| Tim23-Tim50 IMS Only -force run |
| ID: | 1488650548 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 470 (463) | ||
| Sequences: | 192 (112.5) | ||
| Seq/Len: | 0.415 | ||
| Nf(neff/√len): | 5.2 |
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: 0.415).
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 |
| 274_L | 281_L | 2.581 | 0.96 |
| 27_N | 40_T | 2.499 | 0.95 |
| 405_K | 409_E | 2.413 | 0.94 |
| 91_A | 106_S | 2.257 | 0.90 |
| 275_S | 297_Q | 2.213 | 0.89 |
| 191_I | 196_F | 2.120 | 0.86 |
| 294_Y | 303_P | 1.997 | 0.82 |
| 164_T | 168_E | 1.883 | 0.76 |
| 286_I | 294_Y | 1.866 | 0.75 |
| 88_L | 197_L | 1.861 | 0.75 |
| 345_N | 348_E | 1.776 | 0.70 |
| 15_I | 374_A | 1.768 | 0.69 |
| 294_Y | 304_M | 1.699 | 0.65 |
| 269_V | 295_K | 1.643 | 0.61 |
| 277_L | 284_V | 1.626 | 0.60 |
| 386_K | 394_E | 1.615 | 0.59 |
| 108_M | 111_A | 1.606 | 0.58 |
| 26_Q | 359_D | 1.565 | 0.55 |
| 198_V | 206_H | 1.527 | 0.53 |
| 338_N | 341_E | 1.518 | 0.52 |
| 87_A | 110_A | 1.495 | 0.50 |
| 35_K | 61_L | 1.472 | 0.49 |
| 83_I | 110_A | 1.437 | 0.46 |
| 287_I | 318_L | 1.434 | 0.46 |
| 430_D | 434_G | 1.426 | 0.45 |
| 428_L | 438_S | 1.424 | 0.45 |
| 360_K | 363_G | 1.420 | 0.45 |
| 93_F | 110_A | 1.419 | 0.45 |
| 346_L | 351_D | 1.417 | 0.45 |
| 178_P | 185_R | 1.410 | 0.44 |
| 420_Q | 424_Q | 1.408 | 0.44 |
| 313_D | 317_R | 1.381 | 0.42 |
| 340_F | 396_G | 1.381 | 0.42 |
| 173_D | 177_P | 1.360 | 0.40 |
| 185_R | 306_P | 1.359 | 0.40 |
| 410_E | 413_K | 1.353 | 0.40 |
| 56_A | 274_L | 1.350 | 0.40 |
| 187_L | 325_L | 1.342 | 0.39 |
| 19_S | 23_Q | 1.337 | 0.39 |
| 401_L | 408_E | 1.337 | 0.39 |
| 19_S | 47_K | 1.334 | 0.39 |
| 25_L | 41_V | 1.334 | 0.39 |
| 55_N | 85_A | 1.332 | 0.39 |
| 87_A | 191_I | 1.323 | 0.38 |
| 71_D | 166_F | 1.322 | 0.38 |
| 430_D | 433_E | 1.312 | 0.37 |
| 340_F | 392_I | 1.311 | 0.37 |
| 36_L | 45_I | 1.307 | 0.37 |
| 182_P | 407_I | 1.304 | 0.37 |
| 365_H | 385_T | 1.303 | 0.37 |
| 87_A | 304_M | 1.298 | 0.36 |
| 23_Q | 47_K | 1.293 | 0.36 |
| 314_K | 345_N | 1.289 | 0.36 |
| 155_F | 159_F | 1.287 | 0.35 |
| 170_P | 410_E | 1.287 | 0.35 |
| 441_E | 444_K | 1.283 | 0.35 |
| 178_P | 421_M | 1.283 | 0.35 |
| 223_L | 227_Y | 1.282 | 0.35 |
| 229_I | 408_E | 1.281 | 0.35 |
| 420_Q | 423_G | 1.275 | 0.35 |
| 455_A | 458_E | 1.265 | 0.34 |
| 105_S | 109_V | 1.265 | 0.34 |
| 3_Y | 158_R | 1.260 | 0.34 |
| 15_I | 231_L | 1.260 | 0.34 |
| 245_E | 257_N | 1.243 | 0.33 |
| 367_G | 371_A | 1.241 | 0.32 |
| 251_H | 297_Q | 1.241 | 0.32 |
| 128_R | 158_R | 1.231 | 0.32 |
| 61_L | 70_I | 1.226 | 0.31 |
| 256_Y | 414_I | 1.225 | 0.31 |
| 280_D | 284_V | 1.220 | 0.31 |
| 24_G | 54_N | 1.219 | 0.31 |
| 100_K | 108_M | 1.218 | 0.31 |
| 305_E | 314_K | 1.217 | 0.31 |
| 458_E | 461_K | 1.213 | 0.31 |
| 61_L | 190_V | 1.210 | 0.30 |
| 17_G | 24_G | 1.206 | 0.30 |
| 269_V | 292_N | 1.205 | 0.30 |
| 287_I | 340_F | 1.201 | 0.30 |
| 198_V | 428_L | 1.201 | 0.30 |
| 245_E | 256_Y | 1.196 | 0.30 |
| 454_D | 457_F | 1.195 | 0.30 |
| 413_K | 416_I | 1.195 | 0.30 |
| 222_Y | 225_Q | 1.188 | 0.29 |
| 82_S | 87_A | 1.180 | 0.29 |
| 113_C | 116_W | 1.175 | 0.28 |
| 223_L | 249_P | 1.169 | 0.28 |
| 350_F | 396_G | 1.167 | 0.28 |
| 15_I | 373_T | 1.165 | 0.28 |
| 392_I | 396_G | 1.160 | 0.27 |
| 164_T | 242_K | 1.159 | 0.27 |
| 137_E | 305_E | 1.157 | 0.27 |
| 172_P | 391_L | 1.151 | 0.27 |
| 182_P | 420_Q | 1.148 | 0.27 |
| 187_L | 357_L | 1.146 | 0.27 |
| 226_Y | 390_D | 1.143 | 0.26 |
| 31_N | 184_Q | 1.142 | 0.26 |
| 459_E | 462_K | 1.141 | 0.26 |
| 3_Y | 128_R | 1.140 | 0.26 |
| 244_A | 253_F | 1.138 | 0.26 |
| 73_L | 137_E | 1.138 | 0.26 |
| 352_H | 356_K | 1.136 | 0.26 |
| 70_I | 201_E | 1.136 | 0.26 |
| 242_K | 416_I | 1.134 | 0.26 |
| 115_V | 325_L | 1.133 | 0.26 |
| 222_Y | 320_P | 1.133 | 0.26 |
| 44_H | 240_S | 1.129 | 0.26 |
| 284_V | 329_Q | 1.129 | 0.26 |
| 83_I | 117_C | 1.129 | 0.26 |
| 428_L | 434_G | 1.127 | 0.26 |
| 99_L | 379_N | 1.125 | 0.25 |
| 142_I | 306_P | 1.123 | 0.25 |
| 194_E | 259_F | 1.119 | 0.25 |
| 284_V | 399_N | 1.119 | 0.25 |
| 4_G | 77_H | 1.117 | 0.25 |
| 92_L | 107_A | 1.113 | 0.25 |
| 222_Y | 323_E | 1.113 | 0.25 |
| 326_A | 336_I | 1.112 | 0.25 |
| 354_V | 397_Q | 1.111 | 0.25 |
| 408_E | 454_D | 1.106 | 0.24 |
| 330_T | 352_H | 1.106 | 0.24 |
| 15_I | 259_F | 1.106 | 0.24 |
| 47_K | 192_T | 1.105 | 0.24 |
| 15_I | 82_S | 1.103 | 0.24 |
| 177_P | 252_A | 1.103 | 0.24 |
| 454_D | 458_E | 1.103 | 0.24 |
| 226_Y | 396_G | 1.100 | 0.24 |
| 443_M | 447_L | 1.097 | 0.24 |
| 286_I | 337_L | 1.097 | 0.24 |
| 41_V | 114_A | 1.097 | 0.24 |
| 37_Q | 96_S | 1.096 | 0.24 |
| 11_L | 14_G | 1.094 | 0.24 |
| 137_E | 243_I | 1.094 | 0.24 |
| 166_F | 389_L | 1.092 | 0.24 |
| 267_D | 380_S | 1.092 | 0.24 |
| 47_K | 346_L | 1.091 | 0.24 |
| 18_F | 340_F | 1.089 | 0.24 |
| 164_T | 167_Q | 1.087 | 0.23 |
| 48_R | 51_F | 1.086 | 0.23 |
| 129_D | 143_D | 1.084 | 0.23 |
| 54_N | 215_G | 1.083 | 0.23 |
| 85_A | 438_S | 1.082 | 0.23 |
| 53_G | 246_K | 1.080 | 0.23 |
| 59_L | 244_A | 1.080 | 0.23 |
| 395_E | 411_K | 1.079 | 0.23 |
| 161_S | 427_T | 1.078 | 0.23 |
| 5_T | 10_L | 1.078 | 0.23 |
| 408_E | 411_K | 1.077 | 0.23 |
| 282_S | 285_I | 1.076 | 0.23 |
| 211_A | 218_Y | 1.076 | 0.23 |
| 45_I | 161_S | 1.074 | 0.23 |
| 23_Q | 58_I | 1.073 | 0.23 |
| 181_P | 240_S | 1.073 | 0.23 |
| 293_S | 334_R | 1.073 | 0.23 |
| 449_K | 452_E | 1.070 | 0.23 |
| 196_F | 266_K | 1.069 | 0.22 |
| 456_L | 463_K | 1.069 | 0.22 |
| 359_D | 363_G | 1.068 | 0.22 |
| 408_E | 442_Q | 1.066 | 0.22 |
| 422_G | 438_S | 1.065 | 0.22 |
| 5_T | 39_N | 1.064 | 0.22 |
| 177_P | 336_I | 1.062 | 0.22 |
| 232_F | 297_Q | 1.062 | 0.22 |
| 47_K | 117_C | 1.060 | 0.22 |
| 107_A | 285_I | 1.060 | 0.22 |
| 460_E | 463_K | 1.058 | 0.22 |
| 453_V | 457_F | 1.058 | 0.22 |
| 18_F | 115_V | 1.056 | 0.22 |
| 28_I | 392_I | 1.056 | 0.22 |
| 424_Q | 427_T | 1.056 | 0.22 |
| 88_L | 408_E | 1.053 | 0.22 |
| 4_G | 13_L | 1.051 | 0.22 |
| 2_C | 77_H | 1.051 | 0.22 |
| 28_I | 389_L | 1.051 | 0.22 |
| 163_F | 236_Y | 1.049 | 0.21 |
| 233_S | 274_L | 1.049 | 0.21 |
| 275_S | 286_I | 1.049 | 0.21 |
| 132_P | 135_S | 1.048 | 0.21 |
| 245_E | 261_E | 1.046 | 0.21 |
| 183_Y | 293_S | 1.046 | 0.21 |
| 105_S | 128_R | 1.045 | 0.21 |
| 26_Q | 234_S | 1.045 | 0.21 |
| 454_D | 459_E | 1.045 | 0.21 |
| 431_Y | 436_L | 1.044 | 0.21 |
| 314_K | 348_E | 1.043 | 0.21 |
| 19_S | 44_H | 1.043 | 0.21 |
| 414_I | 430_D | 1.043 | 0.21 |
| 185_R | 421_M | 1.042 | 0.21 |
| 350_F | 385_T | 1.042 | 0.21 |
| 183_Y | 437_P | 1.042 | 0.21 |
| 237_M | 252_A | 1.042 | 0.21 |
| 29_P | 33_P | 1.042 | 0.21 |
| 66_I | 234_S | 1.041 | 0.21 |
| 38_L | 386_K | 1.041 | 0.21 |
| 232_F | 349_E | 1.041 | 0.21 |
| 36_L | 186_P | 1.040 | 0.21 |
| 239_Y | 242_K | 1.040 | 0.21 |
| 35_K | 153_K | 1.039 | 0.21 |
| 50_P | 226_Y | 1.038 | 0.21 |
| 183_Y | 421_M | 1.038 | 0.21 |
| 23_Q | 113_C | 1.038 | 0.21 |
| 184_Q | 326_A | 1.037 | 0.21 |
| 50_P | 390_D | 1.037 | 0.21 |
| 26_Q | 152_Y | 1.036 | 0.21 |
| 404_M | 411_K | 1.036 | 0.21 |
| 387_F | 417_Q | 1.035 | 0.21 |
| 148_L | 191_I | 1.033 | 0.21 |
| 194_E | 295_K | 1.031 | 0.21 |
| 368_G | 371_A | 1.030 | 0.21 |
| 111_A | 117_C | 1.030 | 0.21 |
| 264_V | 292_N | 1.030 | 0.21 |
| 133_Q | 137_E | 1.029 | 0.20 |
| 28_I | 191_I | 1.026 | 0.20 |
| 10_L | 55_N | 1.025 | 0.20 |
| 12_G | 146_Y | 1.025 | 0.20 |
| 53_G | 76_K | 1.024 | 0.20 |
| 75_G | 321_F | 1.024 | 0.20 |
| 358_K | 376_G | 1.024 | 0.20 |
| 407_I | 430_D | 1.018 | 0.20 |
| 301_A | 327_T | 1.018 | 0.20 |
| 35_K | 150_L | 1.018 | 0.20 |
| 194_E | 270_H | 1.017 | 0.20 |
| 419_E | 433_E | 1.017 | 0.20 |
| 105_S | 184_Q | 1.017 | 0.20 |
| 419_E | 434_G | 1.015 | 0.20 |
| 419_E | 422_G | 1.013 | 0.20 |
| 398_K | 419_E | 1.012 | 0.20 |
| 241_D | 326_A | 1.012 | 0.20 |
| 101_P | 327_T | 1.012 | 0.20 |
| 389_L | 392_I | 1.009 | 0.20 |
| 114_A | 231_L | 1.008 | 0.19 |
| 198_V | 209_R | 1.008 | 0.19 |
| 440_E | 444_K | 1.007 | 0.19 |
| 156_K | 378_G | 1.007 | 0.19 |
| 231_L | 321_F | 1.006 | 0.19 |
| 178_P | 427_T | 1.005 | 0.19 |
| 430_D | 435_N | 1.005 | 0.19 |
| 325_L | 367_G | 1.005 | 0.19 |
| 422_G | 428_L | 1.004 | 0.19 |
| 413_K | 421_M | 1.003 | 0.19 |
| 233_S | 281_L | 1.002 | 0.19 |
| 220_L | 229_I | 1.002 | 0.19 |
| 61_L | 114_A | 1.001 | 0.19 |
| 85_A | 316_V | 1.000 | 0.19 |
| 102_M | 106_S | 1.000 | 0.19 |
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 | |
| 3qleA | 1 | 0.3872 | 100 | 0.809 | Contact Map |
| 3shqA | 1 | 0.5617 | 100 | 0.862 | Contact Map |
| 2ghtA | 2 | 0.3489 | 99.9 | 0.887 | Contact Map |
| 2hhlA | 4 | 0.3532 | 99.9 | 0.894 | Contact Map |
| 4xpzA | 1 | 0.5362 | 99.7 | 0.913 | Contact Map |
| 3ef1A | 1 | 0.3766 | 99.7 | 0.915 | Contact Map |
| 4um7A | 4 | 0.3532 | 90.1 | 0.976 | Contact Map |
| 2obbA | 1 | 0.2553 | 87.2 | 0.977 | Contact Map |
| 3umbA | 1 | 0.3213 | 85.8 | 0.977 | Contact Map |
| 2ymmA | 4 | 0.334 | 83.9 | 0.978 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)