| 4AIN_A |
| ID: | 1380272480 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 539 (494) | ||
| Sequences: | 1478 (1030.8) | ||
| Seq/Len: | 2.992 | ||
| Nf(neff/√len): | 46.4 |
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: 2.992).
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 |
| 62_A | 490_L | 3.459 | 1.00 |
| 203_I | 440_S | 3.306 | 1.00 |
| 86_R | 93_A | 3.114 | 1.00 |
| 92_E | 350_R | 3.086 | 1.00 |
| 89_R | 92_E | 2.992 | 1.00 |
| 279_F | 413_M | 2.984 | 1.00 |
| 181_F | 198_I | 2.825 | 1.00 |
| 279_F | 283_V | 2.788 | 1.00 |
| 240_V | 464_L | 2.584 | 1.00 |
| 96_F | 259_G | 2.554 | 1.00 |
| 35_V | 39_G | 2.386 | 1.00 |
| 25_P | 200_I | 2.333 | 1.00 |
| 55_V | 487_T | 2.269 | 1.00 |
| 27_L | 454_A | 2.262 | 1.00 |
| 222_G | 238_T | 2.216 | 1.00 |
| 429_A | 459_T | 2.183 | 1.00 |
| 379_T | 407_L | 2.124 | 1.00 |
| 40_F | 43_S | 2.119 | 1.00 |
| 237_W | 241_G | 2.079 | 1.00 |
| 73_F | 497_M | 2.069 | 1.00 |
| 281_F | 375_I | 2.067 | 1.00 |
| 247_T | 460_A | 2.042 | 1.00 |
| 134_D | 137_N | 2.038 | 1.00 |
| 252_F | 256_S | 2.006 | 1.00 |
| 78_A | 359_L | 1.981 | 1.00 |
| 36_W | 43_S | 1.959 | 1.00 |
| 100_S | 267_N | 1.953 | 1.00 |
| 192_G | 195_G | 1.942 | 0.99 |
| 280_V | 407_L | 1.936 | 0.99 |
| 69_V | 494_I | 1.932 | 0.99 |
| 70_F | 493_V | 1.921 | 0.99 |
| 293_L | 374_S | 1.915 | 0.99 |
| 384_E | 389_S | 1.870 | 0.99 |
| 277_A | 375_I | 1.859 | 0.99 |
| 336_S | 482_T | 1.853 | 0.99 |
| 427_T | 431_S | 1.850 | 0.99 |
| 256_S | 264_Y | 1.835 | 0.99 |
| 66_F | 490_L | 1.792 | 0.99 |
| 178_S | 196_K | 1.789 | 0.99 |
| 66_F | 70_F | 1.783 | 0.99 |
| 92_E | 170_R | 1.769 | 0.99 |
| 123_L | 384_E | 1.762 | 0.99 |
| 146_M | 370_T | 1.762 | 0.99 |
| 80_S | 83_G | 1.762 | 0.99 |
| 281_F | 290_L | 1.753 | 0.99 |
| 78_A | 358_I | 1.749 | 0.99 |
| 253_S | 430_D | 1.727 | 0.99 |
| 292_L | 378_G | 1.724 | 0.99 |
| 67_G | 156_I | 1.719 | 0.98 |
| 185_I | 194_L | 1.716 | 0.98 |
| 244_S | 464_L | 1.714 | 0.98 |
| 273_A | 424_F | 1.711 | 0.98 |
| 354_I | 504_L | 1.704 | 0.98 |
| 491_F | 495_G | 1.698 | 0.98 |
| 235_S | 238_T | 1.697 | 0.98 |
| 222_G | 242_I | 1.696 | 0.98 |
| 75_V | 79_A | 1.673 | 0.98 |
| 433_S | 456_G | 1.663 | 0.98 |
| 466_L | 481_V | 1.663 | 0.98 |
| 73_F | 501_V | 1.661 | 0.98 |
| 153_P | 334_W | 1.632 | 0.98 |
| 150_T | 366_A | 1.623 | 0.98 |
| 422_G | 426_I | 1.621 | 0.98 |
| 232_E | 235_S | 1.619 | 0.98 |
| 126_Y | 385_Q | 1.617 | 0.98 |
| 429_A | 433_S | 1.607 | 0.97 |
| 173_R | 182_V | 1.595 | 0.97 |
| 187_E | 191_E | 1.591 | 0.97 |
| 222_G | 239_I | 1.579 | 0.97 |
| 437_G | 451_V | 1.571 | 0.97 |
| 97_R | 100_S | 1.571 | 0.97 |
| 157_Y | 334_W | 1.565 | 0.97 |
| 255_I | 453_A | 1.548 | 0.97 |
| 404_L | 417_A | 1.544 | 0.96 |
| 241_G | 245_V | 1.540 | 0.96 |
| 251_I | 255_I | 1.539 | 0.96 |
| 71_V | 75_V | 1.532 | 0.96 |
| 222_G | 233_D | 1.532 | 0.96 |
| 251_I | 456_G | 1.524 | 0.96 |
| 81_K | 84_T | 1.519 | 0.96 |
| 68_T | 309_G | 1.518 | 0.96 |
| 51_A | 484_V | 1.511 | 0.96 |
| 231_I | 238_T | 1.492 | 0.95 |
| 76_V | 501_V | 1.492 | 0.95 |
| 107_A | 423_T | 1.491 | 0.95 |
| 402_G | 405_H | 1.477 | 0.95 |
| 89_R | 170_R | 1.473 | 0.95 |
| 86_R | 91_D | 1.472 | 0.95 |
| 51_A | 54_A | 1.467 | 0.95 |
| 382_V | 386_N | 1.466 | 0.95 |
| 265_L | 430_D | 1.461 | 0.95 |
| 457_V | 461_A | 1.454 | 0.95 |
| 36_W | 44_F | 1.447 | 0.94 |
| 117_Y | 120_T | 1.445 | 0.94 |
| 33_T | 208_F | 1.440 | 0.94 |
| 95_E | 350_R | 1.438 | 0.94 |
| 271_V | 275_L | 1.431 | 0.94 |
| 218_A | 242_I | 1.419 | 0.94 |
| 110_M | 153_P | 1.416 | 0.94 |
| 160_V | 496_L | 1.409 | 0.93 |
| 103_S | 107_A | 1.405 | 0.93 |
| 216_L | 329_F | 1.401 | 0.93 |
| 293_L | 371_V | 1.368 | 0.92 |
| 294_P | 298_G | 1.366 | 0.92 |
| 163_A | 496_L | 1.366 | 0.92 |
| 194_L | 197_L | 1.364 | 0.92 |
| 85_I | 504_L | 1.362 | 0.92 |
| 232_E | 238_T | 1.357 | 0.91 |
| 89_R | 172_G | 1.357 | 0.91 |
| 201_L | 492_V | 1.344 | 0.91 |
| 178_S | 250_F | 1.339 | 0.91 |
| 98_T | 356_E | 1.331 | 0.90 |
| 96_F | 347_R | 1.328 | 0.90 |
| 296_S | 374_S | 1.324 | 0.90 |
| 247_T | 250_F | 1.323 | 0.90 |
| 404_L | 413_M | 1.319 | 0.90 |
| 38_I | 465_T | 1.310 | 0.89 |
| 143_S | 303_N | 1.306 | 0.89 |
| 79_A | 359_L | 1.302 | 0.89 |
| 186_G | 192_G | 1.296 | 0.89 |
| 77_I | 354_I | 1.293 | 0.89 |
| 83_G | 355_R | 1.289 | 0.88 |
| 321_E | 325_S | 1.288 | 0.88 |
| 63_F | 332_A | 1.277 | 0.88 |
| 412_I | 415_I | 1.276 | 0.88 |
| 180_A | 496_L | 1.273 | 0.88 |
| 90_I | 170_R | 1.265 | 0.87 |
| 193_W | 197_L | 1.265 | 0.87 |
| 302_S | 306_Q | 1.264 | 0.87 |
| 201_L | 485_A | 1.263 | 0.87 |
| 487_T | 491_F | 1.251 | 0.86 |
| 82_F | 505_S | 1.250 | 0.86 |
| 226_S | 232_E | 1.247 | 0.86 |
| 428_S | 431_S | 1.240 | 0.86 |
| 226_S | 233_D | 1.240 | 0.86 |
| 182_V | 191_E | 1.239 | 0.86 |
| 433_S | 459_T | 1.235 | 0.85 |
| 115_M | 421_L | 1.230 | 0.85 |
| 162_L | 354_I | 1.229 | 0.85 |
| 145_T | 373_F | 1.229 | 0.85 |
| 254_A | 456_G | 1.219 | 0.84 |
| 224_G | 401_F | 1.213 | 0.84 |
| 504_L | 507_D | 1.201 | 0.83 |
| 79_A | 355_R | 1.197 | 0.83 |
| 222_G | 232_E | 1.192 | 0.83 |
| 167_S | 503_D | 1.187 | 0.82 |
| 86_R | 353_S | 1.185 | 0.82 |
| 250_F | 456_G | 1.184 | 0.82 |
| 171_V | 503_D | 1.183 | 0.82 |
| 178_S | 432_A | 1.178 | 0.82 |
| 117_Y | 396_A | 1.177 | 0.81 |
| 185_I | 499_A | 1.176 | 0.81 |
| 173_R | 179_S | 1.168 | 0.81 |
| 254_A | 258_V | 1.165 | 0.81 |
| 225_L | 229_N | 1.165 | 0.81 |
| 213_S | 217_G | 1.165 | 0.81 |
| 184_L | 498_F | 1.161 | 0.80 |
| 238_T | 241_G | 1.159 | 0.80 |
| 183_P | 186_G | 1.158 | 0.80 |
| 53_S | 57_D | 1.158 | 0.80 |
| 409_G | 412_I | 1.156 | 0.80 |
| 281_F | 286_T | 1.154 | 0.80 |
| 374_S | 379_T | 1.152 | 0.80 |
| 54_A | 58_N | 1.149 | 0.79 |
| 68_T | 308_A | 1.149 | 0.79 |
| 182_V | 187_E | 1.148 | 0.79 |
| 268_A | 271_V | 1.148 | 0.79 |
| 44_F | 48_A | 1.147 | 0.79 |
| 100_S | 263_Q | 1.145 | 0.79 |
| 260_K | 264_Y | 1.145 | 0.79 |
| 285_P | 289_I | 1.142 | 0.79 |
| 70_F | 497_M | 1.141 | 0.79 |
| 80_S | 85_I | 1.140 | 0.79 |
| 476_S | 479_Q | 1.136 | 0.78 |
| 62_A | 66_F | 1.134 | 0.78 |
| 185_I | 190_A | 1.121 | 0.77 |
| 175_Q | 178_S | 1.118 | 0.77 |
| 265_L | 423_T | 1.116 | 0.76 |
| 37_G | 44_F | 1.116 | 0.76 |
| 21_S | 196_K | 1.114 | 0.76 |
| 47_F | 51_A | 1.113 | 0.76 |
| 71_V | 155_A | 1.111 | 0.76 |
| 43_S | 47_F | 1.110 | 0.76 |
| 264_Y | 268_A | 1.108 | 0.76 |
| 61_W | 65_L | 1.103 | 0.75 |
| 400_L | 417_A | 1.102 | 0.75 |
| 96_F | 104_M | 1.102 | 0.75 |
| 293_L | 370_T | 1.099 | 0.75 |
| 60_G | 129_G | 1.092 | 0.74 |
| 72_F | 76_V | 1.090 | 0.74 |
| 69_V | 497_M | 1.089 | 0.74 |
| 120_T | 322_W | 1.086 | 0.74 |
| 36_W | 40_F | 1.086 | 0.74 |
| 161_G | 166_Y | 1.084 | 0.73 |
| 453_A | 457_V | 1.082 | 0.73 |
| 173_R | 190_A | 1.081 | 0.73 |
| 21_S | 25_P | 1.079 | 0.73 |
| 86_R | 89_R | 1.078 | 0.73 |
| 410_G | 414_G | 1.076 | 0.73 |
| 46_N | 50_S | 1.072 | 0.72 |
| 24_V | 28_V | 1.072 | 0.72 |
| 167_S | 173_R | 1.071 | 0.72 |
| 158_A | 361_V | 1.069 | 0.72 |
| 65_L | 294_P | 1.067 | 0.72 |
| 343_M | 438_T | 1.064 | 0.71 |
| 144_T | 307_M | 1.056 | 0.71 |
| 337_W | 428_S | 1.055 | 0.71 |
| 429_A | 456_G | 1.055 | 0.71 |
| 138_V | 385_Q | 1.055 | 0.71 |
| 407_L | 412_I | 1.052 | 0.70 |
| 424_F | 428_S | 1.050 | 0.70 |
| 236_D | 468_L | 1.050 | 0.70 |
| 87_L | 354_I | 1.049 | 0.70 |
| 251_I | 453_A | 1.043 | 0.69 |
| 136_H | 140_V | 1.041 | 0.69 |
| 246_L | 422_G | 1.040 | 0.69 |
| 245_V | 249_A | 1.038 | 0.69 |
| 420_L | 423_T | 1.037 | 0.69 |
| 126_Y | 137_N | 1.037 | 0.69 |
| 338_S | 493_V | 1.035 | 0.68 |
| 210_T | 262_I | 1.034 | 0.68 |
| 182_V | 190_A | 1.033 | 0.68 |
| 168_T | 175_Q | 1.032 | 0.68 |
| 171_V | 507_D | 1.031 | 0.68 |
| 99_V | 103_S | 1.031 | 0.68 |
| 363_L | 367_G | 1.029 | 0.68 |
| 236_D | 240_V | 1.028 | 0.68 |
| 470_G | 474_A | 1.027 | 0.68 |
| 449_K | 452_T | 1.017 | 0.66 |
| 327_T | 331_W | 1.016 | 0.66 |
| 186_G | 195_G | 1.015 | 0.66 |
| 255_I | 449_K | 1.015 | 0.66 |
| 112_I | 217_G | 1.014 | 0.66 |
| 76_V | 79_A | 1.014 | 0.66 |
| 268_A | 423_T | 1.013 | 0.66 |
| 383_F | 406_A | 1.012 | 0.66 |
| 459_T | 463_G | 1.012 | 0.66 |
| 295_G | 313_M | 1.010 | 0.66 |
| 58_N | 287_V | 1.009 | 0.66 |
| 345_L | 361_V | 1.008 | 0.65 |
| 222_G | 235_S | 1.006 | 0.65 |
| 119_T | 399_Q | 1.002 | 0.65 |
| 110_M | 114_L | 1.001 | 0.65 |
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 | |
| 4c7rA | 3 | 0.9722 | 100 | 0.052 | Contact Map |
| 2wswA | 1 | 0.9221 | 100 | 0.124 | Contact Map |
| 2xq2A | 1 | 0.7588 | 96.9 | 0.962 | Contact Map |
| 3dh4A | 4 | 0.718 | 94.5 | 0.968 | Contact Map |
| 3l1lA | 1 | 0.6623 | 93.7 | 0.969 | Contact Map |
| 2jlnA | 1 | 0.7199 | 90.5 | 0.972 | Contact Map |
| 4djkA | 2 | 0.6735 | 83.7 | 0.975 | Contact Map |
| 3giaA | 1 | 0.6809 | 83.6 | 0.975 | Contact Map |
| 3effK | 4 | 0.2263 | 11.9 | 0.986 | Contact Map |
| 1q90L | 1 | 0.0594 | 9.5 | 0.986 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)