| 1AOP |
| ID: | 1411595168 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 490 (477) | ||
| Sequences: | 1389 (819) | ||
| Seq/Len: | 2.912 | ||
| Nf(neff/√len): | 37.5 |
HHblits Results: (2013_03)
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: 2.912).
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 |
| 276_W | 325_E | 4.303 | 1.00 |
| 466_E | 474_R | 3.839 | 1.00 |
| 168_G | 196_Y | 3.507 | 1.00 |
| 242_E | 245_R | 3.498 | 1.00 |
| 238_T | 241_A | 3.273 | 1.00 |
| 17_Q | 304_K | 3.267 | 1.00 |
| 21_K | 25_E | 3.203 | 1.00 |
| 157_F | 206_A | 3.111 | 1.00 |
| 397_T | 404_G | 2.921 | 1.00 |
| 218_N | 224_N | 2.816 | 1.00 |
| 234_V | 238_T | 2.815 | 1.00 |
| 324_P | 327_E | 2.730 | 1.00 |
| 155_M | 209_V | 2.698 | 1.00 |
| 189_R | 192_S | 2.512 | 1.00 |
| 310_F | 318_L | 2.502 | 1.00 |
| 201_H | 249_I | 2.450 | 1.00 |
| 25_E | 56_M | 2.431 | 1.00 |
| 139_T | 148_I | 2.407 | 1.00 |
| 24_G | 297_T | 2.366 | 1.00 |
| 198_P | 201_H | 2.116 | 1.00 |
| 237_E | 240_K | 2.099 | 1.00 |
| 309_D | 322_G | 2.095 | 1.00 |
| 299_L | 318_L | 2.073 | 1.00 |
| 76_L | 314_A | 2.065 | 1.00 |
| 4_C | 42_F | 2.059 | 1.00 |
| 34_L | 318_L | 2.038 | 1.00 |
| 443_T | 446_E | 1.996 | 1.00 |
| 34_L | 312_I | 1.992 | 1.00 |
| 140_V | 157_F | 1.970 | 1.00 |
| 26_N | 52_P | 1.970 | 1.00 |
| 139_T | 153_N | 1.967 | 1.00 |
| 18_A | 56_M | 1.963 | 1.00 |
| 155_M | 206_A | 1.947 | 0.99 |
| 212_T | 243_V | 1.935 | 0.99 |
| 157_F | 171_L | 1.928 | 0.99 |
| 46_L | 49_N | 1.862 | 0.99 |
| 239_F | 243_V | 1.840 | 0.99 |
| 22_F | 53_V | 1.812 | 0.99 |
| 26_N | 56_M | 1.803 | 0.99 |
| 423_L | 442_I | 1.788 | 0.99 |
| 275_N | 324_P | 1.787 | 0.99 |
| 280_L | 335_A | 1.782 | 0.99 |
| 457_R | 461_E | 1.753 | 0.99 |
| 351_S | 371_L | 1.751 | 0.99 |
| 244_E | 248_G | 1.743 | 0.99 |
| 227_T | 239_F | 1.732 | 0.98 |
| 467_G | 470_D | 1.691 | 0.98 |
| 275_N | 322_G | 1.685 | 0.98 |
| 231_L | 236_V | 1.664 | 0.98 |
| 17_Q | 301_E | 1.649 | 0.98 |
| 334_I | 338_S | 1.645 | 0.98 |
| 157_F | 169_F | 1.640 | 0.98 |
| 97_I | 206_A | 1.639 | 0.98 |
| 269_V | 277_H | 1.627 | 0.97 |
| 93_W | 169_F | 1.616 | 0.97 |
| 24_G | 296_K | 1.604 | 0.97 |
| 13_T | 304_K | 1.592 | 0.97 |
| 68_A | 228_K | 1.587 | 0.97 |
| 365_A | 421_Y | 1.583 | 0.97 |
| 18_A | 60_V | 1.565 | 0.97 |
| 12_T | 15_Q | 1.556 | 0.96 |
| 242_E | 246_R | 1.555 | 0.96 |
| 78_T | 147_D | 1.548 | 0.96 |
| 345_T | 379_D | 1.547 | 0.96 |
| 362_L | 401_N | 1.542 | 0.96 |
| 162_E | 166_L | 1.536 | 0.96 |
| 151_H | 172_L | 1.535 | 0.96 |
| 136_F | 210_V | 1.526 | 0.96 |
| 208_A | 243_V | 1.514 | 0.96 |
| 137_K | 176_G | 1.511 | 0.96 |
| 462_R | 474_R | 1.497 | 0.95 |
| 173_V | 243_V | 1.496 | 0.95 |
| 69_N | 137_K | 1.493 | 0.95 |
| 43_H | 137_K | 1.477 | 0.95 |
| 33_R | 286_R | 1.473 | 0.95 |
| 462_R | 466_E | 1.472 | 0.95 |
| 97_I | 140_V | 1.469 | 0.95 |
| 209_V | 239_F | 1.464 | 0.95 |
| 194_F | 240_K | 1.463 | 0.95 |
| 238_T | 242_E | 1.458 | 0.94 |
| 69_N | 176_G | 1.451 | 0.94 |
| 155_M | 203_L | 1.442 | 0.94 |
| 442_I | 450_S | 1.442 | 0.94 |
| 171_L | 205_V | 1.441 | 0.94 |
| 270_K | 325_E | 1.414 | 0.93 |
| 70_D | 222_R | 1.414 | 0.93 |
| 224_N | 233_R | 1.411 | 0.93 |
| 327_E | 330_K | 1.410 | 0.93 |
| 18_A | 21_K | 1.408 | 0.93 |
| 52_P | 56_M | 1.404 | 0.93 |
| 234_V | 239_F | 1.402 | 0.93 |
| 152_A | 408_L | 1.389 | 0.92 |
| 313_T | 319_I | 1.384 | 0.92 |
| 170_N | 193_E | 1.380 | 0.92 |
| 172_L | 193_E | 1.375 | 0.92 |
| 68_A | 137_K | 1.375 | 0.92 |
| 62_L | 309_D | 1.373 | 0.92 |
| 207_E | 211_T | 1.360 | 0.91 |
| 392_I | 455_I | 1.356 | 0.91 |
| 189_R | 232_E | 1.351 | 0.91 |
| 4_C | 62_L | 1.348 | 0.91 |
| 241_A | 245_R | 1.339 | 0.90 |
| 16_W | 310_F | 1.332 | 0.90 |
| 384_K | 452_D | 1.328 | 0.90 |
| 402_G | 407_M | 1.317 | 0.89 |
| 134_R | 219_R | 1.309 | 0.89 |
| 291_P | 294_P | 1.307 | 0.89 |
| 32_I | 42_F | 1.304 | 0.89 |
| 143_P | 147_D | 1.296 | 0.88 |
| 218_N | 233_R | 1.287 | 0.88 |
| 166_L | 169_F | 1.287 | 0.88 |
| 329_A | 333_K | 1.284 | 0.88 |
| 326_S | 333_K | 1.272 | 0.87 |
| 348_R | 379_D | 1.260 | 0.86 |
| 43_H | 69_N | 1.241 | 0.85 |
| 270_K | 276_W | 1.238 | 0.85 |
| 21_K | 24_G | 1.237 | 0.85 |
| 355_V | 368_E | 1.233 | 0.85 |
| 208_A | 212_T | 1.232 | 0.85 |
| 6_L | 11_I | 1.230 | 0.85 |
| 23_A | 32_I | 1.229 | 0.84 |
| 2_L | 53_V | 1.216 | 0.84 |
| 24_G | 30_G | 1.210 | 0.83 |
| 89_E | 92_E | 1.210 | 0.83 |
| 301_E | 304_K | 1.207 | 0.83 |
| 9_G | 15_Q | 1.201 | 0.83 |
| 45_I | 50_V | 1.200 | 0.83 |
| 457_R | 471_F | 1.191 | 0.82 |
| 201_H | 204_A | 1.188 | 0.82 |
| 78_T | 143_P | 1.188 | 0.82 |
| 43_H | 176_G | 1.186 | 0.81 |
| 156_N | 178_S | 1.185 | 0.81 |
| 296_K | 300_L | 1.178 | 0.81 |
| 370_F | 444_E | 1.171 | 0.80 |
| 442_I | 447_I | 1.170 | 0.80 |
| 75_V | 94_A | 1.170 | 0.80 |
| 192_S | 232_E | 1.159 | 0.79 |
| 216_W | 234_V | 1.157 | 0.79 |
| 359_T | 367_A | 1.157 | 0.79 |
| 215_D | 246_R | 1.150 | 0.79 |
| 370_F | 396_V | 1.145 | 0.78 |
| 190_T | 434_I | 1.143 | 0.78 |
| 118_V | 206_A | 1.143 | 0.78 |
| 92_E | 96_K | 1.141 | 0.78 |
| 157_F | 202_T | 1.141 | 0.78 |
| 22_F | 56_M | 1.139 | 0.78 |
| 23_A | 353_A | 1.136 | 0.77 |
| 402_G | 406_A | 1.131 | 0.77 |
| 173_V | 236_V | 1.131 | 0.77 |
| 9_G | 74_N | 1.126 | 0.77 |
| 201_H | 247_A | 1.123 | 0.76 |
| 18_A | 59_S | 1.120 | 0.76 |
| 111_I | 251_F | 1.119 | 0.76 |
| 134_R | 412_G | 1.118 | 0.76 |
| 451_L | 455_I | 1.116 | 0.76 |
| 234_V | 242_E | 1.116 | 0.76 |
| 231_L | 234_V | 1.114 | 0.76 |
| 139_T | 150_L | 1.112 | 0.75 |
| 45_I | 53_V | 1.112 | 0.75 |
| 211_T | 246_R | 1.111 | 0.75 |
| 76_L | 153_N | 1.111 | 0.75 |
| 452_D | 456_G | 1.105 | 0.75 |
| 187_Y | 232_E | 1.099 | 0.74 |
| 21_K | 56_M | 1.098 | 0.74 |
| 56_M | 59_S | 1.098 | 0.74 |
| 1_L | 36_N | 1.098 | 0.74 |
| 433_R | 473_V | 1.094 | 0.74 |
| 428_N | 432_T | 1.093 | 0.74 |
| 49_N | 52_P | 1.090 | 0.73 |
| 413_L | 423_L | 1.089 | 0.73 |
| 83_E | 89_E | 1.087 | 0.73 |
| 66_A | 71_M | 1.085 | 0.73 |
| 51_K | 113_L | 1.084 | 0.73 |
| 248_G | 251_F | 1.084 | 0.73 |
| 55_Q | 59_S | 1.079 | 0.72 |
| 331_I | 334_I | 1.077 | 0.72 |
| 155_M | 171_L | 1.074 | 0.72 |
| 471_F | 475_A | 1.067 | 0.71 |
| 171_L | 209_V | 1.065 | 0.71 |
| 389_D | 462_R | 1.065 | 0.71 |
| 194_F | 243_V | 1.062 | 0.70 |
| 428_N | 473_V | 1.061 | 0.70 |
| 377_N | 449_A | 1.060 | 0.70 |
| 275_N | 325_E | 1.060 | 0.70 |
| 138_T | 155_M | 1.058 | 0.70 |
| 278_L | 323_V | 1.057 | 0.70 |
| 100_H | 207_E | 1.057 | 0.70 |
| 174_G | 231_L | 1.056 | 0.70 |
| 302_I | 331_I | 1.055 | 0.70 |
| 7_P | 74_N | 1.055 | 0.70 |
| 204_A | 247_A | 1.052 | 0.69 |
| 80_N | 147_D | 1.052 | 0.69 |
| 235_G | 240_K | 1.049 | 0.69 |
| 330_K | 334_I | 1.048 | 0.69 |
| 320_I | 331_I | 1.045 | 0.69 |
| 305_I | 334_I | 1.045 | 0.69 |
| 164_G | 336_K | 1.044 | 0.69 |
| 34_L | 40_F | 1.043 | 0.68 |
| 36_N | 178_S | 1.041 | 0.68 |
| 461_E | 475_A | 1.036 | 0.68 |
| 444_E | 447_I | 1.034 | 0.68 |
| 19_I | 42_F | 1.034 | 0.68 |
| 141_V | 212_T | 1.033 | 0.67 |
| 370_F | 419_G | 1.029 | 0.67 |
| 328_K | 332_E | 1.024 | 0.66 |
| 5_R | 102_L | 1.023 | 0.66 |
| 1_L | 134_R | 1.022 | 0.66 |
| 95_K | 99_E | 1.019 | 0.66 |
| 54_H | 64_A | 1.018 | 0.66 |
| 221_D | 224_N | 1.018 | 0.66 |
| 303_A | 308_G | 1.016 | 0.66 |
| 134_R | 217_G | 1.015 | 0.65 |
| 2_L | 45_I | 1.014 | 0.65 |
| 374_F | 394_M | 1.014 | 0.65 |
| 305_I | 327_E | 1.012 | 0.65 |
| 424_H | 437_M | 1.011 | 0.65 |
| 84_S | 89_E | 1.001 | 0.64 |
| 423_L | 447_I | 1.001 | 0.64 |
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 | |
| 4g38A | 1 | 0.9163 | 100 | 0.133 | Contact Map |
| 1zj8A | 2 | 0.9082 | 100 | 0.248 | Contact Map |
| 3b0gA | 1 | 0.8755 | 100 | 0.305 | Contact Map |
| 2akjA | 1 | 0.8755 | 100 | 0.311 | Contact Map |
| 3or1A | 2 | 0.5061 | 100 | 0.72 | Contact Map |
| 3mm5A | 2 | 0.598 | 100 | 0.744 | Contact Map |
| 3or1B | 2 | 0.5469 | 100 | 0.746 | Contact Map |
| 3mm5B | 2 | 0.5122 | 100 | 0.776 | Contact Map |
| 4g9pA | 1 | 0.7163 | 97.6 | 0.943 | Contact Map |
| 3noyA | 4 | 0.6592 | 96.7 | 0.95 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)