| spdl1 |
| ID: | 1481365038 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 605 (423) | ||
| Sequences: | 172187 (153485) | ||
| Seq/Len: | 407.061 | ||
| Nf(neff/√len): | 7462.7 |
Jackhmmer Results: (2016_04)
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: 407.061).
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 |
| 123_A | 127_E | 1.781 | 1.00 |
| 382_I | 386_K | 1.754 | 1.00 |
| 279_Y | 283_K | 1.751 | 1.00 |
| 240_L | 244_L | 1.695 | 1.00 |
| 233_N | 237_Q | 1.693 | 1.00 |
| 198_I | 202_M | 1.691 | 1.00 |
| 127_E | 131_K | 1.689 | 1.00 |
| 191_Q | 195_E | 1.686 | 1.00 |
| 170_L | 174_E | 1.678 | 1.00 |
| 212_K | 216_E | 1.677 | 1.00 |
| 326_K | 330_I | 1.677 | 1.00 |
| 300_I | 304_L | 1.676 | 1.00 |
| 177_K | 181_K | 1.666 | 1.00 |
| 205_V | 209_K | 1.659 | 1.00 |
| 286_N | 290_R | 1.635 | 1.00 |
| 330_I | 334_L | 1.635 | 1.00 |
| 148_L | 152_S | 1.633 | 1.00 |
| 113_I | 117_K | 1.607 | 1.00 |
| 219_A | 223_Y | 1.584 | 1.00 |
| 226_L | 230_R | 1.575 | 1.00 |
| 293_M | 297_K | 1.569 | 1.00 |
| 187_L | 191_Q | 1.563 | 1.00 |
| 392_Q | 396_A | 1.547 | 1.00 |
| 212_K | 215_R | 1.540 | 1.00 |
| 316_Q | 320_L | 1.535 | 1.00 |
| 106_V | 110_K | 1.532 | 1.00 |
| 378_L | 382_I | 1.524 | 1.00 |
| 59_K | 63_Q | 1.520 | 1.00 |
| 229_A | 233_N | 1.517 | 1.00 |
| 215_R | 219_A | 1.514 | 1.00 |
| 323_L | 327_N | 1.500 | 1.00 |
| 163_M | 167_Q | 1.492 | 1.00 |
| 286_N | 289_N | 1.474 | 1.00 |
| 323_L | 326_K | 1.471 | 1.00 |
| 254_G | 258_F | 1.470 | 1.00 |
| 69_K | 73_L | 1.467 | 1.00 |
| 289_N | 293_M | 1.467 | 1.00 |
| 240_L | 243_A | 1.416 | 1.00 |
| 403_A | 407_E | 1.412 | 1.00 |
| 424_N | 428_R | 1.399 | 0.99 |
| 272_L | 276_K | 1.387 | 0.99 |
| 179_T | 183_E | 1.386 | 0.99 |
| 226_L | 229_A | 1.383 | 0.99 |
| 73_L | 77_S | 1.382 | 0.99 |
| 344_K | 348_D | 1.375 | 0.99 |
| 115_K | 119_E | 1.374 | 0.99 |
| 170_L | 173_M | 1.369 | 0.99 |
| 184_V | 188_Q | 1.367 | 0.99 |
| 207_R | 211_E | 1.356 | 0.99 |
| 375_L | 379_N | 1.353 | 0.99 |
| 184_V | 187_L | 1.352 | 0.99 |
| 134_V | 138_K | 1.345 | 0.99 |
| 34_Q | 38_Q | 1.340 | 0.99 |
| 198_I | 201_L | 1.329 | 0.99 |
| 120_L | 124_R | 1.327 | 0.99 |
| 337_I | 340_L | 1.325 | 0.99 |
| 141_L | 144_K | 1.323 | 0.99 |
| 221_S | 225_A | 1.323 | 0.99 |
| 134_V | 137_Q | 1.321 | 0.99 |
| 141_L | 145_S | 1.320 | 0.99 |
| 375_L | 378_L | 1.317 | 0.99 |
| 413_N | 417_L | 1.316 | 0.99 |
| 265_R | 269_E | 1.305 | 0.99 |
| 80_C | 84_K | 1.303 | 0.99 |
| 177_K | 180_L | 1.302 | 0.99 |
| 219_A | 222_Y | 1.300 | 0.99 |
| 250_P | 254_G | 1.295 | 0.99 |
| 275_M | 279_Y | 1.294 | 0.99 |
| 242_Q | 246_Q | 1.290 | 0.99 |
| 173_M | 177_K | 1.285 | 0.99 |
| 191_Q | 194_L | 1.271 | 0.99 |
| 235_D | 239_Q | 1.266 | 0.99 |
| 312_E | 316_Q | 1.265 | 0.99 |
| 318_R | 322_M | 1.259 | 0.99 |
| 187_L | 190_R | 1.259 | 0.99 |
| 120_L | 123_A | 1.259 | 0.99 |
| 344_K | 347_Y | 1.258 | 0.99 |
| 163_M | 166_L | 1.256 | 0.99 |
| 332_H | 336_E | 1.254 | 0.99 |
| 337_I | 341_E | 1.249 | 0.99 |
| 27_G | 31_V | 1.247 | 0.99 |
| 200_N | 204_Q | 1.232 | 0.98 |
| 289_N | 292_Q | 1.232 | 0.98 |
| 144_K | 148_L | 1.231 | 0.98 |
| 205_V | 208_L | 1.231 | 0.98 |
| 113_I | 116_L | 1.227 | 0.98 |
| 233_N | 236_L | 1.225 | 0.98 |
| 275_M | 278_K | 1.220 | 0.98 |
| 247_A | 251_N | 1.219 | 0.98 |
| 52_T | 56_E | 1.219 | 0.98 |
| 250_P | 253_K | 1.218 | 0.98 |
| 123_A | 126_S | 1.217 | 0.98 |
| 295_R | 299_Q | 1.212 | 0.98 |
| 279_Y | 282_L | 1.207 | 0.98 |
| 261_V | 265_R | 1.202 | 0.98 |
| 215_R | 218_E | 1.200 | 0.98 |
| 272_L | 275_M | 1.200 | 0.98 |
| 82_A | 86_Q | 1.193 | 0.98 |
| 389_L | 392_Q | 1.188 | 0.98 |
| 61_T | 65_E | 1.187 | 0.98 |
| 136_H | 140_L | 1.185 | 0.98 |
| 410_L | 414_E | 1.183 | 0.98 |
| 346_L | 350_M | 1.181 | 0.98 |
| 405_D | 409_K | 1.180 | 0.98 |
| 417_L | 420_S | 1.178 | 0.98 |
| 420_S | 424_N | 1.178 | 0.98 |
| 384_S | 388_E | 1.177 | 0.98 |
| 178_T | 182_E | 1.173 | 0.98 |
| 410_L | 413_N | 1.172 | 0.98 |
| 150_V | 154_R | 1.171 | 0.98 |
| 274_S | 278_K | 1.170 | 0.97 |
| 370_L | 374_K | 1.167 | 0.97 |
| 228_K | 232_A | 1.157 | 0.97 |
| 417_L | 421_E | 1.156 | 0.97 |
| 340_L | 344_K | 1.154 | 0.97 |
| 281_S | 285_Q | 1.152 | 0.97 |
| 55_Y | 59_K | 1.148 | 0.97 |
| 165_A | 169_E | 1.148 | 0.97 |
| 214_E | 218_E | 1.146 | 0.97 |
| 382_I | 385_T | 1.144 | 0.97 |
| 285_Q | 289_N | 1.142 | 0.97 |
| 125_L | 129_Q | 1.142 | 0.97 |
| 229_A | 232_A | 1.141 | 0.97 |
| 322_M | 326_K | 1.139 | 0.97 |
| 166_L | 170_L | 1.136 | 0.97 |
| 351_E | 355_S | 1.133 | 0.97 |
| 222_Y | 226_L | 1.130 | 0.97 |
| 293_M | 296_M | 1.129 | 0.97 |
| 222_Y | 225_A | 1.129 | 0.97 |
| 413_N | 416_C | 1.127 | 0.97 |
| 102_H | 106_V | 1.126 | 0.97 |
| 73_L | 76_L | 1.125 | 0.97 |
| 326_K | 329_E | 1.120 | 0.96 |
| 194_L | 198_I | 1.117 | 0.96 |
| 239_Q | 242_Q | 1.117 | 0.96 |
| 148_L | 151_M | 1.114 | 0.96 |
| 300_I | 303_L | 1.113 | 0.96 |
| 392_Q | 395_K | 1.111 | 0.96 |
| 391_I | 395_K | 1.110 | 0.96 |
| 199_T | 203_R | 1.110 | 0.96 |
| 330_I | 333_L | 1.109 | 0.96 |
| 298_L | 302_T | 1.107 | 0.96 |
| 69_K | 72_M | 1.107 | 0.96 |
| 193_Q | 197_L | 1.106 | 0.96 |
| 284_K | 288_F | 1.103 | 0.96 |
| 247_A | 250_P | 1.103 | 0.96 |
| 159_M | 163_M | 1.102 | 0.96 |
| 122_E | 126_S | 1.101 | 0.96 |
| 399_E | 403_A | 1.101 | 0.96 |
| 256_S | 260_E | 1.098 | 0.96 |
| 403_A | 406_I | 1.097 | 0.96 |
| 292_Q | 295_R | 1.096 | 0.96 |
| 146_E | 150_V | 1.091 | 0.96 |
| 111_T | 115_K | 1.089 | 0.96 |
| 336_E | 339_N | 1.086 | 0.96 |
| 72_M | 75_S | 1.086 | 0.96 |
| 312_E | 315_Q | 1.083 | 0.96 |
| 251_N | 255_N | 1.082 | 0.96 |
| 186_E | 190_R | 1.076 | 0.95 |
| 313_F | 317_E | 1.071 | 0.95 |
| 80_C | 83_I | 1.071 | 0.95 |
| 164_L | 168_I | 1.071 | 0.95 |
| 243_A | 246_Q | 1.070 | 0.95 |
| 282_L | 286_N | 1.070 | 0.95 |
| 213_E | 217_K | 1.069 | 0.95 |
| 211_E | 215_R | 1.069 | 0.95 |
| 231_V | 235_D | 1.069 | 0.95 |
| 374_K | 378_L | 1.068 | 0.95 |
| 396_A | 400_S | 1.068 | 0.95 |
| 126_S | 129_Q | 1.068 | 0.95 |
| 374_K | 377_N | 1.067 | 0.95 |
| 285_Q | 288_F | 1.067 | 0.95 |
| 211_E | 214_E | 1.066 | 0.95 |
| 225_A | 229_A | 1.064 | 0.95 |
| 232_A | 235_D | 1.063 | 0.95 |
| 66_V | 69_K | 1.063 | 0.95 |
| 387_G | 391_I | 1.061 | 0.95 |
| 139_E | 143_C | 1.060 | 0.95 |
| 169_E | 172_E | 1.060 | 0.95 |
| 243_A | 247_A | 1.059 | 0.95 |
| 108_E | 112_K | 1.058 | 0.95 |
| 71_R | 75_S | 1.057 | 0.95 |
| 172_E | 176_M | 1.056 | 0.95 |
| 249_D | 253_K | 1.056 | 0.95 |
| 329_E | 332_H | 1.053 | 0.95 |
| 324_E | 328_G | 1.052 | 0.95 |
| 252_S | 256_S | 1.052 | 0.95 |
| 76_L | 80_C | 1.050 | 0.94 |
| 162_E | 165_A | 1.049 | 0.94 |
| 65_E | 69_K | 1.047 | 0.94 |
| 368_T | 372_Q | 1.045 | 0.94 |
| 381_E | 384_S | 1.044 | 0.94 |
| 190_R | 193_Q | 1.044 | 0.94 |
| 176_M | 179_T | 1.043 | 0.94 |
| 347_Y | 350_M | 1.042 | 0.94 |
| 178_T | 181_K | 1.040 | 0.94 |
| 339_N | 343_F | 1.040 | 0.94 |
| 180_L | 184_V | 1.039 | 0.94 |
| 338_R | 342_K | 1.038 | 0.94 |
| 373_M | 377_N | 1.036 | 0.94 |
| 241_D | 245_Q | 1.036 | 0.94 |
| 273_I | 277_V | 1.036 | 0.94 |
| 201_L | 205_V | 1.035 | 0.94 |
| 267_A | 271_Q | 1.034 | 0.94 |
| 336_E | 340_L | 1.033 | 0.94 |
| 202_M | 206_D | 1.031 | 0.94 |
| 239_Q | 243_A | 1.031 | 0.94 |
| 189_Y | 193_Q | 1.030 | 0.94 |
| 322_M | 325_Q | 1.030 | 0.94 |
| 340_L | 343_F | 1.029 | 0.94 |
| 389_L | 393_R | 1.028 | 0.94 |
| 64_R | 68_L | 1.027 | 0.94 |
| 412_A | 416_C | 1.027 | 0.94 |
| 105_E | 108_E | 1.027 | 0.94 |
| 135_D | 139_E | 1.026 | 0.94 |
| 197_L | 200_N | 1.025 | 0.93 |
| 127_E | 130_L | 1.024 | 0.93 |
| 227_E | 231_V | 1.024 | 0.93 |
| 140_L | 143_C | 1.023 | 0.93 |
| 271_Q | 274_S | 1.021 | 0.93 |
| 129_Q | 133_Q | 1.021 | 0.93 |
| 311_T | 315_Q | 1.021 | 0.93 |
| 238_V | 242_Q | 1.017 | 0.93 |
| 164_L | 167_Q | 1.017 | 0.93 |
| 210_E | 214_E | 1.016 | 0.93 |
| 182_E | 186_E | 1.015 | 0.93 |
| 331_K | 335_G | 1.014 | 0.93 |
| 266_A | 270_R | 1.013 | 0.93 |
| 137_Q | 141_L | 1.013 | 0.93 |
| 132_H | 136_H | 1.012 | 0.93 |
| 203_R | 207_R | 1.012 | 0.93 |
| 220_V | 224_N | 1.011 | 0.93 |
| 377_N | 381_E | 1.010 | 0.93 |
| 65_E | 68_L | 1.009 | 0.93 |
| 208_L | 212_K | 1.009 | 0.93 |
| 335_G | 339_N | 1.008 | 0.93 |
| 78_C | 82_A | 1.008 | 0.93 |
| 396_A | 399_E | 1.008 | 0.93 |
| 206_D | 210_E | 1.006 | 0.93 |
| 160_S | 164_L | 1.006 | 0.93 |
| 185_N | 188_Q | 1.005 | 0.93 |
| 398_F | 402_R | 1.005 | 0.93 |
| 75_S | 79_E | 1.004 | 0.93 |
| 376_D | 380_K | 1.004 | 0.93 |
| 426_K | 430_K | 1.002 | 0.92 |
| 185_N | 189_Y | 1.002 | 0.92 |
| 408_R | 412_A | 1.002 | 0.92 |
| 180_L | 183_E | 1.001 | 0.92 |
| 287_V | 290_R | 1.001 | 0.92 |
| 124_R | 128_K | 1.001 | 0.92 |
| 380_K | 384_S | 1.001 | 0.92 |
| 315_Q | 318_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 | |
| 1i84S | 2 | 0.1471 | 99.7 | 0.696 | Contact Map |
| 1c1gA | 4 | 0.4694 | 99.4 | 0.758 | Contact Map |
| 4uxvA | 1 | 0.6843 | 98.5 | 0.828 | Contact Map |
| 4b8cD | 4 | 0.0876 | 98.3 | 0.842 | Contact Map |
| 2dfsA | 2 | 0.2281 | 98 | 0.851 | Contact Map |
| 4cgkA | 2 | 0.5504 | 97.4 | 0.869 | Contact Map |
| 2v71A | 2 | 0.2645 | 97.4 | 0.87 | Contact Map |
| 4rsiB | 1 | 0.5587 | 97.3 | 0.873 | Contact Map |
| 1deqA | 4 | 0.2529 | 97.1 | 0.876 | Contact Map |
| 4iloA | 2 | 0.3785 | 96.7 | 0.883 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)