| Lisa N Kinch |
| ID: | 1517540806 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 487 (481) | ||
| Sequences: | 2294 (1347.9) | ||
| Seq/Len: | 4.769 | ||
| Nf(neff/√len): | 61.5 |
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: 4.769).
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 |
| 241_A | 334_L | 4.605 | 1.00 |
| 182_V | 206_V | 4.591 | 1.00 |
| 354_Q | 401_A | 4.228 | 1.00 |
| 296_A | 323_F | 3.920 | 1.00 |
| 148_I | 242_Y | 3.919 | 1.00 |
| 459_T | 462_T | 3.579 | 1.00 |
| 236_I | 296_A | 3.533 | 1.00 |
| 355_L | 369_F | 3.395 | 1.00 |
| 359_M | 369_F | 3.283 | 1.00 |
| 348_D | 405_R | 3.270 | 1.00 |
| 203_A | 221_Y | 3.206 | 1.00 |
| 364_V | 369_F | 3.198 | 1.00 |
| 133_S | 156_V | 2.941 | 1.00 |
| 213_H | 227_E | 2.843 | 1.00 |
| 35_V | 447_Y | 2.791 | 1.00 |
| 302_A | 305_Q | 2.741 | 1.00 |
| 143_L | 263_F | 2.696 | 1.00 |
| 101_Y | 107_H | 2.686 | 1.00 |
| 441_A | 449_E | 2.549 | 1.00 |
| 204_E | 221_Y | 2.520 | 1.00 |
| 428_Y | 456_V | 2.488 | 1.00 |
| 436_Q | 440_A | 2.435 | 1.00 |
| 57_F | 61_F | 2.381 | 1.00 |
| 41_A | 177_L | 2.308 | 1.00 |
| 289_F | 366_Y | 2.300 | 1.00 |
| 254_M | 296_A | 2.270 | 1.00 |
| 30_D | 161_T | 2.246 | 1.00 |
| 226_R | 322_L | 2.238 | 1.00 |
| 355_L | 359_M | 2.159 | 1.00 |
| 428_Y | 464_Q | 2.140 | 1.00 |
| 297_Q | 324_L | 2.123 | 1.00 |
| 249_M | 296_A | 2.121 | 1.00 |
| 395_F | 399_A | 2.090 | 1.00 |
| 187_L | 256_I | 2.078 | 1.00 |
| 206_V | 256_I | 2.061 | 1.00 |
| 38_S | 137_F | 2.026 | 1.00 |
| 234_E | 330_H | 2.021 | 1.00 |
| 427_L | 463_E | 2.016 | 1.00 |
| 141_E | 152_R | 2.011 | 1.00 |
| 95_L | 115_A | 2.005 | 1.00 |
| 155_C | 175_L | 2.005 | 1.00 |
| 34_L | 58_A | 1.996 | 1.00 |
| 374_G | 422_H | 1.987 | 1.00 |
| 420_R | 424_V | 1.982 | 1.00 |
| 73_R | 96_L | 1.960 | 1.00 |
| 75_M | 186_S | 1.929 | 1.00 |
| 345_Q | 408_L | 1.893 | 1.00 |
| 22_T | 120_Y | 1.890 | 1.00 |
| 206_V | 224_M | 1.886 | 1.00 |
| 203_A | 310_F | 1.871 | 1.00 |
| 245_C | 269_L | 1.869 | 1.00 |
| 224_M | 228_I | 1.868 | 1.00 |
| 330_H | 333_D | 1.867 | 1.00 |
| 229_V | 319_A | 1.864 | 1.00 |
| 41_A | 44_L | 1.848 | 1.00 |
| 184_F | 232_N | 1.829 | 1.00 |
| 138_L | 450_V | 1.829 | 1.00 |
| 438_A | 453_L | 1.828 | 1.00 |
| 138_L | 430_L | 1.827 | 1.00 |
| 227_E | 231_R | 1.824 | 1.00 |
| 438_A | 449_E | 1.796 | 1.00 |
| 233_A | 237_A | 1.795 | 1.00 |
| 211_Y | 227_E | 1.789 | 1.00 |
| 58_A | 61_F | 1.787 | 1.00 |
| 33_Q | 158_S | 1.763 | 1.00 |
| 236_I | 249_M | 1.756 | 1.00 |
| 76_V | 189_Y | 1.750 | 1.00 |
| 242_Y | 338_R | 1.747 | 1.00 |
| 184_F | 254_M | 1.729 | 1.00 |
| 222_L | 319_A | 1.713 | 0.99 |
| 434_L | 437_N | 1.694 | 0.99 |
| 331_Y | 335_M | 1.685 | 0.99 |
| 339_L | 355_L | 1.684 | 0.99 |
| 29_I | 64_H | 1.678 | 0.99 |
| 142_A | 146_L | 1.665 | 0.99 |
| 44_L | 108_W | 1.663 | 0.99 |
| 40_S | 458_C | 1.662 | 0.99 |
| 441_A | 446_D | 1.640 | 0.99 |
| 227_E | 230_E | 1.638 | 0.99 |
| 129_V | 169_E | 1.636 | 0.99 |
| 179_Q | 259_I | 1.633 | 0.99 |
| 157_V | 175_L | 1.610 | 0.99 |
| 207_L | 221_Y | 1.603 | 0.99 |
| 200_K | 204_E | 1.566 | 0.99 |
| 238_K | 334_L | 1.556 | 0.99 |
| 150_S | 263_F | 1.522 | 0.99 |
| 330_H | 334_L | 1.521 | 0.99 |
| 386_R | 396_D | 1.510 | 0.98 |
| 274_E | 360_Q | 1.506 | 0.98 |
| 236_I | 323_F | 1.502 | 0.98 |
| 368_L | 372_R | 1.491 | 0.98 |
| 245_C | 276_F | 1.482 | 0.98 |
| 303_L | 306_A | 1.474 | 0.98 |
| 375_D | 463_E | 1.469 | 0.98 |
| 371_R | 463_E | 1.462 | 0.98 |
| 237_A | 334_L | 1.453 | 0.98 |
| 230_E | 326_L | 1.425 | 0.97 |
| 164_W | 168_Q | 1.423 | 0.97 |
| 158_S | 447_Y | 1.414 | 0.97 |
| 207_L | 224_M | 1.411 | 0.97 |
| 128_A | 172_A | 1.407 | 0.97 |
| 454_H | 457_L | 1.404 | 0.97 |
| 335_M | 366_Y | 1.403 | 0.97 |
| 182_V | 187_L | 1.402 | 0.97 |
| 225_F | 229_V | 1.400 | 0.97 |
| 332_L | 336_R | 1.399 | 0.97 |
| 108_W | 177_L | 1.398 | 0.97 |
| 62_S | 157_V | 1.398 | 0.97 |
| 371_R | 374_G | 1.393 | 0.97 |
| 405_R | 409_E | 1.381 | 0.97 |
| 230_E | 330_H | 1.377 | 0.97 |
| 225_F | 320_I | 1.376 | 0.97 |
| 208_T | 215_Q | 1.357 | 0.96 |
| 225_F | 304_A | 1.352 | 0.96 |
| 36_V | 450_V | 1.350 | 0.96 |
| 449_E | 470_Y | 1.339 | 0.96 |
| 456_V | 464_Q | 1.326 | 0.96 |
| 484_S | 487_S | 1.324 | 0.96 |
| 199_L | 309_P | 1.323 | 0.96 |
| 226_R | 319_A | 1.320 | 0.96 |
| 139_A | 266_F | 1.313 | 0.95 |
| 435_A | 457_L | 1.297 | 0.95 |
| 16_L | 20_F | 1.292 | 0.95 |
| 343_V | 409_E | 1.281 | 0.94 |
| 235_L | 249_M | 1.277 | 0.94 |
| 75_M | 109_D | 1.267 | 0.94 |
| 249_M | 254_M | 1.266 | 0.94 |
| 143_L | 260_T | 1.259 | 0.94 |
| 76_V | 120_Y | 1.258 | 0.94 |
| 366_Y | 370_F | 1.256 | 0.94 |
| 36_V | 137_F | 1.254 | 0.94 |
| 133_S | 174_V | 1.253 | 0.94 |
| 96_L | 109_D | 1.248 | 0.93 |
| 110_L | 175_L | 1.238 | 0.93 |
| 35_V | 130_L | 1.237 | 0.93 |
| 220_P | 223_A | 1.236 | 0.93 |
| 452_R | 470_Y | 1.235 | 0.93 |
| 335_M | 352_V | 1.233 | 0.93 |
| 437_N | 449_E | 1.227 | 0.93 |
| 418_Q | 422_H | 1.222 | 0.92 |
| 153_A | 174_V | 1.220 | 0.92 |
| 228_I | 303_L | 1.214 | 0.92 |
| 78_S | 189_Y | 1.209 | 0.92 |
| 75_M | 111_H | 1.209 | 0.92 |
| 148_I | 238_K | 1.207 | 0.92 |
| 234_E | 326_L | 1.204 | 0.92 |
| 342_T | 409_E | 1.203 | 0.92 |
| 38_S | 41_A | 1.202 | 0.92 |
| 78_S | 85_Y | 1.197 | 0.91 |
| 288_S | 291_N | 1.196 | 0.91 |
| 442_A | 447_Y | 1.194 | 0.91 |
| 336_R | 344_A | 1.193 | 0.91 |
| 99_E | 107_H | 1.190 | 0.91 |
| 371_R | 422_H | 1.186 | 0.91 |
| 43_A | 49_P | 1.186 | 0.91 |
| 456_V | 470_Y | 1.184 | 0.91 |
| 291_N | 294_P | 1.184 | 0.91 |
| 107_H | 205_H | 1.179 | 0.91 |
| 25_L | 127_R | 1.177 | 0.91 |
| 139_A | 143_L | 1.174 | 0.90 |
| 23_S | 71_E | 1.165 | 0.90 |
| 269_L | 276_F | 1.163 | 0.90 |
| 76_V | 88_R | 1.162 | 0.90 |
| 297_Q | 301_S | 1.161 | 0.90 |
| 203_A | 224_M | 1.158 | 0.90 |
| 187_L | 203_A | 1.142 | 0.89 |
| 438_A | 450_V | 1.142 | 0.89 |
| 417_R | 420_R | 1.141 | 0.89 |
| 336_R | 345_Q | 1.141 | 0.89 |
| 61_F | 155_C | 1.140 | 0.89 |
| 245_C | 278_C | 1.139 | 0.89 |
| 36_V | 451_R | 1.138 | 0.88 |
| 190_F | 198_Q | 1.135 | 0.88 |
| 430_L | 435_A | 1.128 | 0.88 |
| 94_G | 111_H | 1.126 | 0.88 |
| 275_H | 288_S | 1.125 | 0.88 |
| 46_D | 102_N | 1.123 | 0.88 |
| 37_A | 57_F | 1.122 | 0.88 |
| 203_A | 207_L | 1.122 | 0.88 |
| 200_K | 221_Y | 1.120 | 0.87 |
| 232_N | 296_A | 1.117 | 0.87 |
| 328_Q | 349_E | 1.110 | 0.87 |
| 149_P | 238_K | 1.109 | 0.87 |
| 254_M | 300_L | 1.104 | 0.86 |
| 211_Y | 231_R | 1.104 | 0.86 |
| 281_S | 483_I | 1.100 | 0.86 |
| 459_T | 464_Q | 1.097 | 0.86 |
| 449_E | 452_R | 1.095 | 0.86 |
| 215_Q | 220_P | 1.092 | 0.86 |
| 195_Q | 198_Q | 1.091 | 0.85 |
| 237_A | 241_A | 1.090 | 0.85 |
| 35_V | 158_S | 1.088 | 0.85 |
| 322_L | 326_L | 1.085 | 0.85 |
| 204_E | 207_L | 1.082 | 0.85 |
| 151_S | 259_I | 1.080 | 0.85 |
| 204_E | 220_P | 1.080 | 0.85 |
| 338_R | 367_T | 1.079 | 0.85 |
| 220_P | 224_M | 1.077 | 0.84 |
| 109_D | 181_H | 1.067 | 0.84 |
| 254_M | 299_N | 1.066 | 0.84 |
| 393_K | 397_G | 1.064 | 0.83 |
| 419_T | 423_A | 1.058 | 0.83 |
| 35_V | 450_V | 1.054 | 0.83 |
| 222_L | 311_I | 1.053 | 0.83 |
| 36_V | 454_H | 1.052 | 0.83 |
| 187_L | 202_L | 1.051 | 0.82 |
| 162_P | 168_Q | 1.046 | 0.82 |
| 129_V | 132_S | 1.045 | 0.82 |
| 134_I | 442_A | 1.038 | 0.81 |
| 478_G | 481_L | 1.037 | 0.81 |
| 336_R | 405_R | 1.037 | 0.81 |
| 127_R | 161_T | 1.034 | 0.81 |
| 267_A | 483_I | 1.032 | 0.81 |
| 128_A | 133_S | 1.029 | 0.81 |
| 464_Q | 467_M | 1.029 | 0.81 |
| 214_C | 220_P | 1.029 | 0.81 |
| 199_L | 306_A | 1.026 | 0.80 |
| 358_L | 362_S | 1.024 | 0.80 |
| 76_V | 86_N | 1.023 | 0.80 |
| 111_H | 175_L | 1.023 | 0.80 |
| 72_P | 97_L | 1.020 | 0.80 |
| 237_A | 330_H | 1.019 | 0.80 |
| 240_Q | 327_Y | 1.018 | 0.80 |
| 88_R | 189_Y | 1.018 | 0.80 |
| 59_E | 65_K | 1.016 | 0.79 |
| 275_H | 290_S | 1.007 | 0.79 |
| 228_I | 256_I | 1.006 | 0.78 |
| 30_D | 127_R | 1.006 | 0.78 |
| 273_D | 360_Q | 1.005 | 0.78 |
| 219_E | 224_M | 1.000 | 0.78 |
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 | |
| 2ppqA | 1 | 0.577 | 43.2 | 0.981 | Contact Map |
| 3tm0A | 1 | 0.3696 | 32.7 | 0.983 | Contact Map |
| 3c57A | 2 | 0.1027 | 17.2 | 0.985 | Contact Map |
| 4ocvA | 1 | 0.6242 | 17.2 | 0.985 | Contact Map |
| 4gmuA | 1 | 0.3922 | 15.3 | 0.985 | Contact Map |
| 2pywA | 2 | 0.7146 | 15.2 | 0.985 | Contact Map |
| 2v1nA | 1 | 0.2238 | 11.1 | 0.986 | Contact Map |
| 3atsA | 1 | 0.5072 | 9.6 | 0.986 | Contact Map |
| 1ny9A | 1 | 0.1889 | 9.4 | 0.986 | Contact Map |
| 2olcA | 2 | 0.5277 | 9 | 0.987 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)