| spindly |
| ID: | 1433325920 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 605 (574) | ||
| Sequences: | 4100 (3812.2) | ||
| Seq/Len: | 7.143 | ||
| Nf(neff/√len): | 159.1 |
Jackhmmer Results: (2015_01_07)
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: 7.143).
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 |
| 134_V | 137_Q | 3.120 | 1.00 |
| 337_I | 340_L | 3.034 | 1.00 |
| 279_Y | 282_L | 2.754 | 1.00 |
| 58_E | 63_Q | 2.667 | 1.00 |
| 212_K | 215_R | 2.644 | 1.00 |
| 424_N | 427_L | 2.543 | 1.00 |
| 240_L | 243_A | 2.492 | 1.00 |
| 113_I | 116_L | 2.488 | 1.00 |
| 177_K | 180_L | 2.438 | 1.00 |
| 141_L | 144_K | 2.416 | 1.00 |
| 198_I | 201_L | 2.407 | 1.00 |
| 219_A | 222_Y | 2.389 | 1.00 |
| 293_M | 296_M | 2.301 | 1.00 |
| 191_Q | 194_L | 2.299 | 1.00 |
| 323_L | 326_K | 2.297 | 1.00 |
| 286_N | 289_N | 2.284 | 1.00 |
| 233_N | 236_L | 2.261 | 1.00 |
| 239_Q | 244_L | 2.216 | 1.00 |
| 226_L | 229_A | 2.207 | 1.00 |
| 417_L | 420_S | 2.179 | 1.00 |
| 80_C | 83_I | 2.138 | 1.00 |
| 73_L | 76_L | 2.135 | 1.00 |
| 389_L | 392_Q | 2.132 | 1.00 |
| 133_Q | 138_K | 2.115 | 1.00 |
| 205_V | 208_L | 2.108 | 1.00 |
| 184_V | 187_L | 2.102 | 1.00 |
| 112_K | 117_K | 2.088 | 1.00 |
| 403_A | 406_I | 2.086 | 1.00 |
| 59_K | 62_L | 2.085 | 1.00 |
| 33_S | 38_Q | 2.016 | 1.00 |
| 106_V | 109_L | 1.999 | 1.00 |
| 170_L | 173_M | 1.995 | 1.00 |
| 292_Q | 297_K | 1.972 | 1.00 |
| 120_L | 123_A | 1.936 | 1.00 |
| 338_R | 341_E | 1.927 | 1.00 |
| 272_L | 275_M | 1.875 | 1.00 |
| 336_E | 341_E | 1.873 | 1.00 |
| 410_L | 413_N | 1.837 | 1.00 |
| 300_I | 303_L | 1.821 | 1.00 |
| 79_E | 84_K | 1.804 | 1.00 |
| 66_V | 69_K | 1.796 | 1.00 |
| 13_L | 16_A | 1.789 | 1.00 |
| 430_K | 435_K | 1.783 | 1.00 |
| 140_L | 145_S | 1.757 | 1.00 |
| 381_E | 386_K | 1.755 | 1.00 |
| 431_L | 434_L | 1.748 | 1.00 |
| 367_Y | 372_Q | 1.742 | 1.00 |
| 105_E | 110_K | 1.737 | 1.00 |
| 232_A | 237_Q | 1.731 | 1.00 |
| 329_E | 334_L | 1.717 | 1.00 |
| 72_M | 77_S | 1.716 | 1.00 |
| 127_E | 130_L | 1.713 | 1.00 |
| 382_I | 385_T | 1.702 | 1.00 |
| 330_I | 333_L | 1.684 | 1.00 |
| 218_E | 223_Y | 1.659 | 1.00 |
| 375_L | 378_L | 1.658 | 1.00 |
| 265_R | 268_M | 1.655 | 1.00 |
| 344_K | 347_Y | 1.655 | 1.00 |
| 326_K | 330_I | 1.653 | 1.00 |
| 204_Q | 209_K | 1.643 | 1.00 |
| 20_R | 23_A | 1.642 | 1.00 |
| 190_R | 195_E | 1.641 | 1.00 |
| 119_E | 124_R | 1.639 | 1.00 |
| 233_N | 237_Q | 1.638 | 1.00 |
| 127_E | 131_K | 1.632 | 1.00 |
| 197_L | 202_M | 1.629 | 1.00 |
| 52_T | 55_Y | 1.628 | 1.00 |
| 322_M | 327_N | 1.610 | 1.00 |
| 191_Q | 195_E | 1.588 | 1.00 |
| 69_K | 73_L | 1.585 | 1.00 |
| 289_N | 293_M | 1.578 | 1.00 |
| 278_K | 283_K | 1.571 | 1.00 |
| 351_E | 354_P | 1.571 | 1.00 |
| 285_Q | 290_R | 1.566 | 1.00 |
| 388_E | 393_R | 1.556 | 1.00 |
| 402_R | 407_E | 1.544 | 1.00 |
| 299_Q | 304_L | 1.523 | 0.99 |
| 332_H | 336_E | 1.516 | 0.99 |
| 148_L | 151_M | 1.511 | 0.99 |
| 423_E | 428_R | 1.511 | 0.99 |
| 169_E | 174_E | 1.502 | 0.99 |
| 162_E | 167_Q | 1.501 | 0.99 |
| 215_R | 219_A | 1.488 | 0.99 |
| 183_E | 188_Q | 1.485 | 0.99 |
| 409_K | 414_E | 1.484 | 0.99 |
| 55_Y | 59_K | 1.480 | 0.99 |
| 165_A | 169_E | 1.472 | 0.99 |
| 162_E | 165_A | 1.447 | 0.99 |
| 115_K | 119_E | 1.443 | 0.99 |
| 36_E | 40_Q | 1.441 | 0.99 |
| 239_Q | 242_Q | 1.439 | 0.99 |
| 34_Q | 37_L | 1.428 | 0.99 |
| 396_A | 399_E | 1.421 | 0.99 |
| 27_G | 30_L | 1.416 | 0.99 |
| 26_Y | 31_V | 1.414 | 0.99 |
| 284_K | 288_F | 1.411 | 0.99 |
| 126_S | 131_K | 1.399 | 0.99 |
| 232_A | 235_D | 1.397 | 0.99 |
| 211_E | 216_E | 1.392 | 0.99 |
| 12_R | 17_E | 1.390 | 0.99 |
| 416_C | 421_E | 1.386 | 0.99 |
| 112_K | 115_K | 1.382 | 0.99 |
| 65_E | 70_S | 1.380 | 0.99 |
| 378_L | 382_I | 1.378 | 0.99 |
| 315_Q | 320_L | 1.375 | 0.99 |
| 271_Q | 276_K | 1.372 | 0.99 |
| 401_Q | 405_D | 1.367 | 0.99 |
| 40_Q | 45_R | 1.350 | 0.98 |
| 164_L | 167_Q | 1.342 | 0.98 |
| 213_E | 217_K | 1.339 | 0.98 |
| 420_S | 423_E | 1.337 | 0.98 |
| 135_D | 138_K | 1.335 | 0.98 |
| 77_S | 81_E | 1.333 | 0.98 |
| 126_S | 129_Q | 1.324 | 0.98 |
| 291_E | 295_R | 1.322 | 0.98 |
| 368_T | 371_L | 1.319 | 0.98 |
| 338_R | 342_K | 1.318 | 0.98 |
| 123_A | 127_E | 1.310 | 0.98 |
| 361_L | 364_N | 1.307 | 0.98 |
| 139_E | 143_C | 1.305 | 0.98 |
| 54_S | 58_E | 1.300 | 0.98 |
| 267_A | 271_Q | 1.289 | 0.98 |
| 294_Q | 298_L | 1.287 | 0.98 |
| 330_I | 334_L | 1.287 | 0.98 |
| 69_K | 72_M | 1.283 | 0.98 |
| 163_M | 166_L | 1.281 | 0.98 |
| 324_E | 328_G | 1.280 | 0.97 |
| 176_M | 181_K | 1.273 | 0.97 |
| 324_E | 327_N | 1.269 | 0.97 |
| 214_E | 218_E | 1.266 | 0.97 |
| 316_Q | 319_L | 1.265 | 0.97 |
| 269_E | 273_I | 1.263 | 0.97 |
| 229_A | 233_N | 1.262 | 0.97 |
| 19_E | 24_A | 1.260 | 0.97 |
| 340_L | 344_K | 1.258 | 0.97 |
| 399_E | 403_A | 1.256 | 0.97 |
| 176_M | 179_T | 1.255 | 0.97 |
| 204_Q | 207_R | 1.248 | 0.97 |
| 424_N | 428_R | 1.246 | 0.97 |
| 274_S | 278_K | 1.245 | 0.97 |
| 345_N | 348_D | 1.244 | 0.97 |
| 51_M | 55_Y | 1.241 | 0.97 |
| 143_C | 147_E | 1.238 | 0.97 |
| 194_L | 198_I | 1.238 | 0.97 |
| 275_M | 279_Y | 1.237 | 0.97 |
| 65_E | 68_L | 1.222 | 0.96 |
| 336_E | 339_N | 1.219 | 0.96 |
| 225_A | 230_R | 1.217 | 0.96 |
| 335_G | 339_N | 1.215 | 0.96 |
| 235_D | 239_Q | 1.214 | 0.96 |
| 105_E | 108_E | 1.213 | 0.96 |
| 327_N | 330_I | 1.211 | 0.96 |
| 318_R | 322_M | 1.209 | 0.96 |
| 290_R | 294_Q | 1.208 | 0.96 |
| 282_L | 286_N | 1.207 | 0.96 |
| 220_V | 223_Y | 1.203 | 0.96 |
| 59_K | 63_Q | 1.202 | 0.96 |
| 207_R | 211_E | 1.197 | 0.96 |
| 374_K | 379_N | 1.191 | 0.96 |
| 383_E | 387_G | 1.190 | 0.96 |
| 420_S | 424_N | 1.189 | 0.96 |
| 198_I | 202_M | 1.181 | 0.95 |
| 239_Q | 243_A | 1.180 | 0.95 |
| 317_E | 320_L | 1.177 | 0.95 |
| 265_R | 269_E | 1.177 | 0.95 |
| 147_E | 152_S | 1.176 | 0.95 |
| 413_N | 417_L | 1.174 | 0.95 |
| 411_F | 414_E | 1.171 | 0.95 |
| 110_K | 114_E | 1.171 | 0.95 |
| 427_L | 431_L | 1.170 | 0.95 |
| 75_S | 79_E | 1.168 | 0.95 |
| 41_L | 44_C | 1.168 | 0.95 |
| 108_E | 112_K | 1.162 | 0.95 |
| 397_L | 401_Q | 1.158 | 0.95 |
| 234_Q | 237_Q | 1.154 | 0.95 |
| 376_D | 379_N | 1.154 | 0.95 |
| 11_C | 15_E | 1.144 | 0.94 |
| 246_Q | 251_N | 1.143 | 0.94 |
| 293_M | 297_K | 1.138 | 0.94 |
| 106_V | 110_K | 1.136 | 0.94 |
| 234_Q | 238_V | 1.135 | 0.94 |
| 379_N | 383_E | 1.134 | 0.94 |
| 280_Q | 283_K | 1.134 | 0.94 |
| 348_D | 352_S | 1.131 | 0.94 |
| 5_I | 10_R | 1.125 | 0.94 |
| 158_S | 162_E | 1.124 | 0.94 |
| 121_D | 124_R | 1.123 | 0.94 |
| 63_Q | 67_E | 1.123 | 0.94 |
| 212_K | 216_E | 1.122 | 0.94 |
| 283_K | 287_V | 1.118 | 0.93 |
| 111_T | 115_K | 1.117 | 0.93 |
| 396_A | 400_S | 1.115 | 0.93 |
| 376_D | 380_K | 1.115 | 0.93 |
| 417_L | 421_E | 1.115 | 0.93 |
| 416_C | 420_S | 1.113 | 0.93 |
| 568_V | 572_K | 1.112 | 0.93 |
| 339_N | 343_F | 1.111 | 0.93 |
| 408_R | 412_A | 1.109 | 0.93 |
| 247_A | 250_P | 1.108 | 0.93 |
| 41_L | 45_R | 1.107 | 0.93 |
| 243_A | 247_A | 1.106 | 0.93 |
| 182_E | 186_E | 1.105 | 0.93 |
| 27_G | 31_V | 1.104 | 0.93 |
| 317_E | 321_A | 1.103 | 0.93 |
| 392_Q | 396_A | 1.102 | 0.93 |
| 170_L | 174_E | 1.101 | 0.93 |
| 133_Q | 136_H | 1.100 | 0.93 |
| 190_R | 193_Q | 1.097 | 0.92 |
| 271_Q | 274_S | 1.093 | 0.92 |
| 353_K | 357_D | 1.088 | 0.92 |
| 237_Q | 241_D | 1.087 | 0.92 |
| 363_D | 367_Y | 1.086 | 0.92 |
| 206_D | 209_K | 1.085 | 0.92 |
| 288_F | 292_Q | 1.084 | 0.92 |
| 279_Y | 283_K | 1.082 | 0.92 |
| 432_D | 436_L | 1.080 | 0.92 |
| 220_V | 224_N | 1.079 | 0.92 |
| 373_M | 377_N | 1.079 | 0.92 |
| 50_T | 53_E | 1.078 | 0.92 |
| 419_L | 423_E | 1.073 | 0.91 |
| 142_S | 145_S | 1.072 | 0.91 |
| 147_E | 150_V | 1.072 | 0.91 |
| 121_D | 125_L | 1.072 | 0.91 |
| 171_T | 174_E | 1.072 | 0.91 |
| 49_M | 53_E | 1.071 | 0.91 |
| 387_G | 391_I | 1.071 | 0.91 |
| 163_M | 167_Q | 1.070 | 0.91 |
| 240_L | 244_L | 1.070 | 0.91 |
| 438_Y | 441_E | 1.070 | 0.91 |
| 93_K | 97_Q | 1.070 | 0.91 |
| 122_E | 125_L | 1.069 | 0.91 |
| 258_F | 262_E | 1.069 | 0.91 |
| 314_E | 318_R | 1.067 | 0.91 |
| 413_N | 416_C | 1.067 | 0.91 |
| 48_M | 52_T | 1.064 | 0.91 |
| 299_Q | 302_T | 1.060 | 0.91 |
| 250_P | 254_G | 1.060 | 0.91 |
| 175_S | 179_T | 1.059 | 0.91 |
| 169_E | 172_E | 1.056 | 0.90 |
| 180_L | 183_E | 1.053 | 0.90 |
| 31_V | 35_N | 1.052 | 0.90 |
| 200_N | 204_Q | 1.051 | 0.90 |
| 251_N | 255_N | 1.050 | 0.90 |
| 179_T | 183_E | 1.050 | 0.90 |
| 78_C | 82_A | 1.048 | 0.90 |
| 417_L | 424_N | 1.048 | 0.90 |
| 540_A | 544_A | 1.047 | 0.90 |
| 566_T | 572_K | 1.047 | 0.90 |
| 276_K | 279_Y | 1.047 | 0.90 |
| 72_M | 75_S | 1.046 | 0.90 |
| 331_K | 334_L | 1.044 | 0.90 |
| 528_K | 533_V | 1.042 | 0.90 |
| 38_Q | 42_D | 1.041 | 0.90 |
| 177_K | 181_K | 1.040 | 0.90 |
| 382_I | 386_K | 1.039 | 0.90 |
| 225_A | 229_A | 1.037 | 0.89 |
| 483_Q | 486_E | 1.036 | 0.89 |
| 123_A | 126_S | 1.034 | 0.89 |
| 64_R | 68_L | 1.029 | 0.89 |
| 192_E | 195_E | 1.027 | 0.89 |
| 380_K | 384_S | 1.025 | 0.89 |
| 28_L | 31_V | 1.022 | 0.88 |
| 572_K | 576_S | 1.021 | 0.88 |
| 215_R | 218_E | 1.020 | 0.88 |
| 482_P | 488_Q | 1.018 | 0.88 |
| 428_R | 431_L | 1.017 | 0.88 |
| 142_S | 146_E | 1.015 | 0.88 |
| 403_A | 407_E | 1.015 | 0.88 |
| 117_K | 121_D | 1.013 | 0.88 |
| 167_Q | 171_T | 1.010 | 0.88 |
| 28_L | 32_E | 1.009 | 0.88 |
| 529_E | 535_L | 1.009 | 0.88 |
| 211_E | 214_E | 1.007 | 0.87 |
| 411_F | 415_R | 1.007 | 0.87 |
| 21_L | 24_A | 1.007 | 0.87 |
| 187_L | 191_Q | 1.004 | 0.87 |
| 347_Y | 350_M | 1.004 | 0.87 |
| 58_E | 61_T | 1.003 | 0.87 |
| 381_E | 384_S | 1.001 | 0.87 |
| 242_Q | 246_Q | 1.001 | 0.87 |
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 | 0.688 | Contact Map |
| 1c1gA | 4 | 0.4694 | 99.4 | 0.75 | Contact Map |
| 2xs1A | 1 | 0.6678 | 98.4 | 0.827 | Contact Map |
| 2dfsA | 2 | 0.2149 | 98.1 | 0.839 | Contact Map |
| 3c9iA | 6 | 0.4 | 98.1 | 0.84 | Contact Map |
| 4uxvA | 1 | 0.7008 | 97.9 | 0.847 | Contact Map |
| 2v71A | 2 | 0.2595 | 97.5 | 0.86 | Contact Map |
| 3cazA | 2 | 0.3405 | 97.3 | 0.866 | Contact Map |
| 4rsiB | 1 | 0.5802 | 97 | 0.872 | Contact Map |
| 3o0zA | 4 | 0.2562 | 96.9 | 0.872 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)