| chen-jieduan400 |
| ID: | 1510151135 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 420 (420) | ||
| Sequences: | 1471 (944.3) | ||
| Seq/Len: | 3.502 | ||
| Nf(neff/√len): | 46.1 |
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: 3.502).
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 |
| 15_T | 18_D | 5.679 | 1.00 |
| 10_I | 36_L | 4.382 | 1.00 |
| 105_V | 120_I | 4.181 | 1.00 |
| 17_F | 70_E | 4.083 | 1.00 |
| 133_V | 158_F | 3.456 | 1.00 |
| 221_R | 225_E | 3.110 | 1.00 |
| 44_S | 98_A | 3.028 | 1.00 |
| 41_E | 57_R | 3.018 | 1.00 |
| 23_V | 78_R | 2.986 | 1.00 |
| 16_L | 67_G | 2.977 | 1.00 |
| 65_P | 69_A | 2.904 | 1.00 |
| 220_G | 252_L | 2.745 | 1.00 |
| 151_L | 173_H | 2.666 | 1.00 |
| 34_L | 71_L | 2.529 | 1.00 |
| 136_D | 140_E | 2.519 | 1.00 |
| 104_D | 108_R | 2.504 | 1.00 |
| 241_A | 244_D | 2.500 | 1.00 |
| 36_L | 75_A | 2.496 | 1.00 |
| 69_A | 225_E | 2.490 | 1.00 |
| 58_V | 68_L | 2.446 | 1.00 |
| 24_P | 78_R | 2.436 | 1.00 |
| 64_G | 67_G | 2.398 | 1.00 |
| 8_L | 19_A | 2.376 | 1.00 |
| 68_L | 227_L | 2.310 | 1.00 |
| 117_Y | 214_D | 2.267 | 1.00 |
| 314_R | 317_E | 2.230 | 1.00 |
| 23_V | 75_A | 2.217 | 1.00 |
| 102_W | 202_A | 2.198 | 1.00 |
| 41_E | 60_A | 2.189 | 1.00 |
| 135_G | 153_Y | 2.184 | 1.00 |
| 138_P | 170_R | 2.152 | 1.00 |
| 243_G | 273_Q | 2.150 | 1.00 |
| 27_H | 78_R | 2.137 | 1.00 |
| 170_R | 174_D | 2.135 | 1.00 |
| 382_Q | 393_A | 2.123 | 1.00 |
| 298_E | 302_T | 2.090 | 1.00 |
| 27_H | 80_M | 2.078 | 1.00 |
| 86_I | 233_V | 2.072 | 1.00 |
| 250_A | 277_A | 2.069 | 1.00 |
| 74_A | 78_R | 2.046 | 1.00 |
| 219_I | 231_L | 2.018 | 1.00 |
| 65_P | 221_R | 2.015 | 1.00 |
| 146_V | 160_I | 1.984 | 1.00 |
| 84_V | 228_V | 1.976 | 1.00 |
| 16_L | 39_L | 1.949 | 1.00 |
| 324_R | 355_E | 1.942 | 1.00 |
| 93_V | 202_A | 1.936 | 1.00 |
| 101_W | 117_Y | 1.905 | 1.00 |
| 240_R | 408_L | 1.900 | 1.00 |
| 104_D | 113_E | 1.893 | 1.00 |
| 218_E | 222_W | 1.881 | 1.00 |
| 116_D | 208_D | 1.876 | 1.00 |
| 215_T | 219_I | 1.872 | 1.00 |
| 377_A | 381_A | 1.841 | 0.99 |
| 209_P | 248_R | 1.837 | 0.99 |
| 6_Y | 26_L | 1.831 | 0.99 |
| 197_A | 330_I | 1.809 | 0.99 |
| 136_D | 141_L | 1.794 | 0.99 |
| 143_A | 154_Y | 1.776 | 0.99 |
| 17_F | 20_A | 1.758 | 0.99 |
| 323_K | 418_M | 1.754 | 0.99 |
| 17_F | 67_G | 1.751 | 0.99 |
| 378_V | 396_G | 1.745 | 0.99 |
| 250_A | 258_I | 1.669 | 0.99 |
| 218_E | 221_R | 1.662 | 0.99 |
| 72_S | 227_L | 1.651 | 0.99 |
| 357_A | 417_I | 1.644 | 0.98 |
| 23_V | 71_L | 1.634 | 0.98 |
| 336_R | 350_E | 1.613 | 0.98 |
| 75_A | 80_M | 1.610 | 0.98 |
| 76_H | 229_D | 1.609 | 0.98 |
| 65_P | 218_E | 1.608 | 0.98 |
| 108_R | 162_E | 1.603 | 0.98 |
| 83_V | 257_P | 1.576 | 0.98 |
| 42_S | 59_D | 1.573 | 0.98 |
| 297_G | 301_L | 1.561 | 0.98 |
| 86_I | 219_I | 1.561 | 0.98 |
| 160_I | 164_T | 1.557 | 0.98 |
| 116_D | 210_R | 1.549 | 0.97 |
| 114_Y | 117_Y | 1.547 | 0.97 |
| 415_G | 418_M | 1.540 | 0.97 |
| 20_A | 70_E | 1.540 | 0.97 |
| 68_L | 82_V | 1.527 | 0.97 |
| 33_W | 229_D | 1.510 | 0.97 |
| 20_A | 23_V | 1.493 | 0.97 |
| 243_G | 247_R | 1.491 | 0.97 |
| 260_V | 276_I | 1.469 | 0.96 |
| 365_S | 411_Q | 1.451 | 0.96 |
| 36_L | 82_V | 1.440 | 0.96 |
| 357_A | 414_S | 1.417 | 0.95 |
| 246_L | 260_V | 1.416 | 0.95 |
| 57_R | 60_A | 1.414 | 0.95 |
| 137_G | 182_S | 1.413 | 0.95 |
| 213_D | 252_L | 1.408 | 0.95 |
| 186_A | 333_S | 1.397 | 0.95 |
| 3_A | 32_D | 1.381 | 0.94 |
| 120_I | 129_L | 1.379 | 0.94 |
| 223_I | 256_R | 1.375 | 0.94 |
| 43_E | 200_T | 1.369 | 0.94 |
| 205_R | 208_D | 1.361 | 0.94 |
| 10_I | 75_A | 1.342 | 0.93 |
| 185_R | 189_D | 1.340 | 0.93 |
| 213_D | 248_R | 1.340 | 0.93 |
| 223_I | 228_V | 1.328 | 0.93 |
| 54_D | 57_R | 1.324 | 0.92 |
| 359_A | 384_A | 1.321 | 0.92 |
| 4_S | 32_D | 1.321 | 0.92 |
| 153_Y | 156_H | 1.319 | 0.92 |
| 39_L | 82_V | 1.315 | 0.92 |
| 136_D | 143_A | 1.313 | 0.92 |
| 11_S | 14_F | 1.312 | 0.92 |
| 320_P | 324_R | 1.308 | 0.92 |
| 16_L | 68_L | 1.307 | 0.92 |
| 55_H | 100_R | 1.304 | 0.92 |
| 356_I | 410_F | 1.300 | 0.91 |
| 161_A | 177_H | 1.297 | 0.91 |
| 19_A | 71_L | 1.296 | 0.91 |
| 375_D | 396_G | 1.291 | 0.91 |
| 74_A | 77_E | 1.290 | 0.91 |
| 14_F | 61_A | 1.287 | 0.91 |
| 284_A | 288_I | 1.285 | 0.91 |
| 20_A | 74_A | 1.282 | 0.91 |
| 107_A | 162_E | 1.280 | 0.91 |
| 92_G | 202_A | 1.254 | 0.89 |
| 244_D | 248_R | 1.247 | 0.89 |
| 169_P | 172_V | 1.224 | 0.88 |
| 44_S | 61_A | 1.203 | 0.87 |
| 139_D | 185_R | 1.202 | 0.87 |
| 357_A | 413_T | 1.188 | 0.86 |
| 117_Y | 204_V | 1.185 | 0.85 |
| 69_A | 227_L | 1.185 | 0.85 |
| 22_I | 26_L | 1.184 | 0.85 |
| 152_V | 155_E | 1.170 | 0.84 |
| 73_R | 76_H | 1.168 | 0.84 |
| 356_I | 378_V | 1.167 | 0.84 |
| 75_A | 82_V | 1.165 | 0.84 |
| 130_R | 181_M | 1.162 | 0.84 |
| 135_G | 154_Y | 1.161 | 0.84 |
| 236_P | 246_L | 1.160 | 0.84 |
| 39_L | 84_V | 1.158 | 0.84 |
| 23_V | 80_M | 1.158 | 0.84 |
| 399_L | 410_F | 1.148 | 0.83 |
| 360_L | 414_S | 1.145 | 0.83 |
| 264_I | 270_M | 1.142 | 0.82 |
| 334_E | 415_G | 1.133 | 0.82 |
| 355_E | 384_A | 1.130 | 0.82 |
| 214_D | 217_R | 1.120 | 0.81 |
| 138_P | 173_H | 1.119 | 0.81 |
| 320_P | 359_A | 1.118 | 0.81 |
| 26_L | 31_A | 1.118 | 0.81 |
| 55_H | 101_W | 1.117 | 0.81 |
| 152_V | 157_R | 1.111 | 0.80 |
| 39_L | 68_L | 1.106 | 0.80 |
| 58_V | 64_G | 1.106 | 0.80 |
| 93_V | 102_W | 1.103 | 0.79 |
| 10_I | 20_A | 1.094 | 0.79 |
| 12_A | 59_D | 1.089 | 0.78 |
| 18_D | 21_R | 1.089 | 0.78 |
| 328_R | 354_V | 1.083 | 0.78 |
| 258_I | 277_A | 1.082 | 0.78 |
| 73_R | 227_L | 1.079 | 0.77 |
| 196_F | 263_I | 1.074 | 0.77 |
| 264_I | 283_D | 1.073 | 0.77 |
| 324_R | 358_A | 1.067 | 0.76 |
| 108_R | 113_E | 1.064 | 0.76 |
| 233_V | 236_P | 1.058 | 0.75 |
| 161_A | 164_T | 1.057 | 0.75 |
| 382_Q | 396_G | 1.056 | 0.75 |
| 220_G | 224_A | 1.055 | 0.75 |
| 10_I | 39_L | 1.053 | 0.75 |
| 413_T | 416_M | 1.052 | 0.75 |
| 386_P | 389_E | 1.049 | 0.74 |
| 110_Q | 123_E | 1.047 | 0.74 |
| 16_L | 222_W | 1.045 | 0.74 |
| 73_R | 77_E | 1.040 | 0.74 |
| 72_S | 76_H | 1.039 | 0.73 |
| 40_L | 219_I | 1.038 | 0.73 |
| 196_F | 363_Y | 1.037 | 0.73 |
| 385_A | 388_L | 1.033 | 0.73 |
| 130_R | 179_E | 1.030 | 0.72 |
| 72_S | 75_A | 1.022 | 0.72 |
| 337_R | 405_P | 1.017 | 0.71 |
| 128_R | 174_D | 1.014 | 0.71 |
| 303_Q | 307_E | 1.012 | 0.71 |
| 236_P | 260_V | 1.005 | 0.70 |
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 | |
| 1iv8A | 1 | 0.8786 | 100 | 0.411 | Contact Map |
| 3hjeA | 1 | 0.9048 | 100 | 0.422 | Contact Map |
| 2wc7A | 1 | 0.8262 | 100 | 0.769 | Contact Map |
| 1j0hA | 2 | 0.8238 | 100 | 0.769 | Contact Map |
| 1ea9C | 2 | 0.8286 | 100 | 0.77 | Contact Map |
| 2z1kA | 4 | 0.8405 | 100 | 0.772 | Contact Map |
| 1wzlA | 2 | 0.8238 | 100 | 0.776 | Contact Map |
| 4aefA | 2 | 0.8571 | 100 | 0.779 | Contact Map |
| 4aeeA | 2 | 0.8762 | 100 | 0.78 | Contact Map |
| 1lwjA | 2 | 0.8381 | 100 | 0.781 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)