| TF |
| ID: | 1402261489 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 432 (429) | ||
| Sequences: | 2774 (2041.7) | ||
| Seq/Len: | 6.466 | ||
| Nf(neff/√len): | 98.6 |
Jackhmmer Results: (2014_04_16)
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: 6.466).
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 |
| 210_E | 236_N | 4.111 | 1.00 |
| 323_G | 326_E | 3.972 | 1.00 |
| 205_H | 211_F | 3.853 | 1.00 |
| 158_V | 189_M | 3.535 | 1.00 |
| 214_D | 230_A | 3.394 | 1.00 |
| 142_D | 145_R | 3.364 | 1.00 |
| 184_D | 238_K | 3.159 | 1.00 |
| 124_E | 416_K | 3.060 | 1.00 |
| 212_T | 232_K | 2.805 | 1.00 |
| 205_H | 237_L | 2.715 | 1.00 |
| 153_E | 239_K | 2.692 | 1.00 |
| 116_E | 299_D | 2.635 | 1.00 |
| 172_V | 229_K | 2.618 | 1.00 |
| 275_E | 279_K | 2.588 | 1.00 |
| 366_R | 406_Q | 2.560 | 1.00 |
| 74_N | 105_Y | 2.559 | 1.00 |
| 293_G | 296_K | 2.504 | 1.00 |
| 152_K | 244_E | 2.495 | 1.00 |
| 169_T | 234_A | 2.492 | 1.00 |
| 40_R | 46_K | 2.477 | 1.00 |
| 77_D | 81_K | 2.437 | 1.00 |
| 169_T | 181_K | 2.432 | 1.00 |
| 292_E | 343_R | 2.418 | 1.00 |
| 353_E | 357_T | 2.370 | 1.00 |
| 98_K | 101_E | 2.367 | 1.00 |
| 207_A | 240_V | 2.366 | 1.00 |
| 268_A | 272_K | 2.325 | 1.00 |
| 353_E | 356_R | 2.317 | 1.00 |
| 138_D | 142_D | 2.286 | 1.00 |
| 169_T | 176_E | 2.268 | 1.00 |
| 171_S | 234_A | 2.247 | 1.00 |
| 134_D | 271_R | 2.236 | 1.00 |
| 159_E | 242_E | 2.236 | 1.00 |
| 304_A | 308_D | 2.221 | 1.00 |
| 157_A | 206_K | 2.209 | 1.00 |
| 172_V | 231_A | 2.076 | 1.00 |
| 206_K | 209_E | 2.061 | 1.00 |
| 138_D | 267_R | 2.031 | 1.00 |
| 165_T | 238_K | 2.029 | 1.00 |
| 224_E | 227_K | 2.024 | 1.00 |
| 18_T | 102_D | 2.021 | 1.00 |
| 329_A | 332_L | 2.018 | 1.00 |
| 160_A | 200_D | 2.002 | 1.00 |
| 214_D | 232_K | 1.990 | 1.00 |
| 271_R | 275_E | 1.980 | 1.00 |
| 210_E | 234_A | 1.978 | 1.00 |
| 126_E | 420_K | 1.954 | 1.00 |
| 142_D | 146_K | 1.932 | 1.00 |
| 370_L | 373_E | 1.927 | 1.00 |
| 312_D | 334_R | 1.927 | 1.00 |
| 135_A | 139_G | 1.916 | 1.00 |
| 127_K | 419_E | 1.904 | 1.00 |
| 372_E | 376_S | 1.901 | 1.00 |
| 136_D | 278_L | 1.891 | 1.00 |
| 121_E | 414_K | 1.872 | 1.00 |
| 269_E | 272_K | 1.868 | 1.00 |
| 133_T | 136_D | 1.867 | 1.00 |
| 167_D | 238_K | 1.847 | 1.00 |
| 272_K | 276_R | 1.842 | 1.00 |
| 410_A | 414_K | 1.837 | 1.00 |
| 216_T | 230_A | 1.835 | 1.00 |
| 285_R | 289_Q | 1.834 | 1.00 |
| 342_K | 346_V | 1.822 | 1.00 |
| 146_K | 243_R | 1.817 | 1.00 |
| 212_T | 234_A | 1.814 | 1.00 |
| 292_E | 296_K | 1.790 | 1.00 |
| 338_E | 342_K | 1.786 | 1.00 |
| 158_V | 164_V | 1.785 | 1.00 |
| 140_M | 143_T | 1.780 | 1.00 |
| 156_G | 242_E | 1.735 | 1.00 |
| 135_A | 138_D | 1.721 | 1.00 |
| 264_E | 268_A | 1.721 | 1.00 |
| 253_I | 263_V | 1.687 | 1.00 |
| 145_R | 245_L | 1.678 | 1.00 |
| 73_R | 77_D | 1.644 | 1.00 |
| 77_D | 80_I | 1.619 | 1.00 |
| 260_D | 269_E | 1.600 | 1.00 |
| 145_R | 248_L | 1.598 | 1.00 |
| 160_A | 203_K | 1.593 | 1.00 |
| 96_E | 104_T | 1.592 | 1.00 |
| 165_T | 239_K | 1.592 | 1.00 |
| 250_A | 253_I | 1.586 | 1.00 |
| 381_P | 384_V | 1.581 | 0.99 |
| 202_I | 205_H | 1.576 | 0.99 |
| 384_V | 387_F | 1.564 | 0.99 |
| 126_E | 418_T | 1.549 | 0.99 |
| 14_R | 106_S | 1.539 | 0.99 |
| 335_E | 338_E | 1.539 | 0.99 |
| 12_G | 110_E | 1.535 | 0.99 |
| 120_L | 358_N | 1.533 | 0.99 |
| 144_L | 266_L | 1.506 | 0.99 |
| 118_Q | 298_N | 1.504 | 0.99 |
| 316_R | 319_A | 1.502 | 0.99 |
| 369_G | 372_E | 1.501 | 0.99 |
| 156_G | 162_D | 1.492 | 0.99 |
| 166_I | 235_I | 1.490 | 0.99 |
| 154_K | 240_V | 1.483 | 0.99 |
| 370_L | 405_E | 1.481 | 0.99 |
| 126_E | 289_Q | 1.469 | 0.99 |
| 171_S | 176_E | 1.461 | 0.99 |
| 264_E | 267_R | 1.451 | 0.99 |
| 332_L | 335_E | 1.439 | 0.99 |
| 327_K | 331_E | 1.437 | 0.99 |
| 161_E | 188_A | 1.429 | 0.99 |
| 272_K | 275_E | 1.425 | 0.99 |
| 263_V | 267_R | 1.425 | 0.99 |
| 165_T | 186_V | 1.400 | 0.98 |
| 279_K | 283_R | 1.397 | 0.98 |
| 265_G | 268_A | 1.394 | 0.98 |
| 18_T | 104_T | 1.393 | 0.98 |
| 141_L | 263_V | 1.390 | 0.98 |
| 158_V | 237_L | 1.380 | 0.98 |
| 262_S | 265_G | 1.373 | 0.98 |
| 358_N | 410_A | 1.372 | 0.98 |
| 205_H | 213_I | 1.361 | 0.98 |
| 363_D | 366_R | 1.355 | 0.98 |
| 131_E | 421_E | 1.354 | 0.98 |
| 41_I | 49_V | 1.352 | 0.98 |
| 23_S | 26_T | 1.341 | 0.98 |
| 380_D | 384_V | 1.337 | 0.98 |
| 6_E | 14_R | 1.337 | 0.98 |
| 298_N | 350_L | 1.324 | 0.98 |
| 124_E | 418_T | 1.309 | 0.97 |
| 261_G | 265_G | 1.301 | 0.97 |
| 211_F | 237_L | 1.299 | 0.97 |
| 329_A | 333_P | 1.281 | 0.97 |
| 139_G | 142_D | 1.272 | 0.97 |
| 25_E | 29_K | 1.271 | 0.97 |
| 190_G | 199_E | 1.268 | 0.97 |
| 362_A | 402_A | 1.266 | 0.97 |
| 151_W | 163_R | 1.263 | 0.97 |
| 129_I | 419_E | 1.262 | 0.97 |
| 156_G | 159_E | 1.258 | 0.96 |
| 139_G | 143_T | 1.252 | 0.96 |
| 110_E | 305_A | 1.242 | 0.96 |
| 364_E | 399_R | 1.241 | 0.96 |
| 288_S | 292_E | 1.240 | 0.96 |
| 167_D | 236_N | 1.226 | 0.96 |
| 15_V | 78_A | 1.226 | 0.96 |
| 310_E | 344_R | 1.225 | 0.96 |
| 308_D | 334_R | 1.221 | 0.96 |
| 304_A | 338_E | 1.219 | 0.96 |
| 164_V | 240_V | 1.205 | 0.95 |
| 339_E | 342_K | 1.203 | 0.95 |
| 250_A | 254_K | 1.201 | 0.95 |
| 17_I | 105_Y | 1.197 | 0.95 |
| 362_A | 403_L | 1.197 | 0.95 |
| 51_M | 55_A | 1.195 | 0.95 |
| 302_V | 307_I | 1.194 | 0.95 |
| 80_I | 83_K | 1.190 | 0.95 |
| 33_V | 36_A | 1.188 | 0.95 |
| 201_G | 213_I | 1.181 | 0.94 |
| 119_G | 122_A | 1.176 | 0.94 |
| 155_D | 159_E | 1.175 | 0.94 |
| 141_L | 145_R | 1.163 | 0.94 |
| 49_V | 54_V | 1.159 | 0.94 |
| 79_I | 86_P | 1.150 | 0.93 |
| 382_K | 386_E | 1.150 | 0.93 |
| 20_A | 23_S | 1.141 | 0.93 |
| 293_G | 297_A | 1.140 | 0.93 |
| 163_R | 188_A | 1.136 | 0.93 |
| 29_K | 33_V | 1.136 | 0.93 |
| 32_L | 62_V | 1.134 | 0.93 |
| 409_E | 413_A | 1.134 | 0.93 |
| 207_A | 239_K | 1.125 | 0.92 |
| 124_E | 293_G | 1.125 | 0.92 |
| 276_R | 280_S | 1.122 | 0.92 |
| 369_G | 373_E | 1.119 | 0.92 |
| 253_I | 266_L | 1.119 | 0.92 |
| 52_N | 55_A | 1.117 | 0.92 |
| 251_E | 254_K | 1.117 | 0.92 |
| 283_R | 412_L | 1.114 | 0.92 |
| 202_I | 211_F | 1.114 | 0.92 |
| 311_I | 338_E | 1.114 | 0.92 |
| 368_K | 372_E | 1.112 | 0.92 |
| 188_A | 243_R | 1.104 | 0.91 |
| 16_T | 104_T | 1.102 | 0.91 |
| 134_D | 137_V | 1.101 | 0.91 |
| 351_L | 407_A | 1.101 | 0.91 |
| 166_I | 202_I | 1.100 | 0.91 |
| 10_G | 301_D | 1.100 | 0.91 |
| 290_A | 411_V | 1.099 | 0.91 |
| 366_R | 369_G | 1.097 | 0.91 |
| 165_T | 241_E | 1.095 | 0.91 |
| 141_L | 253_I | 1.089 | 0.91 |
| 316_R | 320_Q | 1.087 | 0.91 |
| 149_A | 243_R | 1.086 | 0.91 |
| 22_D | 25_E | 1.082 | 0.90 |
| 312_D | 316_R | 1.080 | 0.90 |
| 294_L | 350_L | 1.073 | 0.90 |
| 215_V | 231_A | 1.064 | 0.89 |
| 12_G | 108_E | 1.061 | 0.89 |
| 396_D | 399_R | 1.059 | 0.89 |
| 197_G | 200_D | 1.055 | 0.89 |
| 22_D | 102_D | 1.054 | 0.89 |
| 134_D | 138_D | 1.045 | 0.88 |
| 163_R | 241_E | 1.039 | 0.88 |
| 158_V | 240_V | 1.038 | 0.88 |
| 171_S | 181_K | 1.038 | 0.88 |
| 213_I | 235_I | 1.036 | 0.88 |
| 277_E | 281_A | 1.035 | 0.88 |
| 54_V | 58_Y | 1.030 | 0.87 |
| 365_E | 369_G | 1.029 | 0.87 |
| 176_E | 181_K | 1.025 | 0.87 |
| 189_M | 203_K | 1.024 | 0.87 |
| 52_N | 56_Q | 1.022 | 0.87 |
| 154_K | 242_E | 1.020 | 0.87 |
| 72_S | 76_I | 1.020 | 0.87 |
| 19_I | 70_L | 1.019 | 0.86 |
| 317_Q | 321_R | 1.015 | 0.86 |
| 121_E | 358_N | 1.014 | 0.86 |
| 115_V | 353_E | 1.012 | 0.86 |
| 250_A | 262_S | 1.011 | 0.86 |
| 16_T | 106_S | 1.009 | 0.86 |
| 85_N | 112_Y | 1.003 | 0.85 |
| 311_I | 334_R | 1.001 | 0.85 |
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 | |
| 1w26A | 2 | 1 | 100 | 0.09 | Contact Map |
| 1t11A | 2 | 0.8681 | 100 | 0.151 | Contact Map |
| 3gtyX | 1 | 0.9352 | 100 | 0.163 | Contact Map |
| 1p9yA | 2 | 0.2708 | 100 | 0.7 | Contact Map |
| 2d3o1 | 1 | 0.2292 | 100 | 0.72 | Contact Map |
| 2nscA | 1 | 0.2523 | 100 | 0.726 | Contact Map |
| 1zxjA | 4 | 0.4745 | 100 | 0.732 | Contact Map |
| 2nsaA | 1 | 0.3727 | 99.9 | 0.745 | Contact Map |
| 3prbA | 2 | 0.3634 | 99.7 | 0.817 | Contact Map |
| 1hxvA | 1 | 0.1968 | 99.7 | 0.824 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)