| 1PW4 |
| ID: | 1507586679 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 451 (406) | ||
| Sequences: | 66419 (41009.2) | ||
| Seq/Len: | 163.594 | ||
| Nf(neff/√len): | 2035.3 |
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: 163.594).
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 |
| 117_S | 121_V | 4.246 | 1.00 |
| 101_L | 132_F | 3.514 | 1.00 |
| 108_F | 125_L | 3.328 | 1.00 |
| 110_G | 190_Y | 3.267 | 1.00 |
| 103_A | 196_A | 3.048 | 1.00 |
| 300_A | 354_I | 2.875 | 1.00 |
| 154_G | 313_D | 2.814 | 1.00 |
| 98_G | 135_M | 2.758 | 1.00 |
| 105_V | 125_L | 2.738 | 1.00 |
| 118_S | 121_V | 2.712 | 1.00 |
| 120_A | 124_V | 2.702 | 1.00 |
| 74_A | 127_F | 2.663 | 1.00 |
| 91_P | 146_H | 2.622 | 1.00 |
| 262_V | 394_G | 2.608 | 1.00 |
| 152_E | 155_G | 2.595 | 1.00 |
| 286_A | 289_K | 2.589 | 1.00 |
| 266_L | 398_A | 2.577 | 1.00 |
| 82_M | 135_M | 2.402 | 1.00 |
| 375_A | 383_A | 2.377 | 1.00 |
| 105_V | 128_L | 2.362 | 1.00 |
| 60_S | 63_D | 2.291 | 1.00 |
| 26_R | 152_E | 2.263 | 1.00 |
| 105_V | 132_F | 2.233 | 1.00 |
| 119_I | 123_F | 2.194 | 1.00 |
| 87_D | 381_G | 2.185 | 1.00 |
| 337_V | 352_C | 2.158 | 1.00 |
| 78_S | 131_W | 2.096 | 1.00 |
| 148_W | 156_I | 2.096 | 1.00 |
| 304_G | 358_F | 2.036 | 1.00 |
| 246_Q | 250_P | 2.032 | 1.00 |
| 116_T | 121_V | 2.008 | 1.00 |
| 59_F | 119_I | 1.999 | 1.00 |
| 258_A | 390_F | 1.996 | 1.00 |
| 96_P | 204_F | 1.982 | 1.00 |
| 183_N | 187_A | 1.950 | 1.00 |
| 70_G | 127_F | 1.936 | 1.00 |
| 330_L | 359_L | 1.936 | 1.00 |
| 270_G | 403_V | 1.918 | 1.00 |
| 107_L | 193_A | 1.883 | 1.00 |
| 201_L | 205_A | 1.877 | 1.00 |
| 247_Y | 379_A | 1.855 | 1.00 |
| 86_S | 139_P | 1.841 | 1.00 |
| 347_T | 351_I | 1.840 | 1.00 |
| 92_R | 96_P | 1.824 | 1.00 |
| 116_T | 125_L | 1.815 | 1.00 |
| 376_P | 379_A | 1.787 | 1.00 |
| 34_F | 163_A | 1.786 | 1.00 |
| 84_S | 88_R | 1.768 | 1.00 |
| 417_M | 421_G | 1.762 | 1.00 |
| 96_P | 200_A | 1.754 | 1.00 |
| 109_M | 125_L | 1.746 | 1.00 |
| 334_A | 352_C | 1.743 | 1.00 |
| 103_A | 200_A | 1.741 | 1.00 |
| 70_G | 123_F | 1.730 | 1.00 |
| 63_D | 119_I | 1.727 | 1.00 |
| 149_S | 152_E | 1.718 | 1.00 |
| 78_S | 134_G | 1.710 | 1.00 |
| 67_A | 122_M | 1.704 | 1.00 |
| 100_I | 200_A | 1.698 | 1.00 |
| 85_V | 94_F | 1.683 | 1.00 |
| 109_M | 122_M | 1.676 | 1.00 |
| 53_Y | 56_E | 1.672 | 1.00 |
| 90_N | 93_V | 1.653 | 1.00 |
| 334_A | 359_L | 1.650 | 1.00 |
| 310_W | 314_K | 1.621 | 1.00 |
| 327_F | 362_G | 1.585 | 1.00 |
| 184_D | 187_A | 1.580 | 1.00 |
| 103_A | 193_A | 1.556 | 1.00 |
| 121_V | 125_L | 1.542 | 1.00 |
| 334_A | 356_I | 1.532 | 1.00 |
| 93_V | 97_A | 1.510 | 1.00 |
| 289_K | 292_W | 1.510 | 1.00 |
| 59_F | 63_D | 1.495 | 1.00 |
| 297_Y | 357_G | 1.473 | 1.00 |
| 51_M | 64_L | 1.453 | 1.00 |
| 41_Y | 164_H | 1.439 | 1.00 |
| 55_V | 64_L | 1.439 | 1.00 |
| 83_G | 87_D | 1.421 | 1.00 |
| 97_A | 101_L | 1.417 | 1.00 |
| 280_K | 290_S | 1.403 | 0.99 |
| 203_A | 207_M | 1.403 | 0.99 |
| 319_N | 373_E | 1.400 | 0.99 |
| 105_V | 129_C | 1.392 | 0.99 |
| 144_M | 160_W | 1.382 | 0.99 |
| 202_F | 206_M | 1.363 | 0.99 |
| 190_Y | 194_F | 1.363 | 0.99 |
| 120_A | 123_F | 1.361 | 0.99 |
| 345_N | 348_V | 1.358 | 0.99 |
| 107_L | 111_F | 1.350 | 0.99 |
| 285_F | 289_K | 1.348 | 0.99 |
| 178_G | 187_A | 1.347 | 0.99 |
| 309_G | 313_D | 1.344 | 0.99 |
| 308_C | 362_G | 1.340 | 0.99 |
| 180_A | 288_D | 1.335 | 0.99 |
| 29_I | 147_W | 1.328 | 0.99 |
| 74_A | 78_S | 1.327 | 0.99 |
| 78_S | 81_I | 1.326 | 0.99 |
| 247_Y | 250_P | 1.321 | 0.99 |
| 269_Y | 395_G | 1.315 | 0.99 |
| 104_A | 108_F | 1.303 | 0.99 |
| 89_S | 94_F | 1.300 | 0.99 |
| 93_V | 209_D | 1.295 | 0.99 |
| 50_A | 179_M | 1.290 | 0.99 |
| 267_L | 423_S | 1.282 | 0.99 |
| 73_I | 396_S | 1.276 | 0.99 |
| 71_I | 133_Q | 1.276 | 0.99 |
| 87_D | 382_T | 1.273 | 0.99 |
| 278_Y | 283_K | 1.272 | 0.99 |
| 76_G | 396_S | 1.262 | 0.99 |
| 347_T | 350_M | 1.261 | 0.99 |
| 255_W | 259_I | 1.261 | 0.99 |
| 61_R | 408_D | 1.250 | 0.99 |
| 300_A | 304_G | 1.249 | 0.99 |
| 307_L | 310_W | 1.248 | 0.99 |
| 101_L | 105_V | 1.248 | 0.99 |
| 155_G | 310_W | 1.244 | 0.98 |
| 249_L | 255_W | 1.238 | 0.98 |
| 36_G | 136_G | 1.232 | 0.98 |
| 394_G | 398_A | 1.228 | 0.98 |
| 311_M | 315_V | 1.225 | 0.98 |
| 86_S | 91_P | 1.224 | 0.98 |
| 145_V | 153_R | 1.223 | 0.98 |
| 332_T | 420_I | 1.212 | 0.98 |
| 108_F | 111_F | 1.206 | 0.98 |
| 90_N | 94_F | 1.204 | 0.98 |
| 69_S | 396_S | 1.201 | 0.98 |
| 194_F | 198_L | 1.198 | 0.98 |
| 155_G | 313_D | 1.189 | 0.98 |
| 187_A | 190_Y | 1.183 | 0.98 |
| 85_V | 89_S | 1.181 | 0.98 |
| 371_A | 387_T | 1.181 | 0.98 |
| 65_G | 274_W | 1.178 | 0.98 |
| 280_K | 287_L | 1.177 | 0.98 |
| 150_Q | 153_R | 1.176 | 0.98 |
| 81_I | 84_S | 1.176 | 0.98 |
| 27_W | 31_L | 1.176 | 0.98 |
| 103_A | 197_I | 1.173 | 0.98 |
| 36_G | 95_L | 1.172 | 0.98 |
| 329_T | 333_I | 1.161 | 0.97 |
| 55_V | 61_R | 1.161 | 0.97 |
| 332_T | 424_I | 1.161 | 0.97 |
| 35_F | 199_V | 1.159 | 0.97 |
| 106_M | 192_P | 1.155 | 0.97 |
| 331_V | 359_L | 1.151 | 0.97 |
| 264_V | 363_P | 1.149 | 0.97 |
| 146_H | 380_A | 1.145 | 0.97 |
| 28_Q | 206_M | 1.141 | 0.97 |
| 124_V | 128_L | 1.140 | 0.97 |
| 62_G | 408_D | 1.139 | 0.97 |
| 108_F | 121_V | 1.137 | 0.97 |
| 332_T | 427_V | 1.126 | 0.97 |
| 327_F | 363_P | 1.125 | 0.97 |
| 93_V | 96_P | 1.121 | 0.97 |
| 270_G | 419_M | 1.112 | 0.96 |
| 42_L | 171_P | 1.110 | 0.96 |
| 96_P | 100_I | 1.109 | 0.96 |
| 25_L | 28_Q | 1.107 | 0.96 |
| 351_I | 354_I | 1.102 | 0.96 |
| 98_G | 132_F | 1.100 | 0.96 |
| 155_G | 159_V | 1.099 | 0.96 |
| 54_L | 185_W | 1.097 | 0.96 |
| 405_Y | 409_F | 1.097 | 0.96 |
| 92_R | 209_D | 1.096 | 0.96 |
| 334_A | 355_V | 1.095 | 0.96 |
| 109_M | 189_L | 1.076 | 0.95 |
| 153_R | 373_E | 1.075 | 0.95 |
| 332_T | 336_I | 1.074 | 0.95 |
| 263_F | 422_G | 1.069 | 0.95 |
| 177_L | 181_W | 1.068 | 0.95 |
| 279_L | 349_D | 1.068 | 0.95 |
| 303_P | 307_L | 1.068 | 0.95 |
| 43_V | 46_N | 1.067 | 0.95 |
| 107_L | 190_Y | 1.064 | 0.95 |
| 74_A | 130_G | 1.063 | 0.95 |
| 36_G | 99_L | 1.063 | 0.95 |
| 111_F | 190_Y | 1.062 | 0.95 |
| 50_A | 188_A | 1.062 | 0.95 |
| 89_S | 93_V | 1.053 | 0.95 |
| 336_I | 420_I | 1.049 | 0.94 |
| 30_F | 148_W | 1.048 | 0.94 |
| 304_G | 307_L | 1.034 | 0.94 |
| 252_K | 256_Y | 1.033 | 0.94 |
| 50_A | 54_L | 1.030 | 0.94 |
| 174_L | 177_L | 1.027 | 0.94 |
| 68_L | 273_D | 1.026 | 0.94 |
| 140_C | 160_W | 1.024 | 0.93 |
| 38_A | 167_G | 1.022 | 0.93 |
| 99_L | 200_A | 1.021 | 0.93 |
| 91_P | 209_D | 1.020 | 0.93 |
| 44_R | 75_Y | 1.019 | 0.93 |
| 67_A | 119_I | 1.019 | 0.93 |
| 97_A | 100_I | 1.016 | 0.93 |
| 79_K | 388_G | 1.015 | 0.93 |
| 278_Y | 282_V | 1.015 | 0.93 |
| 406_T | 410_F | 1.012 | 0.93 |
| 38_A | 170_I | 1.011 | 0.93 |
| 279_L | 285_F | 1.011 | 0.93 |
| 404_G | 408_D | 1.009 | 0.93 |
| 201_L | 204_F | 1.004 | 0.93 |
| 318_G | 321_G | 1.004 | 0.93 |
| 91_P | 142_R | 1.001 | 0.92 |
| 274_W | 404_G | 1.001 | 0.92 |
| 193_A | 197_I | 1.001 | 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 | |
| 1pw4A | 1 | 0.9557 | 100 | 0.218 | Contact Map |
| 4j05A | 2 | 0.8315 | 100 | 0.32 | Contact Map |
| 3wdoA | 1 | 0.8891 | 100 | 0.341 | Contact Map |
| 4pypA | 1 | 0.8891 | 100 | 0.351 | Contact Map |
| 3o7qA | 1 | 0.847 | 100 | 0.352 | Contact Map |
| 2gfpA | 2 | 0.8226 | 100 | 0.363 | Contact Map |
| 4zw9A | 1 | 0 | 100 | 0.377 | Contact Map |
| 4ldsA | 2 | 0.8869 | 100 | 0.385 | Contact Map |
| 4gc0A | 1 | 0.9268 | 100 | 0.391 | Contact Map |
| 4xnjA | 1 | 0 | 100 | 0.395 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)