_A | 1.014 | 0.93 |
| 47_T | 51_A | 1.013 | 0.93 |
| 169_A | 173_A | 1.012 | 0.93 |
| 220_G | 347_L | 1.009 | 0.93 |
| 309_A | 312_S | 1.009 | 0.93 |
| 72_R | 185_E | 1.007 | 0.93 |
| 88_L | 166_V | 1.005 | 0.93 |
| 219_L | 348_Q | 1.005 | 0.93 |
| 247_E | 251_L | 1.002 | 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 | |
| 2gfpA | 2 | 0.9591 | 100 | 0.184 | Contact Map |
| 1pw4A | 1 | 0.9719 | 100 | 0.191 | Contact Map |
| 3o7qA | 1 | 0.9744 | 100 | 0.219 | Contact Map |
| 3wdoA | 1 | 0.9795 | 100 | 0.221 | Contact Map |
| 4pypA | 1 | 0.9847 | 100 | 0.244 | Contact Map |
| 4j05A | 2 | 0.9284 | 100 | 0.244 | Contact Map |
| 2cfqA | 1 | 0.9744 | 100 | 0.261 | Contact Map |
| 4xnjA | 1 | 0 | 100 | 0.285 | Contact Map |
| 4zw9A | 1 | 0 | 100 | 0.291 | Contact Map |
| 4gc0A | 1 | 0.9872 | 100 | 0.296 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)